From ebcf41c1afa8e65e5c2af14c5b70641ad74f8922 Mon Sep 17 00:00:00 2001
From: Casey Schneider-Mizell <caseysm@gmail.com>
Date: Wed, 10 Jul 2024 11:53:52 -0700
Subject: [PATCH] Segment props (#34)

* initial conversion to hatch

* successfully convert to hatch

* unpin neuroglancer

* basic working seg props

* validated inline properties attr

* allow tag descriptions

* use better contrast controls for mainline

* initial working segment prop map

* working version of mapping sets

* tests + associated changes

* Improve targetsite robustness

* update changelog
---
 -/LICENSE.txt                                 |    9 +
 -/README.md                                   |   21 +
 -/pyproject.toml                              |   61 +
 -/src/_/__about__.py                          |    4 +
 -/src/_/__init__.py                           |    3 +
 -/tests/__init__.py                           |    3 +
 .gitignore                                    |    2 +-
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 .../reference/parser.base.tag_dictionary.html |  732 ------
 .../reference/parser.base.view_settings.html  |  730 ------
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 ...er.helpers.make_pre_post_statebuilder.html |  796 -------
 .../statebuilder.helpers.make_state_url.html  |  756 ------
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 .../statebuilder.helpers.make_url_robust.html |  768 -------
 .../statebuilder.helpers.package_state.html   |  781 -------
 ...der.helpers.sort_dataframe_by_root_id.html |  756 ------
 docs/_site/reference/statebuilder.html        |  563 -----
 docs/_site/search.json                        | 1073 ---------
 .../site_libs/bootstrap/bootstrap-icons.css   | 2018 -----------------
 .../site_libs/bootstrap/bootstrap-icons.woff  |  Bin 164168 -> 0 bytes
 .../site_libs/bootstrap/bootstrap.min.css     |   10 -
 .../site_libs/bootstrap/bootstrap.min.js      |    7 -
 .../site_libs/clipboard/clipboard.min.js      |    7 -
 .../_site/site_libs/quarto-html/anchor.min.js |    9 -
 .../_site/site_libs/quarto-html/popper.min.js |    6 -
 .../quarto-syntax-highlighting.css            |  203 --
 docs/_site/site_libs/quarto-html/quarto.js    |  902 --------
 docs/_site/site_libs/quarto-html/tippy.css    |    1 -
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 .../site_libs/quarto-nav/headroom.min.js      |    7 -
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 docs/about.qmd                                |    5 -
 CHANGELOG.md => docs/changelog.md             |   17 +
 docs/index.md                                 |   46 +
 docs/index.qmd                                |    7 -
 docs/objects.json                             |    1 -
 docs/reference/AnnotationLayerConfig.qmd      |   17 -
 docs/reference/ChainedStateBuilder.qmd        |   34 -
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 docs/reference/SegmentationLayerConfig.qmd    |   44 -
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 docs/reference/easyviewer.md                  |   19 +
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 .../layers.AnnotationLayerConfig.qmd          |   17 -
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 ...tebuilder.layers.AnnotationLayerConfig.qmd |   17 -
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 ...ui.statebuilder.layers.LayerConfigBase.qmd |   15 -
 ...builder.layers.SegmentationLayerConfig.qmd |   44 -
 ...ebuilder.StateBuilder.initialize_state.qmd |   11 -
 ...statebuilder.StateBuilder.render_state.qmd |   21 -
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 docs/reference/parser.base.view_settings.qmd  |   18 -
 docs/reference/parser.md                      |    8 +
 docs/reference/preview.qmd                    |   22 -
 docs/reference/segprops.md                    |   13 +
 .../statebuilder.AnnotationLayerConfig.qmd    |   17 -
 .../statebuilder.BoundingBoxMapper.qmd        |   20 -
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 .../statebuilder.ImageLayerConfig.qmd         |   18 -
 docs/reference/statebuilder.LineMapper.qmd    |   20 -
 docs/reference/statebuilder.PointMapper.qmd   |   19 -
 .../statebuilder.SegmentationLayerConfig.qmd  |   23 -
 docs/reference/statebuilder.SphereMapper.qmd  |   20 -
 .../statebuilder.SplitPointMapper.qmd         |   22 -
 docs/reference/statebuilder.StateBuilder.qmd  |   17 -
 .../statebuilder.helpers.from_client.qmd      |   21 -
 ...builder.helpers.make_line_statebuilder.qmd |   26 -
 ....helpers.make_neuron_neuroglancer_link.qmd |   43 -
 ...uilder.helpers.make_point_statebuilder.qmd |   25 -
 ...der.helpers.make_pre_post_statebuilder.qmd |   28 -
 .../statebuilder.helpers.make_state_url.qmd   |   21 -
 ...helpers.make_synapse_neuroglancer_link.qmd |   38 -
 .../statebuilder.helpers.make_url_robust.qmd  |   24 -
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 ...lder.helpers.sort_dataframe_by_root_id.qmd |   21 -
 docs/reference/statebuilder.md                |   23 +
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 docs/styles.css                               |    1 -
 docs/tutorials/index.qmd                      |    7 -
 docs/tutorials/parser.qmd                     |    7 -
 docs/tutorials/statebuilder.qmd               |   36 -
 docs/usage/parser.md                          |    3 +
 docs/usage/segprops.md                        |    5 +
 docs/usage/statebuilder.md                    |    3 +
 examples/dash_with_statebuilder.py            |    2 +-
 mkdocs.yml                                    |   87 +
 pyproject.toml                                |   53 +
 setup.py                                      |   15 +-
 src/nglui/__init__.py                         |    3 +-
 src/nglui/easyviewer/__init__.py              |   17 +-
 src/nglui/easyviewer/ev_base/__init__.py      |    2 +-
 .../ev_base/annotation_compatibility.py       |    4 +-
 src/nglui/easyviewer/ev_base/base.py          |   70 +-
 src/nglui/easyviewer/ev_base/mainline.py      |  127 +-
 .../easyviewer/ev_base/nglite/__init__.py     |    2 +-
 .../ev_base/nglite/equivalence_map.py         |    3 +-
 .../easyviewer/ev_base/nglite/json_utils.py   |    5 +-
 .../ev_base/nglite/json_wrappers.py           |   11 +-
 .../easyviewer/ev_base/nglite/skeleton.py     |    5 +-
 .../ev_base/nglite/trackable_state.py         |    5 +-
 .../easyviewer/ev_base/nglite/url_state.py    |   41 +-
 src/nglui/easyviewer/ev_base/nglite/viewer.py |    5 +-
 .../easyviewer/ev_base/nglite/viewer_base.py  |    3 +-
 .../ev_base/nglite/viewer_config_state.py     |    3 +-
 .../easyviewer/ev_base/nglite/viewer_state.py |   24 +-
 .../ev_base/nglite_compatibility/__init__.py  |    2 +-
 .../ev_base/nglite_compatibility/base.py      |    3 -
 src/nglui/easyviewer/ev_base/seunglab.py      |   27 +-
 src/nglui/easyviewer/ev_base/utils.py         |   36 +-
 src/nglui/parser/base.py                      |    2 +-
 src/nglui/parser/info.py                      |    2 +-
 src/nglui/segmentprops/__init__.py            |    7 +
 src/nglui/segmentprops/base.py                |  432 ++++
 src/nglui/statebuilder/helpers.py             |   76 +-
 src/nglui/statebuilder/layers.py              |  187 +-
 src/nglui/statebuilder/mappers.py             |   86 +-
 src/nglui/statebuilder/statebuilder.py        |  127 +-
 src/nglui/statebuilder/utils.py               |   21 +-
 tests/conftest.py                             |   20 +-
 tests/test_parser.py                          |    2 +-
 tests/test_segment_props.py                   |   40 +
 tests/test_statebuilder.py                    |   30 +-
 tests/test_viewer.py                          |    1 -
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diff --git a/-/LICENSE.txt b/-/LICENSE.txt
new file mode 100644
index 0000000..d18dcf9
--- /dev/null
+++ b/-/LICENSE.txt
@@ -0,0 +1,9 @@
+MIT License
+
+Copyright (c) 2024-present Casey Schneider-Mizell <caseysm@gmail.com>
+
+Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
diff --git a/-/README.md b/-/README.md
new file mode 100644
index 0000000..f8a094b
--- /dev/null
+++ b/-/README.md
@@ -0,0 +1,21 @@
+# .
+
+[![PyPI - Version](https://img.shields.io/pypi/v/-.svg)](https://pypi.org/project/-)
+[![PyPI - Python Version](https://img.shields.io/pypi/pyversions/-.svg)](https://pypi.org/project/-)
+
+-----
+
+## Table of Contents
+
+- [Installation](#installation)
+- [License](#license)
+
+## Installation
+
+```console
+pip install -
+```
+
+## License
+
+`-` is distributed under the terms of the [MIT](https://spdx.org/licenses/MIT.html) license.
diff --git a/-/pyproject.toml b/-/pyproject.toml
new file mode 100644
index 0000000..c0433a8
--- /dev/null
+++ b/-/pyproject.toml
@@ -0,0 +1,61 @@
+[build-system]
+requires = ["hatchling"]
+build-backend = "hatchling.build"
+
+[project]
+name = "-"
+dynamic = ["version"]
+description = ''
+readme = "README.md"
+requires-python = ">=3.8"
+license = "MIT"
+keywords = []
+authors = [
+  { name = "Casey Schneider-Mizell", email = "caseysm@gmail.com" },
+]
+classifiers = [
+  "Development Status :: 4 - Beta",
+  "Programming Language :: Python",
+  "Programming Language :: Python :: 3.8",
+  "Programming Language :: Python :: 3.9",
+  "Programming Language :: Python :: 3.10",
+  "Programming Language :: Python :: 3.11",
+  "Programming Language :: Python :: 3.12",
+  "Programming Language :: Python :: Implementation :: CPython",
+  "Programming Language :: Python :: Implementation :: PyPy",
+]
+dependencies = []
+
+[project.urls]
+Documentation = "https://github.com/Casey Schneider-Mizell/-#readme"
+Issues = "https://github.com/Casey Schneider-Mizell/-/issues"
+Source = "https://github.com/Casey Schneider-Mizell/-"
+
+[tool.hatch.version]
+path = "src/_/__about__.py"
+
+[tool.hatch.envs.types]
+extra-dependencies = [
+  "mypy>=1.0.0",
+]
+[tool.hatch.envs.types.scripts]
+check = "mypy --install-types --non-interactive {args:src/_ tests}"
+
+[tool.coverage.run]
+source_pkgs = ["_", "tests"]
+branch = true
+parallel = true
+omit = [
+  "src/_/__about__.py",
+]
+
+[tool.coverage.paths]
+_ = ["src/_", "*/-/src/_"]
+tests = ["tests", "*/-/tests"]
+
+[tool.coverage.report]
+exclude_lines = [
+  "no cov",
+  "if __name__ == .__main__.:",
+  "if TYPE_CHECKING:",
+]
diff --git a/-/src/_/__about__.py b/-/src/_/__about__.py
new file mode 100644
index 0000000..2851601
--- /dev/null
+++ b/-/src/_/__about__.py
@@ -0,0 +1,4 @@
+# SPDX-FileCopyrightText: 2024-present Casey Schneider-Mizell <caseysm@gmail.com>
+#
+# SPDX-License-Identifier: MIT
+__version__ = "0.0.1"
diff --git a/-/src/_/__init__.py b/-/src/_/__init__.py
new file mode 100644
index 0000000..832729e
--- /dev/null
+++ b/-/src/_/__init__.py
@@ -0,0 +1,3 @@
+# SPDX-FileCopyrightText: 2024-present Casey Schneider-Mizell <caseysm@gmail.com>
+#
+# SPDX-License-Identifier: MIT
diff --git a/-/tests/__init__.py b/-/tests/__init__.py
new file mode 100644
index 0000000..832729e
--- /dev/null
+++ b/-/tests/__init__.py
@@ -0,0 +1,3 @@
+# SPDX-FileCopyrightText: 2024-present Casey Schneider-Mizell <caseysm@gmail.com>
+#
+# SPDX-License-Identifier: MIT
diff --git a/.gitignore b/.gitignore
index 8b76f7d..1800b33 100644
--- a/.gitignore
+++ b/.gitignore
@@ -110,4 +110,4 @@ var/
 *.orig
 *.sublime-workspace
 
-docs/.quarto/
+docs/_site
\ No newline at end of file
diff --git a/LICENSE.license b/LICENSE.license
deleted file mode 100644
index f49a4e1..0000000
--- a/LICENSE.license
+++ /dev/null
@@ -1,201 +0,0 @@
-                                 Apache License
-                           Version 2.0, January 2004
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\ No newline at end of file
diff --git a/docs/.gitignore b/docs/.gitignore
deleted file mode 100644
index 075b254..0000000
--- a/docs/.gitignore
+++ /dev/null
@@ -1 +0,0 @@
-/.quarto/
diff --git a/docs/_quarto.yml b/docs/_quarto.yml
deleted file mode 100644
index 1d812b9..0000000
--- a/docs/_quarto.yml
+++ /dev/null
@@ -1,91 +0,0 @@
-project:
-  type: website
-
-website:
-  title: "NGLui Documentation"
-  page-navigation: true
-  navbar:
-    left:
-      - href: index.qmd
-        text: About
-      - text: Tutorials
-        menu:
-          - tutorials/statebuilder.qmd
-          - tutorials/parser.qmd
-      - href: reference/index.qmd
-        text: Function Reference
-    tools:
-      - icon: github
-        text: Github
-        href: http://github.com/seung-lab/NeuroglancerAnnotationUI
-
-theme:
-  - flatly
-   
-metadata-files:
-  - _sidebar.yml
-
-quartodoc:
-  style: 'pkgdown'
-  title: ''
-  sidebar: _sidebar.yml
-  dir: reference
-  out_index: _api_index.qmd
-  package: nglui
-
-  sections:
-    - title: StateBuilder Functions
-    - subtitle: Layers
-      desc: Instantiating types of layers
-      contents:
-        - name: statebuilder.ImageLayerConfig
-        - name: statebuilder.SegmentationLayerConfig
-          children: embedded
-        - name: statebuilder.AnnotationLayerConfig
-          children: embedded
-    - subtitle: Mapping Rules
-      desc: Rules for mapping data to annotations
-      contents:
-        - statebuilder.PointMapper
-        - statebuilder.LineMapper
-        - statebuilder.SphereMapper
-        - statebuilder.BoundingBoxMapper
-        - statebuilder.SplitPointMapper
-    - subtitle: StateBuilder Classes
-      desc: Tools for data-generated neuroglancer state creation
-      contents:
-        - name: statebuilder.StateBuilder
-          children: embedded
-        - name: statebuilder.ChainedStateBuilder
-          children: embedded
-    - subtitle: Helpers
-      desc: Tools for common types of states
-      contents:
-        - statebuilder.helpers.from_client
-        - statebuilder.helpers.sort_dataframe_by_root_id
-        - statebuilder.helpers.make_line_statebuilder
-        - statebuilder.helpers.make_point_statebuilder
-        - statebuilder.helpers.make_pre_post_statebuilder
-        - statebuilder.helpers.make_state_url
-        - statebuilder.helpers.make_url_robust
-        - statebuilder.helpers.package_state
-        - statebuilder.helpers.make_synapse_neuroglancer_link
-        - statebuilder.helpers.make_neuron_neuroglancer_link
-    - title: Parser
-    - subtitle: Parser Tools
-      desc: Simple tools for parsing neuroglancer states
-      contents:
-        - parser.base.layer_names
-        - parser.base.image_layers
-        - parser.base.segmentation_layers
-        - parser.base.annotation_layers
-        - parser.base.tag_dictionary
-        - parser.base.get_layer
-        - parser.base.view_settings
-        - parser.base.get_selected_ids
-        - parser.base.point_annotations
-        - parser.base.line_annotations
-        - parser.base.sphere_annotations
-        - parser.base.group_annotations
-        - parser.base.extract_multicut
-        - parser.base.annotation_dataframe
diff --git a/docs/_sidebar.yml b/docs/_sidebar.yml
deleted file mode 100644
index 94d9c89..0000000
--- a/docs/_sidebar.yml
+++ /dev/null
@@ -1,54 +0,0 @@
-website:
-  sidebar:
-  - contents:
-    - reference/index.qmd
-    - contents:
-      - contents:
-        - reference/statebuilder.ImageLayerConfig.qmd
-        - reference/statebuilder.SegmentationLayerConfig.qmd
-        - reference/statebuilder.AnnotationLayerConfig.qmd
-        section: Layers
-      - contents:
-        - reference/statebuilder.PointMapper.qmd
-        - reference/statebuilder.LineMapper.qmd
-        - reference/statebuilder.SphereMapper.qmd
-        - reference/statebuilder.BoundingBoxMapper.qmd
-        - reference/statebuilder.SplitPointMapper.qmd
-        section: Mapping Rules
-      - contents:
-        - reference/statebuilder.StateBuilder.qmd
-        - reference/statebuilder.ChainedStateBuilder.qmd
-        section: StateBuilder Classes
-      - contents:
-        - reference/statebuilder.helpers.from_client.qmd
-        - reference/statebuilder.helpers.sort_dataframe_by_root_id.qmd
-        - reference/statebuilder.helpers.make_line_statebuilder.qmd
-        - reference/statebuilder.helpers.make_point_statebuilder.qmd
-        - reference/statebuilder.helpers.make_pre_post_statebuilder.qmd
-        - reference/statebuilder.helpers.make_state_url.qmd
-        - reference/statebuilder.helpers.make_url_robust.qmd
-        - reference/statebuilder.helpers.package_state.qmd
-        - reference/statebuilder.helpers.make_synapse_neuroglancer_link.qmd
-        - reference/statebuilder.helpers.make_neuron_neuroglancer_link.qmd
-        section: Helpers
-      section: StateBuilder Functions
-    - contents:
-      - contents:
-        - reference/parser.base.layer_names.qmd
-        - reference/parser.base.image_layers.qmd
-        - reference/parser.base.segmentation_layers.qmd
-        - reference/parser.base.annotation_layers.qmd
-        - reference/parser.base.tag_dictionary.qmd
-        - reference/parser.base.get_layer.qmd
-        - reference/parser.base.view_settings.qmd
-        - reference/parser.base.get_selected_ids.qmd
-        - reference/parser.base.point_annotations.qmd
-        - reference/parser.base.line_annotations.qmd
-        - reference/parser.base.sphere_annotations.qmd
-        - reference/parser.base.group_annotations.qmd
-        - reference/parser.base.extract_multicut.qmd
-        - reference/parser.base.annotation_dataframe.qmd
-        section: Parser Tools
-      section: Parser
-    id: reference
-  - id: dummy-sidebar
diff --git a/docs/_site/about.html b/docs/_site/about.html
deleted file mode 100644
index 968c43b..0000000
--- a/docs/_site/about.html
+++ /dev/null
@@ -1,381 +0,0 @@
-<!DOCTYPE html>
-<html xmlns="http://www.w3.org/1999/xhtml" lang="en" xml:lang="en"><head>
-
-<meta charset="utf-8">
-<meta name="generator" content="quarto-1.3.450">
-
-<meta name="viewport" content="width=device-width, initial-scale=1.0, user-scalable=yes">
-
-
-<title>NGLui Documentation - About</title>
-<style>
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-div.columns{display: flex; gap: min(4vw, 1.5em);}
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-    <span class="navbar-title">NGLui Documentation</span>
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- <span class="menu-text">About</span></a>
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- <span class="menu-text">Tutorials</span>
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- <span class="dropdown-text">StateBuilder Tutorial</span></a>
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- <span class="dropdown-text">Parser Tutorial</span></a>
-  </li>  
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diff --git a/docs/_site/reference/AnnotationLayerConfig.html b/docs/_site/reference/AnnotationLayerConfig.html
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index 7baecc0..0000000
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-<tr class="odd">
-<td><code>name</code></td>
-<td>str</td>
-<td>Layer name. By default, ‘annos’</td>
-<td><code>None</code></td>
-</tr>
-<tr class="even">
-<td><code>color</code></td>
-<td>str</td>
-<td>Hex color code with an initial #. By default, None</td>
-<td><code>None</code></td>
-</tr>
-<tr class="odd">
-<td><code>linked_segmentation_layer</code></td>
-<td>str</td>
-<td>Name of a linked segmentation layer for selected ids. By default, None</td>
-<td><code>None</code></td>
-</tr>
-<tr class="even">
-<td><code>mapping_rules</code></td>
-<td>(nglui.statebuilder.mappers.PointMapper, nglui.statebuilder.mappers.LineMapper, nglui.statebuilder.mappers.SphereMapper or list)</td>
-<td>One rule or a list of rules mapping data to annotations. By default, []</td>
-<td><code>[]</code></td>
-</tr>
-<tr class="odd">
-<td><code>array_data</code></td>
-<td>bool</td>
-<td>If True, allows simple mapping where one or more arrays are passed instead of a dataframe. Only allows basic annotation creation, no tags, linked segmentations, or other rich features.</td>
-<td><code>False</code></td>
-</tr>
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-<td><code>None</code></td>
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-<tr class="odd">
-<td><code>active</code></td>
-<td>bool</td>
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-<h1>ChainedStateBuilder</h1>
-<p><code>statebuilder.statebuilder.ChainedStateBuilder(self, statebuilders)</code></p>
-<p>Builds a collection of states that sequentially add annotations based on a sequence of dataframes.</p>
-<section id="parameters" class="level2">
-<h2 class="anchored" data-anchor-id="parameters">Parameters</h2>
-<table class="table">
-<colgroup>
-<col style="width: 15%">
-<col style="width: 7%">
-<col style="width: 65%">
-<col style="width: 11%">
-</colgroup>
-<thead>
-<tr class="header">
-<th>Name</th>
-<th>Type</th>
-<th>Description</th>
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-</tr>
-</thead>
-<tbody>
-<tr class="odd">
-<td><code>statebuilders</code></td>
-<td>list</td>
-<td>List of DataStateBuilders, in same order as dataframes will be passed</td>
-<td><em>required</em></td>
-</tr>
-</tbody>
-</table>
-</section>
-<section id="methods" class="level2">
-<h2 class="anchored" data-anchor-id="methods">Methods</h2>
-<table class="table">
-<thead>
-<tr class="header">
-<th>Name</th>
-<th>Description</th>
-</tr>
-</thead>
-<tbody>
-<tr class="odd">
-<td><a href="#nglui.statebuilder.statebuilder.ChainedStateBuilder.render_state">render_state</a></td>
-<td>Generate a single neuroglancer state by addatively applying an ordered collection of</td>
-</tr>
-</tbody>
-</table>
-<section id="nglui.statebuilder.statebuilder.ChainedStateBuilder.render_state" class="level3">
-<h3 class="anchored" data-anchor-id="nglui.statebuilder.statebuilder.ChainedStateBuilder.render_state">render_state</h3>
-<p><code>statebuilder.statebuilder.ChainedStateBuilder.render_state(data_list=None, base_state=None, return_as='url', url_prefix=default_neuroglancer_base, link_text='Neuroglancer Link', target_site=None)</code></p>
-<p>Generate a single neuroglancer state by addatively applying an ordered collection of dataframes to an collection of StateBuilder renders. Parameters data_list : Collection of DataFrame. The order must match the order of StateBuilders contained in the class on creation. base_state : JSON neuroglancer state (optional, default is None). Used as a base state for adding everything else to. return_as: [‘url’, ‘viewer’, ‘html’, ‘json’]. optional, default=‘url’. Sets how the state is returned. Note that if a viewer is returned, the state is not reset to default. url_prefix: string, optional (default is https://neuromancer-seung-import.appspot.com). Overrides the default neuroglancer url for url generation.</p>
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-<section id="nglui.statebuilder.layers.ImageLayerConfig" class="level1">
-<h1>ImageLayerConfig</h1>
-<p><code>statebuilder.layers.ImageLayerConfig(self, source, name=None, active=False, contrast_controls=False, black=0.0, white=1.0)</code></p>
-<p>Image layer configuration class.</p>
-<p>This provides the rules for setting up an image layer in neuroglancer.</p>
-<section id="parameters" class="level2">
-<h2 class="anchored" data-anchor-id="parameters">Parameters</h2>
-<table class="table">
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-<col style="width: 70%">
-<col style="width: 8%">
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-<thead>
-<tr class="header">
-<th>Name</th>
-<th>Type</th>
-<th>Description</th>
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-</thead>
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-<tr class="odd">
-<td><code>source</code></td>
-<td>str</td>
-<td>Cloudpath to an image source</td>
-<td><em>required</em></td>
-</tr>
-<tr class="even">
-<td><code>name</code></td>
-<td>str</td>
-<td>Name of the image layer. By default, ‘img’.</td>
-<td><code>None</code></td>
-</tr>
-<tr class="odd">
-<td><code>active</code></td>
-<td>bool</td>
-<td>If True, makes the layer active in neuroglancer. Default is False.</td>
-<td><code>False</code></td>
-</tr>
-<tr class="even">
-<td><code>contrast_controls</code></td>
-<td>bool</td>
-<td>If True, gives the layer a user-controllable brightness and contrast shader. Default is False.</td>
-<td><code>False</code></td>
-</tr>
-<tr class="odd">
-<td><code>black</code></td>
-<td>float</td>
-<td>If contrast_controls is True, sets the default black level. Default is 0.0.</td>
-<td><code>0.0</code></td>
-</tr>
-<tr class="even">
-<td><code>white</code></td>
-<td>float</td>
-<td>If contrast_controls is True, sets the default white level. Default is 1.0.</td>
-<td><code>1.0</code></td>
-</tr>
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-<section id="nglui.statebuilder.layers.SegmentationLayerConfig" class="level1">
-<h1>SegmentationLayerConfig</h1>
-<p><code>statebuilder.layers.SegmentationLayerConfig(self, source, name=None, selected_ids_column=None, fixed_ids=None, fixed_id_colors=None, color_column=None, active=False, alpha_selected=0.3, alpha_3d=1, alpha_unselected=0, split_point_map=None, view_kws=None, timestamp=None, data_resolution=None)</code></p>
-<p>Configuration class for segmentation layers</p>
-<section id="parameters" class="level2">
-<h2 class="anchored" data-anchor-id="parameters">Parameters</h2>
-<table class="table">
-<colgroup>
-<col style="width: 8%">
-<col style="width: 11%">
-<col style="width: 75%">
-<col style="width: 4%">
-</colgroup>
-<thead>
-<tr class="header">
-<th>Name</th>
-<th>Type</th>
-<th>Description</th>
-<th>Default</th>
-</tr>
-</thead>
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-<tr class="odd">
-<td><code>source</code></td>
-<td>str</td>
-<td>Segmentation source</td>
-<td><em>required</em></td>
-</tr>
-<tr class="even">
-<td><code>name</code></td>
-<td>(str, optional)</td>
-<td>Layer name.</td>
-<td><code>None</code></td>
-</tr>
-<tr class="odd">
-<td><code>selected_ids_column</code></td>
-<td>str or list-like, optional.</td>
-<td>Column name (or list of column names) to use for selected ids.</td>
-<td><code>None</code></td>
-</tr>
-<tr class="even">
-<td><code>fixed_ids</code></td>
-<td>list-like, optional.</td>
-<td>List of root ids to select directly.</td>
-<td><code>None</code></td>
-</tr>
-<tr class="odd">
-<td><code>fixed_id_colors</code></td>
-<td>list-like, optional.</td>
-<td>List of colors for fixed ids. Should be the same length as fixed_ids, although null entries can be padded with None values.</td>
-<td><code>None</code></td>
-</tr>
-<tr class="even">
-<td><code>color_column</code></td>
-<td>str, optional.</td>
-<td># at the begining. Column to use for color values for selected objects. Values should be RGB hex strings with a</td>
-<td><code>None</code></td>
-</tr>
-<tr class="odd">
-<td><code>active</code></td>
-<td>bool, optional.</td>
-<td>If True, makes the layer selected. Default is False.</td>
-<td><code>False</code></td>
-</tr>
-<tr class="even">
-<td><code>alpha_selected</code></td>
-<td></td>
-<td>Opacity of selected segmentations in the image layer. Optional, default is 0.3.</td>
-<td><code>0.3</code></td>
-</tr>
-<tr class="odd">
-<td><code>alpha_3d</code></td>
-<td></td>
-<td>Opacity of meshes. Optional, default is 1.</td>
-<td><code>1</code></td>
-</tr>
-<tr class="even">
-<td><code>alpha_unselected</code></td>
-<td></td>
-<td>Opacity of unselected segments. Optional, default is 0.</td>
-<td><code>0</code></td>
-</tr>
-<tr class="odd">
-<td><code>split_point_map</code></td>
-<td></td>
-<td>If not None, provides an object to map the dataframe input to multicut points. Default is None.</td>
-<td><code>None</code></td>
-</tr>
-<tr class="even">
-<td><code>view_kws</code></td>
-<td>dict, optional.</td>
-<td>Keyword arguments for viewer.set_segmentation_view_options. Sets selected (and unselected) segmetation alpha values. Defaults to values in DEFAULT_SEGMENTATION_VIEW_KWS dict specified in this module.</td>
-<td><code>None</code></td>
-</tr>
-<tr class="odd">
-<td><code>timestamp</code></td>
-<td>float or datetime, optional.</td>
-<td>Timestamp at which to fix the chunkedgraph in either unix epoch or datetime format. Optional, default is None.</td>
-<td><code>None</code></td>
-</tr>
-</tbody>
-</table>
-</section>
-<section id="methods" class="level2">
-<h2 class="anchored" data-anchor-id="methods">Methods</h2>
-<table class="table">
-<thead>
-<tr class="header">
-<th>Name</th>
-<th>Description</th>
-</tr>
-</thead>
-<tbody>
-<tr class="odd">
-<td><a href="#nglui.statebuilder.layers.SegmentationLayerConfig.add_selection_map">add_selection_map</a></td>
-<td>Add rules for selecting active segment ids and their colors</td>
-</tr>
-</tbody>
-</table>
-<section id="nglui.statebuilder.layers.SegmentationLayerConfig.add_selection_map" class="level3">
-<h3 class="anchored" data-anchor-id="nglui.statebuilder.layers.SegmentationLayerConfig.add_selection_map">add_selection_map</h3>
-<p><code>statebuilder.layers.SegmentationLayerConfig.add_selection_map(selected_ids_column=None, fixed_ids=None, fixed_id_colors=None, color_column=None)</code></p>
-<p>Add rules for selecting active segment ids and their colors</p>
-<section id="parameters-1" class="level4">
-<h4 class="anchored" data-anchor-id="parameters-1">Parameters</h4>
-<table class="table">
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-<col style="width: 15%">
-<col style="width: 8%">
-<col style="width: 68%">
-<col style="width: 7%">
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-<th>Name</th>
-<th>Type</th>
-<th>Description</th>
-<th>Default</th>
-</tr>
-</thead>
-<tbody>
-<tr class="odd">
-<td><code>selected_ids_column</code></td>
-<td>str</td>
-<td>Dataframe column to use for adding selected segment ids to the segmentation layer, by default None</td>
-<td><code>None</code></td>
-</tr>
-<tr class="even">
-<td><code>fixed_ids</code></td>
-<td>int or list</td>
-<td>Add one or more segment ids to be active, independent of the data, by default None</td>
-<td><code>None</code></td>
-</tr>
-<tr class="odd">
-<td><code>fixed_id_colors</code></td>
-<td>list</td>
-<td>Add a list of colors (hex, rgb, or CSS3 string) to assign to the fixed ids, by default None</td>
-<td><code>None</code></td>
-</tr>
-<tr class="even">
-<td><code>color_column</code></td>
-<td>str</td>
-<td>Dataframe column to use for adding selected segment colors, by default None</td>
-<td><code>None</code></td>
-</tr>
-</tbody>
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-<h1>get_object</h1>
-<p><code>get_object(path, object_name=None, parser='numpy', load_aliases=True, dynamic=False, loader=None)</code></p>
-<p>Fetch a griffe object.</p>
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-<p>preview: print a user-friendly preview of a griffe object.</p>
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-<div class="sourceCode" id="cb1"><pre class="sourceCode python code-with-copy"><code class="sourceCode python"><span id="cb1-1"><a href="#cb1-1" aria-hidden="true" tabindex="-1"></a><span class="op">&gt;&gt;&gt;</span> get_function(<span class="st">"quartodoc"</span>, <span class="st">"get_function"</span>)</span>
-<span id="cb1-2"><a href="#cb1-2" aria-hidden="true" tabindex="-1"></a><span class="op">&lt;</span>Function(<span class="st">'get_function'</span>, ...</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
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-<th>Type</th>
-<th>Description</th>
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-<section id="function-intro" class="level1">
-<h1>Function Intro</h1>
-<p>This site provides basic documentation for the functions in <code>NGLui</code>. Please see the <a href="../tutorials/index.html">tutorials</a> for more information about how to use them.</p>
-<p>Note that <code>nglui</code> spans two public submodules responsible for different tasks.</p>
-<ul>
-<li><code>StateBuilder</code> handles data-driven Neuroglancer state generation (hence the package name).</li>
-<li><code>Parser</code> extracts information from Neuroglancer states, as represented by dictionaries.</li>
-</ul>
-<hr>
-</section>
-<section id="section" class="level1 doc doc-index">
-<h1 class="doc doc-index"></h1>
-<section id="statebuilder-functions" class="level2">
-<h2 class="anchored" data-anchor-id="statebuilder-functions">StateBuilder Functions</h2>
-<section id="layers" class="level3">
-<h3 class="anchored" data-anchor-id="layers">Layers</h3>
-<p>Instantiating types of layers</p>
-<table class="table">
-<tbody>
-<tr class="odd">
-<td><a href="../reference/statebuilder.ImageLayerConfig.html#nglui.statebuilder.ImageLayerConfig">statebuilder.ImageLayerConfig</a></td>
-<td>Image layer configuration class.</td>
-</tr>
-<tr class="even">
-<td><a href="../reference/statebuilder.SegmentationLayerConfig.html#nglui.statebuilder.SegmentationLayerConfig">statebuilder.SegmentationLayerConfig</a></td>
-<td>Configuration class for segmentation layers</td>
-</tr>
-<tr class="odd">
-<td><a href="../reference/statebuilder.AnnotationLayerConfig.html#nglui.statebuilder.AnnotationLayerConfig">statebuilder.AnnotationLayerConfig</a></td>
-<td>Configuration class for annotation layers</td>
-</tr>
-</tbody>
-</table>
-</section>
-<section id="mapping-rules" class="level3">
-<h3 class="anchored" data-anchor-id="mapping-rules">Mapping Rules</h3>
-<p>Rules for mapping data to annotations</p>
-<table class="table">
-<tbody>
-<tr class="odd">
-<td><a href="../reference/statebuilder.PointMapper.html#nglui.statebuilder.PointMapper">statebuilder.PointMapper</a></td>
-<td>Sets rules to map dataframes to point annotations</td>
-</tr>
-<tr class="even">
-<td><a href="../reference/statebuilder.LineMapper.html#nglui.statebuilder.LineMapper">statebuilder.LineMapper</a></td>
-<td>Sets rules to map dataframes to line annotations</td>
-</tr>
-<tr class="odd">
-<td><a href="../reference/statebuilder.SphereMapper.html#nglui.statebuilder.SphereMapper">statebuilder.SphereMapper</a></td>
-<td>Sets rules to map dataframes to sphere annotations</td>
-</tr>
-<tr class="even">
-<td><a href="../reference/statebuilder.BoundingBoxMapper.html#nglui.statebuilder.BoundingBoxMapper">statebuilder.BoundingBoxMapper</a></td>
-<td>Sets rules to map dataframes to bounding box annotations</td>
-</tr>
-<tr class="odd">
-<td><a href="../reference/statebuilder.SplitPointMapper.html#nglui.statebuilder.SplitPointMapper">statebuilder.SplitPointMapper</a></td>
-<td>Mapper to create split points in a segmentation layer.</td>
-</tr>
-</tbody>
-</table>
-</section>
-<section id="statebuilder-classes" class="level3">
-<h3 class="anchored" data-anchor-id="statebuilder-classes">StateBuilder Classes</h3>
-<p>Tools for data-generated neuroglancer state creation</p>
-<table class="table">
-<tbody>
-<tr class="odd">
-<td><a href="../reference/statebuilder.StateBuilder.html#nglui.statebuilder.StateBuilder">statebuilder.StateBuilder</a></td>
-<td>A class for schematic mapping data frames into neuroglancer states.</td>
-</tr>
-<tr class="even">
-<td><a href="../reference/statebuilder.ChainedStateBuilder.html#nglui.statebuilder.ChainedStateBuilder">statebuilder.ChainedStateBuilder</a></td>
-<td>Builds a collection of states that sequentially add annotations based on a sequence of dataframes.</td>
-</tr>
-</tbody>
-</table>
-</section>
-<section id="helpers" class="level3">
-<h3 class="anchored" data-anchor-id="helpers">Helpers</h3>
-<p>Tools for common types of states</p>
-<table class="table">
-<tbody>
-<tr class="odd">
-<td><a href="../reference/statebuilder.helpers.from_client.html#nglui.statebuilder.helpers.from_client">statebuilder.helpers.from_client</a></td>
-<td>Generate basic image and segmentation layers from a FrameworkClient</td>
-</tr>
-<tr class="even">
-<td><a href="../reference/statebuilder.helpers.sort_dataframe_by_root_id.html#nglui.statebuilder.helpers.sort_dataframe_by_root_id">statebuilder.helpers.sort_dataframe_by_root_id</a></td>
-<td>Sort a dataframe so that rows belonging to the same root id are together, ordered by how many times the root id appears.</td>
-</tr>
-<tr class="odd">
-<td><a href="../reference/statebuilder.helpers.make_line_statebuilder.html#nglui.statebuilder.helpers.make_line_statebuilder">statebuilder.helpers.make_line_statebuilder</a></td>
-<td>Generate a state builder that puts points on a single column with a linked segmentaton id</td>
-</tr>
-<tr class="even">
-<td><a href="../reference/statebuilder.helpers.make_point_statebuilder.html#nglui.statebuilder.helpers.make_point_statebuilder">statebuilder.helpers.make_point_statebuilder</a></td>
-<td>Generate a state builder that puts points on a single column with a linked segmentaton id</td>
-</tr>
-<tr class="odd">
-<td><a href="../reference/statebuilder.helpers.make_pre_post_statebuilder.html#nglui.statebuilder.helpers.make_pre_post_statebuilder">statebuilder.helpers.make_pre_post_statebuilder</a></td>
-<td>Function to generate ChainedStateBuilder with optional pre and post synaptic</td>
-</tr>
-<tr class="even">
-<td><a href="../reference/statebuilder.helpers.make_state_url.html#nglui.statebuilder.helpers.make_state_url">statebuilder.helpers.make_state_url</a></td>
-<td>Generate a url from a neuroglancer state via a state server.</td>
-</tr>
-<tr class="odd">
-<td><a href="../reference/statebuilder.helpers.make_url_robust.html#nglui.statebuilder.helpers.make_url_robust">statebuilder.helpers.make_url_robust</a></td>
-<td>Generate a url from a neuroglancer state. If too long, return through state server,</td>
-</tr>
-<tr class="even">
-<td><a href="../reference/statebuilder.helpers.package_state.html#nglui.statebuilder.helpers.package_state">statebuilder.helpers.package_state</a></td>
-<td>Automate creating a state from a statebuilder and</td>
-</tr>
-<tr class="odd">
-<td><a href="../reference/statebuilder.helpers.make_synapse_neuroglancer_link.html#nglui.statebuilder.helpers.make_synapse_neuroglancer_link">statebuilder.helpers.make_synapse_neuroglancer_link</a></td>
-<td>Generate a neuroglancer link from a synapse dataframe as returned from CAVEclient.materialize.synapse_query.</td>
-</tr>
-<tr class="even">
-<td><a href="../reference/statebuilder.helpers.make_neuron_neuroglancer_link.html#nglui.statebuilder.helpers.make_neuron_neuroglancer_link">statebuilder.helpers.make_neuron_neuroglancer_link</a></td>
-<td>function to create a neuroglancer link view of a neuron, optionally including inputs and outputs</td>
-</tr>
-</tbody>
-</table>
-</section>
-</section>
-<section id="parser" class="level2">
-<h2 class="anchored" data-anchor-id="parser">Parser</h2>
-<section id="parser-tools" class="level3">
-<h3 class="anchored" data-anchor-id="parser-tools">Parser Tools</h3>
-<p>Simple tools for parsing neuroglancer states</p>
-<table class="table">
-<tbody>
-<tr class="odd">
-<td><a href="../reference/parser.base.layer_names.html#nglui.parser.base.layer_names">parser.base.layer_names</a></td>
-<td>Get all layer names in the state</td>
-</tr>
-<tr class="even">
-<td><a href="../reference/parser.base.image_layers.html#nglui.parser.base.image_layers">parser.base.image_layers</a></td>
-<td>Get all image layer names in the state</td>
-</tr>
-<tr class="odd">
-<td><a href="../reference/parser.base.segmentation_layers.html#nglui.parser.base.segmentation_layers">parser.base.segmentation_layers</a></td>
-<td>Get all segmentation layer names in the state</td>
-</tr>
-<tr class="even">
-<td><a href="../reference/parser.base.annotation_layers.html#nglui.parser.base.annotation_layers">parser.base.annotation_layers</a></td>
-<td>Get all annotation layer names in the state</td>
-</tr>
-<tr class="odd">
-<td><a href="../reference/parser.base.tag_dictionary.html#nglui.parser.base.tag_dictionary">parser.base.tag_dictionary</a></td>
-<td>Get the tag id to string dictionary for a layer</td>
-</tr>
-<tr class="even">
-<td><a href="../reference/parser.base.get_layer.html#nglui.parser.base.get_layer">parser.base.get_layer</a></td>
-<td>Gets the contents of the layer based on the layer name.</td>
-</tr>
-<tr class="odd">
-<td><a href="../reference/parser.base.view_settings.html#nglui.parser.base.view_settings">parser.base.view_settings</a></td>
-<td>Get all data about the view state in neuroglancer: position,</td>
-</tr>
-<tr class="even">
-<td><a href="../reference/parser.base.get_selected_ids.html#nglui.parser.base.get_selected_ids">parser.base.get_selected_ids</a></td>
-<td>Get a list of selected ids in a segmentation layer</td>
-</tr>
-<tr class="odd">
-<td><a href="../reference/parser.base.point_annotations.html#nglui.parser.base.point_annotations">parser.base.point_annotations</a></td>
-<td>Get all point annotation points and other info from a layer.</td>
-</tr>
-<tr class="even">
-<td><a href="../reference/parser.base.line_annotations.html#nglui.parser.base.line_annotations">parser.base.line_annotations</a></td>
-<td>Get all line annotation points and other info from a layer.</td>
-</tr>
-<tr class="odd">
-<td><a href="../reference/parser.base.sphere_annotations.html#nglui.parser.base.sphere_annotations">parser.base.sphere_annotations</a></td>
-<td>Get all sphere annotation points and other info from a layer.</td>
-</tr>
-<tr class="even">
-<td><a href="../reference/parser.base.group_annotations.html#nglui.parser.base.group_annotations">parser.base.group_annotations</a></td>
-<td>All group annotations and their associated points</td>
-</tr>
-<tr class="odd">
-<td><a href="../reference/parser.base.extract_multicut.html#nglui.parser.base.extract_multicut">parser.base.extract_multicut</a></td>
-<td>Extract information entered into the multicut graph operation</td>
-</tr>
-<tr class="even">
-<td><a href="../reference/parser.base.annotation_dataframe.html#nglui.parser.base.annotation_dataframe">parser.base.annotation_dataframe</a></td>
-<td>Return all annotations across all annotation layers in the state.</td>
-</tr>
-</tbody>
-</table>
-
-
-</section>
-</section>
-</section>
-
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-<section id="nglui.statebuilder.layers.AnnotationLayerConfig" class="level1">
-<h1>layers.AnnotationLayerConfig</h1>
-<p><code>statebuilder.layers.AnnotationLayerConfig(self, name=None, color=None, linked_segmentation_layer=None, mapping_rules=[], array_data=False, tags=None, active=True, filter_by_segmentation=False, brackets_show_segmentation=True, selection_shows_segmentation=True, filter_query=None, data_resolution=None)</code></p>
-<p>Configuration class for annotation layers</p>
-<section id="parameters" class="level2">
-<h2 class="anchored" data-anchor-id="parameters">Parameters</h2>
-<table class="table">
-<colgroup>
-<col style="width: 8%">
-<col style="width: 36%">
-<col style="width: 52%">
-<col style="width: 3%">
-</colgroup>
-<thead>
-<tr class="header">
-<th>Name</th>
-<th>Type</th>
-<th>Description</th>
-<th>Default</th>
-</tr>
-</thead>
-<tbody>
-<tr class="odd">
-<td><code>name</code></td>
-<td>str</td>
-<td>Layer name. By default, ‘annos’</td>
-<td><code>None</code></td>
-</tr>
-<tr class="even">
-<td><code>color</code></td>
-<td>str</td>
-<td>Hex color code with an initial #. By default, None</td>
-<td><code>None</code></td>
-</tr>
-<tr class="odd">
-<td><code>linked_segmentation_layer</code></td>
-<td>str</td>
-<td>Name of a linked segmentation layer for selected ids. By default, None</td>
-<td><code>None</code></td>
-</tr>
-<tr class="even">
-<td><code>mapping_rules</code></td>
-<td>(nglui.statebuilder.mappers.PointMapper, nglui.statebuilder.mappers.LineMapper, nglui.statebuilder.mappers.SphereMapper or list)</td>
-<td>One rule or a list of rules mapping data to annotations. By default, []</td>
-<td><code>[]</code></td>
-</tr>
-<tr class="odd">
-<td><code>array_data</code></td>
-<td>bool</td>
-<td>If True, allows simple mapping where one or more arrays are passed instead of a dataframe. Only allows basic annotation creation, no tags, linked segmentations, or other rich features.</td>
-<td><code>False</code></td>
-</tr>
-<tr class="even">
-<td><code>tags</code></td>
-<td>list</td>
-<td>List of tags for the layer.</td>
-<td><code>None</code></td>
-</tr>
-<tr class="odd">
-<td><code>active</code></td>
-<td>bool</td>
-<td>If True, makes the layer selected. Default is True (unlike for image/segmentation layers).</td>
-<td><code>True</code></td>
-</tr>
-</tbody>
-</table>
-
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-<section id="nglui.statebuilder.layers.ImageLayerConfig" class="level1">
-<h1>layers.ImageLayerConfig</h1>
-<p><code>statebuilder.layers.ImageLayerConfig(self, source, name=None, active=False, contrast_controls=False, black=0.0, white=1.0)</code></p>
-<p>Image layer configuration class.</p>
-<p>This provides the rules for setting up an image layer in neuroglancer.</p>
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-<td><code>source</code></td>
-<td>str</td>
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-<td><em>required</em></td>
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-<td><code>name</code></td>
-<td>str</td>
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-<td><code>None</code></td>
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-<td><code>active</code></td>
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-<section id="nglui.statebuilder.layers.SegmentationLayerConfig" class="level1">
-<h1>layers.SegmentationLayerConfig</h1>
-<p><code>statebuilder.layers.SegmentationLayerConfig(self, source, name=None, selected_ids_column=None, fixed_ids=None, fixed_id_colors=None, color_column=None, active=False, alpha_selected=0.3, alpha_3d=1, alpha_unselected=0, split_point_map=None, view_kws=None, timestamp=None, data_resolution=None)</code></p>
-<p>Configuration class for segmentation layers</p>
-<section id="parameters" class="level2">
-<h2 class="anchored" data-anchor-id="parameters">Parameters</h2>
-<table class="table">
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-<col style="width: 8%">
-<col style="width: 11%">
-<col style="width: 75%">
-<col style="width: 4%">
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-<th>Name</th>
-<th>Type</th>
-<th>Description</th>
-<th>Default</th>
-</tr>
-</thead>
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-<tr class="odd">
-<td><code>source</code></td>
-<td>str</td>
-<td>Segmentation source</td>
-<td><em>required</em></td>
-</tr>
-<tr class="even">
-<td><code>name</code></td>
-<td>(str, optional)</td>
-<td>Layer name.</td>
-<td><code>None</code></td>
-</tr>
-<tr class="odd">
-<td><code>selected_ids_column</code></td>
-<td>str or list-like, optional.</td>
-<td>Column name (or list of column names) to use for selected ids.</td>
-<td><code>None</code></td>
-</tr>
-<tr class="even">
-<td><code>fixed_ids</code></td>
-<td>list-like, optional.</td>
-<td>List of root ids to select directly.</td>
-<td><code>None</code></td>
-</tr>
-<tr class="odd">
-<td><code>fixed_id_colors</code></td>
-<td>list-like, optional.</td>
-<td>List of colors for fixed ids. Should be the same length as fixed_ids, although null entries can be padded with None values.</td>
-<td><code>None</code></td>
-</tr>
-<tr class="even">
-<td><code>color_column</code></td>
-<td>str, optional.</td>
-<td># at the begining. Column to use for color values for selected objects. Values should be RGB hex strings with a</td>
-<td><code>None</code></td>
-</tr>
-<tr class="odd">
-<td><code>active</code></td>
-<td>bool, optional.</td>
-<td>If True, makes the layer selected. Default is False.</td>
-<td><code>False</code></td>
-</tr>
-<tr class="even">
-<td><code>alpha_selected</code></td>
-<td></td>
-<td>Opacity of selected segmentations in the image layer. Optional, default is 0.3.</td>
-<td><code>0.3</code></td>
-</tr>
-<tr class="odd">
-<td><code>alpha_3d</code></td>
-<td></td>
-<td>Opacity of meshes. Optional, default is 1.</td>
-<td><code>1</code></td>
-</tr>
-<tr class="even">
-<td><code>alpha_unselected</code></td>
-<td></td>
-<td>Opacity of unselected segments. Optional, default is 0.</td>
-<td><code>0</code></td>
-</tr>
-<tr class="odd">
-<td><code>split_point_map</code></td>
-<td></td>
-<td>If not None, provides an object to map the dataframe input to multicut points. Default is None.</td>
-<td><code>None</code></td>
-</tr>
-<tr class="even">
-<td><code>view_kws</code></td>
-<td>dict, optional.</td>
-<td>Keyword arguments for viewer.set_segmentation_view_options. Sets selected (and unselected) segmetation alpha values. Defaults to values in DEFAULT_SEGMENTATION_VIEW_KWS dict specified in this module.</td>
-<td><code>None</code></td>
-</tr>
-<tr class="odd">
-<td><code>timestamp</code></td>
-<td>float or datetime, optional.</td>
-<td>Timestamp at which to fix the chunkedgraph in either unix epoch or datetime format. Optional, default is None.</td>
-<td><code>None</code></td>
-</tr>
-</tbody>
-</table>
-</section>
-<section id="methods" class="level2">
-<h2 class="anchored" data-anchor-id="methods">Methods</h2>
-<table class="table">
-<thead>
-<tr class="header">
-<th>Name</th>
-<th>Description</th>
-</tr>
-</thead>
-<tbody>
-<tr class="odd">
-<td><a href="#nglui.statebuilder.layers.SegmentationLayerConfig.add_selection_map">add_selection_map</a></td>
-<td>Add rules for selecting active segment ids and their colors</td>
-</tr>
-</tbody>
-</table>
-<section id="nglui.statebuilder.layers.SegmentationLayerConfig.add_selection_map" class="level3">
-<h3 class="anchored" data-anchor-id="nglui.statebuilder.layers.SegmentationLayerConfig.add_selection_map">add_selection_map</h3>
-<p><code>statebuilder.layers.SegmentationLayerConfig.add_selection_map(selected_ids_column=None, fixed_ids=None, fixed_id_colors=None, color_column=None)</code></p>
-<p>Add rules for selecting active segment ids and their colors</p>
-<section id="parameters-1" class="level4">
-<h4 class="anchored" data-anchor-id="parameters-1">Parameters</h4>
-<table class="table">
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-<col style="width: 15%">
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-<col style="width: 7%">
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-<th>Name</th>
-<th>Type</th>
-<th>Description</th>
-<th>Default</th>
-</tr>
-</thead>
-<tbody>
-<tr class="odd">
-<td><code>selected_ids_column</code></td>
-<td>str</td>
-<td>Dataframe column to use for adding selected segment ids to the segmentation layer, by default None</td>
-<td><code>None</code></td>
-</tr>
-<tr class="even">
-<td><code>fixed_ids</code></td>
-<td>int or list</td>
-<td>Add one or more segment ids to be active, independent of the data, by default None</td>
-<td><code>None</code></td>
-</tr>
-<tr class="odd">
-<td><code>fixed_id_colors</code></td>
-<td>list</td>
-<td>Add a list of colors (hex, rgb, or CSS3 string) to assign to the fixed ids, by default None</td>
-<td><code>None</code></td>
-</tr>
-<tr class="even">
-<td><code>color_column</code></td>
-<td>str</td>
-<td>Dataframe column to use for adding selected segment colors, by default None</td>
-<td><code>None</code></td>
-</tr>
-</tbody>
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-
-<section id="nglui.statebuilder.layers" class="level1">
-<h1>layers</h1>
-<p><code>statebuilder.layers</code></p>
-<section id="classes" class="level2">
-<h2 class="anchored" data-anchor-id="classes">Classes</h2>
-<table class="table">
-<thead>
-<tr class="header">
-<th>Name</th>
-<th>Description</th>
-</tr>
-</thead>
-<tbody>
-<tr class="odd">
-<td><a href="#nglui.statebuilder.layers.AnnotationLayerConfig">AnnotationLayerConfig</a></td>
-<td>Configuration class for annotation layers</td>
-</tr>
-<tr class="even">
-<td><a href="#nglui.statebuilder.layers.ImageLayerConfig">ImageLayerConfig</a></td>
-<td>Image layer configuration class.</td>
-</tr>
-<tr class="odd">
-<td><a href="#nglui.statebuilder.layers.LayerConfigBase">LayerConfigBase</a></td>
-<td>Base class for configuring layers</td>
-</tr>
-<tr class="even">
-<td><a href="#nglui.statebuilder.layers.SegmentationLayerConfig">SegmentationLayerConfig</a></td>
-<td>Configuration class for segmentation layers</td>
-</tr>
-</tbody>
-</table>
-</section>
-<section id="nglui.statebuilder.layers.AnnotationLayerConfig" class="level2">
-<h2 class="anchored" data-anchor-id="nglui.statebuilder.layers.AnnotationLayerConfig">AnnotationLayerConfig</h2>
-<p><code>statebuilder.layers.AnnotationLayerConfig(self, name=None, color=None, linked_segmentation_layer=None, mapping_rules=[], array_data=False, tags=None, active=True, filter_by_segmentation=False, brackets_show_segmentation=True, selection_shows_segmentation=True, filter_query=None, data_resolution=None)</code></p>
-<p>Configuration class for annotation layers</p>
-<section id="parameters" class="level3">
-<h3 class="anchored" data-anchor-id="parameters">Parameters</h3>
-<table class="table">
-<colgroup>
-<col style="width: 8%">
-<col style="width: 36%">
-<col style="width: 52%">
-<col style="width: 3%">
-</colgroup>
-<thead>
-<tr class="header">
-<th>Name</th>
-<th>Type</th>
-<th>Description</th>
-<th>Default</th>
-</tr>
-</thead>
-<tbody>
-<tr class="odd">
-<td><code>name</code></td>
-<td>str</td>
-<td>Layer name. By default, ‘annos’</td>
-<td><code>None</code></td>
-</tr>
-<tr class="even">
-<td><code>color</code></td>
-<td>str</td>
-<td>Hex color code with an initial #. By default, None</td>
-<td><code>None</code></td>
-</tr>
-<tr class="odd">
-<td><code>linked_segmentation_layer</code></td>
-<td>str</td>
-<td>Name of a linked segmentation layer for selected ids. By default, None</td>
-<td><code>None</code></td>
-</tr>
-<tr class="even">
-<td><code>mapping_rules</code></td>
-<td>(nglui.statebuilder.mappers.PointMapper, nglui.statebuilder.mappers.LineMapper, nglui.statebuilder.mappers.SphereMapper or list)</td>
-<td>One rule or a list of rules mapping data to annotations. By default, []</td>
-<td><code>[]</code></td>
-</tr>
-<tr class="odd">
-<td><code>array_data</code></td>
-<td>bool</td>
-<td>If True, allows simple mapping where one or more arrays are passed instead of a dataframe. Only allows basic annotation creation, no tags, linked segmentations, or other rich features.</td>
-<td><code>False</code></td>
-</tr>
-<tr class="even">
-<td><code>tags</code></td>
-<td>list</td>
-<td>List of tags for the layer.</td>
-<td><code>None</code></td>
-</tr>
-<tr class="odd">
-<td><code>active</code></td>
-<td>bool</td>
-<td>If True, makes the layer selected. Default is True (unlike for image/segmentation layers).</td>
-<td><code>True</code></td>
-</tr>
-</tbody>
-</table>
-</section>
-</section>
-<section id="nglui.statebuilder.layers.ImageLayerConfig" class="level2">
-<h2 class="anchored" data-anchor-id="nglui.statebuilder.layers.ImageLayerConfig">ImageLayerConfig</h2>
-<p><code>statebuilder.layers.ImageLayerConfig(self, source, name=None, active=False, contrast_controls=False, black=0.0, white=1.0)</code></p>
-<p>Image layer configuration class.</p>
-<p>This provides the rules for setting up an image layer in neuroglancer.</p>
-<section id="parameters-1" class="level3">
-<h3 class="anchored" data-anchor-id="parameters-1">Parameters</h3>
-<table class="table">
-<colgroup>
-<col style="width: 15%">
-<col style="width: 5%">
-<col style="width: 70%">
-<col style="width: 8%">
-</colgroup>
-<thead>
-<tr class="header">
-<th>Name</th>
-<th>Type</th>
-<th>Description</th>
-<th>Default</th>
-</tr>
-</thead>
-<tbody>
-<tr class="odd">
-<td><code>source</code></td>
-<td>str</td>
-<td>Cloudpath to an image source</td>
-<td><em>required</em></td>
-</tr>
-<tr class="even">
-<td><code>name</code></td>
-<td>str</td>
-<td>Name of the image layer. By default, ‘img’.</td>
-<td><code>None</code></td>
-</tr>
-<tr class="odd">
-<td><code>active</code></td>
-<td>bool</td>
-<td>If True, makes the layer active in neuroglancer. Default is False.</td>
-<td><code>False</code></td>
-</tr>
-<tr class="even">
-<td><code>contrast_controls</code></td>
-<td>bool</td>
-<td>If True, gives the layer a user-controllable brightness and contrast shader. Default is False.</td>
-<td><code>False</code></td>
-</tr>
-<tr class="odd">
-<td><code>black</code></td>
-<td>float</td>
-<td>If contrast_controls is True, sets the default black level. Default is 0.0.</td>
-<td><code>0.0</code></td>
-</tr>
-<tr class="even">
-<td><code>white</code></td>
-<td>float</td>
-<td>If contrast_controls is True, sets the default white level. Default is 1.0.</td>
-<td><code>1.0</code></td>
-</tr>
-</tbody>
-</table>
-</section>
-</section>
-<section id="nglui.statebuilder.layers.LayerConfigBase" class="level2">
-<h2 class="anchored" data-anchor-id="nglui.statebuilder.layers.LayerConfigBase">LayerConfigBase</h2>
-<p><code>statebuilder.layers.LayerConfigBase(self, name, type, source, color, active)</code></p>
-<p>Base class for configuring layers</p>
-<section id="parameters-2" class="level3">
-<h3 class="anchored" data-anchor-id="parameters-2">Parameters</h3>
-<table class="table">
-<colgroup>
-<col style="width: 13%">
-<col style="width: 10%">
-<col style="width: 60%">
-<col style="width: 16%">
-</colgroup>
-<thead>
-<tr class="header">
-<th>Name</th>
-<th>Type</th>
-<th>Description</th>
-<th>Default</th>
-</tr>
-</thead>
-<tbody>
-<tr class="odd">
-<td><code>name</code></td>
-<td>str</td>
-<td>Layer name for reference and display</td>
-<td><em>required</em></td>
-</tr>
-<tr class="even">
-<td><code>type</code></td>
-<td>str</td>
-<td>Layer type. Usually handled by the subclass</td>
-<td><em>required</em></td>
-</tr>
-<tr class="odd">
-<td><code>source</code></td>
-<td>str</td>
-<td>Datasource for the layer</td>
-<td><em>required</em></td>
-</tr>
-<tr class="even">
-<td><code>color</code></td>
-<td>str</td>
-<td>Hex string (with starting hash).</td>
-<td><em>required</em></td>
-</tr>
-<tr class="odd">
-<td><code>active</code></td>
-<td>(bool)</td>
-<td>If True, becomes a selected layer.</td>
-<td><em>required</em></td>
-</tr>
-</tbody>
-</table>
-</section>
-</section>
-<section id="nglui.statebuilder.layers.SegmentationLayerConfig" class="level2">
-<h2 class="anchored" data-anchor-id="nglui.statebuilder.layers.SegmentationLayerConfig">SegmentationLayerConfig</h2>
-<p><code>statebuilder.layers.SegmentationLayerConfig(self, source, name=None, selected_ids_column=None, fixed_ids=None, fixed_id_colors=None, color_column=None, active=False, alpha_selected=0.3, alpha_3d=1, alpha_unselected=0, split_point_map=None, view_kws=None, timestamp=None, data_resolution=None)</code></p>
-<p>Configuration class for segmentation layers</p>
-<section id="parameters-3" class="level3">
-<h3 class="anchored" data-anchor-id="parameters-3">Parameters</h3>
-<table class="table">
-<colgroup>
-<col style="width: 8%">
-<col style="width: 11%">
-<col style="width: 75%">
-<col style="width: 4%">
-</colgroup>
-<thead>
-<tr class="header">
-<th>Name</th>
-<th>Type</th>
-<th>Description</th>
-<th>Default</th>
-</tr>
-</thead>
-<tbody>
-<tr class="odd">
-<td><code>source</code></td>
-<td>str</td>
-<td>Segmentation source</td>
-<td><em>required</em></td>
-</tr>
-<tr class="even">
-<td><code>name</code></td>
-<td>(str, optional)</td>
-<td>Layer name.</td>
-<td><code>None</code></td>
-</tr>
-<tr class="odd">
-<td><code>selected_ids_column</code></td>
-<td>str or list-like, optional.</td>
-<td>Column name (or list of column names) to use for selected ids.</td>
-<td><code>None</code></td>
-</tr>
-<tr class="even">
-<td><code>fixed_ids</code></td>
-<td>list-like, optional.</td>
-<td>List of root ids to select directly.</td>
-<td><code>None</code></td>
-</tr>
-<tr class="odd">
-<td><code>fixed_id_colors</code></td>
-<td>list-like, optional.</td>
-<td>List of colors for fixed ids. Should be the same length as fixed_ids, although null entries can be padded with None values.</td>
-<td><code>None</code></td>
-</tr>
-<tr class="even">
-<td><code>color_column</code></td>
-<td>str, optional.</td>
-<td># at the begining. Column to use for color values for selected objects. Values should be RGB hex strings with a</td>
-<td><code>None</code></td>
-</tr>
-<tr class="odd">
-<td><code>active</code></td>
-<td>bool, optional.</td>
-<td>If True, makes the layer selected. Default is False.</td>
-<td><code>False</code></td>
-</tr>
-<tr class="even">
-<td><code>alpha_selected</code></td>
-<td></td>
-<td>Opacity of selected segmentations in the image layer. Optional, default is 0.3.</td>
-<td><code>0.3</code></td>
-</tr>
-<tr class="odd">
-<td><code>alpha_3d</code></td>
-<td></td>
-<td>Opacity of meshes. Optional, default is 1.</td>
-<td><code>1</code></td>
-</tr>
-<tr class="even">
-<td><code>alpha_unselected</code></td>
-<td></td>
-<td>Opacity of unselected segments. Optional, default is 0.</td>
-<td><code>0</code></td>
-</tr>
-<tr class="odd">
-<td><code>split_point_map</code></td>
-<td></td>
-<td>If not None, provides an object to map the dataframe input to multicut points. Default is None.</td>
-<td><code>None</code></td>
-</tr>
-<tr class="even">
-<td><code>view_kws</code></td>
-<td>dict, optional.</td>
-<td>Keyword arguments for viewer.set_segmentation_view_options. Sets selected (and unselected) segmetation alpha values. Defaults to values in DEFAULT_SEGMENTATION_VIEW_KWS dict specified in this module.</td>
-<td><code>None</code></td>
-</tr>
-<tr class="odd">
-<td><code>timestamp</code></td>
-<td>float or datetime, optional.</td>
-<td>Timestamp at which to fix the chunkedgraph in either unix epoch or datetime format. Optional, default is None.</td>
-<td><code>None</code></td>
-</tr>
-</tbody>
-</table>
-</section>
-<section id="methods" class="level3">
-<h3 class="anchored" data-anchor-id="methods">Methods</h3>
-<table class="table">
-<thead>
-<tr class="header">
-<th>Name</th>
-<th>Description</th>
-</tr>
-</thead>
-<tbody>
-<tr class="odd">
-<td><a href="#nglui.statebuilder.layers.SegmentationLayerConfig.add_selection_map">add_selection_map</a></td>
-<td>Add rules for selecting active segment ids and their colors</td>
-</tr>
-</tbody>
-</table>
-<section id="nglui.statebuilder.layers.SegmentationLayerConfig.add_selection_map" class="level4">
-<h4 class="anchored" data-anchor-id="nglui.statebuilder.layers.SegmentationLayerConfig.add_selection_map">add_selection_map</h4>
-<p><code>statebuilder.layers.SegmentationLayerConfig.add_selection_map(selected_ids_column=None, fixed_ids=None, fixed_id_colors=None, color_column=None)</code></p>
-<p>Add rules for selecting active segment ids and their colors</p>
-<section id="parameters-4" class="level5">
-<h5 class="anchored" data-anchor-id="parameters-4">Parameters</h5>
-<table class="table">
-<colgroup>
-<col style="width: 15%">
-<col style="width: 8%">
-<col style="width: 68%">
-<col style="width: 7%">
-</colgroup>
-<thead>
-<tr class="header">
-<th>Name</th>
-<th>Type</th>
-<th>Description</th>
-<th>Default</th>
-</tr>
-</thead>
-<tbody>
-<tr class="odd">
-<td><code>selected_ids_column</code></td>
-<td>str</td>
-<td>Dataframe column to use for adding selected segment ids to the segmentation layer, by default None</td>
-<td><code>None</code></td>
-</tr>
-<tr class="even">
-<td><code>fixed_ids</code></td>
-<td>int or list</td>
-<td>Add one or more segment ids to be active, independent of the data, by default None</td>
-<td><code>None</code></td>
-</tr>
-<tr class="odd">
-<td><code>fixed_id_colors</code></td>
-<td>list</td>
-<td>Add a list of colors (hex, rgb, or CSS3 string) to assign to the fixed ids, by default None</td>
-<td><code>None</code></td>
-</tr>
-<tr class="even">
-<td><code>color_column</code></td>
-<td>str</td>
-<td>Dataframe column to use for adding selected segment colors, by default None</td>
-<td><code>None</code></td>
-</tr>
-</tbody>
-</table>
-
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-</section>
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-<section id="nglui.statebuilder.layers.AnnotationLayerConfig" class="level1">
-<h1>AnnotationLayerConfig</h1>
-<p><code>statebuilder.layers.AnnotationLayerConfig(self, name=None, color=None, linked_segmentation_layer=None, mapping_rules=[], array_data=False, tags=None, active=True, filter_by_segmentation=False, brackets_show_segmentation=True, selection_shows_segmentation=True, filter_query=None, data_resolution=None)</code></p>
-<p>Configuration class for annotation layers</p>
-<section id="parameters" class="level2">
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-<th>Name</th>
-<th>Type</th>
-<th>Description</th>
-<th>Default</th>
-</tr>
-</thead>
-<tbody>
-<tr class="odd">
-<td><code>name</code></td>
-<td>str</td>
-<td>Layer name. By default, ‘annos’</td>
-<td><code>None</code></td>
-</tr>
-<tr class="even">
-<td><code>color</code></td>
-<td>str</td>
-<td>Hex color code with an initial #. By default, None</td>
-<td><code>None</code></td>
-</tr>
-<tr class="odd">
-<td><code>linked_segmentation_layer</code></td>
-<td>str</td>
-<td>Name of a linked segmentation layer for selected ids. By default, None</td>
-<td><code>None</code></td>
-</tr>
-<tr class="even">
-<td><code>mapping_rules</code></td>
-<td>(nglui.statebuilder.mappers.PointMapper, nglui.statebuilder.mappers.LineMapper, nglui.statebuilder.mappers.SphereMapper or list)</td>
-<td>One rule or a list of rules mapping data to annotations. By default, []</td>
-<td><code>[]</code></td>
-</tr>
-<tr class="odd">
-<td><code>array_data</code></td>
-<td>bool</td>
-<td>If True, allows simple mapping where one or more arrays are passed instead of a dataframe. Only allows basic annotation creation, no tags, linked segmentations, or other rich features.</td>
-<td><code>False</code></td>
-</tr>
-<tr class="even">
-<td><code>tags</code></td>
-<td>list</td>
-<td>List of tags for the layer.</td>
-<td><code>None</code></td>
-</tr>
-<tr class="odd">
-<td><code>active</code></td>
-<td>bool</td>
-<td>If True, makes the layer selected. Default is True (unlike for image/segmentation layers).</td>
-<td><code>True</code></td>
-</tr>
-</tbody>
-</table>
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-<p>Image layer configuration class.</p>
-<p>This provides the rules for setting up an image layer in neuroglancer.</p>
-<section id="parameters" class="level2">
-<h2 class="anchored" data-anchor-id="parameters">Parameters</h2>
-<table class="table">
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-<td><code>source</code></td>
-<td>str</td>
-<td>Cloudpath to an image source</td>
-<td><em>required</em></td>
-</tr>
-<tr class="even">
-<td><code>name</code></td>
-<td>str</td>
-<td>Name of the image layer. By default, ‘img’.</td>
-<td><code>None</code></td>
-</tr>
-<tr class="odd">
-<td><code>active</code></td>
-<td>bool</td>
-<td>If True, makes the layer active in neuroglancer. Default is False.</td>
-<td><code>False</code></td>
-</tr>
-<tr class="even">
-<td><code>contrast_controls</code></td>
-<td>bool</td>
-<td>If True, gives the layer a user-controllable brightness and contrast shader. Default is False.</td>
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-<h1>LayerConfigBase</h1>
-<p><code>statebuilder.layers.LayerConfigBase(self, name, type, source, color, active)</code></p>
-<p>Base class for configuring layers</p>
-<section id="parameters" class="level2">
-<h2 class="anchored" data-anchor-id="parameters">Parameters</h2>
-<table class="table">
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-<tr class="odd">
-<td><code>name</code></td>
-<td>str</td>
-<td>Layer name for reference and display</td>
-<td><em>required</em></td>
-</tr>
-<tr class="even">
-<td><code>type</code></td>
-<td>str</td>
-<td>Layer type. Usually handled by the subclass</td>
-<td><em>required</em></td>
-</tr>
-<tr class="odd">
-<td><code>source</code></td>
-<td>str</td>
-<td>Datasource for the layer</td>
-<td><em>required</em></td>
-</tr>
-<tr class="even">
-<td><code>color</code></td>
-<td>str</td>
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-<td><em>required</em></td>
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-<section id="nglui.statebuilder.layers.SegmentationLayerConfig" class="level1">
-<h1>SegmentationLayerConfig</h1>
-<p><code>statebuilder.layers.SegmentationLayerConfig(self, source, name=None, selected_ids_column=None, fixed_ids=None, fixed_id_colors=None, color_column=None, active=False, alpha_selected=0.3, alpha_3d=1, alpha_unselected=0, split_point_map=None, view_kws=None, timestamp=None, data_resolution=None)</code></p>
-<p>Configuration class for segmentation layers</p>
-<section id="parameters" class="level2">
-<h2 class="anchored" data-anchor-id="parameters">Parameters</h2>
-<table class="table">
-<colgroup>
-<col style="width: 8%">
-<col style="width: 11%">
-<col style="width: 75%">
-<col style="width: 4%">
-</colgroup>
-<thead>
-<tr class="header">
-<th>Name</th>
-<th>Type</th>
-<th>Description</th>
-<th>Default</th>
-</tr>
-</thead>
-<tbody>
-<tr class="odd">
-<td><code>source</code></td>
-<td>str</td>
-<td>Segmentation source</td>
-<td><em>required</em></td>
-</tr>
-<tr class="even">
-<td><code>name</code></td>
-<td>(str, optional)</td>
-<td>Layer name.</td>
-<td><code>None</code></td>
-</tr>
-<tr class="odd">
-<td><code>selected_ids_column</code></td>
-<td>str or list-like, optional.</td>
-<td>Column name (or list of column names) to use for selected ids.</td>
-<td><code>None</code></td>
-</tr>
-<tr class="even">
-<td><code>fixed_ids</code></td>
-<td>list-like, optional.</td>
-<td>List of root ids to select directly.</td>
-<td><code>None</code></td>
-</tr>
-<tr class="odd">
-<td><code>fixed_id_colors</code></td>
-<td>list-like, optional.</td>
-<td>List of colors for fixed ids. Should be the same length as fixed_ids, although null entries can be padded with None values.</td>
-<td><code>None</code></td>
-</tr>
-<tr class="even">
-<td><code>color_column</code></td>
-<td>str, optional.</td>
-<td># at the begining. Column to use for color values for selected objects. Values should be RGB hex strings with a</td>
-<td><code>None</code></td>
-</tr>
-<tr class="odd">
-<td><code>active</code></td>
-<td>bool, optional.</td>
-<td>If True, makes the layer selected. Default is False.</td>
-<td><code>False</code></td>
-</tr>
-<tr class="even">
-<td><code>alpha_selected</code></td>
-<td></td>
-<td>Opacity of selected segmentations in the image layer. Optional, default is 0.3.</td>
-<td><code>0.3</code></td>
-</tr>
-<tr class="odd">
-<td><code>alpha_3d</code></td>
-<td></td>
-<td>Opacity of meshes. Optional, default is 1.</td>
-<td><code>1</code></td>
-</tr>
-<tr class="even">
-<td><code>alpha_unselected</code></td>
-<td></td>
-<td>Opacity of unselected segments. Optional, default is 0.</td>
-<td><code>0</code></td>
-</tr>
-<tr class="odd">
-<td><code>split_point_map</code></td>
-<td></td>
-<td>If not None, provides an object to map the dataframe input to multicut points. Default is None.</td>
-<td><code>None</code></td>
-</tr>
-<tr class="even">
-<td><code>view_kws</code></td>
-<td>dict, optional.</td>
-<td>Keyword arguments for viewer.set_segmentation_view_options. Sets selected (and unselected) segmetation alpha values. Defaults to values in DEFAULT_SEGMENTATION_VIEW_KWS dict specified in this module.</td>
-<td><code>None</code></td>
-</tr>
-<tr class="odd">
-<td><code>timestamp</code></td>
-<td>float or datetime, optional.</td>
-<td>Timestamp at which to fix the chunkedgraph in either unix epoch or datetime format. Optional, default is None.</td>
-<td><code>None</code></td>
-</tr>
-</tbody>
-</table>
-</section>
-<section id="methods" class="level2">
-<h2 class="anchored" data-anchor-id="methods">Methods</h2>
-<table class="table">
-<thead>
-<tr class="header">
-<th>Name</th>
-<th>Description</th>
-</tr>
-</thead>
-<tbody>
-<tr class="odd">
-<td><a href="#nglui.statebuilder.layers.SegmentationLayerConfig.add_selection_map">add_selection_map</a></td>
-<td>Add rules for selecting active segment ids and their colors</td>
-</tr>
-</tbody>
-</table>
-<section id="nglui.statebuilder.layers.SegmentationLayerConfig.add_selection_map" class="level3">
-<h3 class="anchored" data-anchor-id="nglui.statebuilder.layers.SegmentationLayerConfig.add_selection_map">add_selection_map</h3>
-<p><code>statebuilder.layers.SegmentationLayerConfig.add_selection_map(selected_ids_column=None, fixed_ids=None, fixed_id_colors=None, color_column=None)</code></p>
-<p>Add rules for selecting active segment ids and their colors</p>
-<section id="parameters-1" class="level4">
-<h4 class="anchored" data-anchor-id="parameters-1">Parameters</h4>
-<table class="table">
-<colgroup>
-<col style="width: 15%">
-<col style="width: 8%">
-<col style="width: 68%">
-<col style="width: 7%">
-</colgroup>
-<thead>
-<tr class="header">
-<th>Name</th>
-<th>Type</th>
-<th>Description</th>
-<th>Default</th>
-</tr>
-</thead>
-<tbody>
-<tr class="odd">
-<td><code>selected_ids_column</code></td>
-<td>str</td>
-<td>Dataframe column to use for adding selected segment ids to the segmentation layer, by default None</td>
-<td><code>None</code></td>
-</tr>
-<tr class="even">
-<td><code>fixed_ids</code></td>
-<td>int or list</td>
-<td>Add one or more segment ids to be active, independent of the data, by default None</td>
-<td><code>None</code></td>
-</tr>
-<tr class="odd">
-<td><code>fixed_id_colors</code></td>
-<td>list</td>
-<td>Add a list of colors (hex, rgb, or CSS3 string) to assign to the fixed ids, by default None</td>
-<td><code>None</code></td>
-</tr>
-<tr class="even">
-<td><code>color_column</code></td>
-<td>str</td>
-<td>Dataframe column to use for adding selected segment colors, by default None</td>
-<td><code>None</code></td>
-</tr>
-</tbody>
-</table>
-
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-</section>
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diff --git a/docs/_site/reference/nglui.statebuilder.statebuilder.StateBuilder.render_state.html b/docs/_site/reference/nglui.statebuilder.statebuilder.StateBuilder.render_state.html
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-<td>string or neuroglancer.neuroglancer.Viewer</td>
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-<section id="nglui.parser.base.annotation_dataframe" class="level1">
-<h1>parser.base.annotation_dataframe</h1>
-<p><code>parser.base.annotation_dataframe(state)</code></p>
-<p>Return all annotations across all annotation layers in the state.</p>
-<section id="parameters" class="level2">
-<h2 class="anchored" data-anchor-id="parameters">Parameters</h2>
-<table class="table">
-<thead>
-<tr class="header">
-<th>Name</th>
-<th>Type</th>
-<th>Description</th>
-<th>Default</th>
-</tr>
-</thead>
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-<tr class="odd">
-<td><code>state</code></td>
-<td>dict</td>
-<td>Neuroglancer state dictionary</td>
-<td><em>required</em></td>
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-<tr class="header">
-<th>Type</th>
-<th>Description</th>
-</tr>
-</thead>
-<tbody>
-<tr class="odd">
-<td>pandas.pandas.DataFrame</td>
-<td>Dataframe with columns layer, anno_type, point, pointB, linked_segmentation, tags, anno_id, group_id, description.</td>
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-<p><code>parser.base.extract_multicut(state, seg_layer=None)</code></p>
-<p>Extract information entered into the multicut graph operation</p>
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-<td>int</td>
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-<p><code>parser.base.get_layer(state, layer_name)</code></p>
-<p>Gets the contents of the layer based on the layer name.</p>
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-<section id="nglui.parser.base.group_annotations" class="level1">
-<h1>parser.base.group_annotations</h1>
-<p><code>parser.base.group_annotations(state, layer_name, description=False, linked_segmentations=False, tags=False)</code></p>
-<p>All group annotations and their associated points</p>
-<section id="parameters" class="level2">
-<h2 class="anchored" data-anchor-id="parameters">Parameters</h2>
-<table class="table">
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-<col style="width: 10%">
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-<th>Name</th>
-<th>Type</th>
-<th>Description</th>
-<th>Default</th>
-</tr>
-</thead>
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-<tr class="odd">
-<td><code>state</code></td>
-<td>dict</td>
-<td>Neuroglancer state as JSON dict</td>
-<td><em>required</em></td>
-</tr>
-<tr class="even">
-<td><code>layer_name</code></td>
-<td>str</td>
-<td>Annotation layer name</td>
-<td><em>required</em></td>
-</tr>
-<tr class="odd">
-<td><code>description</code></td>
-<td>bool</td>
-<td>If True, also returns descriptions as well. By default False</td>
-<td><code>False</code></td>
-</tr>
-<tr class="even">
-<td><code>linked_segmentations</code></td>
-<td>bool</td>
-<td>If True, also returns list of linked segmentations, by default False</td>
-<td><code>False</code></td>
-</tr>
-<tr class="odd">
-<td><code>tags</code></td>
-<td>bool</td>
-<td>If True, also returns list of tags, by default False</td>
-<td><code>False</code></td>
-</tr>
-</tbody>
-</table>
-</section>
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-<th>Type</th>
-<th>Description</th>
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-</thead>
-<tbody>
-<tr class="odd">
-<td>list</td>
-<td>List of N 3-element points</td>
-</tr>
-<tr class="even">
-<td>list</td>
-<td>List of N id strings for groups.</td>
-</tr>
-<tr class="odd">
-<td>list</td>
-<td>List of N strings (or None), only returned if description=True.</td>
-</tr>
-<tr class="even">
-<td>list</td>
-<td>List of N lists of object ids. Only returned if linked_segmentations=True.</td>
-</tr>
-<tr class="odd">
-<td>list</td>
-<td>List of N lists of tag ids. Only returned if tags=True.</td>
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-<p>Get all image layer names in the state</p>
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-<section id="nglui.parser.base.layer_names" class="level1">
-<h1>parser.base.layer_names</h1>
-<p><code>parser.base.layer_names(state)</code></p>
-<p>Get all layer names in the state</p>
-<section id="parameters" class="level2">
-<h2 class="anchored" data-anchor-id="parameters">Parameters</h2>
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-<th>Name</th>
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-<tr class="odd">
-<td><code>state</code></td>
-<td>dict</td>
-<td>Neuroglancer state as a JSON dict</td>
-<td><em>required</em></td>
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-<th>Type</th>
-<th>Description</th>
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-<section id="nglui.parser.base.line_annotations" class="level1">
-<h1>parser.base.line_annotations</h1>
-<p><code>parser.base.line_annotations(state, layer_name, description=False, linked_segmentations=False, tags=False, group=False)</code></p>
-<p>Get all line annotation points and other info from a layer.</p>
-<section id="parameters" class="level2">
-<h2 class="anchored" data-anchor-id="parameters">Parameters</h2>
-<table class="table">
-<colgroup>
-<col style="width: 21%">
-<col style="width: 7%">
-<col style="width: 61%">
-<col style="width: 10%">
-</colgroup>
-<thead>
-<tr class="header">
-<th>Name</th>
-<th>Type</th>
-<th>Description</th>
-<th>Default</th>
-</tr>
-</thead>
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-<tr class="odd">
-<td><code>state</code></td>
-<td>dict</td>
-<td>Neuroglancer state as JSON dict</td>
-<td><em>required</em></td>
-</tr>
-<tr class="even">
-<td><code>layer_name</code></td>
-<td>str</td>
-<td>Layer name</td>
-<td><em>required</em></td>
-</tr>
-<tr class="odd">
-<td><code>description</code></td>
-<td>bool</td>
-<td>If True, also returns descriptions as well. By default False</td>
-<td><code>False</code></td>
-</tr>
-<tr class="even">
-<td><code>linked_segmentations</code></td>
-<td>bool</td>
-<td>If True, also returns list of linked segmentations, by default False</td>
-<td><code>False</code></td>
-</tr>
-<tr class="odd">
-<td><code>tags</code></td>
-<td>bool</td>
-<td>If True, also returns list of tags, by default False</td>
-<td><code>False</code></td>
-</tr>
-</tbody>
-</table>
-</section>
-<section id="returns" class="level2">
-<h2 class="anchored" data-anchor-id="returns">Returns</h2>
-<table class="table">
-<colgroup>
-<col style="width: 8%">
-<col style="width: 91%">
-</colgroup>
-<thead>
-<tr class="header">
-<th>Type</th>
-<th>Description</th>
-</tr>
-</thead>
-<tbody>
-<tr class="odd">
-<td>list</td>
-<td>List of N 3-element points (as list) of the first point in each line.</td>
-</tr>
-<tr class="even">
-<td>list</td>
-<td>List of N 3-element points (as list) of the second point in each line.</td>
-</tr>
-<tr class="odd">
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-<h1>parser.base.point_annotations</h1>
-<p><code>parser.base.point_annotations(state, layer_name, description=False, linked_segmentations=False, tags=False, group=False)</code></p>
-<p>Get all point annotation points and other info from a layer.</p>
-<section id="parameters" class="level2">
-<h2 class="anchored" data-anchor-id="parameters">Parameters</h2>
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-<th>Name</th>
-<th>Type</th>
-<th>Description</th>
-<th>Default</th>
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-<td><code>state</code></td>
-<td>dict</td>
-<td>Neuroglancer state as JSON dict</td>
-<td><em>required</em></td>
-</tr>
-<tr class="even">
-<td><code>layer_name</code></td>
-<td>str</td>
-<td>Layer name</td>
-<td><em>required</em></td>
-</tr>
-<tr class="odd">
-<td><code>description</code></td>
-<td>bool</td>
-<td>If True, also returns descriptions as well. By default False</td>
-<td><code>False</code></td>
-</tr>
-<tr class="even">
-<td><code>linked_segmentations</code></td>
-<td>bool</td>
-<td>If True, also returns list of linked segmentations, by default False</td>
-<td><code>False</code></td>
-</tr>
-<tr class="odd">
-<td><code>tags</code></td>
-<td>bool</td>
-<td>If True, also returns list of tags, by default False</td>
-<td><code>False</code></td>
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-</tbody>
-</table>
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-<th>Type</th>
-<th>Description</th>
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-<tbody>
-<tr class="odd">
-<td>list</td>
-<td>List of N 3-element points (as list)</td>
-</tr>
-<tr class="even">
-<td>list</td>
-<td>List of N strings (or None), only returned if description=True.</td>
-</tr>
-<tr class="odd">
-<td>list</td>
-<td>List of N lists of object ids. Only returned if linked_segmentations=True.</td>
-</tr>
-<tr class="even">
-<td>list</td>
-<td>List of N lists of tag ids. Only returned if tags=True.</td>
-</tr>
-<tr class="odd">
-<td>list</td>
-<td>List of group ids (as string) or None for annotations. Only returned if group=True</td>
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-<p><code>parser.base.segmentation_layers(state)</code></p>
-<p>Get all segmentation layer names in the state</p>
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diff --git a/docs/_site/reference/parser.base.sphere_annotations.html b/docs/_site/reference/parser.base.sphere_annotations.html
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-<p><code>parser.base.sphere_annotations(state, layer_name, description=False, linked_segmentations=False, tags=False, group=False)</code></p>
-<p>Get all sphere annotation points and other info from a layer.</p>
-<section id="parameters" class="level2">
-<h2 class="anchored" data-anchor-id="parameters">Parameters</h2>
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-<th>Name</th>
-<th>Type</th>
-<th>Description</th>
-<th>Default</th>
-</tr>
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-<tbody>
-<tr class="odd">
-<td><code>state</code></td>
-<td>dict</td>
-<td>Neuroglancer state as JSON dict</td>
-<td><em>required</em></td>
-</tr>
-<tr class="even">
-<td><code>layer_name</code></td>
-<td>str</td>
-<td>Layer name</td>
-<td><em>required</em></td>
-</tr>
-<tr class="odd">
-<td><code>description</code></td>
-<td>bool</td>
-<td>If True, also returns descriptions as well. By default False</td>
-<td><code>False</code></td>
-</tr>
-<tr class="even">
-<td><code>linked_segmentations</code></td>
-<td>bool</td>
-<td>If True, also returns list of linked segmentations, by default False</td>
-<td><code>False</code></td>
-</tr>
-<tr class="odd">
-<td><code>tags</code></td>
-<td>bool</td>
-<td>If True, also returns list of tags, by default False</td>
-<td><code>False</code></td>
-</tr>
-</tbody>
-</table>
-</section>
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-</tr>
-</thead>
-<tbody>
-<tr class="odd">
-<td>list</td>
-<td>List of N 3-element center points (as list)</td>
-</tr>
-<tr class="even">
-<td>list</td>
-<td>List of N 3-element radii for each axis of the ellipsoid.</td>
-</tr>
-<tr class="odd">
-<td>list</td>
-<td>List of N strings (or None), only returned if description=True.</td>
-</tr>
-<tr class="even">
-<td>list</td>
-<td>List of N lists of object ids. Only returned if linked_segmentations=True.</td>
-</tr>
-<tr class="odd">
-<td>list</td>
-<td>List of N lists of tag ids. Only returned if tags=True.</td>
-</tr>
-<tr class="even">
-<td>list</td>
-<td>List of group ids (as string) or None for annotations. Only returned if group=True</td>
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-<p><code>parser.base.tag_dictionary(state, layer_name)</code></p>
-<p>Get the tag id to string dictionary for a layer</p>
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-<td><code>name</code></td>
-<td>str</td>
-<td>Layer name. By default, ‘annos’</td>
-<td><code>None</code></td>
-</tr>
-<tr class="even">
-<td><code>color</code></td>
-<td>str</td>
-<td>Hex color code with an initial #. By default, None</td>
-<td><code>None</code></td>
-</tr>
-<tr class="odd">
-<td><code>linked_segmentation_layer</code></td>
-<td>str</td>
-<td>Name of a linked segmentation layer for selected ids. By default, None</td>
-<td><code>None</code></td>
-</tr>
-<tr class="even">
-<td><code>mapping_rules</code></td>
-<td>(nglui.statebuilder.mappers.PointMapper, nglui.statebuilder.mappers.LineMapper, nglui.statebuilder.mappers.SphereMapper or list)</td>
-<td>One rule or a list of rules mapping data to annotations. By default, []</td>
-<td><code>[]</code></td>
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-<tr class="odd">
-<td><code>array_data</code></td>
-<td>bool</td>
-<td>If True, allows simple mapping where one or more arrays are passed instead of a dataframe. Only allows basic annotation creation, no tags, linked segmentations, or other rich features.</td>
-<td><code>False</code></td>
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-<td><code>tags</code></td>
-<td>list</td>
-<td>List of tags for the layer.</td>
-<td><code>None</code></td>
-</tr>
-<tr class="odd">
-<td><code>active</code></td>
-<td>bool</td>
-<td>If True, makes the layer selected. Default is True (unlike for image/segmentation layers).</td>
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-<section id="nglui.statebuilder.BoundingBoxMapper" class="level1">
-<h1>statebuilder.BoundingBoxMapper</h1>
-<p><code>statebuilder.BoundingBoxMapper(self, point_column_a=None, point_column_b=None, description_column=None, linked_segmentation_column=None, tag_column=None, group_column=None, gather_linked_segmentations=True, share_linked_segmentations=False, set_position=True, multipoint=False, collapse_groups=False, split_positions=False, mapping_set=None)</code></p>
-<p>Sets rules to map dataframes to bounding box annotations</p>
-<section id="parameters" class="level2">
-<h2 class="anchored" data-anchor-id="parameters">Parameters</h2>
-<table class="table">
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-<tr class="odd">
-<td><code>point_column_a</code></td>
-<td>str</td>
-<td>Column name with 3d position data for the first point of the bounding box. Must be set if array_data is False (the default)</td>
-<td><code>None</code></td>
-</tr>
-<tr class="even">
-<td><code>point_column_b</code></td>
-<td>str</td>
-<td>Column name with 3d position data for the second point of the bounding box. Must be set if array_data is False (the default)</td>
-<td><code>None</code></td>
-</tr>
-<tr class="odd">
-<td><code>description_column</code></td>
-<td>str</td>
-<td>Column name with string data for annotation descriptions</td>
-<td><code>None</code></td>
-</tr>
-<tr class="even">
-<td><code>linked_segmentation_column</code></td>
-<td>str</td>
-<td>Column name for root ids to link to annotations</td>
-<td><code>None</code></td>
-</tr>
-<tr class="odd">
-<td><code>tag_column</code></td>
-<td>str</td>
-<td>Column name for categorical tag data. Tags must match those set in the annotation layer.</td>
-<td><code>None</code></td>
-</tr>
-<tr class="even">
-<td><code>group_column</code></td>
-<td>str</td>
-<td>Column name for grouping data. Data in this row should be numeric with possible NaNs. Rows with the same non-NaN value will be collected into a grouped annotation.</td>
-<td><code>None</code></td>
-</tr>
-<tr class="odd">
-<td><code>set_position</code></td>
-<td>bool</td>
-<td>If set to True, moves the position to center on the first point in the data (using point_column_a).</td>
-<td><code>True</code></td>
-</tr>
-<tr class="even">
-<td><code>multipoint</code></td>
-<td></td>
-<td>If True, permits multiple points in a given row, sharing data in other columns. Each point row must have the same number of points. Default is False.</td>
-<td><code>False</code></td>
-</tr>
-<tr class="odd">
-<td><code>collapse_groups</code></td>
-<td></td>
-<td>If True, groups are toggled closed in the annotation view.</td>
-<td><code>False</code></td>
-</tr>
-<tr class="even">
-<td><code>mapping_set</code></td>
-<td></td>
-<td>If set, assumes data is passed as a dictionary and uses this string to as the key for the data to use.</td>
-<td><code>None</code></td>
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diff --git a/docs/_site/reference/statebuilder.ImageLayerConfig.html b/docs/_site/reference/statebuilder.ImageLayerConfig.html
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-<section id="nglui.statebuilder.ImageLayerConfig" class="level1">
-<h1>statebuilder.ImageLayerConfig</h1>
-<p><code>statebuilder.ImageLayerConfig(self, source, name=None, active=False, contrast_controls=False, black=0.0, white=1.0)</code></p>
-<p>Image layer configuration class.</p>
-<p>This provides the rules for setting up an image layer in neuroglancer.</p>
-<section id="parameters" class="level2">
-<h2 class="anchored" data-anchor-id="parameters">Parameters</h2>
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-<th>Name</th>
-<th>Type</th>
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-<td><code>source</code></td>
-<td>str</td>
-<td>Cloudpath to an image source</td>
-<td><em>required</em></td>
-</tr>
-<tr class="even">
-<td><code>name</code></td>
-<td>str</td>
-<td>Name of the image layer. By default, ‘img’.</td>
-<td><code>None</code></td>
-</tr>
-<tr class="odd">
-<td><code>active</code></td>
-<td>bool</td>
-<td>If True, makes the layer active in neuroglancer. Default is False.</td>
-<td><code>False</code></td>
-</tr>
-<tr class="even">
-<td><code>contrast_controls</code></td>
-<td>bool</td>
-<td>If True, gives the layer a user-controllable brightness and contrast shader. Default is False.</td>
-<td><code>False</code></td>
-</tr>
-<tr class="odd">
-<td><code>black</code></td>
-<td>float</td>
-<td>If contrast_controls is True, sets the default black level. Default is 0.0.</td>
-<td><code>0.0</code></td>
-</tr>
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-<td><code>white</code></td>
-<td>float</td>
-<td>If contrast_controls is True, sets the default white level. Default is 1.0.</td>
-<td><code>1.0</code></td>
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-<h1>statebuilder.LineMapper</h1>
-<p><code>statebuilder.LineMapper(self, point_column_a=None, point_column_b=None, description_column=None, linked_segmentation_column=None, tag_column=None, group_column=None, gather_linked_segmentations=True, share_linked_segmentations=False, set_position=True, multipoint=False, collapse_groups=False, split_positions=False, mapping_set=None)</code></p>
-<p>Sets rules to map dataframes to line annotations</p>
-<section id="parameters" class="level2">
-<h2 class="anchored" data-anchor-id="parameters">Parameters</h2>
-<table class="table">
-<colgroup>
-<col style="width: 14%">
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-<col style="width: 77%">
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-<th>Name</th>
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-<th>Description</th>
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-<td><code>point_column_a</code></td>
-<td>str</td>
-<td>Column name with 3d position data for the first point of the line. Must be set if array_data is False (the default)</td>
-<td><code>None</code></td>
-</tr>
-<tr class="even">
-<td><code>point_column_b</code></td>
-<td>str</td>
-<td>Column name with 3d position data for the first point of the line. Must be set if array_data is False (the default)</td>
-<td><code>None</code></td>
-</tr>
-<tr class="odd">
-<td><code>description_column</code></td>
-<td>str</td>
-<td>Column name with string data for annotation descriptions</td>
-<td><code>None</code></td>
-</tr>
-<tr class="even">
-<td><code>linked_segmentation_column</code></td>
-<td>str</td>
-<td>Column name for root ids to link to annotations</td>
-<td><code>None</code></td>
-</tr>
-<tr class="odd">
-<td><code>tag_column</code></td>
-<td>str</td>
-<td>Column name for categorical tag data. Tags must match those set in the annotation layer.</td>
-<td><code>None</code></td>
-</tr>
-<tr class="even">
-<td><code>group_column</code></td>
-<td>str</td>
-<td>Column name for grouping data. Data in this row should be numeric with possible NaNs. Rows with the same non-NaN value will be collected into a grouped annotation.</td>
-<td><code>None</code></td>
-</tr>
-<tr class="odd">
-<td><code>set_position</code></td>
-<td>bool</td>
-<td>If set to True, moves the position to center on the first point in the data (using point_column_a).</td>
-<td><code>True</code></td>
-</tr>
-<tr class="even">
-<td><code>multipoint</code></td>
-<td></td>
-<td>If True, permits multiple points in a given row, sharing data in other columns. Each point row must have the same number of points. Default is False.</td>
-<td><code>False</code></td>
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-<tr class="odd">
-<td><code>collapse_groups</code></td>
-<td></td>
-<td>If True, groups are toggled closed in the annotation view.</td>
-<td><code>False</code></td>
-</tr>
-<tr class="even">
-<td><code>mapping_set</code></td>
-<td></td>
-<td>If set, assumes data is passed as a dictionary and uses this string to as the key for the data to use.</td>
-<td><code>None</code></td>
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-<section id="nglui.statebuilder.PointMapper" class="level1">
-<h1>statebuilder.PointMapper</h1>
-<p><code>statebuilder.PointMapper(self, point_column=None, description_column=None, linked_segmentation_column=None, tag_column=None, group_column=None, gather_linked_segmentations=True, share_linked_segmentations=False, set_position=True, multipoint=False, collapse_groups=False, split_positions=False, mapping_set=None)</code></p>
-<p>Sets rules to map dataframes to point annotations</p>
-<section id="parameters" class="level2">
-<h2 class="anchored" data-anchor-id="parameters">Parameters</h2>
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-<th>Name</th>
-<th>Type</th>
-<th>Description</th>
-<th>Default</th>
-</tr>
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-<tr class="odd">
-<td><code>point_column</code></td>
-<td>str</td>
-<td>Column name with 3d position data</td>
-<td><code>None</code></td>
-</tr>
-<tr class="even">
-<td><code>description_column</code></td>
-<td>str</td>
-<td>Column name with string data for annotation descriptions</td>
-<td><code>None</code></td>
-</tr>
-<tr class="odd">
-<td><code>linked_segmentation_column</code></td>
-<td>str</td>
-<td>Column name for root ids to link to annotations</td>
-<td><code>None</code></td>
-</tr>
-<tr class="even">
-<td><code>tag_column</code></td>
-<td>str</td>
-<td>Column name for categorical tag data. Tags must match those set in the annotation layer.</td>
-<td><code>None</code></td>
-</tr>
-<tr class="odd">
-<td><code>group_column</code></td>
-<td>str</td>
-<td>Column name for grouping data. Data in this row should be numeric with possible NaNs. Rows with the same non-NaN value will be collected into a grouped annotation.</td>
-<td><code>None</code></td>
-</tr>
-<tr class="even">
-<td><code>set_position</code></td>
-<td>bool</td>
-<td>If set to True, moves the position to center on the first point in the data.</td>
-<td><code>True</code></td>
-</tr>
-<tr class="odd">
-<td><code>multipoint</code></td>
-<td></td>
-<td>If True, permits multiple points in a given row, sharing data in other columns. Default is False.</td>
-<td><code>False</code></td>
-</tr>
-<tr class="even">
-<td><code>collapse_groups</code></td>
-<td></td>
-<td>If True, groups are toggled closed in the annotation view.</td>
-<td><code>False</code></td>
-</tr>
-<tr class="odd">
-<td><code>mapping_set</code></td>
-<td></td>
-<td>If given, assumes data is passed as a dictionary and uses this string to as the key for the data to use.</td>
-<td><code>None</code></td>
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-<section id="nglui.statebuilder.SegmentationLayerConfig" class="level1">
-<h1>statebuilder.SegmentationLayerConfig</h1>
-<p><code>statebuilder.SegmentationLayerConfig(self, source, name=None, selected_ids_column=None, fixed_ids=None, fixed_id_colors=None, color_column=None, active=False, alpha_selected=0.3, alpha_3d=1, alpha_unselected=0, split_point_map=None, view_kws=None, timestamp=None, data_resolution=None)</code></p>
-<p>Configuration class for segmentation layers</p>
-<section id="parameters" class="level2">
-<h2 class="anchored" data-anchor-id="parameters">Parameters</h2>
-<table class="table">
-<colgroup>
-<col style="width: 8%">
-<col style="width: 11%">
-<col style="width: 75%">
-<col style="width: 4%">
-</colgroup>
-<thead>
-<tr class="header">
-<th>Name</th>
-<th>Type</th>
-<th>Description</th>
-<th>Default</th>
-</tr>
-</thead>
-<tbody>
-<tr class="odd">
-<td><code>source</code></td>
-<td>str</td>
-<td>Segmentation source</td>
-<td><em>required</em></td>
-</tr>
-<tr class="even">
-<td><code>name</code></td>
-<td>(str, optional)</td>
-<td>Layer name.</td>
-<td><code>None</code></td>
-</tr>
-<tr class="odd">
-<td><code>selected_ids_column</code></td>
-<td>str or list-like, optional.</td>
-<td>Column name (or list of column names) to use for selected ids.</td>
-<td><code>None</code></td>
-</tr>
-<tr class="even">
-<td><code>fixed_ids</code></td>
-<td>list-like, optional.</td>
-<td>List of root ids to select directly.</td>
-<td><code>None</code></td>
-</tr>
-<tr class="odd">
-<td><code>fixed_id_colors</code></td>
-<td>list-like, optional.</td>
-<td>List of colors for fixed ids. Should be the same length as fixed_ids, although null entries can be padded with None values.</td>
-<td><code>None</code></td>
-</tr>
-<tr class="even">
-<td><code>color_column</code></td>
-<td>str, optional.</td>
-<td># at the begining. Column to use for color values for selected objects. Values should be RGB hex strings with a</td>
-<td><code>None</code></td>
-</tr>
-<tr class="odd">
-<td><code>active</code></td>
-<td>bool, optional.</td>
-<td>If True, makes the layer selected. Default is False.</td>
-<td><code>False</code></td>
-</tr>
-<tr class="even">
-<td><code>alpha_selected</code></td>
-<td></td>
-<td>Opacity of selected segmentations in the image layer. Optional, default is 0.3.</td>
-<td><code>0.3</code></td>
-</tr>
-<tr class="odd">
-<td><code>alpha_3d</code></td>
-<td></td>
-<td>Opacity of meshes. Optional, default is 1.</td>
-<td><code>1</code></td>
-</tr>
-<tr class="even">
-<td><code>alpha_unselected</code></td>
-<td></td>
-<td>Opacity of unselected segments. Optional, default is 0.</td>
-<td><code>0</code></td>
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-<td>If not None, provides an object to map the dataframe input to multicut points. Default is None.</td>
-<td><code>None</code></td>
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-<td><code>view_kws</code></td>
-<td>dict, optional.</td>
-<td>Keyword arguments for viewer.set_segmentation_view_options. Sets selected (and unselected) segmetation alpha values. Defaults to values in DEFAULT_SEGMENTATION_VIEW_KWS dict specified in this module.</td>
-<td><code>None</code></td>
-</tr>
-<tr class="odd">
-<td><code>timestamp</code></td>
-<td>float or datetime, optional.</td>
-<td>Timestamp at which to fix the chunkedgraph in either unix epoch or datetime format. Optional, default is None.</td>
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diff --git a/docs/_site/reference/statebuilder.SphereMapper.html b/docs/_site/reference/statebuilder.SphereMapper.html
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-<section id="nglui.statebuilder.SphereMapper" class="level1">
-<h1>statebuilder.SphereMapper</h1>
-<p><code>statebuilder.SphereMapper(self, center_column=None, radius_column=None, description_column=None, linked_segmentation_column=None, tag_column=None, group_column=None, gather_linked_segmentations=True, share_linked_segmentations=False, z_multiplier=0.1, set_position=True, multipoint=False, collapse_groups=False, split_positions=False, mapping_set=None)</code></p>
-<p>Sets rules to map dataframes to sphere annotations</p>
-<section id="parameters" class="level2">
-<h2 class="anchored" data-anchor-id="parameters">Parameters</h2>
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-<td><code>center_column</code></td>
-<td>str</td>
-<td>Column name with 3d position data for the center of the sphere</td>
-<td><code>None</code></td>
-</tr>
-<tr class="even">
-<td><code>radius_column</code></td>
-<td>str</td>
-<td>Column name with a radius for the sphere (in nm)</td>
-<td><code>None</code></td>
-</tr>
-<tr class="odd">
-<td><code>description_column</code></td>
-<td>str</td>
-<td>Column name with string data for annotation descriptions</td>
-<td><code>None</code></td>
-</tr>
-<tr class="even">
-<td><code>linked_segmentation_column</code></td>
-<td>str</td>
-<td>Column name for root ids to link to annotations</td>
-<td><code>None</code></td>
-</tr>
-<tr class="odd">
-<td><code>tag_column</code></td>
-<td>str</td>
-<td>Column name for categorical tag data. Tags must match those set in the annotation layer.</td>
-<td><code>None</code></td>
-</tr>
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-<td><code>group_column</code></td>
-<td>str</td>
-<td>Column name for grouping data. Data in this row should be numeric with possible NaNs. Rows with the same non-NaN value will be collected into a grouped annotation.</td>
-<td><code>None</code></td>
-</tr>
-<tr class="odd">
-<td><code>set_position</code></td>
-<td>bool</td>
-<td>If set to True, moves the position to center on the first point in the data.</td>
-<td><code>True</code></td>
-</tr>
-<tr class="even">
-<td><code>multipoint</code></td>
-<td></td>
-<td>If True, permits multiple points in a given row, sharing data in other columns. Each point row must have the same number of points. Default is False.</td>
-<td><code>False</code></td>
-</tr>
-<tr class="odd">
-<td><code>collapse_groups</code></td>
-<td></td>
-<td>If True, groups are toggled closed in the annotation view.</td>
-<td><code>False</code></td>
-</tr>
-<tr class="even">
-<td><code>mapping_set</code></td>
-<td></td>
-<td>If set, assumes data is passed as a dictionary and uses this string to as the key for the data to use.</td>
-<td><code>None</code></td>
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-<section id="nglui.statebuilder.SplitPointMapper" class="level1">
-<h1>statebuilder.SplitPointMapper</h1>
-<p><code>statebuilder.SplitPointMapper(self, id_column, point_column, team_column, team_names=['red', 'blue'], supervoxel_column=None, focus=True, mapping_set=None)</code></p>
-<p>Mapper to create split points in a segmentation layer.</p>
-<section id="parameters" class="level2">
-<h2 class="anchored" data-anchor-id="parameters">Parameters</h2>
-<table class="table">
-<colgroup>
-<col style="width: 10%">
-<col style="width: 6%">
-<col style="width: 73%">
-<col style="width: 9%">
-</colgroup>
-<thead>
-<tr class="header">
-<th>Name</th>
-<th>Type</th>
-<th>Description</th>
-<th>Default</th>
-</tr>
-</thead>
-<tbody>
-<tr class="odd">
-<td><code>id_column</code></td>
-<td>str</td>
-<td>Column name for segment ids. The id column must contain the same id in all rows.</td>
-<td><em>required</em></td>
-</tr>
-<tr class="even">
-<td><code>point_column</code></td>
-<td>str</td>
-<td>Name of the column containing points in space.</td>
-<td><em>required</em></td>
-</tr>
-<tr class="odd">
-<td><code>team_column</code></td>
-<td>str</td>
-<td>Name of the column describing the team for the points. The contents of the column should have two values, by default “red” and “blue”.</td>
-<td><em>required</em></td>
-</tr>
-<tr class="even">
-<td><code>team_names</code></td>
-<td>list</td>
-<td>List of two values for the team names used in the team column. The first is mapped to red points, the second blue. Default is [“red”, “blue”].</td>
-<td><code>['red', 'blue']</code></td>
-</tr>
-<tr class="odd">
-<td><code>supervoxel_column</code></td>
-<td>str or None</td>
-<td>Name of a column providing supervoxel ids. If None (default), the supervoxel must be looked up on the server.</td>
-<td><code>None</code></td>
-</tr>
-<tr class="even">
-<td><code>focus</code></td>
-<td>bool</td>
-<td>If True, sets the focus on the split tool and sets the position to the center of split points. Default is True.</td>
-<td><code>True</code></td>
-</tr>
-</tbody>
-</table>
-</section>
-<section id="returns" class="level2">
-<h2 class="anchored" data-anchor-id="returns">Returns</h2>
-<table class="table">
-<colgroup>
-<col style="width: 80%">
-<col style="width: 20%">
-</colgroup>
-<thead>
-<tr class="header">
-<th>Type</th>
-<th>Description</th>
-</tr>
-</thead>
-<tbody>
-<tr class="odd">
-<td>SplitPointMapper instance to pass to a segmentation layer.</td>
-<td></td>
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-<h1>statebuilder.StateBuilder</h1>
-<p><code>statebuilder.StateBuilder(self, layers=[], base_state=None, url_prefix=None, state_server=None, resolution=None, view_kws={}, client=None, target_site=None)</code></p>
-<p>A class for schematic mapping data frames into neuroglancer states.</p>
-<section id="parameters" class="level2">
-<h2 class="anchored" data-anchor-id="parameters">Parameters</h2>
-<table class="table">
-<colgroup>
-<col style="width: 1%">
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-<col style="width: 96%">
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-<td><code>layers</code></td>
-<td></td>
-<td></td>
-<td><code>[]</code></td>
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-<tr class="even">
-<td><code>base_state</code></td>
-<td></td>
-<td></td>
-<td><code>None</code></td>
-</tr>
-<tr class="odd">
-<td><code>url_prefix</code></td>
-<td></td>
-<td>Defaults to None, which will use https://neuromancer-seung-import.appspot.com</td>
-<td><code>None</code></td>
-</tr>
-<tr class="even">
-<td><code>state_server</code></td>
-<td></td>
-<td></td>
-<td><code>None</code></td>
-</tr>
-<tr class="odd">
-<td><code>resolution</code></td>
-<td></td>
-<td></td>
-<td><code>None</code></td>
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-<tr class="even">
-<td><code>view_kws</code></td>
-<td></td>
-<td>keys are: show_slices: Boolean sets if slices are shown in the 3d view. Defaults to False. layout: str <code>xy-3d</code>/<code>xz-3d</code>/<code>yz-3d</code> (sections plus 3d pane), <code>xy</code>/<code>yz</code>/<code>xz</code>/<code>3d</code> (only one pane), or <code>4panel</code> (all panes). Default is <code>xy-3d</code>. show_axis_lines: Boolean determines if the axis lines are shown in the middle of each view. show_scale_bar: Boolean toggles showing the scale bar. orthographic : Boolean toggles orthographic view in the 3d pane. position* : 3-element vector determines the centered location. zoom_image : float Zoom level for the imagery in units of nm per voxel. Defaults to 8. zoom_3d : float Zoom level for the 3d pane. Defaults to 2000. Smaller numbers are more zoomed in. background_color : str or list Sets the background color of the 3d view. Arguments can be rgb values, hex colors, or named web colors. Defaults to black.</td>
-<td><code>{}</code></td>
-</tr>
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-<td><code>client</code></td>
-<td></td>
-<td></td>
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-<p><code>statebuilder.helpers.from_client(client, image_name=None, segmentation_name=None, contrast=None)</code></p>
-<p>Generate basic image and segmentation layers from a FrameworkClient</p>
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-<td>Name for the image layer, by default None.</td>
-<td><code>None</code></td>
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-<td>str</td>
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-<section id="nglui.statebuilder.helpers.make_line_statebuilder" class="level1">
-<h1>statebuilder.helpers.make_line_statebuilder</h1>
-<p><code>statebuilder.helpers.make_line_statebuilder(client, point_column_a='pre_pt_position', point_column_b='post_pt_position', linked_seg_column='pt_root_id', description_column=None, tag_column=None, data_resolution=None, group_column=None, contrast=None, view_kws=None, point_layer_name='lines', color=None, split_positions=False)</code></p>
-<p>Generate a state builder that puts points on a single column with a linked segmentaton id</p>
-<section id="parameters" class="level2">
-<h2 class="anchored" data-anchor-id="parameters">Parameters</h2>
-<table class="table">
-<colgroup>
-<col style="width: 11%">
-<col style="width: 11%">
-<col style="width: 65%">
-<col style="width: 11%">
-</colgroup>
-<thead>
-<tr class="header">
-<th>Name</th>
-<th>Type</th>
-<th>Description</th>
-<th>Default</th>
-</tr>
-</thead>
-<tbody>
-<tr class="odd">
-<td><code>client</code></td>
-<td>caveclient.CAVEclient</td>
-<td>CAVEclient configured for the datastack desired</td>
-<td><em>required</em></td>
-</tr>
-<tr class="even">
-<td><code>point_column_a</code></td>
-<td>str</td>
-<td>column in dataframe to pull points from. Defaults to “pre_pt_position”.</td>
-<td><code>'pre_pt_position'</code></td>
-</tr>
-<tr class="odd">
-<td><code>point_column_b</code></td>
-<td>str</td>
-<td>column in dataframe to pull points from. Defaults to “post_pt_position”.</td>
-<td><code>'post_pt_position'</code></td>
-</tr>
-<tr class="even">
-<td><code>linked_seg_column</code></td>
-<td>str</td>
-<td>column to link to segmentation, None for no column. Defaults to “pt_root_id”.</td>
-<td><code>'pt_root_id'</code></td>
-</tr>
-<tr class="odd">
-<td><code>group_column</code></td>
-<td>str, or list</td>
-<td>column(s) to group annotations by, None for no grouping (default=None)</td>
-<td><code>None</code></td>
-</tr>
-<tr class="even">
-<td><code>tag_column</code></td>
-<td>str</td>
-<td>column to use for tags, None for no tags (default=None)</td>
-<td><code>None</code></td>
-</tr>
-<tr class="odd">
-<td><code>description_column</code></td>
-<td>str</td>
-<td>column to use for descriptions, None for no descriptions (default=None)</td>
-<td><code>None</code></td>
-</tr>
-<tr class="even">
-<td><code>contrast</code></td>
-<td>list</td>
-<td>Two elements specifying the black level and white level as floats between 0 and 1, by default None. If None, no contrast is set.</td>
-<td><code>None</code></td>
-</tr>
-<tr class="odd">
-<td><code>view_kws</code></td>
-<td>dict</td>
-<td>dictionary of view keywords to configure neuroglancer view</td>
-<td><code>None</code></td>
-</tr>
-<tr class="even">
-<td><code>split_positions</code></td>
-<td>bool</td>
-<td>whether the position column into x,y,z columns. Defaults to False.</td>
-<td><code>False</code></td>
-</tr>
-</tbody>
-</table>
-</section>
-<section id="returns" class="level2">
-<h2 class="anchored" data-anchor-id="returns">Returns</h2>
-<table class="table">
-<thead>
-<tr class="header">
-<th>Type</th>
-<th>Description</th>
-</tr>
-</thead>
-<tbody>
-<tr class="odd">
-<td></td>
-<td>A statebuilder to make points with linked segmentations</td>
-</tr>
-</tbody>
-</table>
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diff --git a/docs/_site/reference/statebuilder.helpers.make_neuron_neuroglancer_link.html b/docs/_site/reference/statebuilder.helpers.make_neuron_neuroglancer_link.html
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-<section id="nglui.statebuilder.helpers.make_neuron_neuroglancer_link" class="level1">
-<h1>statebuilder.helpers.make_neuron_neuroglancer_link</h1>
-<p><code>statebuilder.helpers.make_neuron_neuroglancer_link(client, root_ids, return_as='html', shorten='always', show_inputs=False, show_outputs=False, sort_inputs=True, sort_outputs=True, sort_ascending=False, input_color=DEFAULT_POSTSYN_COLOR, output_color=DEFAULT_PRESYN_COLOR, contrast=None, timestamp=None, view_kws=None, point_column='ctr_pt_position', pre_pt_root_id_col='pre_pt_root_id', post_pt_root_id_col='post_pt_root_id', input_layer_name='syns_in', output_layer_name='syns_out', ngl_url=None, link_text='Neuroglancer Link', target_site=None)</code></p>
-<p>function to create a neuroglancer link view of a neuron, optionally including inputs and outputs</p>
-<section id="parameters" class="level2">
-<h2 class="anchored" data-anchor-id="parameters">Parameters</h2>
-<table class="table">
-<colgroup>
-<col style="width: 7%">
-<col style="width: 9%">
-<col style="width: 73%">
-<col style="width: 8%">
-</colgroup>
-<thead>
-<tr class="header">
-<th>Name</th>
-<th>Type</th>
-<th>Description</th>
-<th>Default</th>
-</tr>
-</thead>
-<tbody>
-<tr class="odd">
-<td><code>client</code></td>
-<td>caveclient.CAVEclient</td>
-<td>A CAVEclient configured for the datastack to visualize.</td>
-<td><em>required</em></td>
-</tr>
-<tr class="even">
-<td><code>root_ids</code></td>
-<td>typing.Iterable[int]</td>
-<td>The root_ids to build the visualization around.</td>
-<td><em>required</em></td>
-</tr>
-<tr class="odd">
-<td><code>return_as</code></td>
-<td>str</td>
-<td>How to return the URL or state. Valid options are: - ‘html’: Returns an IPython HTML element. - ‘json’: Returns a dictionary representing the Neuroglancer state. - ‘url’: Returns a URL string. Defaults to ‘html’.</td>
-<td><code>'html'</code></td>
-</tr>
-<tr class="even">
-<td><code>shorten</code></td>
-<td>str</td>
-<td>Whether to shorten the link. Valid options are: - ‘always’: Always shorten the link. - ‘if_long’: Shorten the link if it exceeds MAX_URL_LENGTH. - ‘never’: Never shorten the link. Defaults to ‘if_long’.</td>
-<td><code>'always'</code></td>
-</tr>
-<tr class="odd">
-<td><code>show_inputs</code></td>
-<td>bool</td>
-<td>Whether to include input synapses. Defaults to False.</td>
-<td><code>False</code></td>
-</tr>
-<tr class="even">
-<td><code>show_outputs</code></td>
-<td>bool</td>
-<td>Whether to include output synapses. Defaults to False.</td>
-<td><code>False</code></td>
-</tr>
-<tr class="odd">
-<td><code>sort_inputs</code></td>
-<td>bool</td>
-<td>Whether to sort input synapses by presynaptic root id, ordered by synapse count. Defaults to True.</td>
-<td><code>True</code></td>
-</tr>
-<tr class="even">
-<td><code>sort_outputs</code></td>
-<td>bool</td>
-<td>Whether to sort output synapses by presynaptic root id, ordered by postsynaptic synapse count. Defaults to True.</td>
-<td><code>True</code></td>
-</tr>
-<tr class="odd">
-<td><code>sort_ascending</code></td>
-<td>bool</td>
-<td>If sorting, whether to sort ascending (lowest synapse count to highest). Defaults to False.</td>
-<td><code>False</code></td>
-</tr>
-<tr class="even">
-<td><code>input_color</code></td>
-<td>list(float) or str</td>
-<td>Color of input synapse points as an RGB list [0, 1], hex string, or common name.</td>
-<td><code>DEFAULT_POSTSYN_COLOR</code></td>
-</tr>
-<tr class="odd">
-<td><code>output_color</code></td>
-<td>list(float) or str</td>
-<td>Color of output synapse points as an RGB list [0, 1], hex string, or common name.</td>
-<td><code>DEFAULT_PRESYN_COLOR</code></td>
-</tr>
-<tr class="even">
-<td><code>contrast</code></td>
-<td>list</td>
-<td>List of two floats between 0 and 1, specifying the black and white levels. If None, no contrast is set.</td>
-<td><code>None</code></td>
-</tr>
-<tr class="odd">
-<td><code>timestamp</code></td>
-<td>datetime.datetime.datetime</td>
-<td>Timestamp to use for the query. Defaults to None, which will use the materialized version.</td>
-<td><code>None</code></td>
-</tr>
-<tr class="even">
-<td><code>view_kws</code></td>
-<td>dict</td>
-<td>Dictionary containing viewer settings for Neuroglancer. See nglui.StateBuilder for options. See the previous docstring for details on available keys.</td>
-<td><code>None</code></td>
-</tr>
-<tr class="odd">
-<td><code>point_column</code></td>
-<td>str</td>
-<td>Column to pull synapse positions from. Defaults to “ctr_pt_position”.</td>
-<td><code>'ctr_pt_position'</code></td>
-</tr>
-<tr class="even">
-<td><code>pre_pt_root_id_col</code></td>
-<td>str</td>
-<td>Column to pull presynaptic IDs for synapses from. Defaults to “pre_pt_root_id”.</td>
-<td><code>'pre_pt_root_id'</code></td>
-</tr>
-<tr class="odd">
-<td><code>post_pt_root_id_col</code></td>
-<td>str</td>
-<td>Column to pull postsynaptic IDs for synapses from. Defaults to “post_pt_root_id”.</td>
-<td><code>'post_pt_root_id'</code></td>
-</tr>
-<tr class="even">
-<td><code>input_layer_name</code></td>
-<td>str</td>
-<td>Name of the layer for input synapses. Defaults to “syns_in”.</td>
-<td><code>'syns_in'</code></td>
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-<tr class="odd">
-<td><code>output_layer_name</code></td>
-<td>str</td>
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-<tr class="even">
-<td><code>ngl_url</code></td>
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-</tr>
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-<th>Type</th>
-<th>Description</th>
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-<h1>statebuilder.helpers.make_point_statebuilder</h1>
-<p><code>statebuilder.helpers.make_point_statebuilder(client, point_column='pt_position', linked_seg_column='pt_root_id', data_resolution=None, group_column=None, tag_column=None, description_column=None, contrast=None, view_kws=None, point_layer_name='pts', color=None, split_positions=False)</code></p>
-<p>Generate a state builder that puts points on a single column with a linked segmentaton id</p>
-<section id="parameters" class="level2">
-<h2 class="anchored" data-anchor-id="parameters">Parameters</h2>
-<table class="table">
-<colgroup>
-<col style="width: 11%">
-<col style="width: 11%">
-<col style="width: 67%">
-<col style="width: 8%">
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-<tr class="header">
-<th>Name</th>
-<th>Type</th>
-<th>Description</th>
-<th>Default</th>
-</tr>
-</thead>
-<tbody>
-<tr class="odd">
-<td><code>client</code></td>
-<td>caveclient.CAVEclient</td>
-<td>CAVEclient configured for the datastack desired</td>
-<td><em>required</em></td>
-</tr>
-<tr class="even">
-<td><code>point_column</code></td>
-<td>str</td>
-<td>Column in dataframe to pull points from. Defaults to “pt_position”.</td>
-<td><code>'pt_position'</code></td>
-</tr>
-<tr class="odd">
-<td><code>linked_seg_column</code></td>
-<td>str</td>
-<td>column to link to segmentation, None for no column. Defaults to “pt_root_id”.</td>
-<td><code>'pt_root_id'</code></td>
-</tr>
-<tr class="even">
-<td><code>group_column</code></td>
-<td>str, or list</td>
-<td>column(s) to group annotations by, None for no grouping (default=None)</td>
-<td><code>None</code></td>
-</tr>
-<tr class="odd">
-<td><code>tag_column</code></td>
-<td>str, optional)</td>
-<td>column to use for tags, None for no tags (default=None)</td>
-<td><code>None</code></td>
-</tr>
-<tr class="even">
-<td><code>description_column</code></td>
-<td>str</td>
-<td>column to use for descriptions, None for no descriptions (default=None)</td>
-<td><code>None</code></td>
-</tr>
-<tr class="odd">
-<td><code>contrast</code></td>
-<td>list</td>
-<td>Two elements specifying the black level and white level as floats between 0 and 1, by default None. If None, no contrast is set.</td>
-<td><code>None</code></td>
-</tr>
-<tr class="even">
-<td><code>view_kws</code></td>
-<td>dict</td>
-<td>dictionary of view keywords to configure neuroglancer view</td>
-<td><code>None</code></td>
-</tr>
-<tr class="odd">
-<td><code>split_positions</code></td>
-<td>bool</td>
-<td>whether the position column into x,y,z columns. Defaults to False.</td>
-<td><code>False</code></td>
-</tr>
-</tbody>
-</table>
-</section>
-<section id="returns" class="level2">
-<h2 class="anchored" data-anchor-id="returns">Returns</h2>
-<table class="table">
-<thead>
-<tr class="header">
-<th>Type</th>
-<th>Description</th>
-</tr>
-</thead>
-<tbody>
-<tr class="odd">
-<td></td>
-<td>A statebuilder to make points with linked segmentations</td>
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-<section id="nglui.statebuilder.helpers.make_pre_post_statebuilder" class="level1">
-<h1>statebuilder.helpers.make_pre_post_statebuilder</h1>
-<p><code>statebuilder.helpers.make_pre_post_statebuilder(client, show_inputs=False, show_outputs=False, contrast=None, view_kws=None, point_column='ctr_pt_position', pre_pt_root_id_col='pre_pt_root_id', post_pt_root_id_col='post_pt_root_id', dataframe_resolution_pre=None, dataframe_resolution_post=None, input_layer_name='syns_in', output_layer_name='syns_out', input_layer_color=DEFAULT_POSTSYN_COLOR, output_layer_color=DEFAULT_PRESYN_COLOR, split_positions=False)</code></p>
-<p>Function to generate ChainedStateBuilder with optional pre and post synaptic annotation layers</p>
-<section id="parameters" class="level2">
-<h2 class="anchored" data-anchor-id="parameters">Parameters</h2>
-<table class="table">
-<colgroup>
-<col style="width: 2%">
-<col style="width: 2%">
-<col style="width: 92%">
-<col style="width: 2%">
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-<thead>
-<tr class="header">
-<th>Name</th>
-<th>Type</th>
-<th>Description</th>
-<th>Default</th>
-</tr>
-</thead>
-<tbody>
-<tr class="odd">
-<td><code>client</code></td>
-<td>caveclient.CAVEclient</td>
-<td>a CAVEclient configured for datastack to visualize</td>
-<td><em>required</em></td>
-</tr>
-<tr class="even">
-<td><code>show_inputs</code></td>
-<td>bool</td>
-<td>whether to show input synapses. Defaults to False.</td>
-<td><code>False</code></td>
-</tr>
-<tr class="odd">
-<td><code>show_outputs</code></td>
-<td>bool</td>
-<td>whether to show output synapses.. Defaults to False.</td>
-<td><code>False</code></td>
-</tr>
-<tr class="even">
-<td><code>contrast</code></td>
-<td>list</td>
-<td>Two elements specifying the black level and white level as floats between 0 and 1, by default None. If None, no contrast is set.</td>
-<td><code>None</code></td>
-</tr>
-<tr class="odd">
-<td><code>view_kws</code></td>
-<td>dict</td>
-<td>view_kws to configure statebuilder, see nglui.StateBuilder. Defaults to None. keys are: show_slices: Boolean sets if slices are shown in the 3d view. Defaults to False. layout: str <code>xy-3d</code>/<code>xz-3d</code>/<code>yz-3d</code> (sections plus 3d pane), <code>xy</code>/<code>yz</code>/<code>xz</code>/<code>3d</code> (only one pane), or <code>4panel</code> (all panes). Default is <code>xy-3d</code>. show_axis_lines: Boolean determines if the axis lines are shown in the middle of each view. show_scale_bar: Boolean toggles showing the scale bar. orthographic : Boolean toggles orthographic view in the 3d pane. position* : 3-element vector determines the centered location. zoom_image : float Zoom level for the imagery in units of nm per voxel. Defaults to 8. zoom_3d : float Zoom level for the 3d pane. Defaults to 2000. Smaller numbers are more zoomed in.</td>
-<td><code>None</code></td>
-</tr>
-<tr class="even">
-<td><code>point_column</code></td>
-<td>str</td>
-<td>column to pull points for synapses from. Defaults to “ctr_pt_position”.</td>
-<td><code>'ctr_pt_position'</code></td>
-</tr>
-<tr class="odd">
-<td><code>pre_pt_root_id_col</code></td>
-<td>str</td>
-<td>column to pull pre synaptic ids for synapses from. Defaults to “pre_pt_root_id”.</td>
-<td><code>'pre_pt_root_id'</code></td>
-</tr>
-<tr class="even">
-<td><code>post_pt_root_id_col</code></td>
-<td>str</td>
-<td>column to pull post synaptic ids for synapses from. Defaults to “post_pt_root_id”.</td>
-<td><code>'post_pt_root_id'</code></td>
-</tr>
-<tr class="odd">
-<td><code>input_layer_name</code></td>
-<td>str</td>
-<td>name of layer for inputs. Defaults to “syns_in”.</td>
-<td><code>'syns_in'</code></td>
-</tr>
-<tr class="even">
-<td><code>output_layer_name</code></td>
-<td>str</td>
-<td>name of layer for outputs. Defaults to “syns_out”.</td>
-<td><code>'syns_out'</code></td>
-</tr>
-<tr class="odd">
-<td><code>split_positions</code></td>
-<td>bool</td>
-<td>whether the position column is split into x,y,z columns. Defaults to False.</td>
-<td><code>False</code></td>
-</tr>
-</tbody>
-</table>
-</section>
-<section id="returns" class="level2">
-<h2 class="anchored" data-anchor-id="returns">Returns</h2>
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-<col style="width: 4%">
-<col style="width: 95%">
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-<tr class="header">
-<th>Type</th>
-<th>Description</th>
-</tr>
-</thead>
-<tbody>
-<tr class="odd">
-<td></td>
-<td>An instance of a ChainedStateBuilder configured to accept a list starting with None followed by optionally synapse input dataframe followed by optionally synapse output dataframe.</td>
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-<p><code>statebuilder.helpers.make_state_url(df, sb, client, ngl_url=None, target_site=None)</code></p>
-<p>Generate a url from a neuroglancer state via a state server.</p>
-<section id="parameters" class="level2">
-<h2 class="anchored" data-anchor-id="parameters">Parameters</h2>
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-<td>nglui.statebuilder.statebuilder.nglui.statebuilder.statebuilder.StateBuilder</td>
-<td>Statebuilder to use to render data for link</td>
-<td><em>required</em></td>
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-<td><code>client</code></td>
-<td>caveclient.CAVEclient</td>
-<td>CAVEclient configured with a state server</td>
-<td><em>required</em></td>
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-<tr class="even">
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-<td>str</td>
-<td>Neuroglancer deployment URL, by default None</td>
-<td><code>None</code></td>
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-<tr class="odd">
-<td><code>target_site</code></td>
-<td>str</td>
-<td>Type of neuroglancer deployment to build link for, by default None. This value overrides automatic checking based on the provided url. Use <code>seunglab</code> for a Seung-lab branch and either <code>mainline</code> or <code>cave-explorer</code> for the Cave Explorer or main Google branch.</td>
-<td><code>None</code></td>
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-<th>Type</th>
-<th>Description</th>
-</tr>
-</thead>
-<tbody>
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-<td>str</td>
-<td>Url to the uploaded neuroglancer state.</td>
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-<h1>statebuilder.helpers.make_synapse_neuroglancer_link</h1>
-<p><code>statebuilder.helpers.make_synapse_neuroglancer_link(synapse_df, client, return_as='html', shorten='always', contrast=None, point_column='ctr_pt_position', dataframe_resolution=None, group_connections=True, link_pre_and_post=True, ngl_url=None, view_kws=None, pre_post_columns=None, neuroglancer_link_text='Neuroglancer Link', color=None, split_positions=False, target_site=None)</code></p>
-<p>Generate a neuroglancer link from a synapse dataframe as returned from CAVEclient.materialize.synapse_query.</p>
-<section id="parameters" class="level2">
-<h2 class="anchored" data-anchor-id="parameters">Parameters</h2>
-<table class="table">
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-<th>Type</th>
-<th>Description</th>
-<th>Default</th>
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-<tr class="odd">
-<td><code>synapse_df</code></td>
-<td>pandas.pandas.DataFrame</td>
-<td>DataFrame where each row represents a synapse.</td>
-<td><em>required</em></td>
-</tr>
-<tr class="even">
-<td><code>client</code></td>
-<td>caveclient.caveclient.CAVEclient</td>
-<td>A CAVEclient instance.</td>
-<td><em>required</em></td>
-</tr>
-<tr class="odd">
-<td><code>return_as</code></td>
-<td>str</td>
-<td>How to return the URL. Valid options are: - ‘html’: Returns an IPython HTML element. - ‘url’: Returns a URL string. - ‘json’: Returns a dictionary representing the Neuroglancer state. Defaults to ‘html’.</td>
-<td><code>'html'</code></td>
-</tr>
-<tr class="even">
-<td><code>shorten</code></td>
-<td>str</td>
-<td>Whether to shorten the link. Valid options are: - ‘always’: Always shorten the link. - ‘if_long’: Shorten the link if it exceeds MAX_URL_LENGTH. - ‘never’: Never shorten the link. Defaults to ‘always’.</td>
-<td><code>'always'</code></td>
-</tr>
-<tr class="odd">
-<td><code>contrast</code></td>
-<td>list</td>
-<td>List of two floats between 0 and 1, specifying the black and white levels. If None, no contrast is set.</td>
-<td><code>None</code></td>
-</tr>
-<tr class="even">
-<td><code>point_column</code></td>
-<td>str</td>
-<td>Column in the DataFrame containing synapse positions. Defaults to ‘ctr_pt_position’.</td>
-<td><code>'ctr_pt_position'</code></td>
-</tr>
-<tr class="odd">
-<td><code>dataframe_resolution</code></td>
-<td>list</td>
-<td>List of length 3, specifying the resolution units of the position column. If None, attempts to get the resolution from DataFrame metadata or client.info.viewer_resolution().</td>
-<td><code>None</code></td>
-</tr>
-<tr class="even">
-<td><code>group_connections</code></td>
-<td>bool</td>
-<td>Whether to group synapses within the same connection (between the same neurons). Defaults to True.</td>
-<td><code>True</code></td>
-</tr>
-<tr class="odd">
-<td><code>link_pre_and_post</code></td>
-<td>bool</td>
-<td>Whether to link the synapse annotations to the pre- and post-synaptic partners. Defaults to True.</td>
-<td><code>True</code></td>
-</tr>
-<tr class="even">
-<td><code>ngl_url</code></td>
-<td>str</td>
-<td>URL of the Neuroglancer instance to use. Defaults to client.info.viewer_site() or DEFAULT_NGL.</td>
-<td><code>None</code></td>
-</tr>
-<tr class="odd">
-<td><code>view_kws</code></td>
-<td>dict</td>
-<td>Dictionary containing viewer settings for Neuroglancer. Available keys: - show_slices: Boolean, sets if slices are shown in the 3D view. - layout: str, specifies the viewer layout (e.g., ‘xy-3d’, ‘4panel’). - show_axis_lines: Boolean, determines if axis lines are shown. - show_scale_bar: Boolean, toggles the scale bar. - orthographic: Boolean, toggles orthographic view in the 3D pane. - position: 3-element vector, sets the centered location. - zoom_image: float, zoom level for the imagery in nm per voxel. - zoom_3d: float, zoom level for the 3D pane.</td>
-<td><code>None</code></td>
-</tr>
-<tr class="even">
-<td><code>pre_post_columns</code></td>
-<td>list</td>
-<td>List of two strings, specifying the column names for pre- and post-synaptic root_ids. Defaults to [‘pre_pt_root_id’, ‘post_pt_root_id’].</td>
-<td><code>None</code></td>
-</tr>
-<tr class="odd">
-<td><code>neuroglancer_link_text</code></td>
-<td>str</td>
-<td>Text to use in the returned HTML link. Defaults to ‘Neuroglancer Link’.</td>
-<td><code>'Neuroglancer Link'</code></td>
-</tr>
-<tr class="even">
-<td><code>color</code></td>
-<td>list(float) or str</td>
-<td>Color of synapse points as an RGB list [0, 1], hex string, or common name.</td>
-<td><code>None</code></td>
-</tr>
-<tr class="odd">
-<td><code>split_positions</code></td>
-<td>bool</td>
-<td>Whether the position column is split into x, y, and z columns.</td>
-<td><code>False</code></td>
-</tr>
-<tr class="even">
-<td><code>target_site</code></td>
-<td>str</td>
-<td>Type of neuroglancer deployment to build link for, by default None. This value overrides automatic checking based on the provided url. Use <code>seunglab</code> for a Seung-lab branch and either <code>mainline</code> or <code>cave-explorer</code> for the Cave Explorer or main Google branch.</td>
-<td><code>None</code></td>
-</tr>
-</tbody>
-</table>
-</section>
-<section id="returns" class="level2">
-<h2 class="anchored" data-anchor-id="returns">Returns</h2>
-<table class="table">
-<colgroup>
-<col style="width: 25%">
-<col style="width: 74%">
-</colgroup>
-<thead>
-<tr class="header">
-<th>Type</th>
-<th>Description</th>
-</tr>
-</thead>
-<tbody>
-<tr class="odd">
-<td>IPython.HTML, str, or dict</td>
-<td>Representation of the Neuroglancer state, depending on the <code>return_as</code> parameter.</td>
-</tr>
-</tbody>
-</table>
-</section>
-<section id="raises" class="level2">
-<h2 class="anchored" data-anchor-id="raises">Raises</h2>
-<table class="table">
-<colgroup>
-<col style="width: 15%">
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-</tr>
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-<tbody>
-<tr class="odd">
-<td>ValueError</td>
-<td>If the specified <code>point_column</code> is not found in the DataFrame.</td>
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-<section id="nglui.statebuilder.helpers.make_url_robust" class="level1">
-<h1>statebuilder.helpers.make_url_robust</h1>
-<p><code>statebuilder.helpers.make_url_robust(df, sb, client, shorten='if_long', ngl_url=None, max_url_length=MAX_URL_LENGTH, target_site=None)</code></p>
-<p>Generate a url from a neuroglancer state. If too long, return through state server, othewise return a url containing the data directly.</p>
-<section id="parameters" class="level2">
-<h2 class="anchored" data-anchor-id="parameters">Parameters</h2>
-<table class="table">
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-<td>pandas.pandas.DataFrame</td>
-<td>Dataframe to pass through statebuilder</td>
-<td><em>required</em></td>
-</tr>
-<tr class="even">
-<td><code>sb</code></td>
-<td>nglui.statebuilder.statebuilder.nglui.statebuilder.statebuilder.StateBuilder</td>
-<td>Statebuilder to use to render data for link</td>
-<td><em>required</em></td>
-</tr>
-<tr class="odd">
-<td><code>client</code></td>
-<td>caveclient.CAVEclient</td>
-<td>CAVEclient configured with a state server</td>
-<td><em>required</em></td>
-</tr>
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-<td><code>shorten</code></td>
-<td>str</td>
-<td>How to shorten link. one of ‘if_long’, ‘always’, ‘never’. ‘if_long’ will use the state server to shorten links longer than nglui.statebuilder.MAX_URL_LENGTH (set to 1,750,000). ‘always’ will always use the state server to shorten the url ‘never’ will always return the full url. Defaults to “if_long”.</td>
-<td><code>'if_long'</code></td>
-</tr>
-<tr class="odd">
-<td><code>ngl_url</code></td>
-<td>str</td>
-<td>Neuroglancer deployment URL, by default None</td>
-<td><code>None</code></td>
-</tr>
-<tr class="even">
-<td><code>max_url_length</code></td>
-<td>int</td>
-<td>Maximum length of url to return directly, by default 1_750_000</td>
-<td><code>MAX_URL_LENGTH</code></td>
-</tr>
-<tr class="odd">
-<td><code>target_site</code></td>
-<td>str</td>
-<td>Type of neuroglancer deployment to build link for, by default None. This value overrides automatic checking based on the provided url. Use <code>seunglab</code> for a Seung-lab branch and either <code>mainline</code> or <code>cave-explorer</code> for the Cave Explorer or main Google branch.</td>
-<td><code>None</code></td>
-</tr>
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-<section id="returns" class="level2">
-<h2 class="anchored" data-anchor-id="returns">Returns</h2>
-<table class="table">
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-<tr class="header">
-<th>Type</th>
-<th>Description</th>
-</tr>
-</thead>
-<tbody>
-<tr class="odd">
-<td>str</td>
-<td>URL containing the state created by the statebuilder.</td>
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-<h1>Convert below to numpydoc</h1>
-<section id="parameters" class="level2">
-<h2 class="anchored" data-anchor-id="parameters">Parameters</h2>
-<table class="table">
-<colgroup>
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-<col style="width: 18%">
-<col style="width: 72%">
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-<tr class="odd">
-<td><code>link_text</code></td>
-<td>str</td>
-<td>Text to use for the link, by default “Neuroglancer Link”</td>
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-<tr class="even">
-<td><code>target_site</code></td>
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-<h1>statebuilder.helpers.sort_dataframe_by_root_id</h1>
-<p><code>statebuilder.helpers.sort_dataframe_by_root_id(df, root_id_column, ascending=False, num_column='n_times', drop=False)</code></p>
-<p>Sort a dataframe so that rows belonging to the same root id are together, ordered by how many times the root id appears.</p>
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-<td>str</td>
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-<td><em>required</em></td>
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-<td><code>ascending</code></td>
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-
-<section id="nglui.statebuilder.statebuilder.StateBuilder" class="level1">
-<h1>StateBuilder</h1>
-<p><code>statebuilder.statebuilder.StateBuilder(self, layers=[], base_state=None, url_prefix=None, state_server=None, resolution=None, view_kws={}, client=None, target_site=None)</code></p>
-<p>A class for schematic mapping data frames into neuroglancer states.</p>
-<section id="parameters" class="level2">
-<h2 class="anchored" data-anchor-id="parameters">Parameters</h2>
-<table class="table">
-<colgroup>
-<col style="width: 1%">
-<col style="width: 0%">
-<col style="width: 96%">
-<col style="width: 1%">
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-<thead>
-<tr class="header">
-<th>Name</th>
-<th>Type</th>
-<th>Description</th>
-<th>Default</th>
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-<tbody>
-<tr class="odd">
-<td><code>layers</code></td>
-<td></td>
-<td></td>
-<td><code>[]</code></td>
-</tr>
-<tr class="even">
-<td><code>base_state</code></td>
-<td></td>
-<td></td>
-<td><code>None</code></td>
-</tr>
-<tr class="odd">
-<td><code>url_prefix</code></td>
-<td></td>
-<td>Defaults to None, which will use https://neuromancer-seung-import.appspot.com</td>
-<td><code>None</code></td>
-</tr>
-<tr class="even">
-<td><code>state_server</code></td>
-<td></td>
-<td></td>
-<td><code>None</code></td>
-</tr>
-<tr class="odd">
-<td><code>resolution</code></td>
-<td></td>
-<td></td>
-<td><code>None</code></td>
-</tr>
-<tr class="even">
-<td><code>view_kws</code></td>
-<td></td>
-<td>keys are: show_slices: Boolean sets if slices are shown in the 3d view. Defaults to False. layout: str <code>xy-3d</code>/<code>xz-3d</code>/<code>yz-3d</code> (sections plus 3d pane), <code>xy</code>/<code>yz</code>/<code>xz</code>/<code>3d</code> (only one pane), or <code>4panel</code> (all panes). Default is <code>xy-3d</code>. show_axis_lines: Boolean determines if the axis lines are shown in the middle of each view. show_scale_bar: Boolean toggles showing the scale bar. orthographic : Boolean toggles orthographic view in the 3d pane. position* : 3-element vector determines the centered location. zoom_image : float Zoom level for the imagery in units of nm per voxel. Defaults to 8. zoom_3d : float Zoom level for the 3d pane. Defaults to 2000. Smaller numbers are more zoomed in. background_color : str or list Sets the background color of the 3d view. Arguments can be rgb values, hex colors, or named web colors. Defaults to black.</td>
-<td><code>{}</code></td>
-</tr>
-<tr class="odd">
-<td><code>client</code></td>
-<td></td>
-<td></td>
-<td><code>None</code></td>
-</tr>
-</tbody>
-</table>
-</section>
-<section id="methods" class="level2">
-<h2 class="anchored" data-anchor-id="methods">Methods</h2>
-<table class="table">
-<thead>
-<tr class="header">
-<th>Name</th>
-<th>Description</th>
-</tr>
-</thead>
-<tbody>
-<tr class="odd">
-<td><a href="#nglui.statebuilder.statebuilder.StateBuilder.initialize_state">initialize_state</a></td>
-<td>Generate a new Neuroglancer state with layers as needed for the schema.</td>
-</tr>
-<tr class="even">
-<td><a href="#nglui.statebuilder.statebuilder.StateBuilder.render_state">render_state</a></td>
-<td>Build a Neuroglancer state out of a DataFrame.</td>
-</tr>
-</tbody>
-</table>
-<section id="nglui.statebuilder.statebuilder.StateBuilder.initialize_state" class="level3">
-<h3 class="anchored" data-anchor-id="nglui.statebuilder.statebuilder.StateBuilder.initialize_state">initialize_state</h3>
-<p><code>statebuilder.statebuilder.StateBuilder.initialize_state(base_state=None, target_site=None)</code></p>
-<p>Generate a new Neuroglancer state with layers as needed for the schema.</p>
-<section id="parameters-1" class="level4">
-<h4 class="anchored" data-anchor-id="parameters-1">Parameters</h4>
-<table class="table">
-<colgroup>
-<col style="width: 12%">
-<col style="width: 7%">
-<col style="width: 70%">
-<col style="width: 10%">
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-<tr class="header">
-<th>Name</th>
-<th>Type</th>
-<th>Description</th>
-<th>Default</th>
-</tr>
-</thead>
-<tbody>
-<tr class="odd">
-<td><code>base_state</code></td>
-<td>str</td>
-<td>Optional initial state to build on, described by its JSON. By default None.</td>
-<td><code>None</code></td>
-</tr>
-</tbody>
-</table>
-</section>
-</section>
-<section id="nglui.statebuilder.statebuilder.StateBuilder.render_state" class="level3">
-<h3 class="anchored" data-anchor-id="nglui.statebuilder.statebuilder.StateBuilder.render_state">render_state</h3>
-<p><code>statebuilder.statebuilder.StateBuilder.render_state(data=None, base_state=None, return_as='url', url_prefix=None, link_text='Neuroglancer Link', target_site=None)</code></p>
-<p>Build a Neuroglancer state out of a DataFrame.</p>
-<section id="parameters-2" class="level4">
-<h4 class="anchored" data-anchor-id="parameters-2">Parameters</h4>
-<table class="table">
-<colgroup>
-<col style="width: 2%">
-<col style="width: 16%">
-<col style="width: 76%">
-<col style="width: 4%">
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-<thead>
-<tr class="header">
-<th>Name</th>
-<th>Type</th>
-<th>Description</th>
-<th>Default</th>
-</tr>
-</thead>
-<tbody>
-<tr class="odd">
-<td><code>data</code></td>
-<td>pandas.pandas.DataFrame</td>
-<td>DataFrame to use as a point source. By default None, for which it will return only the base_state and any fixed values.</td>
-<td><code>None</code></td>
-</tr>
-<tr class="even">
-<td><code>base_state</code></td>
-<td>dict</td>
-<td>Initial state to build on, expressed as Neuroglancer JSON. By default None</td>
-<td><code>None</code></td>
-</tr>
-<tr class="odd">
-<td><code>return_as</code></td>
-<td>[url, nglui.statebuilder.statebuilder.StateBuilder.viewer, html, json, dict, shared]</td>
-<td>Choice of output types. Note that if a viewer is returned, the state is not reset. url : Returns the raw url describing the state viewer : Returns an EasyViewer object holding the state information html : Returns an HTML link to the url, useful for notebooks. json : Returns a JSON string describing the state. dict : Returns a dict version of the JSON state. By default ‘url’</td>
-<td><code>'url'</code></td>
-</tr>
-<tr class="even">
-<td><code>url_prefix</code></td>
-<td>str</td>
-<td>Neuroglancer URL prefix to use. By default None, for which it will open with the class default.</td>
-<td><code>None</code></td>
-</tr>
-<tr class="odd">
-<td><code>link_text</code></td>
-<td>str</td>
-<td>Text to use for the link when returning as html, by default ‘Neuroglancer Link’</td>
-<td><code>'Neuroglancer Link'</code></td>
-</tr>
-</tbody>
-</table>
-</section>
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-<th>Type</th>
-<th>Description</th>
-</tr>
-</thead>
-<tbody>
-<tr class="odd">
-<td>string or neuroglancer.neuroglancer.Viewer</td>
-<td>A link to or viewer for a Neuroglancer state with layers, annotations, and selected objects determined by the data.</td>
-</tr>
-</tbody>
-</table>
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-    "text": "statebuilder.layers.ImageLayerConfig(self, source, name=None, active=False, contrast_controls=False, black=0.0, white=1.0)\nImage layer configuration class.\nThis provides the rules for setting up an image layer in neuroglancer.\n\n\n\n\n\n\n\n\n\n\n\nName\nType\nDescription\nDefault\n\n\n\n\nsource\nstr\nCloudpath to an image source\nrequired\n\n\nname\nstr\nName of the image layer. By default, ‘img’.\nNone\n\n\nactive\nbool\nIf True, makes the layer active in neuroglancer. Default is False.\nFalse\n\n\ncontrast_controls\nbool\nIf True, gives the layer a user-controllable brightness and contrast shader. Default is False.\nFalse\n\n\nblack\nfloat\nIf contrast_controls is True, sets the default black level. Default is 0.0.\n0.0\n\n\nwhite\nfloat\nIf contrast_controls is True, sets the default white level. Default is 1.0.\n1.0"
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-    "text": "Name\nType\nDescription\nDefault\n\n\n\n\nsource\nstr\nCloudpath to an image source\nrequired\n\n\nname\nstr\nName of the image layer. By default, ‘img’.\nNone\n\n\nactive\nbool\nIf True, makes the layer active in neuroglancer. Default is False.\nFalse\n\n\ncontrast_controls\nbool\nIf True, gives the layer a user-controllable brightness and contrast shader. Default is False.\nFalse\n\n\nblack\nfloat\nIf contrast_controls is True, sets the default black level. Default is 0.0.\n0.0\n\n\nwhite\nfloat\nIf contrast_controls is True, sets the default white level. Default is 1.0.\n1.0"
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-    "text": "Name\nType\nDescription\nDefault\n\n\n\n\nstate\ndict\nNeuroglancer state as JSON dict\nrequired\n\n\nlayer_name\nstr\nAnnotation layer name\nrequired\n\n\ndescription\nbool\nIf True, also returns descriptions as well. By default False\nFalse\n\n\nlinked_segmentations\nbool\nIf True, also returns list of linked segmentations, by default False\nFalse\n\n\ntags\nbool\nIf True, also returns list of tags, by default False\nFalse"
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-    "text": "statebuilder.statebuilder.StateBuilder(self, layers=[], base_state=None, url_prefix=None, state_server=None, resolution=None, view_kws={}, client=None, target_site=None)\nA class for schematic mapping data frames into neuroglancer states.\n\n\n\n\n\n\n\n\n\n\n\nName\nType\nDescription\nDefault\n\n\n\n\nlayers\n\n\n[]\n\n\nbase_state\n\n\nNone\n\n\nurl_prefix\n\nDefaults to None, which will use https://neuromancer-seung-import.appspot.com\nNone\n\n\nstate_server\n\n\nNone\n\n\nresolution\n\n\nNone\n\n\nview_kws\n\nkeys are: show_slices: Boolean sets if slices are shown in the 3d view. Defaults to False. layout: str xy-3d/xz-3d/yz-3d (sections plus 3d pane), xy/yz/xz/3d (only one pane), or 4panel (all panes). Default is xy-3d. show_axis_lines: Boolean determines if the axis lines are shown in the middle of each view. show_scale_bar: Boolean toggles showing the scale bar. orthographic : Boolean toggles orthographic view in the 3d pane. position* : 3-element vector determines the centered location. zoom_image : float Zoom level for the imagery in units of nm per voxel. Defaults to 8. zoom_3d : float Zoom level for the 3d pane. Defaults to 2000. Smaller numbers are more zoomed in. background_color : str or list Sets the background color of the 3d view. Arguments can be rgb values, hex colors, or named web colors. Defaults to black.\n{}\n\n\nclient\n\n\nNone\n\n\n\n\n\n\n\n\n\nName\nDescription\n\n\n\n\ninitialize_state\nGenerate a new Neuroglancer state with layers as needed for the schema.\n\n\nrender_state\nBuild a Neuroglancer state out of a DataFrame.\n\n\n\n\n\nstatebuilder.statebuilder.StateBuilder.initialize_state(base_state=None, target_site=None)\nGenerate a new Neuroglancer state with layers as needed for the schema.\n\n\n\n\n\n\n\n\n\n\n\nName\nType\nDescription\nDefault\n\n\n\n\nbase_state\nstr\nOptional initial state to build on, described by its JSON. By default None.\nNone\n\n\n\n\n\n\n\nstatebuilder.statebuilder.StateBuilder.render_state(data=None, base_state=None, return_as='url', url_prefix=None, link_text='Neuroglancer Link', target_site=None)\nBuild a Neuroglancer state out of a DataFrame.\n\n\n\n\n\n\n\n\n\n\n\nName\nType\nDescription\nDefault\n\n\n\n\ndata\npandas.pandas.DataFrame\nDataFrame to use as a point source. By default None, for which it will return only the base_state and any fixed values.\nNone\n\n\nbase_state\ndict\nInitial state to build on, expressed as Neuroglancer JSON. By default None\nNone\n\n\nreturn_as\n[url, nglui.statebuilder.statebuilder.StateBuilder.viewer, html, json, dict, shared]\nChoice of output types. Note that if a viewer is returned, the state is not reset. url : Returns the raw url describing the state viewer : Returns an EasyViewer object holding the state information html : Returns an HTML link to the url, useful for notebooks. json : Returns a JSON string describing the state. dict : Returns a dict version of the JSON state. By default ‘url’\n'url'\n\n\nurl_prefix\nstr\nNeuroglancer URL prefix to use. By default None, for which it will open with the class default.\nNone\n\n\nlink_text\nstr\nText to use for the link when returning as html, by default ‘Neuroglancer Link’\n'Neuroglancer Link'\n\n\n\n\n\n\n\n\n\n\n\n\n\nType\nDescription\n\n\n\n\nstring or neuroglancer.neuroglancer.Viewer\nA link to or viewer for a Neuroglancer state with layers, annotations, and selected objects determined by the data."
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-    "text": "statebuilder.ChainedStateBuilder(self, statebuilders)\nBuilds a collection of states that sequentially add annotations based on a sequence of dataframes.\n\n\n\n\n\n\n\n\n\n\n\nName\nType\nDescription\nDefault\n\n\n\n\nstatebuilders\nlist\nList of DataStateBuilders, in same order as dataframes will be passed\nrequired"
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-    "text": "statebuilder.layers.SegmentationLayerConfig(self, source, name=None, selected_ids_column=None, fixed_ids=None, fixed_id_colors=None, color_column=None, active=False, alpha_selected=0.3, alpha_3d=1, alpha_unselected=0, split_point_map=None, view_kws=None, timestamp=None, data_resolution=None)\nConfiguration class for segmentation layers\n\n\n\n\n\n\n\n\n\n\n\nName\nType\nDescription\nDefault\n\n\n\n\nsource\nstr\nSegmentation source\nrequired\n\n\nname\n(str, optional)\nLayer name.\nNone\n\n\nselected_ids_column\nstr or list-like, optional.\nColumn name (or list of column names) to use for selected ids.\nNone\n\n\nfixed_ids\nlist-like, optional.\nList of root ids to select directly.\nNone\n\n\nfixed_id_colors\nlist-like, optional.\nList of colors for fixed ids. Should be the same length as fixed_ids, although null entries can be padded with None values.\nNone\n\n\ncolor_column\nstr, optional.\n# at the begining. Column to use for color values for selected objects. Values should be RGB hex strings with a\nNone\n\n\nactive\nbool, optional.\nIf True, makes the layer selected. Default is False.\nFalse\n\n\nalpha_selected\n\nOpacity of selected segmentations in the image layer. Optional, default is 0.3.\n0.3\n\n\nalpha_3d\n\nOpacity of meshes. Optional, default is 1.\n1\n\n\nalpha_unselected\n\nOpacity of unselected segments. Optional, default is 0.\n0\n\n\nsplit_point_map\n\nIf not None, provides an object to map the dataframe input to multicut points. Default is None.\nNone\n\n\nview_kws\ndict, optional.\nKeyword arguments for viewer.set_segmentation_view_options. Sets selected (and unselected) segmetation alpha values. Defaults to values in DEFAULT_SEGMENTATION_VIEW_KWS dict specified in this module.\nNone\n\n\ntimestamp\nfloat or datetime, optional.\nTimestamp at which to fix the chunkedgraph in either unix epoch or datetime format. Optional, default is None.\nNone\n\n\n\n\n\n\n\n\n\nName\nDescription\n\n\n\n\nadd_selection_map\nAdd rules for selecting active segment ids and their colors\n\n\n\n\n\nstatebuilder.layers.SegmentationLayerConfig.add_selection_map(selected_ids_column=None, fixed_ids=None, fixed_id_colors=None, color_column=None)\nAdd rules for selecting active segment ids and their colors\n\n\n\n\n\n\n\n\n\n\n\nName\nType\nDescription\nDefault\n\n\n\n\nselected_ids_column\nstr\nDataframe column to use for adding selected segment ids to the segmentation layer, by default None\nNone\n\n\nfixed_ids\nint or list\nAdd one or more segment ids to be active, independent of the data, by default None\nNone\n\n\nfixed_id_colors\nlist\nAdd a list of colors (hex, rgb, or CSS3 string) to assign to the fixed ids, by default None\nNone\n\n\ncolor_column\nstr\nDataframe column to use for adding selected segment colors, by default None\nNone"
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-    "text": "Name\nType\nDescription\nDefault\n\n\n\n\nsource\nstr\nSegmentation source\nrequired\n\n\nname\n(str, optional)\nLayer name.\nNone\n\n\nselected_ids_column\nstr or list-like, optional.\nColumn name (or list of column names) to use for selected ids.\nNone\n\n\nfixed_ids\nlist-like, optional.\nList of root ids to select directly.\nNone\n\n\nfixed_id_colors\nlist-like, optional.\nList of colors for fixed ids. Should be the same length as fixed_ids, although null entries can be padded with None values.\nNone\n\n\ncolor_column\nstr, optional.\n# at the begining. Column to use for color values for selected objects. Values should be RGB hex strings with a\nNone\n\n\nactive\nbool, optional.\nIf True, makes the layer selected. Default is False.\nFalse\n\n\nalpha_selected\n\nOpacity of selected segmentations in the image layer. Optional, default is 0.3.\n0.3\n\n\nalpha_3d\n\nOpacity of meshes. Optional, default is 1.\n1\n\n\nalpha_unselected\n\nOpacity of unselected segments. Optional, default is 0.\n0\n\n\nsplit_point_map\n\nIf not None, provides an object to map the dataframe input to multicut points. Default is None.\nNone\n\n\nview_kws\ndict, optional.\nKeyword arguments for viewer.set_segmentation_view_options. Sets selected (and unselected) segmetation alpha values. Defaults to values in DEFAULT_SEGMENTATION_VIEW_KWS dict specified in this module.\nNone\n\n\ntimestamp\nfloat or datetime, optional.\nTimestamp at which to fix the chunkedgraph in either unix epoch or datetime format. Optional, default is None.\nNone"
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-    "text": "Name\nDescription\n\n\n\n\nadd_selection_map\nAdd rules for selecting active segment ids and their colors\n\n\n\n\n\nstatebuilder.layers.SegmentationLayerConfig.add_selection_map(selected_ids_column=None, fixed_ids=None, fixed_id_colors=None, color_column=None)\nAdd rules for selecting active segment ids and their colors\n\n\n\n\n\n\n\n\n\n\n\nName\nType\nDescription\nDefault\n\n\n\n\nselected_ids_column\nstr\nDataframe column to use for adding selected segment ids to the segmentation layer, by default None\nNone\n\n\nfixed_ids\nint or list\nAdd one or more segment ids to be active, independent of the data, by default None\nNone\n\n\nfixed_id_colors\nlist\nAdd a list of colors (hex, rgb, or CSS3 string) to assign to the fixed ids, by default None\nNone\n\n\ncolor_column\nstr\nDataframe column to use for adding selected segment colors, by default None\nNone"
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-    "text": "statebuilder.layers.LayerConfigBase(self, name, type, source, color, active)\nBase class for configuring layers\n\n\n\n\n\n\n\n\n\n\n\nName\nType\nDescription\nDefault\n\n\n\n\nname\nstr\nLayer name for reference and display\nrequired\n\n\ntype\nstr\nLayer type. Usually handled by the subclass\nrequired\n\n\nsource\nstr\nDatasource for the layer\nrequired\n\n\ncolor\nstr\nHex string (with starting hash).\nrequired\n\n\nactive\n(bool)\nIf True, becomes a selected layer.\nrequired"
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-    "text": "Name\nType\nDescription\nDefault\n\n\n\n\nname\nstr\nLayer name for reference and display\nrequired\n\n\ntype\nstr\nLayer type. Usually handled by the subclass\nrequired\n\n\nsource\nstr\nDatasource for the layer\nrequired\n\n\ncolor\nstr\nHex string (with starting hash).\nrequired\n\n\nactive\n(bool)\nIf True, becomes a selected layer.\nrequired"
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-    "text": "parser.base.point_annotations(state, layer_name, description=False, linked_segmentations=False, tags=False, group=False)\nGet all point annotation points and other info from a layer.\n\n\n\n\n\n\n\n\n\n\n\nName\nType\nDescription\nDefault\n\n\n\n\nstate\ndict\nNeuroglancer state as JSON dict\nrequired\n\n\nlayer_name\nstr\nLayer name\nrequired\n\n\ndescription\nbool\nIf True, also returns descriptions as well. By default False\nFalse\n\n\nlinked_segmentations\nbool\nIf True, also returns list of linked segmentations, by default False\nFalse\n\n\ntags\nbool\nIf True, also returns list of tags, by default False\nFalse\n\n\n\n\n\n\n\n\n\n\n\n\n\nType\nDescription\n\n\n\n\nlist\nList of N 3-element points (as list)\n\n\nlist\nList of N strings (or None), only returned if description=True.\n\n\nlist\nList of N lists of object ids. Only returned if linked_segmentations=True.\n\n\nlist\nList of N lists of tag ids. Only returned if tags=True.\n\n\nlist\nList of group ids (as string) or None for annotations. Only returned if group=True"
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-    "text": "Name\nType\nDescription\nDefault\n\n\n\n\nstate\ndict\nNeuroglancer state as JSON dict\nrequired\n\n\nlayer_name\nstr\nLayer name\nrequired\n\n\ndescription\nbool\nIf True, also returns descriptions as well. By default False\nFalse\n\n\nlinked_segmentations\nbool\nIf True, also returns list of linked segmentations, by default False\nFalse\n\n\ntags\nbool\nIf True, also returns list of tags, by default False\nFalse"
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-    "text": "Type\nDescription\n\n\n\n\nlist\nList of N 3-element points (as list)\n\n\nlist\nList of N strings (or None), only returned if description=True.\n\n\nlist\nList of N lists of object ids. Only returned if linked_segmentations=True.\n\n\nlist\nList of N lists of tag ids. Only returned if tags=True.\n\n\nlist\nList of group ids (as string) or None for annotations. Only returned if group=True"
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-    "text": "parser.base.get_layer(state, layer_name)\nGets the contents of the layer based on the layer name.\n\n\n\n\n\n\n\n\n\n\n\nName\nType\nDescription\nDefault\n\n\n\n\nstate\ndict\nNeuroglancer state as a JSON dict\nrequired\n\n\nlayer_name\nstr\nName of layer\nrequired\n\n\n\n\n\n\n\n\n\nType\nDescription\n\n\n\n\ndict\nLayer data contents"
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-    "text": "Name\nType\nDescription\nDefault\n\n\n\n\nstate\ndict\nNeuroglancer state as a JSON dict\nrequired\n\n\nlayer_name\nstr\nName of layer\nrequired"
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-    "text": "Type\nDescription\n\n\n\n\ndict\nLayer data contents"
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-    "text": "This site provides basic documentation for the functions in NGLui. Please see the tutorials for more information about how to use them.\nNote that nglui spans two public submodules responsible for different tasks.\n\nStateBuilder handles data-driven Neuroglancer state generation (hence the package name).\nParser extracts information from Neuroglancer states, as represented by dictionaries."
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-    "text": "StateBuilder Functions\n\nLayers\nInstantiating types of layers\n\n\n\nstatebuilder.ImageLayerConfig\nImage layer configuration class.\n\n\nstatebuilder.SegmentationLayerConfig\nConfiguration class for segmentation layers\n\n\nstatebuilder.AnnotationLayerConfig\nConfiguration class for annotation layers\n\n\n\n\n\nMapping Rules\nRules for mapping data to annotations\n\n\n\nstatebuilder.PointMapper\nSets rules to map dataframes to point annotations\n\n\nstatebuilder.LineMapper\nSets rules to map dataframes to line annotations\n\n\nstatebuilder.SphereMapper\nSets rules to map dataframes to sphere annotations\n\n\nstatebuilder.BoundingBoxMapper\nSets rules to map dataframes to bounding box annotations\n\n\nstatebuilder.SplitPointMapper\nMapper to create split points in a segmentation layer.\n\n\n\n\n\nStateBuilder Classes\nTools for data-generated neuroglancer state creation\n\n\n\nstatebuilder.StateBuilder\nA class for schematic mapping data frames into neuroglancer states.\n\n\nstatebuilder.ChainedStateBuilder\nBuilds a collection of states that sequentially add annotations based on a sequence of dataframes.\n\n\n\n\n\nHelpers\nTools for common types of states\n\n\n\nstatebuilder.helpers.from_client\nGenerate basic image and segmentation layers from a FrameworkClient\n\n\nstatebuilder.helpers.sort_dataframe_by_root_id\nSort a dataframe so that rows belonging to the same root id are together, ordered by how many times the root id appears.\n\n\nstatebuilder.helpers.make_line_statebuilder\nGenerate a state builder that puts points on a single column with a linked segmentaton id\n\n\nstatebuilder.helpers.make_point_statebuilder\nGenerate a state builder that puts points on a single column with a linked segmentaton id\n\n\nstatebuilder.helpers.make_pre_post_statebuilder\nFunction to generate ChainedStateBuilder with optional pre and post synaptic\n\n\nstatebuilder.helpers.make_state_url\nGenerate a url from a neuroglancer state via a state server.\n\n\nstatebuilder.helpers.make_url_robust\nGenerate a url from a neuroglancer state. If too long, return through state server,\n\n\nstatebuilder.helpers.package_state\nAutomate creating a state from a statebuilder and\n\n\nstatebuilder.helpers.make_synapse_neuroglancer_link\nGenerate a neuroglancer link from a synapse dataframe as returned from CAVEclient.materialize.synapse_query.\n\n\nstatebuilder.helpers.make_neuron_neuroglancer_link\nfunction to create a neuroglancer link view of a neuron, optionally including inputs and outputs"
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-    "text": "Parser\n\nParser Tools\nSimple tools for parsing neuroglancer states\n\n\n\nparser.base.layer_names\nGet all layer names in the state\n\n\nparser.base.image_layers\nGet all image layer names in the state\n\n\nparser.base.segmentation_layers\nGet all segmentation layer names in the state\n\n\nparser.base.annotation_layers\nGet all annotation layer names in the state\n\n\nparser.base.tag_dictionary\nGet the tag id to string dictionary for a layer\n\n\nparser.base.get_layer\nGets the contents of the layer based on the layer name.\n\n\nparser.base.view_settings\nGet all data about the view state in neuroglancer: position,\n\n\nparser.base.get_selected_ids\nGet a list of selected ids in a segmentation layer\n\n\nparser.base.point_annotations\nGet all point annotation points and other info from a layer.\n\n\nparser.base.line_annotations\nGet all line annotation points and other info from a layer.\n\n\nparser.base.sphere_annotations\nGet all sphere annotation points and other info from a layer.\n\n\nparser.base.group_annotations\nAll group annotations and their associated points\n\n\nparser.base.extract_multicut\nExtract information entered into the multicut graph operation\n\n\nparser.base.annotation_dataframe\nReturn all annotations across all annotation layers in the state."
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-    "text": "statebuilder.layers.AnnotationLayerConfig(self, name=None, color=None, linked_segmentation_layer=None, mapping_rules=[], array_data=False, tags=None, active=True, filter_by_segmentation=False, brackets_show_segmentation=True, selection_shows_segmentation=True, filter_query=None, data_resolution=None)\nConfiguration class for annotation layers\n\n\n\n\n\n\n\n\n\n\n\nName\nType\nDescription\nDefault\n\n\n\n\nname\nstr\nLayer name. By default, ‘annos’\nNone\n\n\ncolor\nstr\nHex color code with an initial #. By default, None\nNone\n\n\nlinked_segmentation_layer\nstr\nName of a linked segmentation layer for selected ids. By default, None\nNone\n\n\nmapping_rules\n(nglui.statebuilder.mappers.PointMapper, nglui.statebuilder.mappers.LineMapper, nglui.statebuilder.mappers.SphereMapper or list)\nOne rule or a list of rules mapping data to annotations. By default, []\n[]\n\n\narray_data\nbool\nIf True, allows simple mapping where one or more arrays are passed instead of a dataframe. Only allows basic annotation creation, no tags, linked segmentations, or other rich features.\nFalse\n\n\ntags\nlist\nList of tags for the layer.\nNone\n\n\nactive\nbool\nIf True, makes the layer selected. Default is True (unlike for image/segmentation layers).\nTrue"
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-    "text": "Name\nType\nDescription\nDefault\n\n\n\n\nname\nstr\nLayer name. By default, ‘annos’\nNone\n\n\ncolor\nstr\nHex color code with an initial #. By default, None\nNone\n\n\nlinked_segmentation_layer\nstr\nName of a linked segmentation layer for selected ids. By default, None\nNone\n\n\nmapping_rules\n(nglui.statebuilder.mappers.PointMapper, nglui.statebuilder.mappers.LineMapper, nglui.statebuilder.mappers.SphereMapper or list)\nOne rule or a list of rules mapping data to annotations. By default, []\n[]\n\n\narray_data\nbool\nIf True, allows simple mapping where one or more arrays are passed instead of a dataframe. Only allows basic annotation creation, no tags, linked segmentations, or other rich features.\nFalse\n\n\ntags\nlist\nList of tags for the layer.\nNone\n\n\nactive\nbool\nIf True, makes the layer selected. Default is True (unlike for image/segmentation layers).\nTrue"
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-    "text": "parser.base.get_selected_ids(state, layer=None)\nGet a list of selected ids in a segmentation layer\n\n\n\n\n\n\n\n\n\n\n\nName\nType\nDescription\nDefault\n\n\n\n\nstate\ndict\nState dict\nrequired\n\n\nlayer\nstr\nSegmentation layer name, if needed. If None and only one segmentation layer is present, default to it. By default None\nNone\n\n\n\n\n\n\n\n\n\nType\nDescription\n\n\n\n\nlist\nList of root ids."
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-    "text": "Name\nType\nDescription\nDefault\n\n\n\n\nstate\ndict\nState dict\nrequired\n\n\nlayer\nstr\nSegmentation layer name, if needed. If None and only one segmentation layer is present, default to it. By default None\nNone"
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-    "text": "statebuilder.SplitPointMapper(self, id_column, point_column, team_column, team_names=['red', 'blue'], supervoxel_column=None, focus=True, mapping_set=None)\nMapper to create split points in a segmentation layer.\n\n\n\n\n\n\n\n\n\n\n\nName\nType\nDescription\nDefault\n\n\n\n\nid_column\nstr\nColumn name for segment ids. The id column must contain the same id in all rows.\nrequired\n\n\npoint_column\nstr\nName of the column containing points in space.\nrequired\n\n\nteam_column\nstr\nName of the column describing the team for the points. The contents of the column should have two values, by default “red” and “blue”.\nrequired\n\n\nteam_names\nlist\nList of two values for the team names used in the team column. The first is mapped to red points, the second blue. Default is [“red”, “blue”].\n['red', 'blue']\n\n\nsupervoxel_column\nstr or None\nName of a column providing supervoxel ids. If None (default), the supervoxel must be looked up on the server.\nNone\n\n\nfocus\nbool\nIf True, sets the focus on the split tool and sets the position to the center of split points. Default is True.\nTrue\n\n\n\n\n\n\n\n\n\n\n\n\n\nType\nDescription\n\n\n\n\nSplitPointMapper instance to pass to a segmentation layer."
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-    "text": "Name\nType\nDescription\nDefault\n\n\n\n\nid_column\nstr\nColumn name for segment ids. The id column must contain the same id in all rows.\nrequired\n\n\npoint_column\nstr\nName of the column containing points in space.\nrequired\n\n\nteam_column\nstr\nName of the column describing the team for the points. The contents of the column should have two values, by default “red” and “blue”.\nrequired\n\n\nteam_names\nlist\nList of two values for the team names used in the team column. The first is mapped to red points, the second blue. Default is [“red”, “blue”].\n['red', 'blue']\n\n\nsupervoxel_column\nstr or None\nName of a column providing supervoxel ids. If None (default), the supervoxel must be looked up on the server.\nNone\n\n\nfocus\nbool\nIf True, sets the focus on the split tool and sets the position to the center of split points. Default is True.\nTrue"
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-    "text": "statebuilder.helpers.make_synapse_neuroglancer_link(synapse_df, client, return_as='html', shorten='always', contrast=None, point_column='ctr_pt_position', dataframe_resolution=None, group_connections=True, link_pre_and_post=True, ngl_url=None, view_kws=None, pre_post_columns=None, neuroglancer_link_text='Neuroglancer Link', color=None, split_positions=False, target_site=None)\nGenerate a neuroglancer link from a synapse dataframe as returned from CAVEclient.materialize.synapse_query.\n\n\n\n\n\n\n\n\n\n\n\nName\nType\nDescription\nDefault\n\n\n\n\nsynapse_df\npandas.pandas.DataFrame\nDataFrame where each row represents a synapse.\nrequired\n\n\nclient\ncaveclient.caveclient.CAVEclient\nA CAVEclient instance.\nrequired\n\n\nreturn_as\nstr\nHow to return the URL. Valid options are: - ‘html’: Returns an IPython HTML element. - ‘url’: Returns a URL string. - ‘json’: Returns a dictionary representing the Neuroglancer state. Defaults to ‘html’.\n'html'\n\n\nshorten\nstr\nWhether to shorten the link. Valid options are: - ‘always’: Always shorten the link. - ‘if_long’: Shorten the link if it exceeds MAX_URL_LENGTH. - ‘never’: Never shorten the link. Defaults to ‘always’.\n'always'\n\n\ncontrast\nlist\nList of two floats between 0 and 1, specifying the black and white levels. If None, no contrast is set.\nNone\n\n\npoint_column\nstr\nColumn in the DataFrame containing synapse positions. Defaults to ‘ctr_pt_position’.\n'ctr_pt_position'\n\n\ndataframe_resolution\nlist\nList of length 3, specifying the resolution units of the position column. If None, attempts to get the resolution from DataFrame metadata or client.info.viewer_resolution().\nNone\n\n\ngroup_connections\nbool\nWhether to group synapses within the same connection (between the same neurons). Defaults to True.\nTrue\n\n\nlink_pre_and_post\nbool\nWhether to link the synapse annotations to the pre- and post-synaptic partners. Defaults to True.\nTrue\n\n\nngl_url\nstr\nURL of the Neuroglancer instance to use. Defaults to client.info.viewer_site() or DEFAULT_NGL.\nNone\n\n\nview_kws\ndict\nDictionary containing viewer settings for Neuroglancer. Available keys: - show_slices: Boolean, sets if slices are shown in the 3D view. - layout: str, specifies the viewer layout (e.g., ‘xy-3d’, ‘4panel’). - show_axis_lines: Boolean, determines if axis lines are shown. - show_scale_bar: Boolean, toggles the scale bar. - orthographic: Boolean, toggles orthographic view in the 3D pane. - position: 3-element vector, sets the centered location. - zoom_image: float, zoom level for the imagery in nm per voxel. - zoom_3d: float, zoom level for the 3D pane.\nNone\n\n\npre_post_columns\nlist\nList of two strings, specifying the column names for pre- and post-synaptic root_ids. Defaults to [‘pre_pt_root_id’, ‘post_pt_root_id’].\nNone\n\n\nneuroglancer_link_text\nstr\nText to use in the returned HTML link. Defaults to ‘Neuroglancer Link’.\n'Neuroglancer Link'\n\n\ncolor\nlist(float) or str\nColor of synapse points as an RGB list [0, 1], hex string, or common name.\nNone\n\n\nsplit_positions\nbool\nWhether the position column is split into x, y, and z columns.\nFalse\n\n\ntarget_site\nstr\nType of neuroglancer deployment to build link for, by default None. This value overrides automatic checking based on the provided url. Use seunglab for a Seung-lab branch and either mainline or cave-explorer for the Cave Explorer or main Google branch.\nNone\n\n\n\n\n\n\n\n\n\n\n\n\n\nType\nDescription\n\n\n\n\nIPython.HTML, str, or dict\nRepresentation of the Neuroglancer state, depending on the return_as parameter.\n\n\n\n\n\n\n\n\n\n\n\n\n\nType\nDescription\n\n\n\n\nValueError\nIf the specified point_column is not found in the DataFrame."
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-    "text": "Name\nType\nDescription\nDefault\n\n\n\n\nsynapse_df\npandas.pandas.DataFrame\nDataFrame where each row represents a synapse.\nrequired\n\n\nclient\ncaveclient.caveclient.CAVEclient\nA CAVEclient instance.\nrequired\n\n\nreturn_as\nstr\nHow to return the URL. Valid options are: - ‘html’: Returns an IPython HTML element. - ‘url’: Returns a URL string. - ‘json’: Returns a dictionary representing the Neuroglancer state. Defaults to ‘html’.\n'html'\n\n\nshorten\nstr\nWhether to shorten the link. Valid options are: - ‘always’: Always shorten the link. - ‘if_long’: Shorten the link if it exceeds MAX_URL_LENGTH. - ‘never’: Never shorten the link. Defaults to ‘always’.\n'always'\n\n\ncontrast\nlist\nList of two floats between 0 and 1, specifying the black and white levels. If None, no contrast is set.\nNone\n\n\npoint_column\nstr\nColumn in the DataFrame containing synapse positions. Defaults to ‘ctr_pt_position’.\n'ctr_pt_position'\n\n\ndataframe_resolution\nlist\nList of length 3, specifying the resolution units of the position column. If None, attempts to get the resolution from DataFrame metadata or client.info.viewer_resolution().\nNone\n\n\ngroup_connections\nbool\nWhether to group synapses within the same connection (between the same neurons). Defaults to True.\nTrue\n\n\nlink_pre_and_post\nbool\nWhether to link the synapse annotations to the pre- and post-synaptic partners. Defaults to True.\nTrue\n\n\nngl_url\nstr\nURL of the Neuroglancer instance to use. Defaults to client.info.viewer_site() or DEFAULT_NGL.\nNone\n\n\nview_kws\ndict\nDictionary containing viewer settings for Neuroglancer. Available keys: - show_slices: Boolean, sets if slices are shown in the 3D view. - layout: str, specifies the viewer layout (e.g., ‘xy-3d’, ‘4panel’). - show_axis_lines: Boolean, determines if axis lines are shown. - show_scale_bar: Boolean, toggles the scale bar. - orthographic: Boolean, toggles orthographic view in the 3D pane. - position: 3-element vector, sets the centered location. - zoom_image: float, zoom level for the imagery in nm per voxel. - zoom_3d: float, zoom level for the 3D pane.\nNone\n\n\npre_post_columns\nlist\nList of two strings, specifying the column names for pre- and post-synaptic root_ids. Defaults to [‘pre_pt_root_id’, ‘post_pt_root_id’].\nNone\n\n\nneuroglancer_link_text\nstr\nText to use in the returned HTML link. Defaults to ‘Neuroglancer Link’.\n'Neuroglancer Link'\n\n\ncolor\nlist(float) or str\nColor of synapse points as an RGB list [0, 1], hex string, or common name.\nNone\n\n\nsplit_positions\nbool\nWhether the position column is split into x, y, and z columns.\nFalse\n\n\ntarget_site\nstr\nType of neuroglancer deployment to build link for, by default None. This value overrides automatic checking based on the provided url. Use seunglab for a Seung-lab branch and either mainline or cave-explorer for the Cave Explorer or main Google branch.\nNone"
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-    "text": "Type\nDescription\n\n\n\n\nIPython.HTML, str, or dict\nRepresentation of the Neuroglancer state, depending on the return_as parameter."
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-    "text": "Type\nDescription\n\n\n\n\nValueError\nIf the specified point_column is not found in the DataFrame."
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-    "text": "statebuilder.statebuilder.StateBuilder.initialize_state(base_state=None, target_site=None)\nGenerate a new Neuroglancer state with layers as needed for the schema.\n\n\n\n\n\n\n\n\n\n\n\nName\nType\nDescription\nDefault\n\n\n\n\nbase_state\nstr\nOptional initial state to build on, described by its JSON. By default None.\nNone"
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-    "text": "Name\nType\nDescription\nDefault\n\n\n\n\nbase_state\nstr\nOptional initial state to build on, described by its JSON. By default None.\nNone"
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-    "text": "statebuilder.helpers.package_state(df, sb, client, shorten='if_long', return_as='url', ngl_url=None, link_text='Neuroglancer Link', target_site=None)\nAutomate creating a state from a statebuilder and a dataframe, return it in the desired format, shortening if desired."
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-    "text": "Parameters\n\n\n\n\n\n\n\n\n\nName\nType\nDescription\nDefault\n\n\n\n\ndf\npandas.pandas.DataFrame\nDataframe to pass through statebuilder\nrequired\n\n\nsb\nnglui.statebuilder.statebuilder.nglui.statebuilder.statebuilder.StateBuilder\nStatebuilder to use to render data for link\nrequired\n\n\nclient\ncaveclient.CAVEclient\nCAVEclient configured with a state server\nrequired\n\n\nshorten\nstr\nHow to shorten link. one of ‘if_long’, ‘always’, ‘never’. ‘if_long’ will use the state server to shorten links longer than nglui.statebuilder.MAX_URL_LENGTH (set to 1,750,000). ‘always’ will always use the state server to shorten the url ‘never’ will always return the full url. Defaults to “if_long”.\n'if_long'\n\n\nreturn_as\nstr\nHow to return the state. one of ‘html’, ‘url’, ‘json’. ‘html’ will return an ipython clickable link ‘url’ will return a string with the url ‘json’ will return the state as a dictionary\n'url'\n\n\nngl_url\nstr\nNeuroglancer deployment URL, by default None\nNone\n\n\nlink_text\nstr\nText to use for the link, by default “Neuroglancer Link”\n'Neuroglancer Link'\n\n\ntarget_site\nstr\nType of neuroglancer deployment to build link for, by default None. This value overrides automatic checking based on the provided url. Use seunglab for a Seung-lab branch and either mainline or cave-explorer for the Cave Explorer or main Google branch.\nNone"
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-    "text": "Returns\n\n\n\n\n\n\n\nType\nDescription\n\n\n\n\n(IPython.display.HTML, str or dict)\nstate in format specified by return_as"
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-    "text": "parser.base.line_annotations(state, layer_name, description=False, linked_segmentations=False, tags=False, group=False)\nGet all line annotation points and other info from a layer.\n\n\n\n\n\n\n\n\n\n\n\nName\nType\nDescription\nDefault\n\n\n\n\nstate\ndict\nNeuroglancer state as JSON dict\nrequired\n\n\nlayer_name\nstr\nLayer name\nrequired\n\n\ndescription\nbool\nIf True, also returns descriptions as well. By default False\nFalse\n\n\nlinked_segmentations\nbool\nIf True, also returns list of linked segmentations, by default False\nFalse\n\n\ntags\nbool\nIf True, also returns list of tags, by default False\nFalse\n\n\n\n\n\n\n\n\n\n\n\n\n\nType\nDescription\n\n\n\n\nlist\nList of N 3-element points (as list) of the first point in each line.\n\n\nlist\nList of N 3-element points (as list) of the second point in each line.\n\n\nlist\nList of N strings (or None), only returned if description=True.\n\n\nlist\nList of N lists of object ids. Only returned if linked_segmentations=True.\n\n\nlist\nList of N lists of tag ids. Only returned if tags=True.\n\n\nlist\nList of group ids (as string) or None for annotations. Only returned if group=True"
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-    "text": "Name\nType\nDescription\nDefault\n\n\n\n\nstate\ndict\nNeuroglancer state as JSON dict\nrequired\n\n\nlayer_name\nstr\nLayer name\nrequired\n\n\ndescription\nbool\nIf True, also returns descriptions as well. By default False\nFalse\n\n\nlinked_segmentations\nbool\nIf True, also returns list of linked segmentations, by default False\nFalse\n\n\ntags\nbool\nIf True, also returns list of tags, by default False\nFalse"
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-    "text": "Type\nDescription\n\n\n\n\nlist\nList of N 3-element points (as list) of the first point in each line.\n\n\nlist\nList of N 3-element points (as list) of the second point in each line.\n\n\nlist\nList of N strings (or None), only returned if description=True.\n\n\nlist\nList of N lists of object ids. Only returned if linked_segmentations=True.\n\n\nlist\nList of N lists of tag ids. Only returned if tags=True.\n\n\nlist\nList of group ids (as string) or None for annotations. Only returned if group=True"
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-    "text": "statebuilder.AnnotationLayerConfig(self, name=None, color=None, linked_segmentation_layer=None, mapping_rules=[], array_data=False, tags=None, active=True, filter_by_segmentation=False, brackets_show_segmentation=True, selection_shows_segmentation=True, filter_query=None, data_resolution=None)\nConfiguration class for annotation layers\n\n\n\n\n\n\n\n\n\n\n\nName\nType\nDescription\nDefault\n\n\n\n\nname\nstr\nLayer name. By default, ‘annos’\nNone\n\n\ncolor\nstr\nHex color code with an initial #. By default, None\nNone\n\n\nlinked_segmentation_layer\nstr\nName of a linked segmentation layer for selected ids. By default, None\nNone\n\n\nmapping_rules\n(nglui.statebuilder.mappers.PointMapper, nglui.statebuilder.mappers.LineMapper, nglui.statebuilder.mappers.SphereMapper or list)\nOne rule or a list of rules mapping data to annotations. By default, []\n[]\n\n\narray_data\nbool\nIf True, allows simple mapping where one or more arrays are passed instead of a dataframe. Only allows basic annotation creation, no tags, linked segmentations, or other rich features.\nFalse\n\n\ntags\nlist\nList of tags for the layer.\nNone\n\n\nactive\nbool\nIf True, makes the layer selected. Default is True (unlike for image/segmentation layers).\nTrue"
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-    "text": "Name\nType\nDescription\nDefault\n\n\n\n\nname\nstr\nLayer name. By default, ‘annos’\nNone\n\n\ncolor\nstr\nHex color code with an initial #. By default, None\nNone\n\n\nlinked_segmentation_layer\nstr\nName of a linked segmentation layer for selected ids. By default, None\nNone\n\n\nmapping_rules\n(nglui.statebuilder.mappers.PointMapper, nglui.statebuilder.mappers.LineMapper, nglui.statebuilder.mappers.SphereMapper or list)\nOne rule or a list of rules mapping data to annotations. By default, []\n[]\n\n\narray_data\nbool\nIf True, allows simple mapping where one or more arrays are passed instead of a dataframe. Only allows basic annotation creation, no tags, linked segmentations, or other rich features.\nFalse\n\n\ntags\nlist\nList of tags for the layer.\nNone\n\n\nactive\nbool\nIf True, makes the layer selected. Default is True (unlike for image/segmentation layers).\nTrue"
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-    "text": "statebuilder.LineMapper(self, point_column_a=None, point_column_b=None, description_column=None, linked_segmentation_column=None, tag_column=None, group_column=None, gather_linked_segmentations=True, share_linked_segmentations=False, set_position=True, multipoint=False, collapse_groups=False, split_positions=False, mapping_set=None)\nSets rules to map dataframes to line annotations\n\n\n\n\n\n\n\n\n\n\n\nName\nType\nDescription\nDefault\n\n\n\n\npoint_column_a\nstr\nColumn name with 3d position data for the first point of the line. Must be set if array_data is False (the default)\nNone\n\n\npoint_column_b\nstr\nColumn name with 3d position data for the first point of the line. Must be set if array_data is False (the default)\nNone\n\n\ndescription_column\nstr\nColumn name with string data for annotation descriptions\nNone\n\n\nlinked_segmentation_column\nstr\nColumn name for root ids to link to annotations\nNone\n\n\ntag_column\nstr\nColumn name for categorical tag data. Tags must match those set in the annotation layer.\nNone\n\n\ngroup_column\nstr\nColumn name for grouping data. Data in this row should be numeric with possible NaNs. Rows with the same non-NaN value will be collected into a grouped annotation.\nNone\n\n\nset_position\nbool\nIf set to True, moves the position to center on the first point in the data (using point_column_a).\nTrue\n\n\nmultipoint\n\nIf True, permits multiple points in a given row, sharing data in other columns. Each point row must have the same number of points. Default is False.\nFalse\n\n\ncollapse_groups\n\nIf True, groups are toggled closed in the annotation view.\nFalse\n\n\nmapping_set\n\nIf set, assumes data is passed as a dictionary and uses this string to as the key for the data to use.\nNone"
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-    "text": "Name\nType\nDescription\nDefault\n\n\n\n\npoint_column_a\nstr\nColumn name with 3d position data for the first point of the line. Must be set if array_data is False (the default)\nNone\n\n\npoint_column_b\nstr\nColumn name with 3d position data for the first point of the line. Must be set if array_data is False (the default)\nNone\n\n\ndescription_column\nstr\nColumn name with string data for annotation descriptions\nNone\n\n\nlinked_segmentation_column\nstr\nColumn name for root ids to link to annotations\nNone\n\n\ntag_column\nstr\nColumn name for categorical tag data. Tags must match those set in the annotation layer.\nNone\n\n\ngroup_column\nstr\nColumn name for grouping data. Data in this row should be numeric with possible NaNs. Rows with the same non-NaN value will be collected into a grouped annotation.\nNone\n\n\nset_position\nbool\nIf set to True, moves the position to center on the first point in the data (using point_column_a).\nTrue\n\n\nmultipoint\n\nIf True, permits multiple points in a given row, sharing data in other columns. Each point row must have the same number of points. Default is False.\nFalse\n\n\ncollapse_groups\n\nIf True, groups are toggled closed in the annotation view.\nFalse\n\n\nmapping_set\n\nIf set, assumes data is passed as a dictionary and uses this string to as the key for the data to use.\nNone"
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-    "text": "statebuilder.layers.SegmentationLayerConfig(self, source, name=None, selected_ids_column=None, fixed_ids=None, fixed_id_colors=None, color_column=None, active=False, alpha_selected=0.3, alpha_3d=1, alpha_unselected=0, split_point_map=None, view_kws=None, timestamp=None, data_resolution=None)\nConfiguration class for segmentation layers\n\n\n\n\n\n\n\n\n\n\n\nName\nType\nDescription\nDefault\n\n\n\n\nsource\nstr\nSegmentation source\nrequired\n\n\nname\n(str, optional)\nLayer name.\nNone\n\n\nselected_ids_column\nstr or list-like, optional.\nColumn name (or list of column names) to use for selected ids.\nNone\n\n\nfixed_ids\nlist-like, optional.\nList of root ids to select directly.\nNone\n\n\nfixed_id_colors\nlist-like, optional.\nList of colors for fixed ids. Should be the same length as fixed_ids, although null entries can be padded with None values.\nNone\n\n\ncolor_column\nstr, optional.\n# at the begining. Column to use for color values for selected objects. Values should be RGB hex strings with a\nNone\n\n\nactive\nbool, optional.\nIf True, makes the layer selected. Default is False.\nFalse\n\n\nalpha_selected\n\nOpacity of selected segmentations in the image layer. Optional, default is 0.3.\n0.3\n\n\nalpha_3d\n\nOpacity of meshes. Optional, default is 1.\n1\n\n\nalpha_unselected\n\nOpacity of unselected segments. Optional, default is 0.\n0\n\n\nsplit_point_map\n\nIf not None, provides an object to map the dataframe input to multicut points. Default is None.\nNone\n\n\nview_kws\ndict, optional.\nKeyword arguments for viewer.set_segmentation_view_options. Sets selected (and unselected) segmetation alpha values. Defaults to values in DEFAULT_SEGMENTATION_VIEW_KWS dict specified in this module.\nNone\n\n\ntimestamp\nfloat or datetime, optional.\nTimestamp at which to fix the chunkedgraph in either unix epoch or datetime format. Optional, default is None.\nNone\n\n\n\n\n\n\n\n\n\nName\nDescription\n\n\n\n\nadd_selection_map\nAdd rules for selecting active segment ids and their colors\n\n\n\n\n\nstatebuilder.layers.SegmentationLayerConfig.add_selection_map(selected_ids_column=None, fixed_ids=None, fixed_id_colors=None, color_column=None)\nAdd rules for selecting active segment ids and their colors\n\n\n\n\n\n\n\n\n\n\n\nName\nType\nDescription\nDefault\n\n\n\n\nselected_ids_column\nstr\nDataframe column to use for adding selected segment ids to the segmentation layer, by default None\nNone\n\n\nfixed_ids\nint or list\nAdd one or more segment ids to be active, independent of the data, by default None\nNone\n\n\nfixed_id_colors\nlist\nAdd a list of colors (hex, rgb, or CSS3 string) to assign to the fixed ids, by default None\nNone\n\n\ncolor_column\nstr\nDataframe column to use for adding selected segment colors, by default None\nNone"
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-    "text": "Name\nType\nDescription\nDefault\n\n\n\n\nsource\nstr\nSegmentation source\nrequired\n\n\nname\n(str, optional)\nLayer name.\nNone\n\n\nselected_ids_column\nstr or list-like, optional.\nColumn name (or list of column names) to use for selected ids.\nNone\n\n\nfixed_ids\nlist-like, optional.\nList of root ids to select directly.\nNone\n\n\nfixed_id_colors\nlist-like, optional.\nList of colors for fixed ids. Should be the same length as fixed_ids, although null entries can be padded with None values.\nNone\n\n\ncolor_column\nstr, optional.\n# at the begining. Column to use for color values for selected objects. Values should be RGB hex strings with a\nNone\n\n\nactive\nbool, optional.\nIf True, makes the layer selected. Default is False.\nFalse\n\n\nalpha_selected\n\nOpacity of selected segmentations in the image layer. Optional, default is 0.3.\n0.3\n\n\nalpha_3d\n\nOpacity of meshes. Optional, default is 1.\n1\n\n\nalpha_unselected\n\nOpacity of unselected segments. Optional, default is 0.\n0\n\n\nsplit_point_map\n\nIf not None, provides an object to map the dataframe input to multicut points. Default is None.\nNone\n\n\nview_kws\ndict, optional.\nKeyword arguments for viewer.set_segmentation_view_options. Sets selected (and unselected) segmetation alpha values. Defaults to values in DEFAULT_SEGMENTATION_VIEW_KWS dict specified in this module.\nNone\n\n\ntimestamp\nfloat or datetime, optional.\nTimestamp at which to fix the chunkedgraph in either unix epoch or datetime format. Optional, default is None.\nNone"
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-    "text": "statebuilder.helpers.make_line_statebuilder(client, point_column_a='pre_pt_position', point_column_b='post_pt_position', linked_seg_column='pt_root_id', description_column=None, tag_column=None, data_resolution=None, group_column=None, contrast=None, view_kws=None, point_layer_name='lines', color=None, split_positions=False)\nGenerate a state builder that puts points on a single column with a linked segmentaton id\n\n\n\n\n\n\n\n\n\n\n\nName\nType\nDescription\nDefault\n\n\n\n\nclient\ncaveclient.CAVEclient\nCAVEclient configured for the datastack desired\nrequired\n\n\npoint_column_a\nstr\ncolumn in dataframe to pull points from. Defaults to “pre_pt_position”.\n'pre_pt_position'\n\n\npoint_column_b\nstr\ncolumn in dataframe to pull points from. Defaults to “post_pt_position”.\n'post_pt_position'\n\n\nlinked_seg_column\nstr\ncolumn to link to segmentation, None for no column. Defaults to “pt_root_id”.\n'pt_root_id'\n\n\ngroup_column\nstr, or list\ncolumn(s) to group annotations by, None for no grouping (default=None)\nNone\n\n\ntag_column\nstr\ncolumn to use for tags, None for no tags (default=None)\nNone\n\n\ndescription_column\nstr\ncolumn to use for descriptions, None for no descriptions (default=None)\nNone\n\n\ncontrast\nlist\nTwo elements specifying the black level and white level as floats between 0 and 1, by default None. If None, no contrast is set.\nNone\n\n\nview_kws\ndict\ndictionary of view keywords to configure neuroglancer view\nNone\n\n\nsplit_positions\nbool\nwhether the position column into x,y,z columns. Defaults to False.\nFalse\n\n\n\n\n\n\n\n\n\nType\nDescription\n\n\n\n\n\nA statebuilder to make points with linked segmentations"
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-    "text": "Name\nType\nDescription\nDefault\n\n\n\n\nclient\ncaveclient.CAVEclient\nCAVEclient configured for the datastack desired\nrequired\n\n\npoint_column_a\nstr\ncolumn in dataframe to pull points from. Defaults to “pre_pt_position”.\n'pre_pt_position'\n\n\npoint_column_b\nstr\ncolumn in dataframe to pull points from. Defaults to “post_pt_position”.\n'post_pt_position'\n\n\nlinked_seg_column\nstr\ncolumn to link to segmentation, None for no column. Defaults to “pt_root_id”.\n'pt_root_id'\n\n\ngroup_column\nstr, or list\ncolumn(s) to group annotations by, None for no grouping (default=None)\nNone\n\n\ntag_column\nstr\ncolumn to use for tags, None for no tags (default=None)\nNone\n\n\ndescription_column\nstr\ncolumn to use for descriptions, None for no descriptions (default=None)\nNone\n\n\ncontrast\nlist\nTwo elements specifying the black level and white level as floats between 0 and 1, by default None. If None, no contrast is set.\nNone\n\n\nview_kws\ndict\ndictionary of view keywords to configure neuroglancer view\nNone\n\n\nsplit_positions\nbool\nwhether the position column into x,y,z columns. Defaults to False.\nFalse"
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-    "text": "parser.base.extract_multicut(state, seg_layer=None)\nExtract information entered into the multicut graph operation\n\n\n\n\n\n\n\n\n\n\n\nName\nType\nDescription\nDefault\n\n\n\n\nstate\ndict\nNeuroglancer state\nrequired\n\n\nseg_layer\nstr\nName of a segmentation layer or None. If None, the function will check how many segmentation layers there are and, if only one exits, choose it. If more than one segmentation layer is present, it errors. By default None\nNone\n\n\n\n\n\n\n\n\n\n\n\n\n\nType\nDescription\n\n\n\n\nnumpy.numpy.array\nNx3 array of points selected\n\n\nnumpy.numpy.array\nN array with ‘source’ or ‘sink’, depending on which side the point is on.\n\n\nnumpy.numpy.array\nN array with selected supervoxel. If only points are selected (e.g. via clicking on the mesh), the value will be NaN.\n\n\nint\nRoot id of the object to split"
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-    "text": "Name\nType\nDescription\nDefault\n\n\n\n\nstate\ndict\nNeuroglancer state\nrequired\n\n\nseg_layer\nstr\nName of a segmentation layer or None. If None, the function will check how many segmentation layers there are and, if only one exits, choose it. If more than one segmentation layer is present, it errors. By default None\nNone"
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-    "text": "Type\nDescription\n\n\n\n\nnumpy.numpy.array\nNx3 array of points selected\n\n\nnumpy.numpy.array\nN array with ‘source’ or ‘sink’, depending on which side the point is on.\n\n\nnumpy.numpy.array\nN array with selected supervoxel. If only points are selected (e.g. via clicking on the mesh), the value will be NaN.\n\n\nint\nRoot id of the object to split"
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-    "text": "Background\nNeuroglancer is a web application for viewing large volumetric imagery and segmentation data, as well as meshes and annotations like points or lines. Data in Neuroglancer is organized into layers, where each layer is configured to show information like images, segmentation, or annotations. Each layer can show one type of data and has different properties associated with it. In addition, Neuroglancer also stores the exact view that the user sees — what location in the data is centered, the orientation and zoom level of the camera, and more. Collectively, the information underlying both layers and the user view is refered to as the “state,” which is stored as a collection of key/value pairs.\nStateBuilder follows this model by defining a set of rules for initializing layers. For layers that contain properties like selected segment ids or annotations, this configuration involves specifying how to map DataFrame columns to selected segmentations or annotations such as synapses. The general pattern is that you build up a collection of configurations for individual layers, assemble them into a StateBuilder object, and then pass a dataframe through this object to render out a state."
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-    "text": "Simple Layers and StateBuilder\nfrom nglui import statebuilder\n\nimg = statebuilder.ImageLayerConfig(\n    source=client.info.image_source(),\n    contrast_controls=True, # this just puts in the code needed to manually adjust contrast\n)\n\nseg = statebuilder.SegmentationLayerConfig(\n    source=client.info.segmentation_source(),\n)"
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-    "title": "Docs",
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-    "text": "This is a Quarto website.\nTo learn more about Quarto websites visit https://quarto.org/docs/websites."
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-    "title": "About",
-    "section": "",
-    "text": "About this site"
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-    "text": "Tutorials\nDo one thing, then another."
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-    "text": "parser.base.segmentation_layers(state)\nGet all segmentation layer names in the state\n\n\n\n\n\nName\nType\nDescription\nDefault\n\n\n\n\nstate\ndict\nNeuroglancer state as a JSON dict\nrequired\n\n\n\n\n\n\n\n\n\nType\nDescription\n\n\n\n\nlist\nList of layer names"
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-    "text": "Name\nType\nDescription\nDefault\n\n\n\n\nstate\ndict\nNeuroglancer state as a JSON dict\nrequired"
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-    "text": "Type\nDescription\n\n\n\n\nlist\nList of layer names"
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-    "text": "statebuilder.statebuilder.ChainedStateBuilder(self, statebuilders)\nBuilds a collection of states that sequentially add annotations based on a sequence of dataframes.\n\n\n\n\n\n\n\n\n\n\n\nName\nType\nDescription\nDefault\n\n\n\n\nstatebuilders\nlist\nList of DataStateBuilders, in same order as dataframes will be passed\nrequired\n\n\n\n\n\n\n\n\n\nName\nDescription\n\n\n\n\nrender_state\nGenerate a single neuroglancer state by addatively applying an ordered collection of\n\n\n\n\n\nstatebuilder.statebuilder.ChainedStateBuilder.render_state(data_list=None, base_state=None, return_as='url', url_prefix=default_neuroglancer_base, link_text='Neuroglancer Link', target_site=None)\nGenerate a single neuroglancer state by addatively applying an ordered collection of dataframes to an collection of StateBuilder renders. Parameters data_list : Collection of DataFrame. The order must match the order of StateBuilders contained in the class on creation. base_state : JSON neuroglancer state (optional, default is None). Used as a base state for adding everything else to. return_as: [‘url’, ‘viewer’, ‘html’, ‘json’]. optional, default=‘url’. Sets how the state is returned. Note that if a viewer is returned, the state is not reset to default. url_prefix: string, optional (default is https://neuromancer-seung-import.appspot.com). Overrides the default neuroglancer url for url generation."
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-    "text": "Name\nType\nDescription\nDefault\n\n\n\n\nstatebuilders\nlist\nList of DataStateBuilders, in same order as dataframes will be passed\nrequired"
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-    "text": "Name\nDescription\n\n\n\n\nrender_state\nGenerate a single neuroglancer state by addatively applying an ordered collection of\n\n\n\n\n\nstatebuilder.statebuilder.ChainedStateBuilder.render_state(data_list=None, base_state=None, return_as='url', url_prefix=default_neuroglancer_base, link_text='Neuroglancer Link', target_site=None)\nGenerate a single neuroglancer state by addatively applying an ordered collection of dataframes to an collection of StateBuilder renders. Parameters data_list : Collection of DataFrame. The order must match the order of StateBuilders contained in the class on creation. base_state : JSON neuroglancer state (optional, default is None). Used as a base state for adding everything else to. return_as: [‘url’, ‘viewer’, ‘html’, ‘json’]. optional, default=‘url’. Sets how the state is returned. Note that if a viewer is returned, the state is not reset to default. url_prefix: string, optional (default is https://neuromancer-seung-import.appspot.com). Overrides the default neuroglancer url for url generation."
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-    "text": "statebuilder.helpers.make_pre_post_statebuilder(client, show_inputs=False, show_outputs=False, contrast=None, view_kws=None, point_column='ctr_pt_position', pre_pt_root_id_col='pre_pt_root_id', post_pt_root_id_col='post_pt_root_id', dataframe_resolution_pre=None, dataframe_resolution_post=None, input_layer_name='syns_in', output_layer_name='syns_out', input_layer_color=DEFAULT_POSTSYN_COLOR, output_layer_color=DEFAULT_PRESYN_COLOR, split_positions=False)\nFunction to generate ChainedStateBuilder with optional pre and post synaptic annotation layers\n\n\n\n\n\n\n\n\n\n\n\nName\nType\nDescription\nDefault\n\n\n\n\nclient\ncaveclient.CAVEclient\na CAVEclient configured for datastack to visualize\nrequired\n\n\nshow_inputs\nbool\nwhether to show input synapses. Defaults to False.\nFalse\n\n\nshow_outputs\nbool\nwhether to show output synapses.. Defaults to False.\nFalse\n\n\ncontrast\nlist\nTwo elements specifying the black level and white level as floats between 0 and 1, by default None. If None, no contrast is set.\nNone\n\n\nview_kws\ndict\nview_kws to configure statebuilder, see nglui.StateBuilder. Defaults to None. keys are: show_slices: Boolean sets if slices are shown in the 3d view. Defaults to False. layout: str xy-3d/xz-3d/yz-3d (sections plus 3d pane), xy/yz/xz/3d (only one pane), or 4panel (all panes). Default is xy-3d. show_axis_lines: Boolean determines if the axis lines are shown in the middle of each view. show_scale_bar: Boolean toggles showing the scale bar. orthographic : Boolean toggles orthographic view in the 3d pane. position* : 3-element vector determines the centered location. zoom_image : float Zoom level for the imagery in units of nm per voxel. Defaults to 8. zoom_3d : float Zoom level for the 3d pane. Defaults to 2000. Smaller numbers are more zoomed in.\nNone\n\n\npoint_column\nstr\ncolumn to pull points for synapses from. Defaults to “ctr_pt_position”.\n'ctr_pt_position'\n\n\npre_pt_root_id_col\nstr\ncolumn to pull pre synaptic ids for synapses from. Defaults to “pre_pt_root_id”.\n'pre_pt_root_id'\n\n\npost_pt_root_id_col\nstr\ncolumn to pull post synaptic ids for synapses from. Defaults to “post_pt_root_id”.\n'post_pt_root_id'\n\n\ninput_layer_name\nstr\nname of layer for inputs. Defaults to “syns_in”.\n'syns_in'\n\n\noutput_layer_name\nstr\nname of layer for outputs. Defaults to “syns_out”.\n'syns_out'\n\n\nsplit_positions\nbool\nwhether the position column is split into x,y,z columns. Defaults to False.\nFalse\n\n\n\n\n\n\n\n\n\n\n\n\n\nType\nDescription\n\n\n\n\n\nAn instance of a ChainedStateBuilder configured to accept a list starting with None followed by optionally synapse input dataframe followed by optionally synapse output dataframe."
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-    "text": "Name\nType\nDescription\nDefault\n\n\n\n\nclient\ncaveclient.CAVEclient\na CAVEclient configured for datastack to visualize\nrequired\n\n\nshow_inputs\nbool\nwhether to show input synapses. Defaults to False.\nFalse\n\n\nshow_outputs\nbool\nwhether to show output synapses.. Defaults to False.\nFalse\n\n\ncontrast\nlist\nTwo elements specifying the black level and white level as floats between 0 and 1, by default None. If None, no contrast is set.\nNone\n\n\nview_kws\ndict\nview_kws to configure statebuilder, see nglui.StateBuilder. Defaults to None. keys are: show_slices: Boolean sets if slices are shown in the 3d view. Defaults to False. layout: str xy-3d/xz-3d/yz-3d (sections plus 3d pane), xy/yz/xz/3d (only one pane), or 4panel (all panes). Default is xy-3d. show_axis_lines: Boolean determines if the axis lines are shown in the middle of each view. show_scale_bar: Boolean toggles showing the scale bar. orthographic : Boolean toggles orthographic view in the 3d pane. position* : 3-element vector determines the centered location. zoom_image : float Zoom level for the imagery in units of nm per voxel. Defaults to 8. zoom_3d : float Zoom level for the 3d pane. Defaults to 2000. Smaller numbers are more zoomed in.\nNone\n\n\npoint_column\nstr\ncolumn to pull points for synapses from. Defaults to “ctr_pt_position”.\n'ctr_pt_position'\n\n\npre_pt_root_id_col\nstr\ncolumn to pull pre synaptic ids for synapses from. Defaults to “pre_pt_root_id”.\n'pre_pt_root_id'\n\n\npost_pt_root_id_col\nstr\ncolumn to pull post synaptic ids for synapses from. Defaults to “post_pt_root_id”.\n'post_pt_root_id'\n\n\ninput_layer_name\nstr\nname of layer for inputs. Defaults to “syns_in”.\n'syns_in'\n\n\noutput_layer_name\nstr\nname of layer for outputs. Defaults to “syns_out”.\n'syns_out'\n\n\nsplit_positions\nbool\nwhether the position column is split into x,y,z columns. Defaults to False.\nFalse"
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-    "text": "Type\nDescription\n\n\n\n\n\nAn instance of a ChainedStateBuilder configured to accept a list starting with None followed by optionally synapse input dataframe followed by optionally synapse output dataframe."
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-    "text": "statebuilder.helpers.make_point_statebuilder(client, point_column='pt_position', linked_seg_column='pt_root_id', data_resolution=None, group_column=None, tag_column=None, description_column=None, contrast=None, view_kws=None, point_layer_name='pts', color=None, split_positions=False)\nGenerate a state builder that puts points on a single column with a linked segmentaton id\n\n\n\n\n\n\n\n\n\n\n\nName\nType\nDescription\nDefault\n\n\n\n\nclient\ncaveclient.CAVEclient\nCAVEclient configured for the datastack desired\nrequired\n\n\npoint_column\nstr\nColumn in dataframe to pull points from. Defaults to “pt_position”.\n'pt_position'\n\n\nlinked_seg_column\nstr\ncolumn to link to segmentation, None for no column. Defaults to “pt_root_id”.\n'pt_root_id'\n\n\ngroup_column\nstr, or list\ncolumn(s) to group annotations by, None for no grouping (default=None)\nNone\n\n\ntag_column\nstr, optional)\ncolumn to use for tags, None for no tags (default=None)\nNone\n\n\ndescription_column\nstr\ncolumn to use for descriptions, None for no descriptions (default=None)\nNone\n\n\ncontrast\nlist\nTwo elements specifying the black level and white level as floats between 0 and 1, by default None. If None, no contrast is set.\nNone\n\n\nview_kws\ndict\ndictionary of view keywords to configure neuroglancer view\nNone\n\n\nsplit_positions\nbool\nwhether the position column into x,y,z columns. Defaults to False.\nFalse\n\n\n\n\n\n\n\n\n\nType\nDescription\n\n\n\n\n\nA statebuilder to make points with linked segmentations"
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-    "text": "Name\nType\nDescription\nDefault\n\n\n\n\nclient\ncaveclient.CAVEclient\nCAVEclient configured for the datastack desired\nrequired\n\n\npoint_column\nstr\nColumn in dataframe to pull points from. Defaults to “pt_position”.\n'pt_position'\n\n\nlinked_seg_column\nstr\ncolumn to link to segmentation, None for no column. Defaults to “pt_root_id”.\n'pt_root_id'\n\n\ngroup_column\nstr, or list\ncolumn(s) to group annotations by, None for no grouping (default=None)\nNone\n\n\ntag_column\nstr, optional)\ncolumn to use for tags, None for no tags (default=None)\nNone\n\n\ndescription_column\nstr\ncolumn to use for descriptions, None for no descriptions (default=None)\nNone\n\n\ncontrast\nlist\nTwo elements specifying the black level and white level as floats between 0 and 1, by default None. If None, no contrast is set.\nNone\n\n\nview_kws\ndict\ndictionary of view keywords to configure neuroglancer view\nNone\n\n\nsplit_positions\nbool\nwhether the position column into x,y,z columns. Defaults to False.\nFalse"
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-    "text": "Type\nDescription\n\n\n\n\n\nA statebuilder to make points with linked segmentations"
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-    "text": "parser.base.annotation_layers(state)\nGet all annotation layer names in the state\n\n\n\n\n\nName\nType\nDescription\nDefault\n\n\n\n\nstate\ndict\nNeuroglancer state as a JSON dict\nrequired\n\n\n\n\n\n\n\n\n\nType\nDescription\n\n\n\n\nlist\nList of layer names"
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-    "text": "Name\nType\nDescription\nDefault\n\n\n\n\nstate\ndict\nNeuroglancer state as a JSON dict\nrequired"
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-    "text": "statebuilder.layers\n\n\n\n\n\nName\nDescription\n\n\n\n\nAnnotationLayerConfig\nConfiguration class for annotation layers\n\n\nImageLayerConfig\nImage layer configuration class.\n\n\nLayerConfigBase\nBase class for configuring layers\n\n\nSegmentationLayerConfig\nConfiguration class for segmentation layers\n\n\n\n\n\n\nstatebuilder.layers.AnnotationLayerConfig(self, name=None, color=None, linked_segmentation_layer=None, mapping_rules=[], array_data=False, tags=None, active=True, filter_by_segmentation=False, brackets_show_segmentation=True, selection_shows_segmentation=True, filter_query=None, data_resolution=None)\nConfiguration class for annotation layers\n\n\n\n\n\n\n\n\n\n\n\nName\nType\nDescription\nDefault\n\n\n\n\nname\nstr\nLayer name. By default, ‘annos’\nNone\n\n\ncolor\nstr\nHex color code with an initial #. By default, None\nNone\n\n\nlinked_segmentation_layer\nstr\nName of a linked segmentation layer for selected ids. By default, None\nNone\n\n\nmapping_rules\n(nglui.statebuilder.mappers.PointMapper, nglui.statebuilder.mappers.LineMapper, nglui.statebuilder.mappers.SphereMapper or list)\nOne rule or a list of rules mapping data to annotations. By default, []\n[]\n\n\narray_data\nbool\nIf True, allows simple mapping where one or more arrays are passed instead of a dataframe. Only allows basic annotation creation, no tags, linked segmentations, or other rich features.\nFalse\n\n\ntags\nlist\nList of tags for the layer.\nNone\n\n\nactive\nbool\nIf True, makes the layer selected. Default is True (unlike for image/segmentation layers).\nTrue\n\n\n\n\n\n\n\nstatebuilder.layers.ImageLayerConfig(self, source, name=None, active=False, contrast_controls=False, black=0.0, white=1.0)\nImage layer configuration class.\nThis provides the rules for setting up an image layer in neuroglancer.\n\n\n\n\n\n\n\n\n\n\n\nName\nType\nDescription\nDefault\n\n\n\n\nsource\nstr\nCloudpath to an image source\nrequired\n\n\nname\nstr\nName of the image layer. By default, ‘img’.\nNone\n\n\nactive\nbool\nIf True, makes the layer active in neuroglancer. Default is False.\nFalse\n\n\ncontrast_controls\nbool\nIf True, gives the layer a user-controllable brightness and contrast shader. Default is False.\nFalse\n\n\nblack\nfloat\nIf contrast_controls is True, sets the default black level. Default is 0.0.\n0.0\n\n\nwhite\nfloat\nIf contrast_controls is True, sets the default white level. Default is 1.0.\n1.0\n\n\n\n\n\n\n\nstatebuilder.layers.LayerConfigBase(self, name, type, source, color, active)\nBase class for configuring layers\n\n\n\n\n\n\n\n\n\n\n\nName\nType\nDescription\nDefault\n\n\n\n\nname\nstr\nLayer name for reference and display\nrequired\n\n\ntype\nstr\nLayer type. Usually handled by the subclass\nrequired\n\n\nsource\nstr\nDatasource for the layer\nrequired\n\n\ncolor\nstr\nHex string (with starting hash).\nrequired\n\n\nactive\n(bool)\nIf True, becomes a selected layer.\nrequired\n\n\n\n\n\n\n\nstatebuilder.layers.SegmentationLayerConfig(self, source, name=None, selected_ids_column=None, fixed_ids=None, fixed_id_colors=None, color_column=None, active=False, alpha_selected=0.3, alpha_3d=1, alpha_unselected=0, split_point_map=None, view_kws=None, timestamp=None, data_resolution=None)\nConfiguration class for segmentation layers\n\n\n\n\n\n\n\n\n\n\n\nName\nType\nDescription\nDefault\n\n\n\n\nsource\nstr\nSegmentation source\nrequired\n\n\nname\n(str, optional)\nLayer name.\nNone\n\n\nselected_ids_column\nstr or list-like, optional.\nColumn name (or list of column names) to use for selected ids.\nNone\n\n\nfixed_ids\nlist-like, optional.\nList of root ids to select directly.\nNone\n\n\nfixed_id_colors\nlist-like, optional.\nList of colors for fixed ids. Should be the same length as fixed_ids, although null entries can be padded with None values.\nNone\n\n\ncolor_column\nstr, optional.\n# at the begining. Column to use for color values for selected objects. Values should be RGB hex strings with a\nNone\n\n\nactive\nbool, optional.\nIf True, makes the layer selected. Default is False.\nFalse\n\n\nalpha_selected\n\nOpacity of selected segmentations in the image layer. Optional, default is 0.3.\n0.3\n\n\nalpha_3d\n\nOpacity of meshes. Optional, default is 1.\n1\n\n\nalpha_unselected\n\nOpacity of unselected segments. Optional, default is 0.\n0\n\n\nsplit_point_map\n\nIf not None, provides an object to map the dataframe input to multicut points. Default is None.\nNone\n\n\nview_kws\ndict, optional.\nKeyword arguments for viewer.set_segmentation_view_options. Sets selected (and unselected) segmetation alpha values. Defaults to values in DEFAULT_SEGMENTATION_VIEW_KWS dict specified in this module.\nNone\n\n\ntimestamp\nfloat or datetime, optional.\nTimestamp at which to fix the chunkedgraph in either unix epoch or datetime format. Optional, default is None.\nNone\n\n\n\n\n\n\n\n\n\nName\nDescription\n\n\n\n\nadd_selection_map\nAdd rules for selecting active segment ids and their colors\n\n\n\n\n\nstatebuilder.layers.SegmentationLayerConfig.add_selection_map(selected_ids_column=None, fixed_ids=None, fixed_id_colors=None, color_column=None)\nAdd rules for selecting active segment ids and their colors\n\n\n\n\n\n\n\n\n\n\n\nName\nType\nDescription\nDefault\n\n\n\n\nselected_ids_column\nstr\nDataframe column to use for adding selected segment ids to the segmentation layer, by default None\nNone\n\n\nfixed_ids\nint or list\nAdd one or more segment ids to be active, independent of the data, by default None\nNone\n\n\nfixed_id_colors\nlist\nAdd a list of colors (hex, rgb, or CSS3 string) to assign to the fixed ids, by default None\nNone\n\n\ncolor_column\nstr\nDataframe column to use for adding selected segment colors, by default None\nNone"
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-    "text": "Name\nDescription\n\n\n\n\nAnnotationLayerConfig\nConfiguration class for annotation layers\n\n\nImageLayerConfig\nImage layer configuration class.\n\n\nLayerConfigBase\nBase class for configuring layers\n\n\nSegmentationLayerConfig\nConfiguration class for segmentation layers"
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-    "text": "statebuilder.layers.AnnotationLayerConfig(self, name=None, color=None, linked_segmentation_layer=None, mapping_rules=[], array_data=False, tags=None, active=True, filter_by_segmentation=False, brackets_show_segmentation=True, selection_shows_segmentation=True, filter_query=None, data_resolution=None)\nConfiguration class for annotation layers\n\n\n\n\n\n\n\n\n\n\n\nName\nType\nDescription\nDefault\n\n\n\n\nname\nstr\nLayer name. By default, ‘annos’\nNone\n\n\ncolor\nstr\nHex color code with an initial #. By default, None\nNone\n\n\nlinked_segmentation_layer\nstr\nName of a linked segmentation layer for selected ids. By default, None\nNone\n\n\nmapping_rules\n(nglui.statebuilder.mappers.PointMapper, nglui.statebuilder.mappers.LineMapper, nglui.statebuilder.mappers.SphereMapper or list)\nOne rule or a list of rules mapping data to annotations. By default, []\n[]\n\n\narray_data\nbool\nIf True, allows simple mapping where one or more arrays are passed instead of a dataframe. Only allows basic annotation creation, no tags, linked segmentations, or other rich features.\nFalse\n\n\ntags\nlist\nList of tags for the layer.\nNone\n\n\nactive\nbool\nIf True, makes the layer selected. Default is True (unlike for image/segmentation layers).\nTrue"
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-    "text": "statebuilder.layers.ImageLayerConfig(self, source, name=None, active=False, contrast_controls=False, black=0.0, white=1.0)\nImage layer configuration class.\nThis provides the rules for setting up an image layer in neuroglancer.\n\n\n\n\n\n\n\n\n\n\n\nName\nType\nDescription\nDefault\n\n\n\n\nsource\nstr\nCloudpath to an image source\nrequired\n\n\nname\nstr\nName of the image layer. By default, ‘img’.\nNone\n\n\nactive\nbool\nIf True, makes the layer active in neuroglancer. Default is False.\nFalse\n\n\ncontrast_controls\nbool\nIf True, gives the layer a user-controllable brightness and contrast shader. Default is False.\nFalse\n\n\nblack\nfloat\nIf contrast_controls is True, sets the default black level. Default is 0.0.\n0.0\n\n\nwhite\nfloat\nIf contrast_controls is True, sets the default white level. Default is 1.0.\n1.0"
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-    "text": "statebuilder.layers.LayerConfigBase(self, name, type, source, color, active)\nBase class for configuring layers\n\n\n\n\n\n\n\n\n\n\n\nName\nType\nDescription\nDefault\n\n\n\n\nname\nstr\nLayer name for reference and display\nrequired\n\n\ntype\nstr\nLayer type. Usually handled by the subclass\nrequired\n\n\nsource\nstr\nDatasource for the layer\nrequired\n\n\ncolor\nstr\nHex string (with starting hash).\nrequired\n\n\nactive\n(bool)\nIf True, becomes a selected layer.\nrequired"
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-    "text": "statebuilder.layers.SegmentationLayerConfig(self, source, name=None, selected_ids_column=None, fixed_ids=None, fixed_id_colors=None, color_column=None, active=False, alpha_selected=0.3, alpha_3d=1, alpha_unselected=0, split_point_map=None, view_kws=None, timestamp=None, data_resolution=None)\nConfiguration class for segmentation layers\n\n\n\n\n\n\n\n\n\n\n\nName\nType\nDescription\nDefault\n\n\n\n\nsource\nstr\nSegmentation source\nrequired\n\n\nname\n(str, optional)\nLayer name.\nNone\n\n\nselected_ids_column\nstr or list-like, optional.\nColumn name (or list of column names) to use for selected ids.\nNone\n\n\nfixed_ids\nlist-like, optional.\nList of root ids to select directly.\nNone\n\n\nfixed_id_colors\nlist-like, optional.\nList of colors for fixed ids. Should be the same length as fixed_ids, although null entries can be padded with None values.\nNone\n\n\ncolor_column\nstr, optional.\n# at the begining. Column to use for color values for selected objects. Values should be RGB hex strings with a\nNone\n\n\nactive\nbool, optional.\nIf True, makes the layer selected. Default is False.\nFalse\n\n\nalpha_selected\n\nOpacity of selected segmentations in the image layer. Optional, default is 0.3.\n0.3\n\n\nalpha_3d\n\nOpacity of meshes. Optional, default is 1.\n1\n\n\nalpha_unselected\n\nOpacity of unselected segments. Optional, default is 0.\n0\n\n\nsplit_point_map\n\nIf not None, provides an object to map the dataframe input to multicut points. Default is None.\nNone\n\n\nview_kws\ndict, optional.\nKeyword arguments for viewer.set_segmentation_view_options. Sets selected (and unselected) segmetation alpha values. Defaults to values in DEFAULT_SEGMENTATION_VIEW_KWS dict specified in this module.\nNone\n\n\ntimestamp\nfloat or datetime, optional.\nTimestamp at which to fix the chunkedgraph in either unix epoch or datetime format. Optional, default is None.\nNone\n\n\n\n\n\n\n\n\n\nName\nDescription\n\n\n\n\nadd_selection_map\nAdd rules for selecting active segment ids and their colors\n\n\n\n\n\nstatebuilder.layers.SegmentationLayerConfig.add_selection_map(selected_ids_column=None, fixed_ids=None, fixed_id_colors=None, color_column=None)\nAdd rules for selecting active segment ids and their colors\n\n\n\n\n\n\n\n\n\n\n\nName\nType\nDescription\nDefault\n\n\n\n\nselected_ids_column\nstr\nDataframe column to use for adding selected segment ids to the segmentation layer, by default None\nNone\n\n\nfixed_ids\nint or list\nAdd one or more segment ids to be active, independent of the data, by default None\nNone\n\n\nfixed_id_colors\nlist\nAdd a list of colors (hex, rgb, or CSS3 string) to assign to the fixed ids, by default None\nNone\n\n\ncolor_column\nstr\nDataframe column to use for adding selected segment colors, by default None\nNone"
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-    "title": "preview",
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-    "text": "preview(ast, max_depth=999, compact=False, as_string=False)\nPrint a friendly representation of a griffe object (e.g. function, docstring)\n\n\n&gt;&gt;&gt; from quartodoc import get_object\n&gt;&gt;&gt; obj = get_object(\"quartodoc\", \"get_object\")\n&gt;&gt;&gt; preview(obj.docstring.parsed)\n ...\n&gt;&gt;&gt; preview(obj)\n ..."
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-    "title": "preview",
-    "section": "",
-    "text": "&gt;&gt;&gt; from quartodoc import get_object\n&gt;&gt;&gt; obj = get_object(\"quartodoc\", \"get_object\")\n&gt;&gt;&gt; preview(obj.docstring.parsed)\n ...\n&gt;&gt;&gt; preview(obj)\n ..."
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-    "text": "statebuilder.helpers.make_neuron_neuroglancer_link(client, root_ids, return_as='html', shorten='always', show_inputs=False, show_outputs=False, sort_inputs=True, sort_outputs=True, sort_ascending=False, input_color=DEFAULT_POSTSYN_COLOR, output_color=DEFAULT_PRESYN_COLOR, contrast=None, timestamp=None, view_kws=None, point_column='ctr_pt_position', pre_pt_root_id_col='pre_pt_root_id', post_pt_root_id_col='post_pt_root_id', input_layer_name='syns_in', output_layer_name='syns_out', ngl_url=None, link_text='Neuroglancer Link', target_site=None)\nfunction to create a neuroglancer link view of a neuron, optionally including inputs and outputs\n\n\n\n\n\n\n\n\n\n\n\nName\nType\nDescription\nDefault\n\n\n\n\nclient\ncaveclient.CAVEclient\nA CAVEclient configured for the datastack to visualize.\nrequired\n\n\nroot_ids\ntyping.Iterable[int]\nThe root_ids to build the visualization around.\nrequired\n\n\nreturn_as\nstr\nHow to return the URL or state. Valid options are: - ‘html’: Returns an IPython HTML element. - ‘json’: Returns a dictionary representing the Neuroglancer state. - ‘url’: Returns a URL string. Defaults to ‘html’.\n'html'\n\n\nshorten\nstr\nWhether to shorten the link. Valid options are: - ‘always’: Always shorten the link. - ‘if_long’: Shorten the link if it exceeds MAX_URL_LENGTH. - ‘never’: Never shorten the link. Defaults to ‘if_long’.\n'always'\n\n\nshow_inputs\nbool\nWhether to include input synapses. Defaults to False.\nFalse\n\n\nshow_outputs\nbool\nWhether to include output synapses. Defaults to False.\nFalse\n\n\nsort_inputs\nbool\nWhether to sort input synapses by presynaptic root id, ordered by synapse count. Defaults to True.\nTrue\n\n\nsort_outputs\nbool\nWhether to sort output synapses by presynaptic root id, ordered by postsynaptic synapse count. Defaults to True.\nTrue\n\n\nsort_ascending\nbool\nIf sorting, whether to sort ascending (lowest synapse count to highest). Defaults to False.\nFalse\n\n\ninput_color\nlist(float) or str\nColor of input synapse points as an RGB list [0, 1], hex string, or common name.\nDEFAULT_POSTSYN_COLOR\n\n\noutput_color\nlist(float) or str\nColor of output synapse points as an RGB list [0, 1], hex string, or common name.\nDEFAULT_PRESYN_COLOR\n\n\ncontrast\nlist\nList of two floats between 0 and 1, specifying the black and white levels. If None, no contrast is set.\nNone\n\n\ntimestamp\ndatetime.datetime.datetime\nTimestamp to use for the query. Defaults to None, which will use the materialized version.\nNone\n\n\nview_kws\ndict\nDictionary containing viewer settings for Neuroglancer. See nglui.StateBuilder for options. See the previous docstring for details on available keys.\nNone\n\n\npoint_column\nstr\nColumn to pull synapse positions from. Defaults to “ctr_pt_position”.\n'ctr_pt_position'\n\n\npre_pt_root_id_col\nstr\nColumn to pull presynaptic IDs for synapses from. Defaults to “pre_pt_root_id”.\n'pre_pt_root_id'\n\n\npost_pt_root_id_col\nstr\nColumn to pull postsynaptic IDs for synapses from. Defaults to “post_pt_root_id”.\n'post_pt_root_id'\n\n\ninput_layer_name\nstr\nName of the layer for input synapses. Defaults to “syns_in”.\n'syns_in'\n\n\noutput_layer_name\nstr\nName of the layer for output synapses. Defaults to “syns_out”.\n'syns_out'\n\n\nngl_url\nstr\nURL of the Neuroglancer instance to use. Defaults to the default viewer set in the datastack.\nNone\n\n\nlink_text\nstr\nText to use for the HTML return. Defaults to ‘Neuroglancer Link’.\n'Neuroglancer Link'\n\n\n\n\n\n\n\n\n\n\n\n\n\nType\nDescription\n\n\n\n\nValueError\nIf the specified point column is not present in the synapse table.\n\n\n\n\n\n\n\n\n\n\n\n\n\nType\nDescription\n\n\n\n\nIPython.HTML, str, or dict\nRepresentation of the Neuroglancer state, depending on the return_as parameter."
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-    "text": "Name\nType\nDescription\nDefault\n\n\n\n\nclient\ncaveclient.CAVEclient\nA CAVEclient configured for the datastack to visualize.\nrequired\n\n\nroot_ids\ntyping.Iterable[int]\nThe root_ids to build the visualization around.\nrequired\n\n\nreturn_as\nstr\nHow to return the URL or state. Valid options are: - ‘html’: Returns an IPython HTML element. - ‘json’: Returns a dictionary representing the Neuroglancer state. - ‘url’: Returns a URL string. Defaults to ‘html’.\n'html'\n\n\nshorten\nstr\nWhether to shorten the link. Valid options are: - ‘always’: Always shorten the link. - ‘if_long’: Shorten the link if it exceeds MAX_URL_LENGTH. - ‘never’: Never shorten the link. Defaults to ‘if_long’.\n'always'\n\n\nshow_inputs\nbool\nWhether to include input synapses. Defaults to False.\nFalse\n\n\nshow_outputs\nbool\nWhether to include output synapses. Defaults to False.\nFalse\n\n\nsort_inputs\nbool\nWhether to sort input synapses by presynaptic root id, ordered by synapse count. Defaults to True.\nTrue\n\n\nsort_outputs\nbool\nWhether to sort output synapses by presynaptic root id, ordered by postsynaptic synapse count. Defaults to True.\nTrue\n\n\nsort_ascending\nbool\nIf sorting, whether to sort ascending (lowest synapse count to highest). Defaults to False.\nFalse\n\n\ninput_color\nlist(float) or str\nColor of input synapse points as an RGB list [0, 1], hex string, or common name.\nDEFAULT_POSTSYN_COLOR\n\n\noutput_color\nlist(float) or str\nColor of output synapse points as an RGB list [0, 1], hex string, or common name.\nDEFAULT_PRESYN_COLOR\n\n\ncontrast\nlist\nList of two floats between 0 and 1, specifying the black and white levels. If None, no contrast is set.\nNone\n\n\ntimestamp\ndatetime.datetime.datetime\nTimestamp to use for the query. Defaults to None, which will use the materialized version.\nNone\n\n\nview_kws\ndict\nDictionary containing viewer settings for Neuroglancer. See nglui.StateBuilder for options. See the previous docstring for details on available keys.\nNone\n\n\npoint_column\nstr\nColumn to pull synapse positions from. Defaults to “ctr_pt_position”.\n'ctr_pt_position'\n\n\npre_pt_root_id_col\nstr\nColumn to pull presynaptic IDs for synapses from. Defaults to “pre_pt_root_id”.\n'pre_pt_root_id'\n\n\npost_pt_root_id_col\nstr\nColumn to pull postsynaptic IDs for synapses from. Defaults to “post_pt_root_id”.\n'post_pt_root_id'\n\n\ninput_layer_name\nstr\nName of the layer for input synapses. Defaults to “syns_in”.\n'syns_in'\n\n\noutput_layer_name\nstr\nName of the layer for output synapses. Defaults to “syns_out”.\n'syns_out'\n\n\nngl_url\nstr\nURL of the Neuroglancer instance to use. Defaults to the default viewer set in the datastack.\nNone\n\n\nlink_text\nstr\nText to use for the HTML return. Defaults to ‘Neuroglancer Link’.\n'Neuroglancer Link'"
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-    "text": "Type\nDescription\n\n\n\n\nValueError\nIf the specified point column is not present in the synapse table."
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-    "text": "Name\nType\nDescription\nDefault\n\n\n\n\nstate\ndict\nNeuroglancer state as a JSON dict\nrequired"
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-    "text": "statebuilder.statebuilder.StateBuilder.render_state(data=None, base_state=None, return_as='url', url_prefix=None, link_text='Neuroglancer Link', target_site=None)\nBuild a Neuroglancer state out of a DataFrame.\n\n\n\n\n\n\n\n\n\n\n\nName\nType\nDescription\nDefault\n\n\n\n\ndata\npandas.pandas.DataFrame\nDataFrame to use as a point source. By default None, for which it will return only the base_state and any fixed values.\nNone\n\n\nbase_state\ndict\nInitial state to build on, expressed as Neuroglancer JSON. By default None\nNone\n\n\nreturn_as\n[url, nglui.statebuilder.statebuilder.StateBuilder.viewer, html, json, dict, shared]\nChoice of output types. Note that if a viewer is returned, the state is not reset. url : Returns the raw url describing the state viewer : Returns an EasyViewer object holding the state information html : Returns an HTML link to the url, useful for notebooks. json : Returns a JSON string describing the state. dict : Returns a dict version of the JSON state. By default ‘url’\n'url'\n\n\nurl_prefix\nstr\nNeuroglancer URL prefix to use. By default None, for which it will open with the class default.\nNone\n\n\nlink_text\nstr\nText to use for the link when returning as html, by default ‘Neuroglancer Link’\n'Neuroglancer Link'\n\n\n\n\n\n\n\n\n\n\n\n\n\nType\nDescription\n\n\n\n\nstring or neuroglancer.neuroglancer.Viewer\nA link to or viewer for a Neuroglancer state with layers, annotations, and selected objects determined by the data."
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-    "text": "Name\nType\nDescription\nDefault\n\n\n\n\ndata\npandas.pandas.DataFrame\nDataFrame to use as a point source. By default None, for which it will return only the base_state and any fixed values.\nNone\n\n\nbase_state\ndict\nInitial state to build on, expressed as Neuroglancer JSON. By default None\nNone\n\n\nreturn_as\n[url, nglui.statebuilder.statebuilder.StateBuilder.viewer, html, json, dict, shared]\nChoice of output types. Note that if a viewer is returned, the state is not reset. url : Returns the raw url describing the state viewer : Returns an EasyViewer object holding the state information html : Returns an HTML link to the url, useful for notebooks. json : Returns a JSON string describing the state. dict : Returns a dict version of the JSON state. By default ‘url’\n'url'\n\n\nurl_prefix\nstr\nNeuroglancer URL prefix to use. By default None, for which it will open with the class default.\nNone\n\n\nlink_text\nstr\nText to use for the link when returning as html, by default ‘Neuroglancer Link’\n'Neuroglancer Link'"
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-    "text": "Type\nDescription\n\n\n\n\nstring or neuroglancer.neuroglancer.Viewer\nA link to or viewer for a Neuroglancer state with layers, annotations, and selected objects determined by the data."
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-    "text": "statebuilder.helpers.make_url_robust(df, sb, client, shorten='if_long', ngl_url=None, max_url_length=MAX_URL_LENGTH, target_site=None)\nGenerate a url from a neuroglancer state. If too long, return through state server, othewise return a url containing the data directly.\n\n\n\n\n\n\n\n\n\n\n\nName\nType\nDescription\nDefault\n\n\n\n\ndf\npandas.pandas.DataFrame\nDataframe to pass through statebuilder\nrequired\n\n\nsb\nnglui.statebuilder.statebuilder.nglui.statebuilder.statebuilder.StateBuilder\nStatebuilder to use to render data for link\nrequired\n\n\nclient\ncaveclient.CAVEclient\nCAVEclient configured with a state server\nrequired\n\n\nshorten\nstr\nHow to shorten link. one of ‘if_long’, ‘always’, ‘never’. ‘if_long’ will use the state server to shorten links longer than nglui.statebuilder.MAX_URL_LENGTH (set to 1,750,000). ‘always’ will always use the state server to shorten the url ‘never’ will always return the full url. Defaults to “if_long”.\n'if_long'\n\n\nngl_url\nstr\nNeuroglancer deployment URL, by default None\nNone\n\n\nmax_url_length\nint\nMaximum length of url to return directly, by default 1_750_000\nMAX_URL_LENGTH\n\n\ntarget_site\nstr\nType of neuroglancer deployment to build link for, by default None. This value overrides automatic checking based on the provided url. Use seunglab for a Seung-lab branch and either mainline or cave-explorer for the Cave Explorer or main Google branch.\nNone\n\n\n\n\n\n\n\n\n\nType\nDescription\n\n\n\n\nstr\nURL containing the state created by the statebuilder."
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-    "text": "Name\nType\nDescription\nDefault\n\n\n\n\ndf\npandas.pandas.DataFrame\nDataframe to pass through statebuilder\nrequired\n\n\nsb\nnglui.statebuilder.statebuilder.nglui.statebuilder.statebuilder.StateBuilder\nStatebuilder to use to render data for link\nrequired\n\n\nclient\ncaveclient.CAVEclient\nCAVEclient configured with a state server\nrequired\n\n\nshorten\nstr\nHow to shorten link. one of ‘if_long’, ‘always’, ‘never’. ‘if_long’ will use the state server to shorten links longer than nglui.statebuilder.MAX_URL_LENGTH (set to 1,750,000). ‘always’ will always use the state server to shorten the url ‘never’ will always return the full url. Defaults to “if_long”.\n'if_long'\n\n\nngl_url\nstr\nNeuroglancer deployment URL, by default None\nNone\n\n\nmax_url_length\nint\nMaximum length of url to return directly, by default 1_750_000\nMAX_URL_LENGTH\n\n\ntarget_site\nstr\nType of neuroglancer deployment to build link for, by default None. This value overrides automatic checking based on the provided url. Use seunglab for a Seung-lab branch and either mainline or cave-explorer for the Cave Explorer or main Google branch.\nNone"
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-    "text": "get_object(path, object_name=None, parser='numpy', load_aliases=True, dynamic=False, loader=None)\nFetch a griffe object.\n\n\n\n\n\n\n\n\n\n\n\nName\nType\nDescription\nDefault\n\n\n\n\npath\nstr\nAn import path to the object. This should have the form path.to.module:object. For example, quartodoc:get_object or quartodoc:MdRenderer.render.\nrequired\n\n\nobject_name\n‘str | None’\n(Deprecated). A function name.\nNone\n\n\nparser\nstr\nA docstring parser to use.\n'numpy'\n\n\nload_aliases\n\nFor aliases that were imported from other modules, should we load that module?\nTrue\n\n\ndynamic\n\nWhether to dynamically import object. Useful if docstring is not hard-coded, but was set on object by running python code.\nFalse\n\n\n\n\n\n\npreview: print a user-friendly preview of a griffe object.\n\n\n\n&gt;&gt;&gt; get_function(\"quartodoc\", \"get_function\")\n&lt;Function('get_function', ...\n\n\n\n\n\n\nType\nDescription\n\n\n\n\ngriffe.dataclasses.griffe.dataclasses.Object\nabc"
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-    "text": "statebuilder.helpers.from_client(client, image_name=None, segmentation_name=None, contrast=None)\nGenerate basic image and segmentation layers from a FrameworkClient\n\n\n\n\n\n\n\n\n\n\n\nName\nType\nDescription\nDefault\n\n\n\n\nclient\ncaveclient.caveclient.CAVEclient\nA CAVEclient with a specified datastack\nrequired\n\n\nimage_name\nstr\nName for the image layer, by default None.\nNone\n\n\nsegmentation_name\nstr\nName for the segmentation layer, by default None\nNone\n\n\ncontrast\nlist - like\nTwo elements specifying the black level and white level as floats between 0 and 1, by default None. If None, no contrast is set.\nNone\n\n\n\n\n\n\n\n\n\n\n\n\n\nType\nDescription\n\n\n\n\nnglui.statebuilder.layers.ImageLayerConfig\nImage layer with default values from the client\n\n\nnglui.statebuilder.layers.ImageLayerConfig\nSegmentation layer with default values from the client"
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-    "text": "Name\nType\nDescription\nDefault\n\n\n\n\nclient\ncaveclient.caveclient.CAVEclient\nA CAVEclient with a specified datastack\nrequired\n\n\nimage_name\nstr\nName for the image layer, by default None.\nNone\n\n\nsegmentation_name\nstr\nName for the segmentation layer, by default None\nNone\n\n\ncontrast\nlist - like\nTwo elements specifying the black level and white level as floats between 0 and 1, by default None. If None, no contrast is set.\nNone"
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-    "text": "Type\nDescription\n\n\n\n\nnglui.statebuilder.layers.ImageLayerConfig\nImage layer with default values from the client\n\n\nnglui.statebuilder.layers.ImageLayerConfig\nSegmentation layer with default values from the client"
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-    "text": "statebuilder.layers.ImageLayerConfig(self, source, name=None, active=False, contrast_controls=False, black=0.0, white=1.0)\nImage layer configuration class.\nThis provides the rules for setting up an image layer in neuroglancer.\n\n\n\n\n\n\n\n\n\n\n\nName\nType\nDescription\nDefault\n\n\n\n\nsource\nstr\nCloudpath to an image source\nrequired\n\n\nname\nstr\nName of the image layer. By default, ‘img’.\nNone\n\n\nactive\nbool\nIf True, makes the layer active in neuroglancer. Default is False.\nFalse\n\n\ncontrast_controls\nbool\nIf True, gives the layer a user-controllable brightness and contrast shader. Default is False.\nFalse\n\n\nblack\nfloat\nIf contrast_controls is True, sets the default black level. Default is 0.0.\n0.0\n\n\nwhite\nfloat\nIf contrast_controls is True, sets the default white level. Default is 1.0.\n1.0"
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-    "text": "statebuilder.SphereMapper(self, center_column=None, radius_column=None, description_column=None, linked_segmentation_column=None, tag_column=None, group_column=None, gather_linked_segmentations=True, share_linked_segmentations=False, z_multiplier=0.1, set_position=True, multipoint=False, collapse_groups=False, split_positions=False, mapping_set=None)\nSets rules to map dataframes to sphere annotations\n\n\n\n\n\n\n\n\n\n\n\nName\nType\nDescription\nDefault\n\n\n\n\ncenter_column\nstr\nColumn name with 3d position data for the center of the sphere\nNone\n\n\nradius_column\nstr\nColumn name with a radius for the sphere (in nm)\nNone\n\n\ndescription_column\nstr\nColumn name with string data for annotation descriptions\nNone\n\n\nlinked_segmentation_column\nstr\nColumn name for root ids to link to annotations\nNone\n\n\ntag_column\nstr\nColumn name for categorical tag data. Tags must match those set in the annotation layer.\nNone\n\n\ngroup_column\nstr\nColumn name for grouping data. Data in this row should be numeric with possible NaNs. Rows with the same non-NaN value will be collected into a grouped annotation.\nNone\n\n\nset_position\nbool\nIf set to True, moves the position to center on the first point in the data.\nTrue\n\n\nmultipoint\n\nIf True, permits multiple points in a given row, sharing data in other columns. Each point row must have the same number of points. Default is False.\nFalse\n\n\ncollapse_groups\n\nIf True, groups are toggled closed in the annotation view.\nFalse\n\n\nmapping_set\n\nIf set, assumes data is passed as a dictionary and uses this string to as the key for the data to use.\nNone"
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-    "text": "statebuilder.StateBuilder(self, layers=[], base_state=None, url_prefix=None, state_server=None, resolution=None, view_kws={}, client=None, target_site=None)\nA class for schematic mapping data frames into neuroglancer states.\n\n\n\n\n\n\n\n\n\n\n\nName\nType\nDescription\nDefault\n\n\n\n\nlayers\n\n\n[]\n\n\nbase_state\n\n\nNone\n\n\nurl_prefix\n\nDefaults to None, which will use https://neuromancer-seung-import.appspot.com\nNone\n\n\nstate_server\n\n\nNone\n\n\nresolution\n\n\nNone\n\n\nview_kws\n\nkeys are: show_slices: Boolean sets if slices are shown in the 3d view. Defaults to False. layout: str xy-3d/xz-3d/yz-3d (sections plus 3d pane), xy/yz/xz/3d (only one pane), or 4panel (all panes). Default is xy-3d. show_axis_lines: Boolean determines if the axis lines are shown in the middle of each view. show_scale_bar: Boolean toggles showing the scale bar. orthographic : Boolean toggles orthographic view in the 3d pane. position* : 3-element vector determines the centered location. zoom_image : float Zoom level for the imagery in units of nm per voxel. Defaults to 8. zoom_3d : float Zoom level for the 3d pane. Defaults to 2000. Smaller numbers are more zoomed in. background_color : str or list Sets the background color of the 3d view. Arguments can be rgb values, hex colors, or named web colors. Defaults to black.\n{}\n\n\nclient\n\n\nNone"
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-    "text": "Name\nType\nDescription\nDefault\n\n\n\n\nlayers\n\n\n[]\n\n\nbase_state\n\n\nNone\n\n\nurl_prefix\n\nDefaults to None, which will use https://neuromancer-seung-import.appspot.com\nNone\n\n\nstate_server\n\n\nNone\n\n\nresolution\n\n\nNone\n\n\nview_kws\n\nkeys are: show_slices: Boolean sets if slices are shown in the 3d view. Defaults to False. layout: str xy-3d/xz-3d/yz-3d (sections plus 3d pane), xy/yz/xz/3d (only one pane), or 4panel (all panes). Default is xy-3d. show_axis_lines: Boolean determines if the axis lines are shown in the middle of each view. show_scale_bar: Boolean toggles showing the scale bar. orthographic : Boolean toggles orthographic view in the 3d pane. position* : 3-element vector determines the centered location. zoom_image : float Zoom level for the imagery in units of nm per voxel. Defaults to 8. zoom_3d : float Zoom level for the 3d pane. Defaults to 2000. Smaller numbers are more zoomed in. background_color : str or list Sets the background color of the 3d view. Arguments can be rgb values, hex colors, or named web colors. Defaults to black.\n{}\n\n\nclient\n\n\nNone"
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-    "text": "statebuilder.layers.AnnotationLayerConfig(self, name=None, color=None, linked_segmentation_layer=None, mapping_rules=[], array_data=False, tags=None, active=True, filter_by_segmentation=False, brackets_show_segmentation=True, selection_shows_segmentation=True, filter_query=None, data_resolution=None)\nConfiguration class for annotation layers\n\n\n\n\n\n\n\n\n\n\n\nName\nType\nDescription\nDefault\n\n\n\n\nname\nstr\nLayer name. By default, ‘annos’\nNone\n\n\ncolor\nstr\nHex color code with an initial #. By default, None\nNone\n\n\nlinked_segmentation_layer\nstr\nName of a linked segmentation layer for selected ids. By default, None\nNone\n\n\nmapping_rules\n(nglui.statebuilder.mappers.PointMapper, nglui.statebuilder.mappers.LineMapper, nglui.statebuilder.mappers.SphereMapper or list)\nOne rule or a list of rules mapping data to annotations. By default, []\n[]\n\n\narray_data\nbool\nIf True, allows simple mapping where one or more arrays are passed instead of a dataframe. Only allows basic annotation creation, no tags, linked segmentations, or other rich features.\nFalse\n\n\ntags\nlist\nList of tags for the layer.\nNone\n\n\nactive\nbool\nIf True, makes the layer selected. Default is True (unlike for image/segmentation layers).\nTrue"
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-    "text": "Name\nType\nDescription\nDefault\n\n\n\n\nname\nstr\nLayer name. By default, ‘annos’\nNone\n\n\ncolor\nstr\nHex color code with an initial #. By default, None\nNone\n\n\nlinked_segmentation_layer\nstr\nName of a linked segmentation layer for selected ids. By default, None\nNone\n\n\nmapping_rules\n(nglui.statebuilder.mappers.PointMapper, nglui.statebuilder.mappers.LineMapper, nglui.statebuilder.mappers.SphereMapper or list)\nOne rule or a list of rules mapping data to annotations. By default, []\n[]\n\n\narray_data\nbool\nIf True, allows simple mapping where one or more arrays are passed instead of a dataframe. Only allows basic annotation creation, no tags, linked segmentations, or other rich features.\nFalse\n\n\ntags\nlist\nList of tags for the layer.\nNone\n\n\nactive\nbool\nIf True, makes the layer selected. Default is True (unlike for image/segmentation layers).\nTrue"
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-    "text": "parser.base.tag_dictionary(state, layer_name)\nGet the tag id to string dictionary for a layer\n\n\n\n\n\nName\nType\nDescription\nDefault\n\n\n\n\nstate\ndict\n\nrequired\n\n\nlayer_name\n[type]\n[description]\nrequired\n\n\n\n\n\n\n\n\n\nType\nDescription\n\n\n\n\n[type]\n[description]"
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-    "text": "Name\nType\nDescription\nDefault\n\n\n\n\nstate\ndict\n\nrequired\n\n\nlayer_name\n[type]\n[description]\nrequired"
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-    "text": "statebuilder.SegmentationLayerConfig(self, source, name=None, selected_ids_column=None, fixed_ids=None, fixed_id_colors=None, color_column=None, active=False, alpha_selected=0.3, alpha_3d=1, alpha_unselected=0, split_point_map=None, view_kws=None, timestamp=None, data_resolution=None)\nConfiguration class for segmentation layers\n\n\n\n\n\n\n\n\n\n\n\nName\nType\nDescription\nDefault\n\n\n\n\nsource\nstr\nSegmentation source\nrequired\n\n\nname\n(str, optional)\nLayer name.\nNone\n\n\nselected_ids_column\nstr or list-like, optional.\nColumn name (or list of column names) to use for selected ids.\nNone\n\n\nfixed_ids\nlist-like, optional.\nList of root ids to select directly.\nNone\n\n\nfixed_id_colors\nlist-like, optional.\nList of colors for fixed ids. Should be the same length as fixed_ids, although null entries can be padded with None values.\nNone\n\n\ncolor_column\nstr, optional.\n# at the begining. Column to use for color values for selected objects. Values should be RGB hex strings with a\nNone\n\n\nactive\nbool, optional.\nIf True, makes the layer selected. Default is False.\nFalse\n\n\nalpha_selected\n\nOpacity of selected segmentations in the image layer. Optional, default is 0.3.\n0.3\n\n\nalpha_3d\n\nOpacity of meshes. Optional, default is 1.\n1\n\n\nalpha_unselected\n\nOpacity of unselected segments. Optional, default is 0.\n0\n\n\nsplit_point_map\n\nIf not None, provides an object to map the dataframe input to multicut points. Default is None.\nNone\n\n\nview_kws\ndict, optional.\nKeyword arguments for viewer.set_segmentation_view_options. Sets selected (and unselected) segmetation alpha values. Defaults to values in DEFAULT_SEGMENTATION_VIEW_KWS dict specified in this module.\nNone\n\n\ntimestamp\nfloat or datetime, optional.\nTimestamp at which to fix the chunkedgraph in either unix epoch or datetime format. Optional, default is None.\nNone"
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-    "title": "statebuilder.SegmentationLayerConfig",
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-    "text": "Name\nType\nDescription\nDefault\n\n\n\n\nsource\nstr\nSegmentation source\nrequired\n\n\nname\n(str, optional)\nLayer name.\nNone\n\n\nselected_ids_column\nstr or list-like, optional.\nColumn name (or list of column names) to use for selected ids.\nNone\n\n\nfixed_ids\nlist-like, optional.\nList of root ids to select directly.\nNone\n\n\nfixed_id_colors\nlist-like, optional.\nList of colors for fixed ids. Should be the same length as fixed_ids, although null entries can be padded with None values.\nNone\n\n\ncolor_column\nstr, optional.\n# at the begining. Column to use for color values for selected objects. Values should be RGB hex strings with a\nNone\n\n\nactive\nbool, optional.\nIf True, makes the layer selected. Default is False.\nFalse\n\n\nalpha_selected\n\nOpacity of selected segmentations in the image layer. Optional, default is 0.3.\n0.3\n\n\nalpha_3d\n\nOpacity of meshes. Optional, default is 1.\n1\n\n\nalpha_unselected\n\nOpacity of unselected segments. Optional, default is 0.\n0\n\n\nsplit_point_map\n\nIf not None, provides an object to map the dataframe input to multicut points. Default is None.\nNone\n\n\nview_kws\ndict, optional.\nKeyword arguments for viewer.set_segmentation_view_options. Sets selected (and unselected) segmetation alpha values. Defaults to values in DEFAULT_SEGMENTATION_VIEW_KWS dict specified in this module.\nNone\n\n\ntimestamp\nfloat or datetime, optional.\nTimestamp at which to fix the chunkedgraph in either unix epoch or datetime format. Optional, default is None.\nNone"
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-    "text": "statebuilder.layers.AnnotationLayerConfig(self, name=None, color=None, linked_segmentation_layer=None, mapping_rules=[], array_data=False, tags=None, active=True, filter_by_segmentation=False, brackets_show_segmentation=True, selection_shows_segmentation=True, filter_query=None, data_resolution=None)\nConfiguration class for annotation layers\n\n\n\n\n\n\n\n\n\n\n\nName\nType\nDescription\nDefault\n\n\n\n\nname\nstr\nLayer name. By default, ‘annos’\nNone\n\n\ncolor\nstr\nHex color code with an initial #. By default, None\nNone\n\n\nlinked_segmentation_layer\nstr\nName of a linked segmentation layer for selected ids. By default, None\nNone\n\n\nmapping_rules\n(nglui.statebuilder.mappers.PointMapper, nglui.statebuilder.mappers.LineMapper, nglui.statebuilder.mappers.SphereMapper or list)\nOne rule or a list of rules mapping data to annotations. By default, []\n[]\n\n\narray_data\nbool\nIf True, allows simple mapping where one or more arrays are passed instead of a dataframe. Only allows basic annotation creation, no tags, linked segmentations, or other rich features.\nFalse\n\n\ntags\nlist\nList of tags for the layer.\nNone\n\n\nactive\nbool\nIf True, makes the layer selected. Default is True (unlike for image/segmentation layers).\nTrue"
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-    "text": "Name\nType\nDescription\nDefault\n\n\n\n\nname\nstr\nLayer name. By default, ‘annos’\nNone\n\n\ncolor\nstr\nHex color code with an initial #. By default, None\nNone\n\n\nlinked_segmentation_layer\nstr\nName of a linked segmentation layer for selected ids. By default, None\nNone\n\n\nmapping_rules\n(nglui.statebuilder.mappers.PointMapper, nglui.statebuilder.mappers.LineMapper, nglui.statebuilder.mappers.SphereMapper or list)\nOne rule or a list of rules mapping data to annotations. By default, []\n[]\n\n\narray_data\nbool\nIf True, allows simple mapping where one or more arrays are passed instead of a dataframe. Only allows basic annotation creation, no tags, linked segmentations, or other rich features.\nFalse\n\n\ntags\nlist\nList of tags for the layer.\nNone\n\n\nactive\nbool\nIf True, makes the layer selected. Default is True (unlike for image/segmentation layers).\nTrue"
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-    "text": "statebuilder.helpers.make_state_url(df, sb, client, ngl_url=None, target_site=None)\nGenerate a url from a neuroglancer state via a state server.\n\n\n\n\n\n\n\n\n\n\n\nName\nType\nDescription\nDefault\n\n\n\n\ndf\npandas.pandas.DataFrame\nDataframe to pass through statebuilder\nrequired\n\n\nsb\nnglui.statebuilder.statebuilder.nglui.statebuilder.statebuilder.StateBuilder\nStatebuilder to use to render data for link\nrequired\n\n\nclient\ncaveclient.CAVEclient\nCAVEclient configured with a state server\nrequired\n\n\nngl_url\nstr\nNeuroglancer deployment URL, by default None\nNone\n\n\ntarget_site\nstr\nType of neuroglancer deployment to build link for, by default None. This value overrides automatic checking based on the provided url. Use seunglab for a Seung-lab branch and either mainline or cave-explorer for the Cave Explorer or main Google branch.\nNone\n\n\n\n\n\n\n\n\n\nType\nDescription\n\n\n\n\nstr\nUrl to the uploaded neuroglancer state."
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-    "text": "Name\nType\nDescription\nDefault\n\n\n\n\ndf\npandas.pandas.DataFrame\nDataframe to pass through statebuilder\nrequired\n\n\nsb\nnglui.statebuilder.statebuilder.nglui.statebuilder.statebuilder.StateBuilder\nStatebuilder to use to render data for link\nrequired\n\n\nclient\ncaveclient.CAVEclient\nCAVEclient configured with a state server\nrequired\n\n\nngl_url\nstr\nNeuroglancer deployment URL, by default None\nNone\n\n\ntarget_site\nstr\nType of neuroglancer deployment to build link for, by default None. This value overrides automatic checking based on the provided url. Use seunglab for a Seung-lab branch and either mainline or cave-explorer for the Cave Explorer or main Google branch.\nNone"
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-    "text": "Type\nDescription\n\n\n\n\nstr\nUrl to the uploaded neuroglancer state."
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-    "text": "statebuilder.BoundingBoxMapper(self, point_column_a=None, point_column_b=None, description_column=None, linked_segmentation_column=None, tag_column=None, group_column=None, gather_linked_segmentations=True, share_linked_segmentations=False, set_position=True, multipoint=False, collapse_groups=False, split_positions=False, mapping_set=None)\nSets rules to map dataframes to bounding box annotations\n\n\n\n\n\n\n\n\n\n\n\nName\nType\nDescription\nDefault\n\n\n\n\npoint_column_a\nstr\nColumn name with 3d position data for the first point of the bounding box. Must be set if array_data is False (the default)\nNone\n\n\npoint_column_b\nstr\nColumn name with 3d position data for the second point of the bounding box. Must be set if array_data is False (the default)\nNone\n\n\ndescription_column\nstr\nColumn name with string data for annotation descriptions\nNone\n\n\nlinked_segmentation_column\nstr\nColumn name for root ids to link to annotations\nNone\n\n\ntag_column\nstr\nColumn name for categorical tag data. Tags must match those set in the annotation layer.\nNone\n\n\ngroup_column\nstr\nColumn name for grouping data. Data in this row should be numeric with possible NaNs. Rows with the same non-NaN value will be collected into a grouped annotation.\nNone\n\n\nset_position\nbool\nIf set to True, moves the position to center on the first point in the data (using point_column_a).\nTrue\n\n\nmultipoint\n\nIf True, permits multiple points in a given row, sharing data in other columns. Each point row must have the same number of points. Default is False.\nFalse\n\n\ncollapse_groups\n\nIf True, groups are toggled closed in the annotation view.\nFalse\n\n\nmapping_set\n\nIf set, assumes data is passed as a dictionary and uses this string to as the key for the data to use.\nNone"
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-    "text": "Name\nType\nDescription\nDefault\n\n\n\n\npoint_column_a\nstr\nColumn name with 3d position data for the first point of the bounding box. Must be set if array_data is False (the default)\nNone\n\n\npoint_column_b\nstr\nColumn name with 3d position data for the second point of the bounding box. Must be set if array_data is False (the default)\nNone\n\n\ndescription_column\nstr\nColumn name with string data for annotation descriptions\nNone\n\n\nlinked_segmentation_column\nstr\nColumn name for root ids to link to annotations\nNone\n\n\ntag_column\nstr\nColumn name for categorical tag data. Tags must match those set in the annotation layer.\nNone\n\n\ngroup_column\nstr\nColumn name for grouping data. Data in this row should be numeric with possible NaNs. Rows with the same non-NaN value will be collected into a grouped annotation.\nNone\n\n\nset_position\nbool\nIf set to True, moves the position to center on the first point in the data (using point_column_a).\nTrue\n\n\nmultipoint\n\nIf True, permits multiple points in a given row, sharing data in other columns. Each point row must have the same number of points. Default is False.\nFalse\n\n\ncollapse_groups\n\nIf True, groups are toggled closed in the annotation view.\nFalse\n\n\nmapping_set\n\nIf set, assumes data is passed as a dictionary and uses this string to as the key for the data to use.\nNone"
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-    "text": "statebuilder.layers.SegmentationLayerConfig(self, source, name=None, selected_ids_column=None, fixed_ids=None, fixed_id_colors=None, color_column=None, active=False, alpha_selected=0.3, alpha_3d=1, alpha_unselected=0, split_point_map=None, view_kws=None, timestamp=None, data_resolution=None)\nConfiguration class for segmentation layers\n\n\n\n\n\n\n\n\n\n\n\nName\nType\nDescription\nDefault\n\n\n\n\nsource\nstr\nSegmentation source\nrequired\n\n\nname\n(str, optional)\nLayer name.\nNone\n\n\nselected_ids_column\nstr or list-like, optional.\nColumn name (or list of column names) to use for selected ids.\nNone\n\n\nfixed_ids\nlist-like, optional.\nList of root ids to select directly.\nNone\n\n\nfixed_id_colors\nlist-like, optional.\nList of colors for fixed ids. Should be the same length as fixed_ids, although null entries can be padded with None values.\nNone\n\n\ncolor_column\nstr, optional.\n# at the begining. Column to use for color values for selected objects. Values should be RGB hex strings with a\nNone\n\n\nactive\nbool, optional.\nIf True, makes the layer selected. Default is False.\nFalse\n\n\nalpha_selected\n\nOpacity of selected segmentations in the image layer. Optional, default is 0.3.\n0.3\n\n\nalpha_3d\n\nOpacity of meshes. Optional, default is 1.\n1\n\n\nalpha_unselected\n\nOpacity of unselected segments. Optional, default is 0.\n0\n\n\nsplit_point_map\n\nIf not None, provides an object to map the dataframe input to multicut points. Default is None.\nNone\n\n\nview_kws\ndict, optional.\nKeyword arguments for viewer.set_segmentation_view_options. Sets selected (and unselected) segmetation alpha values. Defaults to values in DEFAULT_SEGMENTATION_VIEW_KWS dict specified in this module.\nNone\n\n\ntimestamp\nfloat or datetime, optional.\nTimestamp at which to fix the chunkedgraph in either unix epoch or datetime format. Optional, default is None.\nNone\n\n\n\n\n\n\n\n\n\nName\nDescription\n\n\n\n\nadd_selection_map\nAdd rules for selecting active segment ids and their colors\n\n\n\n\n\nstatebuilder.layers.SegmentationLayerConfig.add_selection_map(selected_ids_column=None, fixed_ids=None, fixed_id_colors=None, color_column=None)\nAdd rules for selecting active segment ids and their colors\n\n\n\n\n\n\n\n\n\n\n\nName\nType\nDescription\nDefault\n\n\n\n\nselected_ids_column\nstr\nDataframe column to use for adding selected segment ids to the segmentation layer, by default None\nNone\n\n\nfixed_ids\nint or list\nAdd one or more segment ids to be active, independent of the data, by default None\nNone\n\n\nfixed_id_colors\nlist\nAdd a list of colors (hex, rgb, or CSS3 string) to assign to the fixed ids, by default None\nNone\n\n\ncolor_column\nstr\nDataframe column to use for adding selected segment colors, by default None\nNone"
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-    "text": "Name\nType\nDescription\nDefault\n\n\n\n\nsource\nstr\nSegmentation source\nrequired\n\n\nname\n(str, optional)\nLayer name.\nNone\n\n\nselected_ids_column\nstr or list-like, optional.\nColumn name (or list of column names) to use for selected ids.\nNone\n\n\nfixed_ids\nlist-like, optional.\nList of root ids to select directly.\nNone\n\n\nfixed_id_colors\nlist-like, optional.\nList of colors for fixed ids. Should be the same length as fixed_ids, although null entries can be padded with None values.\nNone\n\n\ncolor_column\nstr, optional.\n# at the begining. Column to use for color values for selected objects. Values should be RGB hex strings with a\nNone\n\n\nactive\nbool, optional.\nIf True, makes the layer selected. Default is False.\nFalse\n\n\nalpha_selected\n\nOpacity of selected segmentations in the image layer. Optional, default is 0.3.\n0.3\n\n\nalpha_3d\n\nOpacity of meshes. Optional, default is 1.\n1\n\n\nalpha_unselected\n\nOpacity of unselected segments. Optional, default is 0.\n0\n\n\nsplit_point_map\n\nIf not None, provides an object to map the dataframe input to multicut points. Default is None.\nNone\n\n\nview_kws\ndict, optional.\nKeyword arguments for viewer.set_segmentation_view_options. Sets selected (and unselected) segmetation alpha values. Defaults to values in DEFAULT_SEGMENTATION_VIEW_KWS dict specified in this module.\nNone\n\n\ntimestamp\nfloat or datetime, optional.\nTimestamp at which to fix the chunkedgraph in either unix epoch or datetime format. Optional, default is None.\nNone"
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-    "text": "Name\nDescription\n\n\n\n\nadd_selection_map\nAdd rules for selecting active segment ids and their colors\n\n\n\n\n\nstatebuilder.layers.SegmentationLayerConfig.add_selection_map(selected_ids_column=None, fixed_ids=None, fixed_id_colors=None, color_column=None)\nAdd rules for selecting active segment ids and their colors\n\n\n\n\n\n\n\n\n\n\n\nName\nType\nDescription\nDefault\n\n\n\n\nselected_ids_column\nstr\nDataframe column to use for adding selected segment ids to the segmentation layer, by default None\nNone\n\n\nfixed_ids\nint or list\nAdd one or more segment ids to be active, independent of the data, by default None\nNone\n\n\nfixed_id_colors\nlist\nAdd a list of colors (hex, rgb, or CSS3 string) to assign to the fixed ids, by default None\nNone\n\n\ncolor_column\nstr\nDataframe column to use for adding selected segment colors, by default None\nNone"
-  },
-  {
-    "objectID": "reference/parser.base.sphere_annotations.html",
-    "href": "reference/parser.base.sphere_annotations.html",
-    "title": "parser.base.sphere_annotations",
-    "section": "",
-    "text": "parser.base.sphere_annotations(state, layer_name, description=False, linked_segmentations=False, tags=False, group=False)\nGet all sphere annotation points and other info from a layer.\n\n\n\n\n\n\n\n\n\n\n\nName\nType\nDescription\nDefault\n\n\n\n\nstate\ndict\nNeuroglancer state as JSON dict\nrequired\n\n\nlayer_name\nstr\nLayer name\nrequired\n\n\ndescription\nbool\nIf True, also returns descriptions as well. By default False\nFalse\n\n\nlinked_segmentations\nbool\nIf True, also returns list of linked segmentations, by default False\nFalse\n\n\ntags\nbool\nIf True, also returns list of tags, by default False\nFalse\n\n\n\n\n\n\n\n\n\n\n\n\n\nType\nDescription\n\n\n\n\nlist\nList of N 3-element center points (as list)\n\n\nlist\nList of N 3-element radii for each axis of the ellipsoid.\n\n\nlist\nList of N strings (or None), only returned if description=True.\n\n\nlist\nList of N lists of object ids. Only returned if linked_segmentations=True.\n\n\nlist\nList of N lists of tag ids. Only returned if tags=True.\n\n\nlist\nList of group ids (as string) or None for annotations. Only returned if group=True"
-  },
-  {
-    "objectID": "reference/parser.base.sphere_annotations.html#parameters",
-    "href": "reference/parser.base.sphere_annotations.html#parameters",
-    "title": "parser.base.sphere_annotations",
-    "section": "",
-    "text": "Name\nType\nDescription\nDefault\n\n\n\n\nstate\ndict\nNeuroglancer state as JSON dict\nrequired\n\n\nlayer_name\nstr\nLayer name\nrequired\n\n\ndescription\nbool\nIf True, also returns descriptions as well. By default False\nFalse\n\n\nlinked_segmentations\nbool\nIf True, also returns list of linked segmentations, by default False\nFalse\n\n\ntags\nbool\nIf True, also returns list of tags, by default False\nFalse"
-  },
-  {
-    "objectID": "reference/parser.base.sphere_annotations.html#returns",
-    "href": "reference/parser.base.sphere_annotations.html#returns",
-    "title": "parser.base.sphere_annotations",
-    "section": "",
-    "text": "Type\nDescription\n\n\n\n\nlist\nList of N 3-element center points (as list)\n\n\nlist\nList of N 3-element radii for each axis of the ellipsoid.\n\n\nlist\nList of N strings (or None), only returned if description=True.\n\n\nlist\nList of N lists of object ids. Only returned if linked_segmentations=True.\n\n\nlist\nList of N lists of tag ids. Only returned if tags=True.\n\n\nlist\nList of group ids (as string) or None for annotations. Only returned if group=True"
-  }
-]
\ No newline at end of file
diff --git a/docs/_site/site_libs/bootstrap/bootstrap-icons.css b/docs/_site/site_libs/bootstrap/bootstrap-icons.css
deleted file mode 100644
index 94f1940..0000000
--- a/docs/_site/site_libs/bootstrap/bootstrap-icons.css
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diff --git a/docs/_site/site_libs/bootstrap/bootstrap.min.css b/docs/_site/site_libs/bootstrap/bootstrap.min.css
deleted file mode 100644
index 2d28750..0000000
--- a/docs/_site/site_libs/bootstrap/bootstrap.min.css
+++ /dev/null
@@ -1,10 +0,0 @@
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t?t:{}},a(K,t,Y),t}_handleSwipe(){const t=Math.abs(this.touchDeltaX);if(t<=40)return;const e=t/this.touchDeltaX;this.touchDeltaX=0,e&&this._slide(e>0?J:Z)}_addEventListeners(){this._config.keyboard&&j.on(this._element,"keydown.bs.carousel",(t=>this._keydown(t))),"hover"===this._config.pause&&(j.on(this._element,"mouseenter.bs.carousel",(t=>this.pause(t))),j.on(this._element,"mouseleave.bs.carousel",(t=>this.cycle(t)))),this._config.touch&&this._touchSupported&&this._addTouchEventListeners()}_addTouchEventListeners(){const t=t=>this._pointerEvent&&("pen"===t.pointerType||"touch"===t.pointerType),e=e=>{t(e)?this.touchStartX=e.clientX:this._pointerEvent||(this.touchStartX=e.touches[0].clientX)},i=t=>{this.touchDeltaX=t.touches&&t.touches.length>1?0:t.touches[0].clientX-this.touchStartX},n=e=>{t(e)&&(this.touchDeltaX=e.clientX-this.touchStartX),this._handleSwipe(),"hover"===this._config.pause&&(this.pause(),this.touchTimeout&&clearTimeout(this.touchTimeout),this.touchTimeout=setTimeout((t=>this.cycle(t)),500+this._config.interval))};V.find(".carousel-item img",this._element).forEach((t=>{j.on(t,"dragstart.bs.carousel",(t=>t.preventDefault()))})),this._pointerEvent?(j.on(this._element,"pointerdown.bs.carousel",(t=>e(t))),j.on(this._element,"pointerup.bs.carousel",(t=>n(t))),this._element.classList.add("pointer-event")):(j.on(this._element,"touchstart.bs.carousel",(t=>e(t))),j.on(this._element,"touchmove.bs.carousel",(t=>i(t))),j.on(this._element,"touchend.bs.carousel",(t=>n(t))))}_keydown(t){if(/input|textarea/i.test(t.target.tagName))return;const e=tt[t.key];e&&(t.preventDefault(),this._slide(e))}_getItemIndex(t){return this._items=t&&t.parentNode?V.find(".carousel-item",t.parentNode):[],this._items.indexOf(t)}_getItemByOrder(t,e){const i=t===Q;return v(this._items,e,i,this._config.wrap)}_triggerSlideEvent(t,e){const i=this._getItemIndex(t),n=this._getItemIndex(V.findOne(nt,this._element));return j.trigger(this._element,"slide.bs.carousel",{relatedTarget:t,direction:e,from:n,to:i})}_setActiveIndicatorElement(t){if(this._indicatorsElement){const e=V.findOne(".active",this._indicatorsElement);e.classList.remove(it),e.removeAttribute("aria-current");const i=V.find("[data-bs-target]",this._indicatorsElement);for(let e=0;e<i.length;e++)if(Number.parseInt(i[e].getAttribute("data-bs-slide-to"),10)===this._getItemIndex(t)){i[e].classList.add(it),i[e].setAttribute("aria-current","true");break}}}_updateInterval(){const t=this._activeElement||V.findOne(nt,this._element);if(!t)return;const e=Number.parseInt(t.getAttribute("data-bs-interval"),10);e?(this._config.defaultInterval=this._config.defaultInterval||this._config.interval,this._config.interval=e):this._config.interval=this._config.defaultInterval||this._config.interval}_slide(t,e){const i=this._directionToOrder(t),n=V.findOne(nt,this._element),s=this._getItemIndex(n),o=e||this._getItemByOrder(i,n),r=this._getItemIndex(o),a=Boolean(this._interval),l=i===Q,c=l?"carousel-item-start":"carousel-item-end",h=l?"carousel-item-next":"carousel-item-prev",d=this._orderToDirection(i);if(o&&o.classList.contains(it))return void(this._isSliding=!1);if(this._isSliding)return;if(this._triggerSlideEvent(o,d).defaultPrevented)return;if(!n||!o)return;this._isSliding=!0,a&&this.pause(),this._setActiveIndicatorElement(o),this._activeElement=o;const f=()=>{j.trigger(this._element,et,{relatedTarget:o,direction:d,from:s,to:r})};if(this._element.classList.contains("slide")){o.classList.add(h),u(o),n.classList.add(c),o.classList.add(c);const t=()=>{o.classList.remove(c,h),o.classList.add(it),n.classList.remove(it,h,c),this._isSliding=!1,setTimeout(f,0)};this._queueCallback(t,n,!0)}else n.classList.remove(it),o.classList.add(it),this._isSliding=!1,f();a&&this.cycle()}_directionToOrder(t){return[J,Z].includes(t)?m()?t===Z?G:Q:t===Z?Q:G:t}_orderToDirection(t){return[Q,G].includes(t)?m()?t===G?Z:J:t===G?J:Z:t}static carouselInterface(t,e){const i=st.getOrCreateInstance(t,e);let{_config:n}=i;"object"==typeof e&&(n={...n,...e});const s="string"==typeof e?e:n.slide;if("number"==typeof e)i.to(e);else if("string"==typeof s){if(void 0===i[s])throw new TypeError(`No method named "${s}"`);i[s]()}else n.interval&&n.ride&&(i.pause(),i.cycle())}static jQueryInterface(t){return this.each((function(){st.carouselInterface(this,t)}))}static dataApiClickHandler(t){const e=n(this);if(!e||!e.classList.contains("carousel"))return;const i={...U.getDataAttributes(e),...U.getDataAttributes(this)},s=this.getAttribute("data-bs-slide-to");s&&(i.interval=!1),st.carouselInterface(e,i),s&&st.getInstance(e).to(s),t.preventDefault()}}j.on(document,"click.bs.carousel.data-api","[data-bs-slide], [data-bs-slide-to]",st.dataApiClickHandler),j.on(window,"load.bs.carousel.data-api",(()=>{const t=V.find('[data-bs-ride="carousel"]');for(let e=0,i=t.length;e<i;e++)st.carouselInterface(t[e],st.getInstance(t[e]))})),g(st);const ot="collapse",rt={toggle:!0,parent:null},at={toggle:"boolean",parent:"(null|element)"},lt="show",ct="collapse",ht="collapsing",dt="collapsed",ut=":scope .collapse .collapse",ft='[data-bs-toggle="collapse"]';class pt extends B{constructor(t,e){super(t),this._isTransitioning=!1,this._config=this._getConfig(e),this._triggerArray=[];const n=V.find(ft);for(let t=0,e=n.length;t<e;t++){const e=n[t],s=i(e),o=V.find(s).filter((t=>t===this._element));null!==s&&o.length&&(this._selector=s,this._triggerArray.push(e))}this._initializeChildren(),this._config.parent||this._addAriaAndCollapsedClass(this._triggerArray,this._isShown()),this._config.toggle&&this.toggle()}static get Default(){return rt}static get NAME(){return ot}toggle(){this._isShown()?this.hide():this.show()}show(){if(this._isTransitioning||this._isShown())return;let t,e=[];if(this._config.parent){const t=V.find(ut,this._config.parent);e=V.find(".collapse.show, .collapse.collapsing",this._config.parent).filter((e=>!t.includes(e)))}const i=V.findOne(this._selector);if(e.length){const n=e.find((t=>i!==t));if(t=n?pt.getInstance(n):null,t&&t._isTransitioning)return}if(j.trigger(this._element,"show.bs.collapse").defaultPrevented)return;e.forEach((e=>{i!==e&&pt.getOrCreateInstance(e,{toggle:!1}).hide(),t||H.set(e,"bs.collapse",null)}));const n=this._getDimension();this._element.classList.remove(ct),this._element.classList.add(ht),this._element.style[n]=0,this._addAriaAndCollapsedClass(this._triggerArray,!0),this._isTransitioning=!0;const s=`scroll${n[0].toUpperCase()+n.slice(1)}`;this._queueCallback((()=>{this._isTransitioning=!1,this._element.classList.remove(ht),this._element.classList.add(ct,lt),this._element.style[n]="",j.trigger(this._element,"shown.bs.collapse")}),this._element,!0),this._element.style[n]=`${this._element[s]}px`}hide(){if(this._isTransitioning||!this._isShown())return;if(j.trigger(this._element,"hide.bs.collapse").defaultPrevented)return;const t=this._getDimension();this._element.style[t]=`${this._element.getBoundingClientRect()[t]}px`,u(this._element),this._element.classList.add(ht),this._element.classList.remove(ct,lt);const e=this._triggerArray.length;for(let t=0;t<e;t++){const e=this._triggerArray[t],i=n(e);i&&!this._isShown(i)&&this._addAriaAndCollapsedClass([e],!1)}this._isTransitioning=!0,this._element.style[t]="",this._queueCallback((()=>{this._isTransitioning=!1,this._element.classList.remove(ht),this._element.classList.add(ct),j.trigger(this._element,"hidden.bs.collapse")}),this._element,!0)}_isShown(t=this._element){return t.classList.contains(lt)}_getConfig(t){return(t={...rt,...U.getDataAttributes(this._element),...t}).toggle=Boolean(t.toggle),t.parent=r(t.parent),a(ot,t,at),t}_getDimension(){return this._element.classList.contains("collapse-horizontal")?"width":"height"}_initializeChildren(){if(!this._config.parent)return;const t=V.find(ut,this._config.parent);V.find(ft,this._config.parent).filter((e=>!t.includes(e))).forEach((t=>{const e=n(t);e&&this._addAriaAndCollapsedClass([t],this._isShown(e))}))}_addAriaAndCollapsedClass(t,e){t.length&&t.forEach((t=>{e?t.classList.remove(dt):t.classList.add(dt),t.setAttribute("aria-expanded",e)}))}static jQueryInterface(t){return this.each((function(){const e={};"string"==typeof t&&/show|hide/.test(t)&&(e.toggle=!1);const i=pt.getOrCreateInstance(this,e);if("string"==typeof t){if(void 0===i[t])throw new TypeError(`No method named "${t}"`);i[t]()}}))}}j.on(document,"click.bs.collapse.data-api",ft,(function(t){("A"===t.target.tagName||t.delegateTarget&&"A"===t.delegateTarget.tagName)&&t.preventDefault();const e=i(this);V.find(e).forEach((t=>{pt.getOrCreateInstance(t,{toggle:!1}).toggle()}))})),g(pt);var mt="top",gt="bottom",_t="right",bt="left",vt="auto",yt=[mt,gt,_t,bt],wt="start",Et="end",At="clippingParents",Tt="viewport",Ot="popper",Ct="reference",kt=yt.reduce((function(t,e){return t.concat([e+"-"+wt,e+"-"+Et])}),[]),Lt=[].concat(yt,[vt]).reduce((function(t,e){return t.concat([e,e+"-"+wt,e+"-"+Et])}),[]),xt="beforeRead",Dt="read",St="afterRead",Nt="beforeMain",It="main",Pt="afterMain",jt="beforeWrite",Mt="write",Ht="afterWrite",Bt=[xt,Dt,St,Nt,It,Pt,jt,Mt,Ht];function Rt(t){return t?(t.nodeName||"").toLowerCase():null}function Wt(t){if(null==t)return window;if("[object Window]"!==t.toString()){var e=t.ownerDocument;return e&&e.defaultView||window}return t}function $t(t){return t instanceof Wt(t).Element||t instanceof Element}function zt(t){return t instanceof Wt(t).HTMLElement||t instanceof HTMLElement}function qt(t){return"undefined"!=typeof ShadowRoot&&(t instanceof Wt(t).ShadowRoot||t instanceof ShadowRoot)}const Ft={name:"applyStyles",enabled:!0,phase:"write",fn:function(t){var e=t.state;Object.keys(e.elements).forEach((function(t){var i=e.styles[t]||{},n=e.attributes[t]||{},s=e.elements[t];zt(s)&&Rt(s)&&(Object.assign(s.style,i),Object.keys(n).forEach((function(t){var e=n[t];!1===e?s.removeAttribute(t):s.setAttribute(t,!0===e?"":e)})))}))},effect:function(t){var e=t.state,i={popper:{position:e.options.strategy,left:"0",top:"0",margin:"0"},arrow:{position:"absolute"},reference:{}};return Object.assign(e.elements.popper.style,i.popper),e.styles=i,e.elements.arrow&&Object.assign(e.elements.arrow.style,i.arrow),function(){Object.keys(e.elements).forEach((function(t){var n=e.elements[t],s=e.attributes[t]||{},o=Object.keys(e.styles.hasOwnProperty(t)?e.styles[t]:i[t]).reduce((function(t,e){return t[e]="",t}),{});zt(n)&&Rt(n)&&(Object.assign(n.style,o),Object.keys(s).forEach((function(t){n.removeAttribute(t)})))}))}},requires:["computeStyles"]};function Ut(t){return t.split("-")[0]}function Vt(t,e){var i=t.getBoundingClientRect();return{width:i.width/1,height:i.height/1,top:i.top/1,right:i.right/1,bottom:i.bottom/1,left:i.left/1,x:i.left/1,y:i.top/1}}function Kt(t){var e=Vt(t),i=t.offsetWidth,n=t.offsetHeight;return Math.abs(e.width-i)<=1&&(i=e.width),Math.abs(e.height-n)<=1&&(n=e.height),{x:t.offsetLeft,y:t.offsetTop,width:i,height:n}}function Xt(t,e){var i=e.getRootNode&&e.getRootNode();if(t.contains(e))return!0;if(i&&qt(i)){var 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n=Yt(i);if("none"!==n.transform||"none"!==n.perspective||"paint"===n.contain||-1!==["transform","perspective"].indexOf(n.willChange)||e&&"filter"===n.willChange||e&&n.filter&&"none"!==n.filter)return i;i=i.parentNode}return null}(t)||e}function ee(t){return["top","bottom"].indexOf(t)>=0?"x":"y"}var ie=Math.max,ne=Math.min,se=Math.round;function oe(t,e,i){return ie(t,ne(e,i))}function re(t){return Object.assign({},{top:0,right:0,bottom:0,left:0},t)}function ae(t,e){return e.reduce((function(e,i){return e[i]=t,e}),{})}const le={name:"arrow",enabled:!0,phase:"main",fn:function(t){var e,i=t.state,n=t.name,s=t.options,o=i.elements.arrow,r=i.modifiersData.popperOffsets,a=Ut(i.placement),l=ee(a),c=[bt,_t].indexOf(a)>=0?"height":"width";if(o&&r){var h=function(t,e){return re("number"!=typeof(t="function"==typeof 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Be={placement:"bottom",modifiers:[],strategy:"absolute"};function Re(){for(var t=arguments.length,e=new Array(t),i=0;i<t;i++)e[i]=arguments[i];return!e.some((function(t){return!(t&&"function"==typeof t.getBoundingClientRect)}))}function We(t){void 0===t&&(t={});var e=t,i=e.defaultModifiers,n=void 0===i?[]:i,s=e.defaultOptions,o=void 0===s?Be:s;return function(t,e,i){void 0===i&&(i=o);var s,r,a={placement:"bottom",orderedModifiers:[],options:Object.assign({},Be,o),modifiersData:{},elements:{reference:t,popper:e},attributes:{},styles:{}},l=[],c=!1,h={state:a,setOptions:function(i){var s="function"==typeof i?i(a.options):i;d(),a.options=Object.assign({},o,a.options,s),a.scrollParents={reference:$t(t)?Ae(t):t.contextElement?Ae(t.contextElement):[],popper:Ae(e)};var r,c,u=function(t){var e=He(t);return Bt.reduce((function(t,i){return t.concat(e.filter((function(t){return t.phase===i})))}),[])}((r=[].concat(n,a.options.modifiers),c=r.reduce((function(t,e){var i=t[e.name];return 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Fe=Object.freeze({__proto__:null,popperGenerator:We,detectOverflow:ke,createPopperBase:$e,createPopper:qe,createPopperLite:ze,top:mt,bottom:gt,right:_t,left:bt,auto:vt,basePlacements:yt,start:wt,end:Et,clippingParents:At,viewport:Tt,popper:Ot,reference:Ct,variationPlacements:kt,placements:Lt,beforeRead:xt,read:Dt,afterRead:St,beforeMain:Nt,main:It,afterMain:Pt,beforeWrite:jt,write:Mt,afterWrite:Ht,modifierPhases:Bt,applyStyles:Ft,arrow:le,computeStyles:ue,eventListeners:pe,flip:xe,hide:Ne,offset:Ie,popperOffsets:Pe,preventOverflow:je}),Ue="dropdown",Ve="Escape",Ke="Space",Xe="ArrowUp",Ye="ArrowDown",Qe=new 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this._isShown()?this.hide():this.show()}show(){if(c(this._element)||this._isShown(this._menu))return;const t={relatedTarget:this._element};if(j.trigger(this._element,"show.bs.dropdown",t).defaultPrevented)return;const e=hi.getParentFromElement(this._element);this._inNavbar?U.setDataAttribute(this._menu,"popper","none"):this._createPopper(e),"ontouchstart"in document.documentElement&&!e.closest(".navbar-nav")&&[].concat(...document.body.children).forEach((t=>j.on(t,"mouseover",d))),this._element.focus(),this._element.setAttribute("aria-expanded",!0),this._menu.classList.add(Je),this._element.classList.add(Je),j.trigger(this._element,"shown.bs.dropdown",t)}hide(){if(c(this._element)||!this._isShown(this._menu))return;const t={relatedTarget:this._element};this._completeHide(t)}dispose(){this._popper&&this._popper.destroy(),super.dispose()}update(){this._inNavbar=this._detectNavbar(),this._popper&&this._popper.update()}_completeHide(t){j.trigger(this._element,"hide.bs.dropdown",t).defaultPrevented||("ontouchstart"in document.documentElement&&[].concat(...document.body.children).forEach((t=>j.off(t,"mouseover",d))),this._popper&&this._popper.destroy(),this._menu.classList.remove(Je),this._element.classList.remove(Je),this._element.setAttribute("aria-expanded","false"),U.removeDataAttribute(this._menu,"popper"),j.trigger(this._element,"hidden.bs.dropdown",t))}_getConfig(t){if(t={...this.constructor.Default,...U.getDataAttributes(this._element),...t},a(Ue,t,this.constructor.DefaultType),"object"==typeof t.reference&&!o(t.reference)&&"function"!=typeof t.reference.getBoundingClientRect)throw new TypeError(`${Ue.toUpperCase()}: Option "reference" provided type "object" without a required "getBoundingClientRect" 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null!==this._element.closest(".navbar")}_getOffset(){const{offset:t}=this._config;return"string"==typeof t?t.split(",").map((t=>Number.parseInt(t,10))):"function"==typeof t?e=>t(e,this._element):t}_getPopperConfig(){const t={placement:this._getPlacement(),modifiers:[{name:"preventOverflow",options:{boundary:this._config.boundary}},{name:"offset",options:{offset:this._getOffset()}}]};return"static"===this._config.display&&(t.modifiers=[{name:"applyStyles",enabled:!1}]),{...t,..."function"==typeof this._config.popperConfig?this._config.popperConfig(t):this._config.popperConfig}}_selectMenuItem({key:t,target:e}){const i=V.find(".dropdown-menu .dropdown-item:not(.disabled):not(:disabled)",this._menu).filter(l);i.length&&v(i,e,t===Ye,!i.includes(e)).focus()}static jQueryInterface(t){return this.each((function(){const e=hi.getOrCreateInstance(this,t);if("string"==typeof t){if(void 0===e[t])throw new TypeError(`No method named "${t}"`);e[t]()}}))}static clearMenus(t){if(t&&(2===t.button||"keyup"===t.type&&"Tab"!==t.key))return;const e=V.find(ti);for(let i=0,n=e.length;i<n;i++){const n=hi.getInstance(e[i]);if(!n||!1===n._config.autoClose)continue;if(!n._isShown())continue;const s={relatedTarget:n._element};if(t){const e=t.composedPath(),i=e.includes(n._menu);if(e.includes(n._element)||"inside"===n._config.autoClose&&!i||"outside"===n._config.autoClose&&i)continue;if(n._menu.contains(t.target)&&("keyup"===t.type&&"Tab"===t.key||/input|select|option|textarea|form/i.test(t.target.tagName)))continue;"click"===t.type&&(s.clickEvent=t)}n._completeHide(s)}}static getParentFromElement(t){return n(t)||t.parentNode}static dataApiKeydownHandler(t){if(/input|textarea/i.test(t.target.tagName)?t.key===Ke||t.key!==Ve&&(t.key!==Ye&&t.key!==Xe||t.target.closest(ei)):!Qe.test(t.key))return;const e=this.classList.contains(Je);if(!e&&t.key===Ve)return;if(t.preventDefault(),t.stopPropagation(),c(this))return;const i=this.matches(ti)?this:V.prev(this,ti)[0],n=hi.getOrCreateInstance(i);if(t.key!==Ve)return t.key===Xe||t.key===Ye?(e||n.show(),void n._selectMenuItem(t)):void(e&&t.key!==Ke||hi.clearMenus());n.hide()}}j.on(document,Ze,ti,hi.dataApiKeydownHandler),j.on(document,Ze,ei,hi.dataApiKeydownHandler),j.on(document,Ge,hi.clearMenus),j.on(document,"keyup.bs.dropdown.data-api",hi.clearMenus),j.on(document,Ge,ti,(function(t){t.preventDefault(),hi.getOrCreateInstance(this).toggle()})),g(hi);const di=".fixed-top, .fixed-bottom, .is-fixed, .sticky-top",ui=".sticky-top";class fi{constructor(){this._element=document.body}getWidth(){const t=document.documentElement.clientWidth;return Math.abs(window.innerWidth-t)}hide(){const t=this.getWidth();this._disableOverFlow(),this._setElementAttributes(this._element,"paddingRight",(e=>e+t)),this._setElementAttributes(di,"paddingRight",(e=>e+t)),this._setElementAttributes(ui,"marginRight",(e=>e-t))}_disableOverFlow(){this._saveInitialAttribute(this._element,"overflow"),this._element.style.overflow="hidden"}_setElementAttributes(t,e,i){const n=this.getWidth();this._applyManipulationCallback(t,(t=>{if(t!==this._element&&window.innerWidth>t.clientWidth+n)return;this._saveInitialAttribute(t,e);const s=window.getComputedStyle(t)[e];t.style[e]=`${i(Number.parseFloat(s))}px`}))}reset(){this._resetElementAttributes(this._element,"overflow"),this._resetElementAttributes(this._element,"paddingRight"),this._resetElementAttributes(di,"paddingRight"),this._resetElementAttributes(ui,"marginRight")}_saveInitialAttribute(t,e){const i=t.style[e];i&&U.setDataAttribute(t,e,i)}_resetElementAttributes(t,e){this._applyManipulationCallback(t,(t=>{const i=U.getDataAttribute(t,e);void 0===i?t.style.removeProperty(e):(U.removeDataAttribute(t,e),t.style[e]=i)}))}_applyManipulationCallback(t,e){o(t)?e(t):V.find(t,this._element).forEach(e)}isOverflowing(){return this.getWidth()>0}}const pi={className:"modal-backdrop",isVisible:!0,isAnimated:!1,rootElement:"body",clickCallback:null},mi={className:"string",isVisible:"boolean",isAnimated:"boolean",rootElement:"(element|string)",clickCallback:"(function|null)"},gi="show",_i="mousedown.bs.backdrop";class bi{constructor(t){this._config=this._getConfig(t),this._isAppended=!1,this._element=null}show(t){this._config.isVisible?(this._append(),this._config.isAnimated&&u(this._getElement()),this._getElement().classList.add(gi),this._emulateAnimation((()=>{_(t)}))):_(t)}hide(t){this._config.isVisible?(this._getElement().classList.remove(gi),this._emulateAnimation((()=>{this.dispose(),_(t)}))):_(t)}_getElement(){if(!this._element){const t=document.createElement("div");t.className=this._config.className,this._config.isAnimated&&t.classList.add("fade"),this._element=t}return this._element}_getConfig(t){return(t={...pi,..."object"==typeof t?t:{}}).rootElement=r(t.rootElement),a("backdrop",t,mi),t}_append(){this._isAppended||(this._config.rootElement.append(this._getElement()),j.on(this._getElement(),_i,(()=>{_(this._config.clickCallback)})),this._isAppended=!0)}dispose(){this._isAppended&&(j.off(this._element,_i),this._element.remove(),this._isAppended=!1)}_emulateAnimation(t){b(t,this._getElement(),this._config.isAnimated)}}const vi={trapElement:null,autofocus:!0},yi={trapElement:"element",autofocus:"boolean"},wi=".bs.focustrap",Ei="backward";class Ai{constructor(t){this._config=this._getConfig(t),this._isActive=!1,this._lastTabNavDirection=null}activate(){const{trapElement:t,autofocus:e}=this._config;this._isActive||(e&&t.focus(),j.off(document,wi),j.on(document,"focusin.bs.focustrap",(t=>this._handleFocusin(t))),j.on(document,"keydown.tab.bs.focustrap",(t=>this._handleKeydown(t))),this._isActive=!0)}deactivate(){this._isActive&&(this._isActive=!1,j.off(document,wi))}_handleFocusin(t){const{target:e}=t,{trapElement:i}=this._config;if(e===document||e===i||i.contains(e))return;const n=V.focusableChildren(i);0===n.length?i.focus():this._lastTabNavDirection===Ei?n[n.length-1].focus():n[0].focus()}_handleKeydown(t){"Tab"===t.key&&(this._lastTabNavDirection=t.shiftKey?Ei:"forward")}_getConfig(t){return t={...vi,..."object"==typeof t?t:{}},a("focustrap",t,yi),t}}const Ti="modal",Oi="Escape",Ci={backdrop:!0,keyboard:!0,focus:!0},ki={backdrop:"(boolean|string)",keyboard:"boolean",focus:"boolean"},Li="hidden.bs.modal",xi="show.bs.modal",Di="resize.bs.modal",Si="click.dismiss.bs.modal",Ni="keydown.dismiss.bs.modal",Ii="mousedown.dismiss.bs.modal",Pi="modal-open",ji="show",Mi="modal-static";class Hi extends B{constructor(t,e){super(t),this._config=this._getConfig(e),this._dialog=V.findOne(".modal-dialog",this._element),this._backdrop=this._initializeBackDrop(),this._focustrap=this._initializeFocusTrap(),this._isShown=!1,this._ignoreBackdropClick=!1,this._isTransitioning=!1,this._scrollBar=new fi}static get Default(){return Ci}static get NAME(){return Ti}toggle(t){return this._isShown?this.hide():this.show(t)}show(t){this._isShown||this._isTransitioning||j.trigger(this._element,xi,{relatedTarget:t}).defaultPrevented||(this._isShown=!0,this._isAnimated()&&(this._isTransitioning=!0),this._scrollBar.hide(),document.body.classList.add(Pi),this._adjustDialog(),this._setEscapeEvent(),this._setResizeEvent(),j.on(this._dialog,Ii,(()=>{j.one(this._element,"mouseup.dismiss.bs.modal",(t=>{t.target===this._element&&(this._ignoreBackdropClick=!0)}))})),this._showBackdrop((()=>this._showElement(t))))}hide(){if(!this._isShown||this._isTransitioning)return;if(j.trigger(this._element,"hide.bs.modal").defaultPrevented)return;this._isShown=!1;const t=this._isAnimated();t&&(this._isTransitioning=!0),this._setEscapeEvent(),this._setResizeEvent(),this._focustrap.deactivate(),this._element.classList.remove(ji),j.off(this._element,Si),j.off(this._dialog,Ii),this._queueCallback((()=>this._hideModal()),this._element,t)}dispose(){[window,this._dialog].forEach((t=>j.off(t,".bs.modal"))),this._backdrop.dispose(),this._focustrap.deactivate(),super.dispose()}handleUpdate(){this._adjustDialog()}_initializeBackDrop(){return new bi({isVisible:Boolean(this._config.backdrop),isAnimated:this._isAnimated()})}_initializeFocusTrap(){return new Ai({trapElement:this._element})}_getConfig(t){return t={...Ci,...U.getDataAttributes(this._element),..."object"==typeof t?t:{}},a(Ti,t,ki),t}_showElement(t){const e=this._isAnimated(),i=V.findOne(".modal-body",this._dialog);this._element.parentNode&&this._element.parentNode.nodeType===Node.ELEMENT_NODE||document.body.append(this._element),this._element.style.display="block",this._element.removeAttribute("aria-hidden"),this._element.setAttribute("aria-modal",!0),this._element.setAttribute("role","dialog"),this._element.scrollTop=0,i&&(i.scrollTop=0),e&&u(this._element),this._element.classList.add(ji),this._queueCallback((()=>{this._config.focus&&this._focustrap.activate(),this._isTransitioning=!1,j.trigger(this._element,"shown.bs.modal",{relatedTarget:t})}),this._dialog,e)}_setEscapeEvent(){this._isShown?j.on(this._element,Ni,(t=>{this._config.keyboard&&t.key===Oi?(t.preventDefault(),this.hide()):this._config.keyboard||t.key!==Oi||this._triggerBackdropTransition()})):j.off(this._element,Ni)}_setResizeEvent(){this._isShown?j.on(window,Di,(()=>this._adjustDialog())):j.off(window,Di)}_hideModal(){this._element.style.display="none",this._element.setAttribute("aria-hidden",!0),this._element.removeAttribute("aria-modal"),this._element.removeAttribute("role"),this._isTransitioning=!1,this._backdrop.hide((()=>{document.body.classList.remove(Pi),this._resetAdjustments(),this._scrollBar.reset(),j.trigger(this._element,Li)}))}_showBackdrop(t){j.on(this._element,Si,(t=>{this._ignoreBackdropClick?this._ignoreBackdropClick=!1:t.target===t.currentTarget&&(!0===this._config.backdrop?this.hide():"static"===this._config.backdrop&&this._triggerBackdropTransition())})),this._backdrop.show(t)}_isAnimated(){return this._element.classList.contains("fade")}_triggerBackdropTransition(){if(j.trigger(this._element,"hidePrevented.bs.modal").defaultPrevented)return;const{classList:t,scrollHeight:e,style:i}=this._element,n=e>document.documentElement.clientHeight;!n&&"hidden"===i.overflowY||t.contains(Mi)||(n||(i.overflowY="hidden"),t.add(Mi),this._queueCallback((()=>{t.remove(Mi),n||this._queueCallback((()=>{i.overflowY=""}),this._dialog)}),this._dialog),this._element.focus())}_adjustDialog(){const t=this._element.scrollHeight>document.documentElement.clientHeight,e=this._scrollBar.getWidth(),i=e>0;(!i&&t&&!m()||i&&!t&&m())&&(this._element.style.paddingLeft=`${e}px`),(i&&!t&&!m()||!i&&t&&m())&&(this._element.style.paddingRight=`${e}px`)}_resetAdjustments(){this._element.style.paddingLeft="",this._element.style.paddingRight=""}static jQueryInterface(t,e){return this.each((function(){const i=Hi.getOrCreateInstance(this,t);if("string"==typeof t){if(void 0===i[t])throw new TypeError(`No method named "${t}"`);i[t](e)}}))}}j.on(document,"click.bs.modal.data-api",'[data-bs-toggle="modal"]',(function(t){const e=n(this);["A","AREA"].includes(this.tagName)&&t.preventDefault(),j.one(e,xi,(t=>{t.defaultPrevented||j.one(e,Li,(()=>{l(this)&&this.focus()}))}));const i=V.findOne(".modal.show");i&&Hi.getInstance(i).hide(),Hi.getOrCreateInstance(e).toggle(this)})),R(Hi),g(Hi);const Bi="offcanvas",Ri={backdrop:!0,keyboard:!0,scroll:!1},Wi={backdrop:"boolean",keyboard:"boolean",scroll:"boolean"},$i="show",zi=".offcanvas.show",qi="hidden.bs.offcanvas";class Fi extends B{constructor(t,e){super(t),this._config=this._getConfig(e),this._isShown=!1,this._backdrop=this._initializeBackDrop(),this._focustrap=this._initializeFocusTrap(),this._addEventListeners()}static get NAME(){return Bi}static get Default(){return Ri}toggle(t){return this._isShown?this.hide():this.show(t)}show(t){this._isShown||j.trigger(this._element,"show.bs.offcanvas",{relatedTarget:t}).defaultPrevented||(this._isShown=!0,this._element.style.visibility="visible",this._backdrop.show(),this._config.scroll||(new fi).hide(),this._element.removeAttribute("aria-hidden"),this._element.setAttribute("aria-modal",!0),this._element.setAttribute("role","dialog"),this._element.classList.add($i),this._queueCallback((()=>{this._config.scroll||this._focustrap.activate(),j.trigger(this._element,"shown.bs.offcanvas",{relatedTarget:t})}),this._element,!0))}hide(){this._isShown&&(j.trigger(this._element,"hide.bs.offcanvas").defaultPrevented||(this._focustrap.deactivate(),this._element.blur(),this._isShown=!1,this._element.classList.remove($i),this._backdrop.hide(),this._queueCallback((()=>{this._element.setAttribute("aria-hidden",!0),this._element.removeAttribute("aria-modal"),this._element.removeAttribute("role"),this._element.style.visibility="hidden",this._config.scroll||(new fi).reset(),j.trigger(this._element,qi)}),this._element,!0)))}dispose(){this._backdrop.dispose(),this._focustrap.deactivate(),super.dispose()}_getConfig(t){return t={...Ri,...U.getDataAttributes(this._element),..."object"==typeof t?t:{}},a(Bi,t,Wi),t}_initializeBackDrop(){return new bi({className:"offcanvas-backdrop",isVisible:this._config.backdrop,isAnimated:!0,rootElement:this._element.parentNode,clickCallback:()=>this.hide()})}_initializeFocusTrap(){return new Ai({trapElement:this._element})}_addEventListeners(){j.on(this._element,"keydown.dismiss.bs.offcanvas",(t=>{this._config.keyboard&&"Escape"===t.key&&this.hide()}))}static jQueryInterface(t){return this.each((function(){const e=Fi.getOrCreateInstance(this,t);if("string"==typeof t){if(void 0===e[t]||t.startsWith("_")||"constructor"===t)throw new TypeError(`No method named "${t}"`);e[t](this)}}))}}j.on(document,"click.bs.offcanvas.data-api",'[data-bs-toggle="offcanvas"]',(function(t){const e=n(this);if(["A","AREA"].includes(this.tagName)&&t.preventDefault(),c(this))return;j.one(e,qi,(()=>{l(this)&&this.focus()}));const i=V.findOne(zi);i&&i!==e&&Fi.getInstance(i).hide(),Fi.getOrCreateInstance(e).toggle(this)})),j.on(window,"load.bs.offcanvas.data-api",(()=>V.find(zi).forEach((t=>Fi.getOrCreateInstance(t).show())))),R(Fi),g(Fi);const Ui=new Set(["background","cite","href","itemtype","longdesc","poster","src","xlink:href"]),Vi=/^(?:(?:https?|mailto|ftp|tel|file|sms):|[^#&/:?]*(?:[#/?]|$))/i,Ki=/^data:(?:image\/(?:bmp|gif|jpeg|jpg|png|tiff|webp)|video\/(?:mpeg|mp4|ogg|webm)|audio\/(?:mp3|oga|ogg|opus));base64,[\d+/a-z]+=*$/i,Xi=(t,e)=>{const i=t.nodeName.toLowerCase();if(e.includes(i))return!Ui.has(i)||Boolean(Vi.test(t.nodeValue)||Ki.test(t.nodeValue));const n=e.filter((t=>t instanceof RegExp));for(let t=0,e=n.length;t<e;t++)if(n[t].test(i))return!0;return!1};function Yi(t,e,i){if(!t.length)return t;if(i&&"function"==typeof i)return i(t);const n=(new window.DOMParser).parseFromString(t,"text/html"),s=[].concat(...n.body.querySelectorAll("*"));for(let t=0,i=s.length;t<i;t++){const i=s[t],n=i.nodeName.toLowerCase();if(!Object.keys(e).includes(n)){i.remove();continue}const o=[].concat(...i.attributes),r=[].concat(e["*"]||[],e[n]||[]);o.forEach((t=>{Xi(t,r)||i.removeAttribute(t.nodeName)}))}return n.body.innerHTML}const Qi="tooltip",Gi=new Set(["sanitize","allowList","sanitizeFn"]),Zi={animation:"boolean",template:"string",title:"(string|element|function)",trigger:"string",delay:"(number|object)",html:"boolean",selector:"(string|boolean)",placement:"(string|function)",offset:"(array|string|function)",container:"(string|element|boolean)",fallbackPlacements:"array",boundary:"(string|element)",customClass:"(string|function)",sanitize:"boolean",sanitizeFn:"(null|function)",allowList:"object",popperConfig:"(null|object|function)"},Ji={AUTO:"auto",TOP:"top",RIGHT:m()?"left":"right",BOTTOM:"bottom",LEFT:m()?"right":"left"},tn={animation:!0,template:'<div class="tooltip" role="tooltip"><div class="tooltip-arrow"></div><div class="tooltip-inner"></div></div>',trigger:"hover focus",title:"",delay:0,html:!1,selector:!1,placement:"top",offset:[0,0],container:!1,fallbackPlacements:["top","right","bottom","left"],boundary:"clippingParents",customClass:"",sanitize:!0,sanitizeFn:null,allowList:{"*":["class","dir","id","lang","role",/^aria-[\w-]*$/i],a:["target","href","title","rel"],area:[],b:[],br:[],col:[],code:[],div:[],em:[],hr:[],h1:[],h2:[],h3:[],h4:[],h5:[],h6:[],i:[],img:["src","srcset","alt","title","width","height"],li:[],ol:[],p:[],pre:[],s:[],small:[],span:[],sub:[],sup:[],strong:[],u:[],ul:[]},popperConfig:null},en={HIDE:"hide.bs.tooltip",HIDDEN:"hidden.bs.tooltip",SHOW:"show.bs.tooltip",SHOWN:"shown.bs.tooltip",INSERTED:"inserted.bs.tooltip",CLICK:"click.bs.tooltip",FOCUSIN:"focusin.bs.tooltip",FOCUSOUT:"focusout.bs.tooltip",MOUSEENTER:"mouseenter.bs.tooltip",MOUSELEAVE:"mouseleave.bs.tooltip"},nn="fade",sn="show",on="show",rn="out",an=".tooltip-inner",ln=".modal",cn="hide.bs.modal",hn="hover",dn="focus";class un extends B{constructor(t,e){if(void 0===Fe)throw new TypeError("Bootstrap's tooltips require Popper (https://popper.js.org)");super(t),this._isEnabled=!0,this._timeout=0,this._hoverState="",this._activeTrigger={},this._popper=null,this._config=this._getConfig(e),this.tip=null,this._setListeners()}static get Default(){return tn}static get NAME(){return Qi}static get Event(){return en}static get DefaultType(){return Zi}enable(){this._isEnabled=!0}disable(){this._isEnabled=!1}toggleEnabled(){this._isEnabled=!this._isEnabled}toggle(t){if(this._isEnabled)if(t){const e=this._initializeOnDelegatedTarget(t);e._activeTrigger.click=!e._activeTrigger.click,e._isWithActiveTrigger()?e._enter(null,e):e._leave(null,e)}else{if(this.getTipElement().classList.contains(sn))return void this._leave(null,this);this._enter(null,this)}}dispose(){clearTimeout(this._timeout),j.off(this._element.closest(ln),cn,this._hideModalHandler),this.tip&&this.tip.remove(),this._disposePopper(),super.dispose()}show(){if("none"===this._element.style.display)throw new Error("Please use show on visible elements");if(!this.isWithContent()||!this._isEnabled)return;const t=j.trigger(this._element,this.constructor.Event.SHOW),e=h(this._element),i=null===e?this._element.ownerDocument.documentElement.contains(this._element):e.contains(this._element);if(t.defaultPrevented||!i)return;"tooltip"===this.constructor.NAME&&this.tip&&this.getTitle()!==this.tip.querySelector(an).innerHTML&&(this._disposePopper(),this.tip.remove(),this.tip=null);const n=this.getTipElement(),s=(t=>{do{t+=Math.floor(1e6*Math.random())}while(document.getElementById(t));return t})(this.constructor.NAME);n.setAttribute("id",s),this._element.setAttribute("aria-describedby",s),this._config.animation&&n.classList.add(nn);const o="function"==typeof this._config.placement?this._config.placement.call(this,n,this._element):this._config.placement,r=this._getAttachment(o);this._addAttachmentClass(r);const{container:a}=this._config;H.set(n,this.constructor.DATA_KEY,this),this._element.ownerDocument.documentElement.contains(this.tip)||(a.append(n),j.trigger(this._element,this.constructor.Event.INSERTED)),this._popper?this._popper.update():this._popper=qe(this._element,n,this._getPopperConfig(r)),n.classList.add(sn);const l=this._resolvePossibleFunction(this._config.customClass);l&&n.classList.add(...l.split(" ")),"ontouchstart"in document.documentElement&&[].concat(...document.body.children).forEach((t=>{j.on(t,"mouseover",d)}));const c=this.tip.classList.contains(nn);this._queueCallback((()=>{const t=this._hoverState;this._hoverState=null,j.trigger(this._element,this.constructor.Event.SHOWN),t===rn&&this._leave(null,this)}),this.tip,c)}hide(){if(!this._popper)return;const t=this.getTipElement();if(j.trigger(this._element,this.constructor.Event.HIDE).defaultPrevented)return;t.classList.remove(sn),"ontouchstart"in document.documentElement&&[].concat(...document.body.children).forEach((t=>j.off(t,"mouseover",d))),this._activeTrigger.click=!1,this._activeTrigger.focus=!1,this._activeTrigger.hover=!1;const e=this.tip.classList.contains(nn);this._queueCallback((()=>{this._isWithActiveTrigger()||(this._hoverState!==on&&t.remove(),this._cleanTipClass(),this._element.removeAttribute("aria-describedby"),j.trigger(this._element,this.constructor.Event.HIDDEN),this._disposePopper())}),this.tip,e),this._hoverState=""}update(){null!==this._popper&&this._popper.update()}isWithContent(){return Boolean(this.getTitle())}getTipElement(){if(this.tip)return this.tip;const t=document.createElement("div");t.innerHTML=this._config.template;const e=t.children[0];return this.setContent(e),e.classList.remove(nn,sn),this.tip=e,this.tip}setContent(t){this._sanitizeAndSetContent(t,this.getTitle(),an)}_sanitizeAndSetContent(t,e,i){const n=V.findOne(i,t);e||!n?this.setElementContent(n,e):n.remove()}setElementContent(t,e){if(null!==t)return o(e)?(e=r(e),void(this._config.html?e.parentNode!==t&&(t.innerHTML="",t.append(e)):t.textContent=e.textContent)):void(this._config.html?(this._config.sanitize&&(e=Yi(e,this._config.allowList,this._config.sanitizeFn)),t.innerHTML=e):t.textContent=e)}getTitle(){const t=this._element.getAttribute("data-bs-original-title")||this._config.title;return this._resolvePossibleFunction(t)}updateAttachment(t){return"right"===t?"end":"left"===t?"start":t}_initializeOnDelegatedTarget(t,e){return e||this.constructor.getOrCreateInstance(t.delegateTarget,this._getDelegateConfig())}_getOffset(){const{offset:t}=this._config;return"string"==typeof t?t.split(",").map((t=>Number.parseInt(t,10))):"function"==typeof t?e=>t(e,this._element):t}_resolvePossibleFunction(t){return"function"==typeof t?t.call(this._element):t}_getPopperConfig(t){const e={placement:t,modifiers:[{name:"flip",options:{fallbackPlacements:this._config.fallbackPlacements}},{name:"offset",options:{offset:this._getOffset()}},{name:"preventOverflow",options:{boundary:this._config.boundary}},{name:"arrow",options:{element:`.${this.constructor.NAME}-arrow`}},{name:"onChange",enabled:!0,phase:"afterWrite",fn:t=>this._handlePopperPlacementChange(t)}],onFirstUpdate:t=>{t.options.placement!==t.placement&&this._handlePopperPlacementChange(t)}};return{...e,..."function"==typeof this._config.popperConfig?this._config.popperConfig(e):this._config.popperConfig}}_addAttachmentClass(t){this.getTipElement().classList.add(`${this._getBasicClassPrefix()}-${this.updateAttachment(t)}`)}_getAttachment(t){return Ji[t.toUpperCase()]}_setListeners(){this._config.trigger.split(" ").forEach((t=>{if("click"===t)j.on(this._element,this.constructor.Event.CLICK,this._config.selector,(t=>this.toggle(t)));else if("manual"!==t){const e=t===hn?this.constructor.Event.MOUSEENTER:this.constructor.Event.FOCUSIN,i=t===hn?this.constructor.Event.MOUSELEAVE:this.constructor.Event.FOCUSOUT;j.on(this._element,e,this._config.selector,(t=>this._enter(t))),j.on(this._element,i,this._config.selector,(t=>this._leave(t)))}})),this._hideModalHandler=()=>{this._element&&this.hide()},j.on(this._element.closest(ln),cn,this._hideModalHandler),this._config.selector?this._config={...this._config,trigger:"manual",selector:""}:this._fixTitle()}_fixTitle(){const t=this._element.getAttribute("title"),e=typeof this._element.getAttribute("data-bs-original-title");(t||"string"!==e)&&(this._element.setAttribute("data-bs-original-title",t||""),!t||this._element.getAttribute("aria-label")||this._element.textContent||this._element.setAttribute("aria-label",t),this._element.setAttribute("title",""))}_enter(t,e){e=this._initializeOnDelegatedTarget(t,e),t&&(e._activeTrigger["focusin"===t.type?dn:hn]=!0),e.getTipElement().classList.contains(sn)||e._hoverState===on?e._hoverState=on:(clearTimeout(e._timeout),e._hoverState=on,e._config.delay&&e._config.delay.show?e._timeout=setTimeout((()=>{e._hoverState===on&&e.show()}),e._config.delay.show):e.show())}_leave(t,e){e=this._initializeOnDelegatedTarget(t,e),t&&(e._activeTrigger["focusout"===t.type?dn:hn]=e._element.contains(t.relatedTarget)),e._isWithActiveTrigger()||(clearTimeout(e._timeout),e._hoverState=rn,e._config.delay&&e._config.delay.hide?e._timeout=setTimeout((()=>{e._hoverState===rn&&e.hide()}),e._config.delay.hide):e.hide())}_isWithActiveTrigger(){for(const 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diff --git a/docs/_site/site_libs/clipboard/clipboard.min.js b/docs/_site/site_libs/clipboard/clipboard.min.js
deleted file mode 100644
index 1103f81..0000000
--- a/docs/_site/site_libs/clipboard/clipboard.min.js
+++ /dev/null
@@ -1,7 +0,0 @@
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- */
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diff --git a/docs/_site/site_libs/quarto-html/anchor.min.js b/docs/_site/site_libs/quarto-html/anchor.min.js
deleted file mode 100644
index 1c2b86f..0000000
--- a/docs/_site/site_libs/quarto-html/anchor.min.js
+++ /dev/null
@@ -1,9 +0,0 @@
-// @license magnet:?xt=urn:btih:d3d9a9a6595521f9666a5e94cc830dab83b65699&dn=expat.txt Expat
-//
-// AnchorJS - v4.3.1 - 2021-04-17
-// https://www.bryanbraun.com/anchorjs/
-// Copyright (c) 2021 Bryan Braun; Licensed MIT
-//
-// @license magnet:?xt=urn:btih:d3d9a9a6595521f9666a5e94cc830dab83b65699&dn=expat.txt Expat
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-// @license-end
\ No newline at end of file
diff --git a/docs/_site/site_libs/quarto-html/popper.min.js b/docs/_site/site_libs/quarto-html/popper.min.js
deleted file mode 100644
index 2269d66..0000000
--- a/docs/_site/site_libs/quarto-html/popper.min.js
+++ /dev/null
@@ -1,6 +0,0 @@
-/**
- * @popperjs/core v2.11.4 - MIT License
- */
-
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diff --git a/docs/_site/site_libs/quarto-html/quarto-syntax-highlighting.css b/docs/_site/site_libs/quarto-html/quarto-syntax-highlighting.css
deleted file mode 100644
index d9fd98f..0000000
--- a/docs/_site/site_libs/quarto-html/quarto-syntax-highlighting.css
+++ /dev/null
@@ -1,203 +0,0 @@
-/* quarto syntax highlight colors */
-:root {
-  --quarto-hl-ot-color: #003B4F;
-  --quarto-hl-at-color: #657422;
-  --quarto-hl-ss-color: #20794D;
-  --quarto-hl-an-color: #5E5E5E;
-  --quarto-hl-fu-color: #4758AB;
-  --quarto-hl-st-color: #20794D;
-  --quarto-hl-cf-color: #003B4F;
-  --quarto-hl-op-color: #5E5E5E;
-  --quarto-hl-er-color: #AD0000;
-  --quarto-hl-bn-color: #AD0000;
-  --quarto-hl-al-color: #AD0000;
-  --quarto-hl-va-color: #111111;
-  --quarto-hl-bu-color: inherit;
-  --quarto-hl-ex-color: inherit;
-  --quarto-hl-pp-color: #AD0000;
-  --quarto-hl-in-color: #5E5E5E;
-  --quarto-hl-vs-color: #20794D;
-  --quarto-hl-wa-color: #5E5E5E;
-  --quarto-hl-do-color: #5E5E5E;
-  --quarto-hl-im-color: #00769E;
-  --quarto-hl-ch-color: #20794D;
-  --quarto-hl-dt-color: #AD0000;
-  --quarto-hl-fl-color: #AD0000;
-  --quarto-hl-co-color: #5E5E5E;
-  --quarto-hl-cv-color: #5E5E5E;
-  --quarto-hl-cn-color: #8f5902;
-  --quarto-hl-sc-color: #5E5E5E;
-  --quarto-hl-dv-color: #AD0000;
-  --quarto-hl-kw-color: #003B4F;
-}
-
-/* other quarto variables */
-:root {
-  --quarto-font-monospace: SFMono-Regular, Menlo, Monaco, Consolas, "Liberation Mono", "Courier New", monospace;
-}
-
-pre > code.sourceCode > span {
-  color: #003B4F;
-}
-
-code span {
-  color: #003B4F;
-}
-
-code.sourceCode > span {
-  color: #003B4F;
-}
-
-div.sourceCode,
-div.sourceCode pre.sourceCode {
-  color: #003B4F;
-}
-
-code span.ot {
-  color: #003B4F;
-  font-style: inherit;
-}
-
-code span.at {
-  color: #657422;
-  font-style: inherit;
-}
-
-code span.ss {
-  color: #20794D;
-  font-style: inherit;
-}
-
-code span.an {
-  color: #5E5E5E;
-  font-style: inherit;
-}
-
-code span.fu {
-  color: #4758AB;
-  font-style: inherit;
-}
-
-code span.st {
-  color: #20794D;
-  font-style: inherit;
-}
-
-code span.cf {
-  color: #003B4F;
-  font-style: inherit;
-}
-
-code span.op {
-  color: #5E5E5E;
-  font-style: inherit;
-}
-
-code span.er {
-  color: #AD0000;
-  font-style: inherit;
-}
-
-code span.bn {
-  color: #AD0000;
-  font-style: inherit;
-}
-
-code span.al {
-  color: #AD0000;
-  font-style: inherit;
-}
-
-code span.va {
-  color: #111111;
-  font-style: inherit;
-}
-
-code span.bu {
-  font-style: inherit;
-}
-
-code span.ex {
-  font-style: inherit;
-}
-
-code span.pp {
-  color: #AD0000;
-  font-style: inherit;
-}
-
-code span.in {
-  color: #5E5E5E;
-  font-style: inherit;
-}
-
-code span.vs {
-  color: #20794D;
-  font-style: inherit;
-}
-
-code span.wa {
-  color: #5E5E5E;
-  font-style: italic;
-}
-
-code span.do {
-  color: #5E5E5E;
-  font-style: italic;
-}
-
-code span.im {
-  color: #00769E;
-  font-style: inherit;
-}
-
-code span.ch {
-  color: #20794D;
-  font-style: inherit;
-}
-
-code span.dt {
-  color: #AD0000;
-  font-style: inherit;
-}
-
-code span.fl {
-  color: #AD0000;
-  font-style: inherit;
-}
-
-code span.co {
-  color: #5E5E5E;
-  font-style: inherit;
-}
-
-code span.cv {
-  color: #5E5E5E;
-  font-style: italic;
-}
-
-code span.cn {
-  color: #8f5902;
-  font-style: inherit;
-}
-
-code span.sc {
-  color: #5E5E5E;
-  font-style: inherit;
-}
-
-code span.dv {
-  color: #AD0000;
-  font-style: inherit;
-}
-
-code span.kw {
-  color: #003B4F;
-  font-style: inherit;
-}
-
-.prevent-inlining {
-  content: "</";
-}
-
-/*# sourceMappingURL=debc5d5d77c3f9108843748ff7464032.css.map */
diff --git a/docs/_site/site_libs/quarto-html/quarto.js b/docs/_site/site_libs/quarto-html/quarto.js
deleted file mode 100644
index c3935c7..0000000
--- a/docs/_site/site_libs/quarto-html/quarto.js
+++ /dev/null
@@ -1,902 +0,0 @@
-const sectionChanged = new CustomEvent("quarto-sectionChanged", {
-  detail: {},
-  bubbles: true,
-  cancelable: false,
-  composed: false,
-});
-
-const layoutMarginEls = () => {
-  // Find any conflicting margin elements and add margins to the
-  // top to prevent overlap
-  const marginChildren = window.document.querySelectorAll(
-    ".column-margin.column-container > * "
-  );
-
-  let lastBottom = 0;
-  for (const marginChild of marginChildren) {
-    if (marginChild.offsetParent !== null) {
-      // clear the top margin so we recompute it
-      marginChild.style.marginTop = null;
-      const top = marginChild.getBoundingClientRect().top + window.scrollY;
-      console.log({
-        childtop: marginChild.getBoundingClientRect().top,
-        scroll: window.scrollY,
-        top,
-        lastBottom,
-      });
-      if (top < lastBottom) {
-        const margin = lastBottom - top;
-        marginChild.style.marginTop = `${margin}px`;
-      }
-      const styles = window.getComputedStyle(marginChild);
-      const marginTop = parseFloat(styles["marginTop"]);
-
-      console.log({
-        top,
-        height: marginChild.getBoundingClientRect().height,
-        marginTop,
-        total: top + marginChild.getBoundingClientRect().height + marginTop,
-      });
-      lastBottom = top + marginChild.getBoundingClientRect().height + marginTop;
-    }
-  }
-};
-
-window.document.addEventListener("DOMContentLoaded", function (_event) {
-  // Recompute the position of margin elements anytime the body size changes
-  if (window.ResizeObserver) {
-    const resizeObserver = new window.ResizeObserver(
-      throttle(layoutMarginEls, 50)
-    );
-    resizeObserver.observe(window.document.body);
-  }
-
-  const tocEl = window.document.querySelector('nav.toc-active[role="doc-toc"]');
-  const sidebarEl = window.document.getElementById("quarto-sidebar");
-  const leftTocEl = window.document.getElementById("quarto-sidebar-toc-left");
-  const marginSidebarEl = window.document.getElementById(
-    "quarto-margin-sidebar"
-  );
-  // function to determine whether the element has a previous sibling that is active
-  const prevSiblingIsActiveLink = (el) => {
-    const sibling = el.previousElementSibling;
-    if (sibling && sibling.tagName === "A") {
-      return sibling.classList.contains("active");
-    } else {
-      return false;
-    }
-  };
-
-  // fire slideEnter for bootstrap tab activations (for htmlwidget resize behavior)
-  function fireSlideEnter(e) {
-    const event = window.document.createEvent("Event");
-    event.initEvent("slideenter", true, true);
-    window.document.dispatchEvent(event);
-  }
-  const tabs = window.document.querySelectorAll('a[data-bs-toggle="tab"]');
-  tabs.forEach((tab) => {
-    tab.addEventListener("shown.bs.tab", fireSlideEnter);
-  });
-
-  // fire slideEnter for tabby tab activations (for htmlwidget resize behavior)
-  document.addEventListener("tabby", fireSlideEnter, false);
-
-  // Track scrolling and mark TOC links as active
-  // get table of contents and sidebar (bail if we don't have at least one)
-  const tocLinks = tocEl
-    ? [...tocEl.querySelectorAll("a[data-scroll-target]")]
-    : [];
-  const makeActive = (link) => tocLinks[link].classList.add("active");
-  const removeActive = (link) => tocLinks[link].classList.remove("active");
-  const removeAllActive = () =>
-    [...Array(tocLinks.length).keys()].forEach((link) => removeActive(link));
-
-  // activate the anchor for a section associated with this TOC entry
-  tocLinks.forEach((link) => {
-    link.addEventListener("click", () => {
-      if (link.href.indexOf("#") !== -1) {
-        const anchor = link.href.split("#")[1];
-        const heading = window.document.querySelector(
-          `[data-anchor-id=${anchor}]`
-        );
-        if (heading) {
-          // Add the class
-          heading.classList.add("reveal-anchorjs-link");
-
-          // function to show the anchor
-          const handleMouseout = () => {
-            heading.classList.remove("reveal-anchorjs-link");
-            heading.removeEventListener("mouseout", handleMouseout);
-          };
-
-          // add a function to clear the anchor when the user mouses out of it
-          heading.addEventListener("mouseout", handleMouseout);
-        }
-      }
-    });
-  });
-
-  const sections = tocLinks.map((link) => {
-    const target = link.getAttribute("data-scroll-target");
-    if (target.startsWith("#")) {
-      return window.document.getElementById(decodeURI(`${target.slice(1)}`));
-    } else {
-      return window.document.querySelector(decodeURI(`${target}`));
-    }
-  });
-
-  const sectionMargin = 200;
-  let currentActive = 0;
-  // track whether we've initialized state the first time
-  let init = false;
-
-  const updateActiveLink = () => {
-    // The index from bottom to top (e.g. reversed list)
-    let sectionIndex = -1;
-    if (
-      window.innerHeight + window.pageYOffset >=
-      window.document.body.offsetHeight
-    ) {
-      sectionIndex = 0;
-    } else {
-      sectionIndex = [...sections].reverse().findIndex((section) => {
-        if (section) {
-          return window.pageYOffset >= section.offsetTop - sectionMargin;
-        } else {
-          return false;
-        }
-      });
-    }
-    if (sectionIndex > -1) {
-      const current = sections.length - sectionIndex - 1;
-      if (current !== currentActive) {
-        removeAllActive();
-        currentActive = current;
-        makeActive(current);
-        if (init) {
-          window.dispatchEvent(sectionChanged);
-        }
-        init = true;
-      }
-    }
-  };
-
-  const inHiddenRegion = (top, bottom, hiddenRegions) => {
-    for (const region of hiddenRegions) {
-      if (top <= region.bottom && bottom >= region.top) {
-        return true;
-      }
-    }
-    return false;
-  };
-
-  const categorySelector = "header.quarto-title-block .quarto-category";
-  const activateCategories = (href) => {
-    // Find any categories
-    // Surround them with a link pointing back to:
-    // #category=Authoring
-    try {
-      const categoryEls = window.document.querySelectorAll(categorySelector);
-      for (const categoryEl of categoryEls) {
-        const categoryText = categoryEl.textContent;
-        if (categoryText) {
-          const link = `${href}#category=${encodeURIComponent(categoryText)}`;
-          const linkEl = window.document.createElement("a");
-          linkEl.setAttribute("href", link);
-          for (const child of categoryEl.childNodes) {
-            linkEl.append(child);
-          }
-          categoryEl.appendChild(linkEl);
-        }
-      }
-    } catch {
-      // Ignore errors
-    }
-  };
-  function hasTitleCategories() {
-    return window.document.querySelector(categorySelector) !== null;
-  }
-
-  function offsetRelativeUrl(url) {
-    const offset = getMeta("quarto:offset");
-    return offset ? offset + url : url;
-  }
-
-  function offsetAbsoluteUrl(url) {
-    const offset = getMeta("quarto:offset");
-    const baseUrl = new URL(offset, window.location);
-
-    const projRelativeUrl = url.replace(baseUrl, "");
-    if (projRelativeUrl.startsWith("/")) {
-      return projRelativeUrl;
-    } else {
-      return "/" + projRelativeUrl;
-    }
-  }
-
-  // read a meta tag value
-  function getMeta(metaName) {
-    const metas = window.document.getElementsByTagName("meta");
-    for (let i = 0; i < metas.length; i++) {
-      if (metas[i].getAttribute("name") === metaName) {
-        return metas[i].getAttribute("content");
-      }
-    }
-    return "";
-  }
-
-  async function findAndActivateCategories() {
-    const currentPagePath = offsetAbsoluteUrl(window.location.href);
-    const response = await fetch(offsetRelativeUrl("listings.json"));
-    if (response.status == 200) {
-      return response.json().then(function (listingPaths) {
-        const listingHrefs = [];
-        for (const listingPath of listingPaths) {
-          const pathWithoutLeadingSlash = listingPath.listing.substring(1);
-          for (const item of listingPath.items) {
-            if (
-              item === currentPagePath ||
-              item === currentPagePath + "index.html"
-            ) {
-              // Resolve this path against the offset to be sure
-              // we already are using the correct path to the listing
-              // (this adjusts the listing urls to be rooted against
-              // whatever root the page is actually running against)
-              const relative = offsetRelativeUrl(pathWithoutLeadingSlash);
-              const baseUrl = window.location;
-              const resolvedPath = new URL(relative, baseUrl);
-              listingHrefs.push(resolvedPath.pathname);
-              break;
-            }
-          }
-        }
-
-        // Look up the tree for a nearby linting and use that if we find one
-        const nearestListing = findNearestParentListing(
-          offsetAbsoluteUrl(window.location.pathname),
-          listingHrefs
-        );
-        if (nearestListing) {
-          activateCategories(nearestListing);
-        } else {
-          // See if the referrer is a listing page for this item
-          const referredRelativePath = offsetAbsoluteUrl(document.referrer);
-          const referrerListing = listingHrefs.find((listingHref) => {
-            const isListingReferrer =
-              listingHref === referredRelativePath ||
-              listingHref === referredRelativePath + "index.html";
-            return isListingReferrer;
-          });
-
-          if (referrerListing) {
-            // Try to use the referrer if possible
-            activateCategories(referrerListing);
-          } else if (listingHrefs.length > 0) {
-            // Otherwise, just fall back to the first listing
-            activateCategories(listingHrefs[0]);
-          }
-        }
-      });
-    }
-  }
-  if (hasTitleCategories()) {
-    findAndActivateCategories();
-  }
-
-  const findNearestParentListing = (href, listingHrefs) => {
-    if (!href || !listingHrefs) {
-      return undefined;
-    }
-    // Look up the tree for a nearby linting and use that if we find one
-    const relativeParts = href.substring(1).split("/");
-    while (relativeParts.length > 0) {
-      const path = relativeParts.join("/");
-      for (const listingHref of listingHrefs) {
-        if (listingHref.startsWith(path)) {
-          return listingHref;
-        }
-      }
-      relativeParts.pop();
-    }
-
-    return undefined;
-  };
-
-  const manageSidebarVisiblity = (el, placeholderDescriptor) => {
-    let isVisible = true;
-    let elRect;
-
-    return (hiddenRegions) => {
-      if (el === null) {
-        return;
-      }
-
-      // Find the last element of the TOC
-      const lastChildEl = el.lastElementChild;
-
-      if (lastChildEl) {
-        // Converts the sidebar to a menu
-        const convertToMenu = () => {
-          for (const child of el.children) {
-            child.style.opacity = 0;
-            child.style.overflow = "hidden";
-          }
-
-          nexttick(() => {
-            const toggleContainer = window.document.createElement("div");
-            toggleContainer.style.width = "100%";
-            toggleContainer.classList.add("zindex-over-content");
-            toggleContainer.classList.add("quarto-sidebar-toggle");
-            toggleContainer.classList.add("headroom-target"); // Marks this to be managed by headeroom
-            toggleContainer.id = placeholderDescriptor.id;
-            toggleContainer.style.position = "fixed";
-
-            const toggleIcon = window.document.createElement("i");
-            toggleIcon.classList.add("quarto-sidebar-toggle-icon");
-            toggleIcon.classList.add("bi");
-            toggleIcon.classList.add("bi-caret-down-fill");
-
-            const toggleTitle = window.document.createElement("div");
-            const titleEl = window.document.body.querySelector(
-              placeholderDescriptor.titleSelector
-            );
-            if (titleEl) {
-              toggleTitle.append(
-                titleEl.textContent || titleEl.innerText,
-                toggleIcon
-              );
-            }
-            toggleTitle.classList.add("zindex-over-content");
-            toggleTitle.classList.add("quarto-sidebar-toggle-title");
-            toggleContainer.append(toggleTitle);
-
-            const toggleContents = window.document.createElement("div");
-            toggleContents.classList = el.classList;
-            toggleContents.classList.add("zindex-over-content");
-            toggleContents.classList.add("quarto-sidebar-toggle-contents");
-            for (const child of el.children) {
-              if (child.id === "toc-title") {
-                continue;
-              }
-
-              const clone = child.cloneNode(true);
-              clone.style.opacity = 1;
-              clone.style.display = null;
-              toggleContents.append(clone);
-            }
-            toggleContents.style.height = "0px";
-            const positionToggle = () => {
-              // position the element (top left of parent, same width as parent)
-              if (!elRect) {
-                elRect = el.getBoundingClientRect();
-              }
-              toggleContainer.style.left = `${elRect.left}px`;
-              toggleContainer.style.top = `${elRect.top}px`;
-              toggleContainer.style.width = `${elRect.width}px`;
-            };
-            positionToggle();
-
-            toggleContainer.append(toggleContents);
-            el.parentElement.prepend(toggleContainer);
-
-            // Process clicks
-            let tocShowing = false;
-            // Allow the caller to control whether this is dismissed
-            // when it is clicked (e.g. sidebar navigation supports
-            // opening and closing the nav tree, so don't dismiss on click)
-            const clickEl = placeholderDescriptor.dismissOnClick
-              ? toggleContainer
-              : toggleTitle;
-
-            const closeToggle = () => {
-              if (tocShowing) {
-                toggleContainer.classList.remove("expanded");
-                toggleContents.style.height = "0px";
-                tocShowing = false;
-              }
-            };
-
-            // Get rid of any expanded toggle if the user scrolls
-            window.document.addEventListener(
-              "scroll",
-              throttle(() => {
-                closeToggle();
-              }, 50)
-            );
-
-            // Handle positioning of the toggle
-            window.addEventListener(
-              "resize",
-              throttle(() => {
-                elRect = undefined;
-                positionToggle();
-              }, 50)
-            );
-
-            window.addEventListener("quarto-hrChanged", () => {
-              elRect = undefined;
-            });
-
-            // Process the click
-            clickEl.onclick = () => {
-              if (!tocShowing) {
-                toggleContainer.classList.add("expanded");
-                toggleContents.style.height = null;
-                tocShowing = true;
-              } else {
-                closeToggle();
-              }
-            };
-          });
-        };
-
-        // Converts a sidebar from a menu back to a sidebar
-        const convertToSidebar = () => {
-          for (const child of el.children) {
-            child.style.opacity = 1;
-            child.style.overflow = null;
-          }
-
-          const placeholderEl = window.document.getElementById(
-            placeholderDescriptor.id
-          );
-          if (placeholderEl) {
-            placeholderEl.remove();
-          }
-
-          el.classList.remove("rollup");
-        };
-
-        if (isReaderMode()) {
-          convertToMenu();
-          isVisible = false;
-        } else {
-          // Find the top and bottom o the element that is being managed
-          const elTop = el.offsetTop;
-          const elBottom =
-            elTop + lastChildEl.offsetTop + lastChildEl.offsetHeight;
-
-          if (!isVisible) {
-            // If the element is current not visible reveal if there are
-            // no conflicts with overlay regions
-            if (!inHiddenRegion(elTop, elBottom, hiddenRegions)) {
-              convertToSidebar();
-              isVisible = true;
-            }
-          } else {
-            // If the element is visible, hide it if it conflicts with overlay regions
-            // and insert a placeholder toggle (or if we're in reader mode)
-            if (inHiddenRegion(elTop, elBottom, hiddenRegions)) {
-              convertToMenu();
-              isVisible = false;
-            }
-          }
-        }
-      }
-    };
-  };
-
-  const tabEls = document.querySelectorAll('a[data-bs-toggle="tab"]');
-  for (const tabEl of tabEls) {
-    const id = tabEl.getAttribute("data-bs-target");
-    if (id) {
-      const columnEl = document.querySelector(
-        `${id} .column-margin, .tabset-margin-content`
-      );
-      if (columnEl)
-        tabEl.addEventListener("shown.bs.tab", function (event) {
-          const el = event.srcElement;
-          if (el) {
-            const visibleCls = `${el.id}-margin-content`;
-            // walk up until we find a parent tabset
-            let panelTabsetEl = el.parentElement;
-            while (panelTabsetEl) {
-              if (panelTabsetEl.classList.contains("panel-tabset")) {
-                break;
-              }
-              panelTabsetEl = panelTabsetEl.parentElement;
-            }
-
-            if (panelTabsetEl) {
-              const prevSib = panelTabsetEl.previousElementSibling;
-              if (
-                prevSib &&
-                prevSib.classList.contains("tabset-margin-container")
-              ) {
-                const childNodes = prevSib.querySelectorAll(
-                  ".tabset-margin-content"
-                );
-                for (const childEl of childNodes) {
-                  if (childEl.classList.contains(visibleCls)) {
-                    childEl.classList.remove("collapse");
-                  } else {
-                    childEl.classList.add("collapse");
-                  }
-                }
-              }
-            }
-          }
-
-          layoutMarginEls();
-        });
-    }
-  }
-
-  // Manage the visibility of the toc and the sidebar
-  const marginScrollVisibility = manageSidebarVisiblity(marginSidebarEl, {
-    id: "quarto-toc-toggle",
-    titleSelector: "#toc-title",
-    dismissOnClick: true,
-  });
-  const sidebarScrollVisiblity = manageSidebarVisiblity(sidebarEl, {
-    id: "quarto-sidebarnav-toggle",
-    titleSelector: ".title",
-    dismissOnClick: false,
-  });
-  let tocLeftScrollVisibility;
-  if (leftTocEl) {
-    tocLeftScrollVisibility = manageSidebarVisiblity(leftTocEl, {
-      id: "quarto-lefttoc-toggle",
-      titleSelector: "#toc-title",
-      dismissOnClick: true,
-    });
-  }
-
-  // Find the first element that uses formatting in special columns
-  const conflictingEls = window.document.body.querySelectorAll(
-    '[class^="column-"], [class*=" column-"], aside, [class*="margin-caption"], [class*=" margin-caption"], [class*="margin-ref"], [class*=" margin-ref"]'
-  );
-
-  // Filter all the possibly conflicting elements into ones
-  // the do conflict on the left or ride side
-  const arrConflictingEls = Array.from(conflictingEls);
-  const leftSideConflictEls = arrConflictingEls.filter((el) => {
-    if (el.tagName === "ASIDE") {
-      return false;
-    }
-    return Array.from(el.classList).find((className) => {
-      return (
-        className !== "column-body" &&
-        className.startsWith("column-") &&
-        !className.endsWith("right") &&
-        !className.endsWith("container") &&
-        className !== "column-margin"
-      );
-    });
-  });
-  const rightSideConflictEls = arrConflictingEls.filter((el) => {
-    if (el.tagName === "ASIDE") {
-      return true;
-    }
-
-    const hasMarginCaption = Array.from(el.classList).find((className) => {
-      return className == "margin-caption";
-    });
-    if (hasMarginCaption) {
-      return true;
-    }
-
-    return Array.from(el.classList).find((className) => {
-      return (
-        className !== "column-body" &&
-        !className.endsWith("container") &&
-        className.startsWith("column-") &&
-        !className.endsWith("left")
-      );
-    });
-  });
-
-  const kOverlapPaddingSize = 10;
-  function toRegions(els) {
-    return els.map((el) => {
-      const boundRect = el.getBoundingClientRect();
-      const top =
-        boundRect.top +
-        document.documentElement.scrollTop -
-        kOverlapPaddingSize;
-      return {
-        top,
-        bottom: top + el.scrollHeight + 2 * kOverlapPaddingSize,
-      };
-    });
-  }
-
-  let hasObserved = false;
-  const visibleItemObserver = (els) => {
-    let visibleElements = [...els];
-    const intersectionObserver = new IntersectionObserver(
-      (entries, _observer) => {
-        entries.forEach((entry) => {
-          if (entry.isIntersecting) {
-            if (visibleElements.indexOf(entry.target) === -1) {
-              visibleElements.push(entry.target);
-            }
-          } else {
-            visibleElements = visibleElements.filter((visibleEntry) => {
-              return visibleEntry !== entry;
-            });
-          }
-        });
-
-        if (!hasObserved) {
-          hideOverlappedSidebars();
-        }
-        hasObserved = true;
-      },
-      {}
-    );
-    els.forEach((el) => {
-      intersectionObserver.observe(el);
-    });
-
-    return {
-      getVisibleEntries: () => {
-        return visibleElements;
-      },
-    };
-  };
-
-  const rightElementObserver = visibleItemObserver(rightSideConflictEls);
-  const leftElementObserver = visibleItemObserver(leftSideConflictEls);
-
-  const hideOverlappedSidebars = () => {
-    marginScrollVisibility(toRegions(rightElementObserver.getVisibleEntries()));
-    sidebarScrollVisiblity(toRegions(leftElementObserver.getVisibleEntries()));
-    if (tocLeftScrollVisibility) {
-      tocLeftScrollVisibility(
-        toRegions(leftElementObserver.getVisibleEntries())
-      );
-    }
-  };
-
-  window.quartoToggleReader = () => {
-    // Applies a slow class (or removes it)
-    // to update the transition speed
-    const slowTransition = (slow) => {
-      const manageTransition = (id, slow) => {
-        const el = document.getElementById(id);
-        if (el) {
-          if (slow) {
-            el.classList.add("slow");
-          } else {
-            el.classList.remove("slow");
-          }
-        }
-      };
-
-      manageTransition("TOC", slow);
-      manageTransition("quarto-sidebar", slow);
-    };
-    const readerMode = !isReaderMode();
-    setReaderModeValue(readerMode);
-
-    // If we're entering reader mode, slow the transition
-    if (readerMode) {
-      slowTransition(readerMode);
-    }
-    highlightReaderToggle(readerMode);
-    hideOverlappedSidebars();
-
-    // If we're exiting reader mode, restore the non-slow transition
-    if (!readerMode) {
-      slowTransition(!readerMode);
-    }
-  };
-
-  const highlightReaderToggle = (readerMode) => {
-    const els = document.querySelectorAll(".quarto-reader-toggle");
-    if (els) {
-      els.forEach((el) => {
-        if (readerMode) {
-          el.classList.add("reader");
-        } else {
-          el.classList.remove("reader");
-        }
-      });
-    }
-  };
-
-  const setReaderModeValue = (val) => {
-    if (window.location.protocol !== "file:") {
-      window.localStorage.setItem("quarto-reader-mode", val);
-    } else {
-      localReaderMode = val;
-    }
-  };
-
-  const isReaderMode = () => {
-    if (window.location.protocol !== "file:") {
-      return window.localStorage.getItem("quarto-reader-mode") === "true";
-    } else {
-      return localReaderMode;
-    }
-  };
-  let localReaderMode = null;
-
-  const tocOpenDepthStr = tocEl?.getAttribute("data-toc-expanded");
-  const tocOpenDepth = tocOpenDepthStr ? Number(tocOpenDepthStr) : 1;
-
-  // Walk the TOC and collapse/expand nodes
-  // Nodes are expanded if:
-  // - they are top level
-  // - they have children that are 'active' links
-  // - they are directly below an link that is 'active'
-  const walk = (el, depth) => {
-    // Tick depth when we enter a UL
-    if (el.tagName === "UL") {
-      depth = depth + 1;
-    }
-
-    // It this is active link
-    let isActiveNode = false;
-    if (el.tagName === "A" && el.classList.contains("active")) {
-      isActiveNode = true;
-    }
-
-    // See if there is an active child to this element
-    let hasActiveChild = false;
-    for (child of el.children) {
-      hasActiveChild = walk(child, depth) || hasActiveChild;
-    }
-
-    // Process the collapse state if this is an UL
-    if (el.tagName === "UL") {
-      if (tocOpenDepth === -1 && depth > 1) {
-        el.classList.add("collapse");
-      } else if (
-        depth <= tocOpenDepth ||
-        hasActiveChild ||
-        prevSiblingIsActiveLink(el)
-      ) {
-        el.classList.remove("collapse");
-      } else {
-        el.classList.add("collapse");
-      }
-
-      // untick depth when we leave a UL
-      depth = depth - 1;
-    }
-    return hasActiveChild || isActiveNode;
-  };
-
-  // walk the TOC and expand / collapse any items that should be shown
-
-  if (tocEl) {
-    walk(tocEl, 0);
-    updateActiveLink();
-  }
-
-  // Throttle the scroll event and walk peridiocally
-  window.document.addEventListener(
-    "scroll",
-    throttle(() => {
-      if (tocEl) {
-        updateActiveLink();
-        walk(tocEl, 0);
-      }
-      if (!isReaderMode()) {
-        hideOverlappedSidebars();
-      }
-    }, 5)
-  );
-  window.addEventListener(
-    "resize",
-    throttle(() => {
-      if (!isReaderMode()) {
-        hideOverlappedSidebars();
-      }
-    }, 10)
-  );
-  hideOverlappedSidebars();
-  highlightReaderToggle(isReaderMode());
-});
-
-// grouped tabsets
-window.addEventListener("pageshow", (_event) => {
-  function getTabSettings() {
-    const data = localStorage.getItem("quarto-persistent-tabsets-data");
-    if (!data) {
-      localStorage.setItem("quarto-persistent-tabsets-data", "{}");
-      return {};
-    }
-    if (data) {
-      return JSON.parse(data);
-    }
-  }
-
-  function setTabSettings(data) {
-    localStorage.setItem(
-      "quarto-persistent-tabsets-data",
-      JSON.stringify(data)
-    );
-  }
-
-  function setTabState(groupName, groupValue) {
-    const data = getTabSettings();
-    data[groupName] = groupValue;
-    setTabSettings(data);
-  }
-
-  function toggleTab(tab, active) {
-    const tabPanelId = tab.getAttribute("aria-controls");
-    const tabPanel = document.getElementById(tabPanelId);
-    if (active) {
-      tab.classList.add("active");
-      tabPanel.classList.add("active");
-    } else {
-      tab.classList.remove("active");
-      tabPanel.classList.remove("active");
-    }
-  }
-
-  function toggleAll(selectedGroup, selectorsToSync) {
-    for (const [thisGroup, tabs] of Object.entries(selectorsToSync)) {
-      const active = selectedGroup === thisGroup;
-      for (const tab of tabs) {
-        toggleTab(tab, active);
-      }
-    }
-  }
-
-  function findSelectorsToSyncByLanguage() {
-    const result = {};
-    const tabs = Array.from(
-      document.querySelectorAll(`div[data-group] a[id^='tabset-']`)
-    );
-    for (const item of tabs) {
-      const div = item.parentElement.parentElement.parentElement;
-      const group = div.getAttribute("data-group");
-      if (!result[group]) {
-        result[group] = {};
-      }
-      const selectorsToSync = result[group];
-      const value = item.innerHTML;
-      if (!selectorsToSync[value]) {
-        selectorsToSync[value] = [];
-      }
-      selectorsToSync[value].push(item);
-    }
-    return result;
-  }
-
-  function setupSelectorSync() {
-    const selectorsToSync = findSelectorsToSyncByLanguage();
-    Object.entries(selectorsToSync).forEach(([group, tabSetsByValue]) => {
-      Object.entries(tabSetsByValue).forEach(([value, items]) => {
-        items.forEach((item) => {
-          item.addEventListener("click", (_event) => {
-            setTabState(group, value);
-            toggleAll(value, selectorsToSync[group]);
-          });
-        });
-      });
-    });
-    return selectorsToSync;
-  }
-
-  const selectorsToSync = setupSelectorSync();
-  for (const [group, selectedName] of Object.entries(getTabSettings())) {
-    const selectors = selectorsToSync[group];
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deleted file mode 100644
index e6ae635..0000000
--- a/docs/_site/site_libs/quarto-html/tippy.css
+++ /dev/null
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diff --git a/docs/_site/site_libs/quarto-html/tippy.umd.min.js b/docs/_site/site_libs/quarto-html/tippy.umd.min.js
deleted file mode 100644
index ca292be..0000000
--- a/docs/_site/site_libs/quarto-html/tippy.umd.min.js
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G={name:"inlinePositioning",defaultValue:!1,fn:function(e){var t,n=e.reference;var r=-1,o=!1,i=[],a={name:"tippyInlinePositioning",enabled:!0,phase:"afterWrite",fn:function(o){var a=o.state;e.props.inlinePositioning&&(-1!==i.indexOf(a.placement)&&(i=[]),t!==a.placement&&-1===i.indexOf(a.placement)&&(i.push(a.placement),e.setProps({getReferenceClientRect:function(){return function(e){return function(e,t,n,r){if(n.length<2||null===e)return t;if(2===n.length&&r>=0&&n[0].left>n[1].right)return n[r]||t;switch(e){case"top":case"bottom":var o=n[0],i=n[n.length-1],a="top"===e,s=o.top,u=i.bottom,c=a?o.left:i.left,p=a?o.right:i.right;return{top:s,bottom:u,left:c,right:p,width:p-c,height:u-s};case"left":case"right":var f=Math.min.apply(Math,n.map((function(e){return e.left}))),l=Math.max.apply(Math,n.map((function(e){return e.right}))),d=n.filter((function(t){return"left"===e?t.left===f:t.right===l})),v=d[0].top,m=d[d.length-1].bottom;return{top:v,bottom:m,left:f,right:l,width:l-f,height:m-v};default:return t}}(p(e),n.getBoundingClientRect(),f(n.getClientRects()),r)}(a.placement)}})),t=a.placement)}};function s(){var t;o||(t=function(e,t){var n;return{popperOptions:Object.assign({},e.popperOptions,{modifiers:[].concat(((null==(n=e.popperOptions)?void 0:n.modifiers)||[]).filter((function(e){return e.name!==t.name})),[t])})}}(e.props,a),o=!0,e.setProps(t),o=!1)}return{onCreate:s,onAfterUpdate:s,onTrigger:function(t,n){if(m(n)){var o=f(e.reference.getClientRects()),i=o.find((function(e){return e.left-2<=n.clientX&&e.right+2>=n.clientX&&e.top-2<=n.clientY&&e.bottom+2>=n.clientY})),a=o.indexOf(i);r=a>-1?a:r}},onHidden:function(){r=-1}}}};var K={name:"sticky",defaultValue:!1,fn:function(e){var t=e.reference,n=e.popper;function r(t){return!0===e.props.sticky||e.props.sticky===t}var o=null,i=null;function a(){var 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h(y,t)}return i.indexOf(e)>=0?h(y,e):void 0}},y.showNext=function(){var e=i[0];if(!r)return y.show(0);var t=i.indexOf(r);y.show(i[t+1]||e)},y.showPrevious=function(){var e=i[i.length-1];if(!r)return y.show(e);var t=i.indexOf(r),n=i[t-1]||e;y.show(n)};var E=y.setProps;return y.setProps=function(e){c=e.overrides||c,E(e)},y.setInstances=function(e){m(!0),p.forEach((function(e){return e()})),o=e,m(!1),v(),l(),p=g(y),y.setProps({triggerTarget:a})},p=g(y),y},F.delegate=function(e,n){var r=[],o=[],i=!1,a=n.target,c=s(n,["target"]),p=Object.assign({},c,{trigger:"manual",touch:!1}),f=Object.assign({touch:R.touch},c,{showOnCreate:!0}),l=F(e,p);function d(e){if(e.target&&!i){var t=e.target.closest(a);if(t){var r=t.getAttribute("data-tippy-trigger")||n.trigger||R.trigger;if(!t._tippy&&!("touchstart"===e.type&&"boolean"==typeof f.touch||"touchstart"!==e.type&&r.indexOf(X[e.type])<0)){var s=F(t,f);s&&(o=o.concat(s))}}}}function v(e,t,n,o){void 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-
diff --git a/docs/_site/site_libs/quarto-nav/headroom.min.js b/docs/_site/site_libs/quarto-nav/headroom.min.js
deleted file mode 100644
index b08f1df..0000000
--- a/docs/_site/site_libs/quarto-nav/headroom.min.js
+++ /dev/null
@@ -1,7 +0,0 @@
-/*!
- * headroom.js v0.12.0 - Give your page some headroom. Hide your header until you need it
- * Copyright (c) 2020 Nick Williams - http://wicky.nillia.ms/headroom.js
- * License: MIT
- */
-
-!function(t,n){"object"==typeof exports&&"undefined"!=typeof module?module.exports=n():"function"==typeof define&&define.amd?define(n):(t=t||self).Headroom=n()}(this,function(){"use strict";function t(){return"undefined"!=typeof window}function d(t){return function(t){return t&&t.document&&function(t){return 9===t.nodeType}(t.document)}(t)?function(t){var n=t.document,o=n.body,s=n.documentElement;return{scrollHeight:function(){return Math.max(o.scrollHeight,s.scrollHeight,o.offsetHeight,s.offsetHeight,o.clientHeight,s.clientHeight)},height:function(){return t.innerHeight||s.clientHeight||o.clientHeight},scrollY:function(){return void 0!==t.pageYOffset?t.pageYOffset:(s||o.parentNode||o).scrollTop}}}(t):function(t){return{scrollHeight:function(){return Math.max(t.scrollHeight,t.offsetHeight,t.clientHeight)},height:function(){return Math.max(t.offsetHeight,t.clientHeight)},scrollY:function(){return t.scrollTop}}}(t)}function n(t,s,e){var n,o=function(){var n=!1;try{var t={get passive(){n=!0}};window.addEventListener("test",t,t),window.removeEventListener("test",t,t)}catch(t){n=!1}return n}(),i=!1,r=d(t),l=r.scrollY(),a={};function c(){var t=Math.round(r.scrollY()),n=r.height(),o=r.scrollHeight();a.scrollY=t,a.lastScrollY=l,a.direction=l<t?"down":"up",a.distance=Math.abs(t-l),a.isOutOfBounds=t<0||o<t+n,a.top=t<=s.offset[a.direction],a.bottom=o<=t+n,a.toleranceExceeded=a.distance>s.tolerance[a.direction],e(a),l=t,i=!1}function h(){i||(i=!0,n=requestAnimationFrame(c))}var u=!!o&&{passive:!0,capture:!1};return t.addEventListener("scroll",h,u),c(),{destroy:function(){cancelAnimationFrame(n),t.removeEventListener("scroll",h,u)}}}function o(t){return t===Object(t)?t:{down:t,up:t}}function s(t,n){n=n||{},Object.assign(this,s.options,n),this.classes=Object.assign({},s.options.classes,n.classes),this.elem=t,this.tolerance=o(this.tolerance),this.offset=o(this.offset),this.initialised=!1,this.frozen=!1}return s.prototype={constructor:s,init:function(){return s.cutsTheMustard&&!this.initialised&&(this.addClass("initial"),this.initialised=!0,setTimeout(function(t){t.scrollTracker=n(t.scroller,{offset:t.offset,tolerance:t.tolerance},t.update.bind(t))},100,this)),this},destroy:function(){this.initialised=!1,Object.keys(this.classes).forEach(this.removeClass,this),this.scrollTracker.destroy()},unpin:function(){!this.hasClass("pinned")&&this.hasClass("unpinned")||(this.addClass("unpinned"),this.removeClass("pinned"),this.onUnpin&&this.onUnpin.call(this))},pin:function(){this.hasClass("unpinned")&&(this.addClass("pinned"),this.removeClass("unpinned"),this.onPin&&this.onPin.call(this))},freeze:function(){this.frozen=!0,this.addClass("frozen")},unfreeze:function(){this.frozen=!1,this.removeClass("frozen")},top:function(){this.hasClass("top")||(this.addClass("top"),this.removeClass("notTop"),this.onTop&&this.onTop.call(this))},notTop:function(){this.hasClass("notTop")||(this.addClass("notTop"),this.removeClass("top"),this.onNotTop&&this.onNotTop.call(this))},bottom:function(){this.hasClass("bottom")||(this.addClass("bottom"),this.removeClass("notBottom"),this.onBottom&&this.onBottom.call(this))},notBottom:function(){this.hasClass("notBottom")||(this.addClass("notBottom"),this.removeClass("bottom"),this.onNotBottom&&this.onNotBottom.call(this))},shouldUnpin:function(t){return"down"===t.direction&&!t.top&&t.toleranceExceeded},shouldPin:function(t){return"up"===t.direction&&t.toleranceExceeded||t.top},addClass:function(t){this.elem.classList.add.apply(this.elem.classList,this.classes[t].split(" "))},removeClass:function(t){this.elem.classList.remove.apply(this.elem.classList,this.classes[t].split(" "))},hasClass:function(t){return this.classes[t].split(" ").every(function(t){return this.classList.contains(t)},this.elem)},update:function(t){t.isOutOfBounds||!0!==this.frozen&&(t.top?this.top():this.notTop(),t.bottom?this.bottom():this.notBottom(),this.shouldUnpin(t)?this.unpin():this.shouldPin(t)&&this.pin())}},s.options={tolerance:{up:0,down:0},offset:0,scroller:t()?window:null,classes:{frozen:"headroom--frozen",pinned:"headroom--pinned",unpinned:"headroom--unpinned",top:"headroom--top",notTop:"headroom--not-top",bottom:"headroom--bottom",notBottom:"headroom--not-bottom",initial:"headroom"}},s.cutsTheMustard=!!(t()&&function(){}.bind&&"classList"in document.documentElement&&Object.assign&&Object.keys&&requestAnimationFrame),s});
diff --git a/docs/_site/site_libs/quarto-nav/quarto-nav.js b/docs/_site/site_libs/quarto-nav/quarto-nav.js
deleted file mode 100644
index 3b21201..0000000
--- a/docs/_site/site_libs/quarto-nav/quarto-nav.js
+++ /dev/null
@@ -1,277 +0,0 @@
-const headroomChanged = new CustomEvent("quarto-hrChanged", {
-  detail: {},
-  bubbles: true,
-  cancelable: false,
-  composed: false,
-});
-
-window.document.addEventListener("DOMContentLoaded", function () {
-  let init = false;
-
-  // Manage the back to top button, if one is present.
-  let lastScrollTop = window.pageYOffset || document.documentElement.scrollTop;
-  const scrollDownBuffer = 5;
-  const scrollUpBuffer = 35;
-  const btn = document.getElementById("quarto-back-to-top");
-  const hideBackToTop = () => {
-    btn.style.display = "none";
-  };
-  const showBackToTop = () => {
-    btn.style.display = "inline-block";
-  };
-  if (btn) {
-    window.document.addEventListener(
-      "scroll",
-      function () {
-        const currentScrollTop =
-          window.pageYOffset || document.documentElement.scrollTop;
-
-        // Shows and hides the button 'intelligently' as the user scrolls
-        if (currentScrollTop - scrollDownBuffer > lastScrollTop) {
-          hideBackToTop();
-          lastScrollTop = currentScrollTop <= 0 ? 0 : currentScrollTop;
-        } else if (currentScrollTop < lastScrollTop - scrollUpBuffer) {
-          showBackToTop();
-          lastScrollTop = currentScrollTop <= 0 ? 0 : currentScrollTop;
-        }
-
-        // Show the button at the bottom, hides it at the top
-        if (currentScrollTop <= 0) {
-          hideBackToTop();
-        } else if (
-          window.innerHeight + currentScrollTop >=
-          document.body.offsetHeight
-        ) {
-          showBackToTop();
-        }
-      },
-      false
-    );
-  }
-
-  function throttle(func, wait) {
-    var timeout;
-    return function () {
-      const context = this;
-      const args = arguments;
-      const later = function () {
-        clearTimeout(timeout);
-        timeout = null;
-        func.apply(context, args);
-      };
-
-      if (!timeout) {
-        timeout = setTimeout(later, wait);
-      }
-    };
-  }
-
-  function headerOffset() {
-    // Set an offset if there is are fixed top navbar
-    const headerEl = window.document.querySelector("header.fixed-top");
-    if (headerEl) {
-      return headerEl.clientHeight;
-    } else {
-      return 0;
-    }
-  }
-
-  function footerOffset() {
-    const footerEl = window.document.querySelector("footer.footer");
-    if (footerEl) {
-      return footerEl.clientHeight;
-    } else {
-      return 0;
-    }
-  }
-
-  function updateDocumentOffsetWithoutAnimation() {
-    updateDocumentOffset(false);
-  }
-
-  function updateDocumentOffset(animated) {
-    // set body offset
-    const topOffset = headerOffset();
-    const bodyOffset = topOffset + footerOffset();
-    const bodyEl = window.document.body;
-    bodyEl.setAttribute("data-bs-offset", topOffset);
-    bodyEl.style.paddingTop = topOffset + "px";
-
-    // deal with sidebar offsets
-    const sidebars = window.document.querySelectorAll(
-      ".sidebar, .headroom-target"
-    );
-    sidebars.forEach((sidebar) => {
-      if (!animated) {
-        sidebar.classList.add("notransition");
-        // Remove the no transition class after the animation has time to complete
-        setTimeout(function () {
-          sidebar.classList.remove("notransition");
-        }, 201);
-      }
-
-      if (window.Headroom && sidebar.classList.contains("sidebar-unpinned")) {
-        sidebar.style.top = "0";
-        sidebar.style.maxHeight = "100vh";
-      } else {
-        sidebar.style.top = topOffset + "px";
-        sidebar.style.maxHeight = "calc(100vh - " + topOffset + "px)";
-      }
-    });
-
-    // allow space for footer
-    const mainContainer = window.document.querySelector(".quarto-container");
-    if (mainContainer) {
-      mainContainer.style.minHeight = "calc(100vh - " + bodyOffset + "px)";
-    }
-
-    // link offset
-    let linkStyle = window.document.querySelector("#quarto-target-style");
-    if (!linkStyle) {
-      linkStyle = window.document.createElement("style");
-      linkStyle.setAttribute("id", "quarto-target-style");
-      window.document.head.appendChild(linkStyle);
-    }
-    while (linkStyle.firstChild) {
-      linkStyle.removeChild(linkStyle.firstChild);
-    }
-    if (topOffset > 0) {
-      linkStyle.appendChild(
-        window.document.createTextNode(`
-      section:target::before {
-        content: "";
-        display: block;
-        height: ${topOffset}px;
-        margin: -${topOffset}px 0 0;
-      }`)
-      );
-    }
-    if (init) {
-      window.dispatchEvent(headroomChanged);
-    }
-    init = true;
-  }
-
-  // initialize headroom
-  var header = window.document.querySelector("#quarto-header");
-  if (header && window.Headroom) {
-    const headroom = new window.Headroom(header, {
-      tolerance: 5,
-      onPin: function () {
-        const sidebars = window.document.querySelectorAll(
-          ".sidebar, .headroom-target"
-        );
-        sidebars.forEach((sidebar) => {
-          sidebar.classList.remove("sidebar-unpinned");
-        });
-        updateDocumentOffset();
-      },
-      onUnpin: function () {
-        const sidebars = window.document.querySelectorAll(
-          ".sidebar, .headroom-target"
-        );
-        sidebars.forEach((sidebar) => {
-          sidebar.classList.add("sidebar-unpinned");
-        });
-        updateDocumentOffset();
-      },
-    });
-    headroom.init();
-
-    let frozen = false;
-    window.quartoToggleHeadroom = function () {
-      if (frozen) {
-        headroom.unfreeze();
-        frozen = false;
-      } else {
-        headroom.freeze();
-        frozen = true;
-      }
-    };
-  }
-
-  window.addEventListener(
-    "hashchange",
-    function (e) {
-      if (
-        getComputedStyle(document.documentElement).scrollBehavior !== "smooth"
-      ) {
-        window.scrollTo(0, window.pageYOffset - headerOffset());
-      }
-    },
-    false
-  );
-
-  // Observe size changed for the header
-  const headerEl = window.document.querySelector("header.fixed-top");
-  if (headerEl && window.ResizeObserver) {
-    const observer = new window.ResizeObserver(
-      updateDocumentOffsetWithoutAnimation
-    );
-    observer.observe(headerEl, {
-      attributes: true,
-      childList: true,
-      characterData: true,
-    });
-  } else {
-    window.addEventListener(
-      "resize",
-      throttle(updateDocumentOffsetWithoutAnimation, 50)
-    );
-  }
-  setTimeout(updateDocumentOffsetWithoutAnimation, 250);
-
-  // fixup index.html links if we aren't on the filesystem
-  if (window.location.protocol !== "file:") {
-    const links = window.document.querySelectorAll("a");
-    for (let i = 0; i < links.length; i++) {
-      if (links[i].href) {
-        links[i].href = links[i].href.replace(/\/index\.html/, "/");
-      }
-    }
-
-    // Fixup any sharing links that require urls
-    // Append url to any sharing urls
-    const sharingLinks = window.document.querySelectorAll(
-      "a.sidebar-tools-main-item"
-    );
-    for (let i = 0; i < sharingLinks.length; i++) {
-      const sharingLink = sharingLinks[i];
-      const href = sharingLink.getAttribute("href");
-      if (href) {
-        sharingLink.setAttribute(
-          "href",
-          href.replace("|url|", window.location.href)
-        );
-      }
-    }
-
-    // Scroll the active navigation item into view, if necessary
-    const navSidebar = window.document.querySelector("nav#quarto-sidebar");
-    if (navSidebar) {
-      // Find the active item
-      const activeItem = navSidebar.querySelector("li.sidebar-item a.active");
-      if (activeItem) {
-        // Wait for the scroll height and height to resolve by observing size changes on the
-        // nav element that is scrollable
-        const resizeObserver = new ResizeObserver((_entries) => {
-          // The bottom of the element
-          const elBottom = activeItem.offsetTop;
-          const viewBottom = navSidebar.scrollTop + navSidebar.clientHeight;
-
-          // The element height and scroll height are the same, then we are still loading
-          if (viewBottom !== navSidebar.scrollHeight) {
-            // Determine if the item isn't visible and scroll to it
-            if (elBottom >= viewBottom) {
-              navSidebar.scrollTop = elBottom;
-            }
-
-            // stop observing now since we've completed the scroll
-            resizeObserver.unobserve(navSidebar);
-          }
-        });
-        resizeObserver.observe(navSidebar);
-      }
-    }
-  }
-});
diff --git a/docs/_site/site_libs/quarto-search/autocomplete.umd.js b/docs/_site/site_libs/quarto-search/autocomplete.umd.js
deleted file mode 100644
index 619c57c..0000000
--- a/docs/_site/site_libs/quarto-search/autocomplete.umd.js
+++ /dev/null
@@ -1,3 +0,0 @@
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diff --git a/docs/_site/site_libs/quarto-search/fuse.min.js b/docs/_site/site_libs/quarto-search/fuse.min.js
deleted file mode 100644
index adc2835..0000000
--- a/docs/_site/site_libs/quarto-search/fuse.min.js
+++ /dev/null
@@ -1,9 +0,0 @@
-/**
- * Fuse.js v6.6.2 - Lightweight fuzzy-search (http://fusejs.io)
- *
- * Copyright (c) 2022 Kiro Risk (http://kiro.me)
- * All Rights Reserved. Apache Software License 2.0
- *
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ve(e,t){t.score=e.score}function ge(e,t){var n=arguments.length>2&&void 0!==arguments[2]?arguments[2]:{},r=n.includeMatches,i=void 0===r?I.includeMatches:r,o=n.includeScore,c=void 0===o?I.includeScore:o,a=[];return i&&a.push(de),c&&a.push(ve),e.map((function(e){var n=e.idx,r={item:t[n],refIndex:n};return a.length&&a.forEach((function(t){t(e,r)})),r}))}var ye=function(){function e(n){var i=arguments.length>1&&void 0!==arguments[1]?arguments[1]:{},o=arguments.length>2?arguments[2]:void 0;r(this,e),this.options=t(t({},I),i),this.options.useExtendedSearch,this._keyStore=new S(this.options.keys),this.setCollection(n,o)}return o(e,[{key:"setCollection",value:function(e,t){if(this._docs=e,t&&!(t instanceof $))throw new Error("Incorrect 'index' type");this._myIndex=t||F(this.options.keys,this._docs,{getFn:this.options.getFn,fieldNormWeight:this.options.fieldNormWeight})}},{key:"add",value:function(e){k(e)&&(this._docs.push(e),this._myIndex.add(e))}},{key:"remove",value:function(){for(var e=arguments.length>0&&void 0!==arguments[0]?arguments[0]:function(){return!1},t=[],n=0,r=this._docs.length;n<r;n+=1){var i=this._docs[n];e(i,n)&&(this.removeAt(n),n-=1,r-=1,t.push(i))}return t}},{key:"removeAt",value:function(e){this._docs.splice(e,1),this._myIndex.removeAt(e)}},{key:"getIndex",value:function(){return this._myIndex}},{key:"search",value:function(e){var t=arguments.length>1&&void 0!==arguments[1]?arguments[1]:{},n=t.limit,r=void 0===n?-1:n,i=this.options,o=i.includeMatches,c=i.includeScore,a=i.shouldSort,s=i.sortFn,u=i.ignoreFieldNorm,h=g(e)?g(this._docs[0])?this._searchStringList(e):this._searchObjectList(e):this._searchLogical(e);return fe(h,{ignoreFieldNorm:u}),a&&h.sort(s),y(r)&&r>-1&&(h=h.slice(0,r)),ge(h,this._docs,{includeMatches:o,includeScore:c})}},{key:"_searchStringList",value:function(e){var t=re(e,this.options),n=this._myIndex.records,r=[];return n.forEach((function(e){var n=e.v,i=e.i,o=e.n;if(k(n)){var c=t.searchIn(n),a=c.isMatch,s=c.score,u=c.indices;a&&r.push({item:n,idx:i,matches:[{score:s,value:n,norm:o,indices:u}]})}})),r}},{key:"_searchLogical",value:function(e){var t=this,n=function(e,t){var n=(arguments.length>2&&void 0!==arguments[2]?arguments[2]:{}).auto,r=void 0===n||n,i=function e(n){var i=Object.keys(n),o=ue(n);if(!o&&i.length>1&&!se(n))return e(le(n));if(he(n)){var c=o?n[ce]:i[0],a=o?n[ae]:n[c];if(!g(a))throw new Error(x(c));var s={keyId:j(c),pattern:a};return r&&(s.searcher=re(a,t)),s}var u={children:[],operator:i[0]};return i.forEach((function(t){var r=n[t];v(r)&&r.forEach((function(t){u.children.push(e(t))}))})),u};return se(e)||(e=le(e)),i(e)}(e,this.options),r=function e(n,r,i){if(!n.children){var o=n.keyId,c=n.searcher,a=t._findMatches({key:t._keyStore.get(o),value:t._myIndex.getValueForItemAtKeyId(r,o),searcher:c});return a&&a.length?[{idx:i,item:r,matches:a}]:[]}for(var s=[],u=0,h=n.children.length;u<h;u+=1){var l=e(n.children[u],r,i);if(l.length)s.push.apply(s,f(l));else if(n.operator===ie)return[]}return s},i=this._myIndex.records,o={},c=[];return i.forEach((function(e){var t=e.$,i=e.i;if(k(t)){var a=r(n,t,i);a.length&&(o[i]||(o[i]={idx:i,item:t,matches:[]},c.push(o[i])),a.forEach((function(e){var t,n=e.matches;(t=o[i].matches).push.apply(t,f(n))})))}})),c}},{key:"_searchObjectList",value:function(e){var t=this,n=re(e,this.options),r=this._myIndex,i=r.keys,o=r.records,c=[];return o.forEach((function(e){var r=e.$,o=e.i;if(k(r)){var a=[];i.forEach((function(e,i){a.push.apply(a,f(t._findMatches({key:e,value:r[i],searcher:n})))})),a.length&&c.push({idx:o,item:r,matches:a})}})),c}},{key:"_findMatches",value:function(e){var t=e.key,n=e.value,r=e.searcher;if(!k(n))return[];var i=[];if(v(n))n.forEach((function(e){var n=e.v,o=e.i,c=e.n;if(k(n)){var a=r.searchIn(n),s=a.isMatch,u=a.score,h=a.indices;s&&i.push({score:u,key:t,value:n,idx:o,norm:c,indices:h})}}));else{var o=n.v,c=n.n,a=r.searchIn(o),s=a.isMatch,u=a.score,h=a.indices;s&&i.push({score:u,key:t,value:o,norm:c,indices:h})}return i}}]),e}();return ye.version="6.6.2",ye.createIndex=F,ye.parseIndex=function(e){var t=arguments.length>1&&void 0!==arguments[1]?arguments[1]:{},n=t.getFn,r=void 0===n?I.getFn:n,i=t.fieldNormWeight,o=void 0===i?I.fieldNormWeight:i,c=e.keys,a=e.records,s=new $({getFn:r,fieldNormWeight:o});return s.setKeys(c),s.setIndexRecords(a),s},ye.config=I,function(){ne.push.apply(ne,arguments)}(te),ye},"object"==typeof exports&&"undefined"!=typeof module?module.exports=t():"function"==typeof define&&define.amd?define(t):(e="undefined"!=typeof globalThis?globalThis:e||self).Fuse=t();
\ No newline at end of file
diff --git a/docs/_site/site_libs/quarto-search/quarto-search.js b/docs/_site/site_libs/quarto-search/quarto-search.js
deleted file mode 100644
index f5d852d..0000000
--- a/docs/_site/site_libs/quarto-search/quarto-search.js
+++ /dev/null
@@ -1,1140 +0,0 @@
-const kQueryArg = "q";
-const kResultsArg = "show-results";
-
-// If items don't provide a URL, then both the navigator and the onSelect
-// function aren't called (and therefore, the default implementation is used)
-//
-// We're using this sentinel URL to signal to those handlers that this
-// item is a more item (along with the type) and can be handled appropriately
-const kItemTypeMoreHref = "0767FDFD-0422-4E5A-BC8A-3BE11E5BBA05";
-
-window.document.addEventListener("DOMContentLoaded", function (_event) {
-  // Ensure that search is available on this page. If it isn't,
-  // should return early and not do anything
-  var searchEl = window.document.getElementById("quarto-search");
-  if (!searchEl) return;
-
-  const { autocomplete } = window["@algolia/autocomplete-js"];
-
-  let quartoSearchOptions = {};
-  let language = {};
-  const searchOptionEl = window.document.getElementById(
-    "quarto-search-options"
-  );
-  if (searchOptionEl) {
-    const jsonStr = searchOptionEl.textContent;
-    quartoSearchOptions = JSON.parse(jsonStr);
-    language = quartoSearchOptions.language;
-  }
-
-  // note the search mode
-  if (quartoSearchOptions.type === "overlay") {
-    searchEl.classList.add("type-overlay");
-  } else {
-    searchEl.classList.add("type-textbox");
-  }
-
-  // Used to determine highlighting behavior for this page
-  // A `q` query param is expected when the user follows a search
-  // to this page
-  const currentUrl = new URL(window.location);
-  const query = currentUrl.searchParams.get(kQueryArg);
-  const showSearchResults = currentUrl.searchParams.get(kResultsArg);
-  const mainEl = window.document.querySelector("main");
-
-  // highlight matches on the page
-  if (query !== null && mainEl) {
-    // perform any highlighting
-    highlight(escapeRegExp(query), mainEl);
-
-    // fix up the URL to remove the q query param
-    const replacementUrl = new URL(window.location);
-    replacementUrl.searchParams.delete(kQueryArg);
-    window.history.replaceState({}, "", replacementUrl);
-  }
-
-  // function to clear highlighting on the page when the search query changes
-  // (e.g. if the user edits the query or clears it)
-  let highlighting = true;
-  const resetHighlighting = (searchTerm) => {
-    if (mainEl && highlighting && query !== null && searchTerm !== query) {
-      clearHighlight(query, mainEl);
-      highlighting = false;
-    }
-  };
-
-  // Clear search highlighting when the user scrolls sufficiently
-  const resetFn = () => {
-    resetHighlighting("");
-    window.removeEventListener("quarto-hrChanged", resetFn);
-    window.removeEventListener("quarto-sectionChanged", resetFn);
-  };
-
-  // Register this event after the initial scrolling and settling of events
-  // on the page
-  window.addEventListener("quarto-hrChanged", resetFn);
-  window.addEventListener("quarto-sectionChanged", resetFn);
-
-  // Responsively switch to overlay mode if the search is present on the navbar
-  // Note that switching the sidebar to overlay mode requires more coordinate (not just
-  // the media query since we generate different HTML for sidebar overlays than we do
-  // for sidebar input UI)
-  const detachedMediaQuery =
-    quartoSearchOptions.type === "overlay" ? "all" : "(max-width: 991px)";
-
-  // If configured, include the analytics client to send insights
-  const plugins = configurePlugins(quartoSearchOptions);
-
-  let lastState = null;
-  const { setIsOpen, setQuery, setCollections } = autocomplete({
-    container: searchEl,
-    detachedMediaQuery: detachedMediaQuery,
-    defaultActiveItemId: 0,
-    panelContainer: "#quarto-search-results",
-    panelPlacement: quartoSearchOptions["panel-placement"],
-    debug: false,
-    openOnFocus: true,
-    plugins,
-    classNames: {
-      form: "d-flex",
-    },
-    translations: {
-      clearButtonTitle: language["search-clear-button-title"],
-      detachedCancelButtonText: language["search-detached-cancel-button-title"],
-      submitButtonTitle: language["search-submit-button-title"],
-    },
-    initialState: {
-      query,
-    },
-    getItemUrl({ item }) {
-      return item.href;
-    },
-    onStateChange({ state }) {
-      // Perhaps reset highlighting
-      resetHighlighting(state.query);
-
-      // If the panel just opened, ensure the panel is positioned properly
-      if (state.isOpen) {
-        if (lastState && !lastState.isOpen) {
-          setTimeout(() => {
-            positionPanel(quartoSearchOptions["panel-placement"]);
-          }, 150);
-        }
-      }
-
-      // Perhaps show the copy link
-      showCopyLink(state.query, quartoSearchOptions);
-
-      lastState = state;
-    },
-    reshape({ sources, state }) {
-      return sources.map((source) => {
-        try {
-          const items = source.getItems();
-
-          // Validate the items
-          validateItems(items);
-
-          // group the items by document
-          const groupedItems = new Map();
-          items.forEach((item) => {
-            const hrefParts = item.href.split("#");
-            const baseHref = hrefParts[0];
-            const isDocumentItem = hrefParts.length === 1;
-
-            const items = groupedItems.get(baseHref);
-            if (!items) {
-              groupedItems.set(baseHref, [item]);
-            } else {
-              // If the href for this item matches the document
-              // exactly, place this item first as it is the item that represents
-              // the document itself
-              if (isDocumentItem) {
-                items.unshift(item);
-              } else {
-                items.push(item);
-              }
-              groupedItems.set(baseHref, items);
-            }
-          });
-
-          const reshapedItems = [];
-          let count = 1;
-          for (const [_key, value] of groupedItems) {
-            const firstItem = value[0];
-            reshapedItems.push({
-              ...firstItem,
-              type: kItemTypeDoc,
-            });
-
-            const collapseMatches = quartoSearchOptions["collapse-after"];
-            const collapseCount =
-              typeof collapseMatches === "number" ? collapseMatches : 1;
-
-            if (value.length > 1) {
-              const target = `search-more-${count}`;
-              const isExpanded =
-                state.context.expanded &&
-                state.context.expanded.includes(target);
-
-              const remainingCount = value.length - collapseCount;
-
-              for (let i = 1; i < value.length; i++) {
-                if (collapseMatches && i === collapseCount) {
-                  reshapedItems.push({
-                    target,
-                    title: isExpanded
-                      ? language["search-hide-matches-text"]
-                      : remainingCount === 1
-                      ? `${remainingCount} ${language["search-more-match-text"]}`
-                      : `${remainingCount} ${language["search-more-matches-text"]}`,
-                    type: kItemTypeMore,
-                    href: kItemTypeMoreHref,
-                  });
-                }
-
-                if (isExpanded || !collapseMatches || i < collapseCount) {
-                  reshapedItems.push({
-                    ...value[i],
-                    type: kItemTypeItem,
-                    target,
-                  });
-                }
-              }
-            }
-            count += 1;
-          }
-
-          return {
-            ...source,
-            getItems() {
-              return reshapedItems;
-            },
-          };
-        } catch (error) {
-          // Some form of error occurred
-          return {
-            ...source,
-            getItems() {
-              return [
-                {
-                  title: error.name || "An Error Occurred While Searching",
-                  text:
-                    error.message ||
-                    "An unknown error occurred while attempting to perform the requested search.",
-                  type: kItemTypeError,
-                },
-              ];
-            },
-          };
-        }
-      });
-    },
-    navigator: {
-      navigate({ itemUrl }) {
-        if (itemUrl !== offsetURL(kItemTypeMoreHref)) {
-          window.location.assign(itemUrl);
-        }
-      },
-      navigateNewTab({ itemUrl }) {
-        if (itemUrl !== offsetURL(kItemTypeMoreHref)) {
-          const windowReference = window.open(itemUrl, "_blank", "noopener");
-          if (windowReference) {
-            windowReference.focus();
-          }
-        }
-      },
-      navigateNewWindow({ itemUrl }) {
-        if (itemUrl !== offsetURL(kItemTypeMoreHref)) {
-          window.open(itemUrl, "_blank", "noopener");
-        }
-      },
-    },
-    getSources({ state, setContext, setActiveItemId, refresh }) {
-      return [
-        {
-          sourceId: "documents",
-          getItemUrl({ item }) {
-            if (item.href) {
-              return offsetURL(item.href);
-            } else {
-              return undefined;
-            }
-          },
-          onSelect({
-            item,
-            state,
-            setContext,
-            setIsOpen,
-            setActiveItemId,
-            refresh,
-          }) {
-            if (item.type === kItemTypeMore) {
-              toggleExpanded(item, state, setContext, setActiveItemId, refresh);
-
-              // Toggle more
-              setIsOpen(true);
-            }
-          },
-          getItems({ query }) {
-            if (query === null || query === "") {
-              return [];
-            }
-
-            const limit = quartoSearchOptions.limit;
-            if (quartoSearchOptions.algolia) {
-              return algoliaSearch(query, limit, quartoSearchOptions.algolia);
-            } else {
-              // Fuse search options
-              const fuseSearchOptions = {
-                isCaseSensitive: false,
-                shouldSort: true,
-                minMatchCharLength: 2,
-                limit: limit,
-              };
-
-              return readSearchData().then(function (fuse) {
-                return fuseSearch(query, fuse, fuseSearchOptions);
-              });
-            }
-          },
-          templates: {
-            noResults({ createElement }) {
-              const hasQuery = lastState.query;
-
-              return createElement(
-                "div",
-                {
-                  class: `quarto-search-no-results${
-                    hasQuery ? "" : " no-query"
-                  }`,
-                },
-                language["search-no-results-text"]
-              );
-            },
-            header({ items, createElement }) {
-              // count the documents
-              const count = items.filter((item) => {
-                return item.type === kItemTypeDoc;
-              }).length;
-
-              if (count > 0) {
-                return createElement(
-                  "div",
-                  { class: "search-result-header" },
-                  `${count} ${language["search-matching-documents-text"]}`
-                );
-              } else {
-                return createElement(
-                  "div",
-                  { class: "search-result-header-no-results" },
-                  ``
-                );
-              }
-            },
-            footer({ _items, createElement }) {
-              if (
-                quartoSearchOptions.algolia &&
-                quartoSearchOptions.algolia["show-logo"]
-              ) {
-                const libDir = quartoSearchOptions.algolia["libDir"];
-                const logo = createElement("img", {
-                  src: offsetURL(
-                    `${libDir}/quarto-search/search-by-algolia.svg`
-                  ),
-                  class: "algolia-search-logo",
-                });
-                return createElement(
-                  "a",
-                  { href: "http://www.algolia.com/" },
-                  logo
-                );
-              }
-            },
-
-            item({ item, createElement }) {
-              return renderItem(
-                item,
-                createElement,
-                state,
-                setActiveItemId,
-                setContext,
-                refresh
-              );
-            },
-          },
-        },
-      ];
-    },
-  });
-
-  window.quartoOpenSearch = () => {
-    setIsOpen(false);
-    setIsOpen(true);
-    focusSearchInput();
-  };
-
-  // Remove the labeleledby attribute since it is pointing
-  // to a non-existent label
-  if (quartoSearchOptions.type === "overlay") {
-    const inputEl = window.document.querySelector(
-      "#quarto-search .aa-Autocomplete"
-    );
-    if (inputEl) {
-      inputEl.removeAttribute("aria-labelledby");
-    }
-  }
-
-  // If the main document scrolls dismiss the search results
-  // (otherwise, since they're floating in the document they can scroll with the document)
-  window.document.body.onscroll = () => {
-    setIsOpen(false);
-  };
-
-  if (showSearchResults) {
-    setIsOpen(true);
-    focusSearchInput();
-  }
-});
-
-function configurePlugins(quartoSearchOptions) {
-  const autocompletePlugins = [];
-  const algoliaOptions = quartoSearchOptions.algolia;
-  if (
-    algoliaOptions &&
-    algoliaOptions["analytics-events"] &&
-    algoliaOptions["search-only-api-key"] &&
-    algoliaOptions["application-id"]
-  ) {
-    const apiKey = algoliaOptions["search-only-api-key"];
-    const appId = algoliaOptions["application-id"];
-
-    // Aloglia insights may not be loaded because they require cookie consent
-    // Use deferred loading so events will start being recorded when/if consent
-    // is granted.
-    const algoliaInsightsDeferredPlugin = deferredLoadPlugin(() => {
-      if (
-        window.aa &&
-        window["@algolia/autocomplete-plugin-algolia-insights"]
-      ) {
-        window.aa("init", {
-          appId,
-          apiKey,
-          useCookie: true,
-        });
-
-        const { createAlgoliaInsightsPlugin } =
-          window["@algolia/autocomplete-plugin-algolia-insights"];
-        // Register the insights client
-        const algoliaInsightsPlugin = createAlgoliaInsightsPlugin({
-          insightsClient: window.aa,
-          onItemsChange({ insights, insightsEvents }) {
-            const events = insightsEvents.map((event) => {
-              const maxEvents = event.objectIDs.slice(0, 20);
-              return {
-                ...event,
-                objectIDs: maxEvents,
-              };
-            });
-
-            insights.viewedObjectIDs(...events);
-          },
-        });
-        return algoliaInsightsPlugin;
-      }
-    });
-
-    // Add the plugin
-    autocompletePlugins.push(algoliaInsightsDeferredPlugin);
-    return autocompletePlugins;
-  }
-}
-
-// For plugins that may not load immediately, create a wrapper
-// plugin and forward events and plugin data once the plugin
-// is initialized. This is useful for cases like cookie consent
-// which may prevent the analytics insights event plugin from initializing
-// immediately.
-function deferredLoadPlugin(createPlugin) {
-  let plugin = undefined;
-  let subscribeObj = undefined;
-  const wrappedPlugin = () => {
-    if (!plugin && subscribeObj) {
-      plugin = createPlugin();
-      if (plugin && plugin.subscribe) {
-        plugin.subscribe(subscribeObj);
-      }
-    }
-    return plugin;
-  };
-
-  return {
-    subscribe: (obj) => {
-      subscribeObj = obj;
-    },
-    onStateChange: (obj) => {
-      const plugin = wrappedPlugin();
-      if (plugin && plugin.onStateChange) {
-        plugin.onStateChange(obj);
-      }
-    },
-    onSubmit: (obj) => {
-      const plugin = wrappedPlugin();
-      if (plugin && plugin.onSubmit) {
-        plugin.onSubmit(obj);
-      }
-    },
-    onReset: (obj) => {
-      const plugin = wrappedPlugin();
-      if (plugin && plugin.onReset) {
-        plugin.onReset(obj);
-      }
-    },
-    getSources: (obj) => {
-      const plugin = wrappedPlugin();
-      if (plugin && plugin.getSources) {
-        return plugin.getSources(obj);
-      } else {
-        return Promise.resolve([]);
-      }
-    },
-    data: (obj) => {
-      const plugin = wrappedPlugin();
-      if (plugin && plugin.data) {
-        plugin.data(obj);
-      }
-    },
-  };
-}
-
-function validateItems(items) {
-  // Validate the first item
-  if (items.length > 0) {
-    const item = items[0];
-    const missingFields = [];
-    if (item.href == undefined) {
-      missingFields.push("href");
-    }
-    if (!item.title == undefined) {
-      missingFields.push("title");
-    }
-    if (!item.text == undefined) {
-      missingFields.push("text");
-    }
-
-    if (missingFields.length === 1) {
-      throw {
-        name: `Error: Search index is missing the <code>${missingFields[0]}</code> field.`,
-        message: `The items being returned for this search do not include all the required fields. Please ensure that your index items include the <code>${missingFields[0]}</code> field or use <code>index-fields</code> in your <code>_quarto.yml</code> file to specify the field names.`,
-      };
-    } else if (missingFields.length > 1) {
-      const missingFieldList = missingFields
-        .map((field) => {
-          return `<code>${field}</code>`;
-        })
-        .join(", ");
-
-      throw {
-        name: `Error: Search index is missing the following fields: ${missingFieldList}.`,
-        message: `The items being returned for this search do not include all the required fields. Please ensure that your index items includes the following fields: ${missingFieldList}, or use <code>index-fields</code> in your <code>_quarto.yml</code> file to specify the field names.`,
-      };
-    }
-  }
-}
-
-let lastQuery = null;
-function showCopyLink(query, options) {
-  const language = options.language;
-  lastQuery = query;
-  // Insert share icon
-  const inputSuffixEl = window.document.body.querySelector(
-    ".aa-Form .aa-InputWrapperSuffix"
-  );
-
-  if (inputSuffixEl) {
-    let copyButtonEl = window.document.body.querySelector(
-      ".aa-Form .aa-InputWrapperSuffix .aa-CopyButton"
-    );
-
-    if (copyButtonEl === null) {
-      copyButtonEl = window.document.createElement("button");
-      copyButtonEl.setAttribute("class", "aa-CopyButton");
-      copyButtonEl.setAttribute("type", "button");
-      copyButtonEl.setAttribute("title", language["search-copy-link-title"]);
-      copyButtonEl.onmousedown = (e) => {
-        e.preventDefault();
-        e.stopPropagation();
-      };
-
-      const linkIcon = "bi-clipboard";
-      const checkIcon = "bi-check2";
-
-      const shareIconEl = window.document.createElement("i");
-      shareIconEl.setAttribute("class", `bi ${linkIcon}`);
-      copyButtonEl.appendChild(shareIconEl);
-      inputSuffixEl.prepend(copyButtonEl);
-
-      const clipboard = new window.ClipboardJS(".aa-CopyButton", {
-        text: function (_trigger) {
-          const copyUrl = new URL(window.location);
-          copyUrl.searchParams.set(kQueryArg, lastQuery);
-          copyUrl.searchParams.set(kResultsArg, "1");
-          return copyUrl.toString();
-        },
-      });
-      clipboard.on("success", function (e) {
-        // Focus the input
-
-        // button target
-        const button = e.trigger;
-        const icon = button.querySelector("i.bi");
-
-        // flash "checked"
-        icon.classList.add(checkIcon);
-        icon.classList.remove(linkIcon);
-        setTimeout(function () {
-          icon.classList.remove(checkIcon);
-          icon.classList.add(linkIcon);
-        }, 1000);
-      });
-    }
-
-    // If there is a query, show the link icon
-    if (copyButtonEl) {
-      if (lastQuery && options["copy-button"]) {
-        copyButtonEl.style.display = "flex";
-      } else {
-        copyButtonEl.style.display = "none";
-      }
-    }
-  }
-}
-
-/* Search Index Handling */
-// create the index
-var fuseIndex = undefined;
-async function readSearchData() {
-  // Initialize the search index on demand
-  if (fuseIndex === undefined) {
-    // create fuse index
-    const options = {
-      keys: [
-        { name: "title", weight: 20 },
-        { name: "section", weight: 20 },
-        { name: "text", weight: 10 },
-      ],
-      ignoreLocation: true,
-      threshold: 0.1,
-    };
-    const fuse = new window.Fuse([], options);
-
-    // fetch the main search.json
-    const response = await fetch(offsetURL("search.json"));
-    if (response.status == 200) {
-      return response.json().then(function (searchDocs) {
-        searchDocs.forEach(function (searchDoc) {
-          fuse.add(searchDoc);
-        });
-        fuseIndex = fuse;
-        return fuseIndex;
-      });
-    } else {
-      return Promise.reject(
-        new Error(
-          "Unexpected status from search index request: " + response.status
-        )
-      );
-    }
-  }
-  return fuseIndex;
-}
-
-function inputElement() {
-  return window.document.body.querySelector(".aa-Form .aa-Input");
-}
-
-function focusSearchInput() {
-  setTimeout(() => {
-    const inputEl = inputElement();
-    if (inputEl) {
-      inputEl.focus();
-    }
-  }, 50);
-}
-
-/* Panels */
-const kItemTypeDoc = "document";
-const kItemTypeMore = "document-more";
-const kItemTypeItem = "document-item";
-const kItemTypeError = "error";
-
-function renderItem(
-  item,
-  createElement,
-  state,
-  setActiveItemId,
-  setContext,
-  refresh
-) {
-  switch (item.type) {
-    case kItemTypeDoc:
-      return createDocumentCard(
-        createElement,
-        "file-richtext",
-        item.title,
-        item.section,
-        item.text,
-        item.href
-      );
-    case kItemTypeMore:
-      return createMoreCard(
-        createElement,
-        item,
-        state,
-        setActiveItemId,
-        setContext,
-        refresh
-      );
-    case kItemTypeItem:
-      return createSectionCard(
-        createElement,
-        item.section,
-        item.text,
-        item.href
-      );
-    case kItemTypeError:
-      return createErrorCard(createElement, item.title, item.text);
-    default:
-      return undefined;
-  }
-}
-
-function createDocumentCard(createElement, icon, title, section, text, href) {
-  const iconEl = createElement("i", {
-    class: `bi bi-${icon} search-result-icon`,
-  });
-  const titleEl = createElement("p", { class: "search-result-title" }, title);
-  const titleContainerEl = createElement(
-    "div",
-    { class: "search-result-title-container" },
-    [iconEl, titleEl]
-  );
-
-  const textEls = [];
-  if (section) {
-    const sectionEl = createElement(
-      "p",
-      { class: "search-result-section" },
-      section
-    );
-    textEls.push(sectionEl);
-  }
-  const descEl = createElement("p", {
-    class: "search-result-text",
-    dangerouslySetInnerHTML: {
-      __html: text,
-    },
-  });
-  textEls.push(descEl);
-
-  const textContainerEl = createElement(
-    "div",
-    { class: "search-result-text-container" },
-    textEls
-  );
-
-  const containerEl = createElement(
-    "div",
-    {
-      class: "search-result-container",
-    },
-    [titleContainerEl, textContainerEl]
-  );
-
-  const linkEl = createElement(
-    "a",
-    {
-      href: offsetURL(href),
-      class: "search-result-link",
-    },
-    containerEl
-  );
-
-  const classes = ["search-result-doc", "search-item"];
-  if (!section) {
-    classes.push("document-selectable");
-  }
-
-  return createElement(
-    "div",
-    {
-      class: classes.join(" "),
-    },
-    linkEl
-  );
-}
-
-function createMoreCard(
-  createElement,
-  item,
-  state,
-  setActiveItemId,
-  setContext,
-  refresh
-) {
-  const moreCardEl = createElement(
-    "div",
-    {
-      class: "search-result-more search-item",
-      onClick: (e) => {
-        // Handle expanding the sections by adding the expanded
-        // section to the list of expanded sections
-        toggleExpanded(item, state, setContext, setActiveItemId, refresh);
-        e.stopPropagation();
-      },
-    },
-    item.title
-  );
-
-  return moreCardEl;
-}
-
-function toggleExpanded(item, state, setContext, setActiveItemId, refresh) {
-  const expanded = state.context.expanded || [];
-  if (expanded.includes(item.target)) {
-    setContext({
-      expanded: expanded.filter((target) => target !== item.target),
-    });
-  } else {
-    setContext({ expanded: [...expanded, item.target] });
-  }
-
-  refresh();
-  setActiveItemId(item.__autocomplete_id);
-}
-
-function createSectionCard(createElement, section, text, href) {
-  const sectionEl = createSection(createElement, section, text, href);
-  return createElement(
-    "div",
-    {
-      class: "search-result-doc-section search-item",
-    },
-    sectionEl
-  );
-}
-
-function createSection(createElement, title, text, href) {
-  const descEl = createElement("p", {
-    class: "search-result-text",
-    dangerouslySetInnerHTML: {
-      __html: text,
-    },
-  });
-
-  const titleEl = createElement("p", { class: "search-result-section" }, title);
-  const linkEl = createElement(
-    "a",
-    {
-      href: offsetURL(href),
-      class: "search-result-link",
-    },
-    [titleEl, descEl]
-  );
-  return linkEl;
-}
-
-function createErrorCard(createElement, title, text) {
-  const descEl = createElement("p", {
-    class: "search-error-text",
-    dangerouslySetInnerHTML: {
-      __html: text,
-    },
-  });
-
-  const titleEl = createElement("p", {
-    class: "search-error-title",
-    dangerouslySetInnerHTML: {
-      __html: `<i class="bi bi-exclamation-circle search-error-icon"></i> ${title}`,
-    },
-  });
-  const errorEl = createElement("div", { class: "search-error" }, [
-    titleEl,
-    descEl,
-  ]);
-  return errorEl;
-}
-
-function positionPanel(pos) {
-  const panelEl = window.document.querySelector(
-    "#quarto-search-results .aa-Panel"
-  );
-  const inputEl = window.document.querySelector(
-    "#quarto-search .aa-Autocomplete"
-  );
-
-  if (panelEl && inputEl) {
-    panelEl.style.top = `${Math.round(panelEl.offsetTop)}px`;
-    if (pos === "start") {
-      panelEl.style.left = `${Math.round(inputEl.left)}px`;
-    } else {
-      panelEl.style.right = `${Math.round(inputEl.offsetRight)}px`;
-    }
-  }
-}
-
-/* Highlighting */
-// highlighting functions
-function highlightMatch(query, text) {
-  if (text) {
-    const start = text.toLowerCase().indexOf(query.toLowerCase());
-    if (start !== -1) {
-      const startMark = "<mark class='search-match'>";
-      const endMark = "</mark>";
-
-      const end = start + query.length;
-      text =
-        text.slice(0, start) +
-        startMark +
-        text.slice(start, end) +
-        endMark +
-        text.slice(end);
-      const startInfo = clipStart(text, start);
-      const endInfo = clipEnd(
-        text,
-        startInfo.position + startMark.length + endMark.length
-      );
-      text =
-        startInfo.prefix +
-        text.slice(startInfo.position, endInfo.position) +
-        endInfo.suffix;
-
-      return text;
-    } else {
-      return text;
-    }
-  } else {
-    return text;
-  }
-}
-
-function clipStart(text, pos) {
-  const clipStart = pos - 50;
-  if (clipStart < 0) {
-    // This will just return the start of the string
-    return {
-      position: 0,
-      prefix: "",
-    };
-  } else {
-    // We're clipping before the start of the string, walk backwards to the first space.
-    const spacePos = findSpace(text, pos, -1);
-    return {
-      position: spacePos.position,
-      prefix: "",
-    };
-  }
-}
-
-function clipEnd(text, pos) {
-  const clipEnd = pos + 200;
-  if (clipEnd > text.length) {
-    return {
-      position: text.length,
-      suffix: "",
-    };
-  } else {
-    const spacePos = findSpace(text, clipEnd, 1);
-    return {
-      position: spacePos.position,
-      suffix: spacePos.clipped ? "…" : "",
-    };
-  }
-}
-
-function findSpace(text, start, step) {
-  let stepPos = start;
-  while (stepPos > -1 && stepPos < text.length) {
-    const char = text[stepPos];
-    if (char === " " || char === "," || char === ":") {
-      return {
-        position: step === 1 ? stepPos : stepPos - step,
-        clipped: stepPos > 1 && stepPos < text.length,
-      };
-    }
-    stepPos = stepPos + step;
-  }
-
-  return {
-    position: stepPos - step,
-    clipped: false,
-  };
-}
-
-// removes highlighting as implemented by the mark tag
-function clearHighlight(searchterm, el) {
-  const childNodes = el.childNodes;
-  for (let i = childNodes.length - 1; i >= 0; i--) {
-    const node = childNodes[i];
-    if (node.nodeType === Node.ELEMENT_NODE) {
-      if (
-        node.tagName === "MARK" &&
-        node.innerText.toLowerCase() === searchterm.toLowerCase()
-      ) {
-        el.replaceChild(document.createTextNode(node.innerText), node);
-      } else {
-        clearHighlight(searchterm, node);
-      }
-    }
-  }
-}
-
-function escapeRegExp(string) {
-  return string.replace(/[.*+?^${}()|[\]\\]/g, "\\$&"); // $& means the whole matched string
-}
-
-// highlight matches
-function highlight(term, el) {
-  const termRegex = new RegExp(term, "ig");
-  const childNodes = el.childNodes;
-
-  // walk back to front avoid mutating elements in front of us
-  for (let i = childNodes.length - 1; i >= 0; i--) {
-    const node = childNodes[i];
-
-    if (node.nodeType === Node.TEXT_NODE) {
-      // Search text nodes for text to highlight
-      const text = node.nodeValue;
-
-      let startIndex = 0;
-      let matchIndex = text.search(termRegex);
-      if (matchIndex > -1) {
-        const markFragment = document.createDocumentFragment();
-        while (matchIndex > -1) {
-          const prefix = text.slice(startIndex, matchIndex);
-          markFragment.appendChild(document.createTextNode(prefix));
-
-          const mark = document.createElement("mark");
-          mark.appendChild(
-            document.createTextNode(
-              text.slice(matchIndex, matchIndex + term.length)
-            )
-          );
-          markFragment.appendChild(mark);
-
-          startIndex = matchIndex + term.length;
-          matchIndex = text.slice(startIndex).search(new RegExp(term, "ig"));
-          if (matchIndex > -1) {
-            matchIndex = startIndex + matchIndex;
-          }
-        }
-        if (startIndex < text.length) {
-          markFragment.appendChild(
-            document.createTextNode(text.slice(startIndex, text.length))
-          );
-        }
-
-        el.replaceChild(markFragment, node);
-      }
-    } else if (node.nodeType === Node.ELEMENT_NODE) {
-      // recurse through elements
-      highlight(term, node);
-    }
-  }
-}
-
-/* Link Handling */
-// get the offset from this page for a given site root relative url
-function offsetURL(url) {
-  var offset = getMeta("quarto:offset");
-  return offset ? offset + url : url;
-}
-
-// read a meta tag value
-function getMeta(metaName) {
-  var metas = window.document.getElementsByTagName("meta");
-  for (let i = 0; i < metas.length; i++) {
-    if (metas[i].getAttribute("name") === metaName) {
-      return metas[i].getAttribute("content");
-    }
-  }
-  return "";
-}
-
-function algoliaSearch(query, limit, algoliaOptions) {
-  const { getAlgoliaResults } = window["@algolia/autocomplete-preset-algolia"];
-
-  const applicationId = algoliaOptions["application-id"];
-  const searchOnlyApiKey = algoliaOptions["search-only-api-key"];
-  const indexName = algoliaOptions["index-name"];
-  const indexFields = algoliaOptions["index-fields"];
-  const searchClient = window.algoliasearch(applicationId, searchOnlyApiKey);
-  const searchParams = algoliaOptions["params"];
-  const searchAnalytics = !!algoliaOptions["analytics-events"];
-
-  return getAlgoliaResults({
-    searchClient,
-    queries: [
-      {
-        indexName: indexName,
-        query,
-        params: {
-          hitsPerPage: limit,
-          clickAnalytics: searchAnalytics,
-          ...searchParams,
-        },
-      },
-    ],
-    transformResponse: (response) => {
-      if (!indexFields) {
-        return response.hits.map((hit) => {
-          return hit.map((item) => {
-            return {
-              ...item,
-              text: highlightMatch(query, item.text),
-            };
-          });
-        });
-      } else {
-        const remappedHits = response.hits.map((hit) => {
-          return hit.map((item) => {
-            const newItem = { ...item };
-            ["href", "section", "title", "text"].forEach((keyName) => {
-              const mappedName = indexFields[keyName];
-              if (
-                mappedName &&
-                item[mappedName] !== undefined &&
-                mappedName !== keyName
-              ) {
-                newItem[keyName] = item[mappedName];
-                delete newItem[mappedName];
-              }
-            });
-            newItem.text = highlightMatch(query, newItem.text);
-            return newItem;
-          });
-        });
-        return remappedHits;
-      }
-    },
-  });
-}
-
-function fuseSearch(query, fuse, fuseOptions) {
-  return fuse.search(query, fuseOptions).map((result) => {
-    const addParam = (url, name, value) => {
-      const anchorParts = url.split("#");
-      const baseUrl = anchorParts[0];
-      const sep = baseUrl.search("\\?") > 0 ? "&" : "?";
-      anchorParts[0] = baseUrl + sep + name + "=" + value;
-      return anchorParts.join("#");
-    };
-
-    return {
-      title: result.item.title,
-      section: result.item.section,
-      href: addParam(result.item.href, kQueryArg, query),
-      text: highlightMatch(query, result.item.text),
-    };
-  });
-}
diff --git a/docs/_site/tutorials/index.html b/docs/_site/tutorials/index.html
deleted file mode 100644
index 22c0e5b..0000000
--- a/docs/_site/tutorials/index.html
+++ /dev/null
@@ -1,369 +0,0 @@
-<!DOCTYPE html>
-<html xmlns="http://www.w3.org/1999/xhtml" lang="en" xml:lang="en"><head>
-
-<meta charset="utf-8">
-<meta name="generator" content="quarto-1.3.450">
-
-<meta name="viewport" content="width=device-width, initial-scale=1.0, user-scalable=yes">
-
-
-<title>NGLui Documentation – index</title>
-<style>
-code{white-space: pre-wrap;}
-span.smallcaps{font-variant: small-caps;}
-div.columns{display: flex; gap: min(4vw, 1.5em);}
-div.column{flex: auto; overflow-x: auto;}
-div.hanging-indent{margin-left: 1.5em; text-indent: -1.5em;}
-ul.task-list{list-style: none;}
-ul.task-list li input[type="checkbox"] {
-  width: 0.8em;
-  margin: 0 0.8em 0.2em -1em; /* quarto-specific, see https://github.com/quarto-dev/quarto-cli/issues/4556 */ 
-  vertical-align: middle;
-}
-</style>
-
-
-<script src="../site_libs/quarto-nav/quarto-nav.js"></script>
-<script src="../site_libs/quarto-nav/headroom.min.js"></script>
-<script src="../site_libs/clipboard/clipboard.min.js"></script>
-<script src="../site_libs/quarto-search/autocomplete.umd.js"></script>
-<script src="../site_libs/quarto-search/fuse.min.js"></script>
-<script src="../site_libs/quarto-search/quarto-search.js"></script>
-<meta name="quarto:offset" content="../">
-<script src="../site_libs/quarto-html/quarto.js"></script>
-<script src="../site_libs/quarto-html/popper.min.js"></script>
-<script src="../site_libs/quarto-html/tippy.umd.min.js"></script>
-<script src="../site_libs/quarto-html/anchor.min.js"></script>
-<link href="../site_libs/quarto-html/tippy.css" rel="stylesheet">
-<link href="../site_libs/quarto-html/quarto-syntax-highlighting.css" rel="stylesheet" id="quarto-text-highlighting-styles">
-<script src="../site_libs/bootstrap/bootstrap.min.js"></script>
-<link href="../site_libs/bootstrap/bootstrap-icons.css" rel="stylesheet">
-<link href="../site_libs/bootstrap/bootstrap.min.css" rel="stylesheet" id="quarto-bootstrap" data-mode="light">
-<script id="quarto-search-options" type="application/json">{
-  "location": "navbar",
-  "copy-button": false,
-  "collapse-after": 3,
-  "panel-placement": "end",
-  "type": "overlay",
-  "limit": 20,
-  "language": {
-    "search-no-results-text": "No results",
-    "search-matching-documents-text": "matching documents",
-    "search-copy-link-title": "Copy link to search",
-    "search-hide-matches-text": "Hide additional matches",
-    "search-more-match-text": "more match in this document",
-    "search-more-matches-text": "more matches in this document",
-    "search-clear-button-title": "Clear",
-    "search-detached-cancel-button-title": "Cancel",
-    "search-submit-button-title": "Submit",
-    "search-label": "Search"
-  }
-}</script>
-
-
-</head>
-
-<body class="nav-fixed fullcontent">
-
-<div id="quarto-search-results"></div>
-  <header id="quarto-header" class="headroom fixed-top">
-    <nav class="navbar navbar-expand-lg navbar-dark ">
-      <div class="navbar-container container-fluid">
-      <div class="navbar-brand-container">
-    <a class="navbar-brand" href="../index.html">
-    <span class="navbar-title">NGLui Documentation</span>
-    </a>
-  </div>
-            <div id="quarto-search" class="" title="Search"></div>
-          <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbarCollapse" aria-controls="navbarCollapse" aria-expanded="false" aria-label="Toggle navigation" onclick="if (window.quartoToggleHeadroom) { window.quartoToggleHeadroom(); }">
-  <span class="navbar-toggler-icon"></span>
-</button>
-          <div class="collapse navbar-collapse" id="navbarCollapse">
-            <ul class="navbar-nav navbar-nav-scroll me-auto">
-  <li class="nav-item">
-    <a class="nav-link" href="../index.html" rel="" target="">
- <span class="menu-text">About</span></a>
-  </li>  
-  <li class="nav-item dropdown ">
-    <a class="nav-link dropdown-toggle" href="#" id="nav-menu-tutorials" role="button" data-bs-toggle="dropdown" aria-expanded="false" rel="" target="">
- <span class="menu-text">Tutorials</span>
-    </a>
-    <ul class="dropdown-menu" aria-labelledby="nav-menu-tutorials">    
-        <li>
-    <a class="dropdown-item" href="../tutorials/statebuilder.html" rel="" target="">
- <span class="dropdown-text">StateBuilder Tutorial</span></a>
-  </li>  
-        <li>
-    <a class="dropdown-item" href="../tutorials/parser.html" rel="" target="">
- <span class="dropdown-text">Parser Tutorial</span></a>
-  </li>  
-    </ul>
-  </li>
-  <li class="nav-item">
-    <a class="nav-link" href="../reference/index.html" rel="" target="">
- <span class="menu-text">Function Reference</span></a>
-  </li>  
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-   
-  <ul>
-  <li><a href="#background" id="toc-background" class="nav-link active" data-scroll-target="#background">Background</a></li>
-  <li><a href="#simple-layers-and-statebuilder" id="toc-simple-layers-and-statebuilder" class="nav-link" data-scroll-target="#simple-layers-and-statebuilder">Simple Layers and StateBuilder</a></li>
-  <li><a href="#data-driven-states" id="toc-data-driven-states" class="nav-link" data-scroll-target="#data-driven-states">Data-driven States</a></li>
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-
-<p>The StateBuilder module is designed to allow rules-based generation of Neuroglancer states based on DataFrames or numpy arrays.</p>
-<section id="background" class="level2">
-<h2 class="anchored" data-anchor-id="background">Background</h2>
-<p><a href="https://github.com/google/neuroglancer">Neuroglancer</a> is a web application for viewing large volumetric imagery and segmentation data, as well as meshes and annotations like points or lines. Data in Neuroglancer is organized into layers, where each layer is configured to show information like images, segmentation, or annotations. Each layer can show one type of data and has different properties associated with it. In addition, Neuroglancer also stores the exact view that the user sees —&nbsp;what location in the data is centered, the orientation and zoom level of the camera, and more. Collectively, the information underlying both layers and the user view is refered to as the “state,” which is stored as a collection of key/value pairs.</p>
-<p>StateBuilder follows this model by defining a set of rules for initializing layers. For layers that contain properties like selected segment ids or annotations, this configuration involves specifying how to map DataFrame columns to selected segmentations or annotations such as synapses. The general pattern is that you build up a collection of configurations for individual layers, assemble them into a <code>StateBuilder</code> object, and then pass a dataframe through this object to render out a state.</p>
-</section>
-<section id="simple-layers-and-statebuilder" class="level2">
-<h2 class="anchored" data-anchor-id="simple-layers-and-statebuilder">Simple Layers and StateBuilder</h2>
-<div class="sourceCode" id="cb1"><pre class="sourceCode python code-with-copy"><code class="sourceCode python"><span id="cb1-1"><a href="#cb1-1" aria-hidden="true" tabindex="-1"></a><span class="im">from</span> nglui <span class="im">import</span> statebuilder</span>
-<span id="cb1-2"><a href="#cb1-2" aria-hidden="true" tabindex="-1"></a></span>
-<span id="cb1-3"><a href="#cb1-3" aria-hidden="true" tabindex="-1"></a>img <span class="op">=</span> statebuilder.ImageLayerConfig(</span>
-<span id="cb1-4"><a href="#cb1-4" aria-hidden="true" tabindex="-1"></a>    source<span class="op">=</span>client.info.image_source(),</span>
-<span id="cb1-5"><a href="#cb1-5" aria-hidden="true" tabindex="-1"></a>    contrast_controls<span class="op">=</span><span class="va">True</span>, <span class="co"># this just puts in the code needed to manually adjust contrast</span></span>
-<span id="cb1-6"><a href="#cb1-6" aria-hidden="true" tabindex="-1"></a>)</span>
-<span id="cb1-7"><a href="#cb1-7" aria-hidden="true" tabindex="-1"></a></span>
-<span id="cb1-8"><a href="#cb1-8" aria-hidden="true" tabindex="-1"></a>seg <span class="op">=</span> statebuilder.SegmentationLayerConfig(</span>
-<span id="cb1-9"><a href="#cb1-9" aria-hidden="true" tabindex="-1"></a>    source<span class="op">=</span>client.info.segmentation_source(),</span>
-<span id="cb1-10"><a href="#cb1-10" aria-hidden="true" tabindex="-1"></a>)</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
-</section>
-<section id="data-driven-states" class="level2">
-<h2 class="anchored" data-anchor-id="data-driven-states">Data-driven States</h2>
-
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diff --git a/docs/about.qmd b/docs/about.qmd
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+++ /dev/null
@@ -1,5 +0,0 @@
----
-title: "About"
----
-
-About this site
diff --git a/CHANGELOG.md b/docs/changelog.md
similarity index 91%
rename from CHANGELOG.md
rename to docs/changelog.md
index f0d899d..c794bd8 100644
--- a/CHANGELOG.md
+++ b/docs/changelog.md
@@ -2,6 +2,23 @@
 
 This project attempts to follow [Semantic Versioning](https://semver.org) and uses [Keep-a-Changelog formatting](https://keepachangelog.com/en/1.0.0/). But I make mistakes sometimes.
 
+## [3.2.0] - 2024-07-10
+
+### Added
+
+- **SegmentProperties** : A new module has been created to build Segment Properties, which are a method of organizing information about segment IDs in a Neuroglancer segmentation layer.
+Segment Properties only work with the newer Google/Spelunker branches, and offer a way to add browsable and searchable metadata to segments that can be viewed in the viewer.
+- **StateBuilder** : Various changes were made to support segment properties from both explicit URLs and from data-driven mapping. See documentation for details.
+
+## Changed
+
+- **StateBuilder** : Image layers for spelunker now use native contrast controls.
+
+### Fixed
+
+- **StateBuilder** : Improvements to the use of `target_site` and `url_prefix` in general when both creating statebuilder and rendering states. In particular, the values in `render_state` should now correctly take precendence over the values in `StateBuilder` when both are set.
+
+
 ## [3.1.0] - 2024-05-29
 
 ### Added
diff --git a/docs/index.md b/docs/index.md
new file mode 100644
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--- /dev/null
+++ b/docs/index.md
@@ -0,0 +1,46 @@
+# NGLui
+
+NGLui is a library for programmatically generating shareable Neuroglancer states in order to explore and visualize large, 3d image datasets.
+It is designed to be used in conjunction with the [Neuroglancer](https://github.com/google/neuroglancer) web viewer and the [CAVE analysis ecosystem](https://caveconnectome.github.io/CAVEclient/).
+It aims to separate the *rules* you want to use to generate states from the *data* you want to visualize, allowing you make reusable code to generate states from different datasets and analyses.
+
+## Installation
+
+NGLui is available on PyPI and can be installed with pip:
+
+```bash
+pip install nglui
+```
+
+If you want to clone the repository and develop on NGLui, note that it uses [Hatch](https://hatch.pypa.io/latest/) for development and packaging.
+
+## Quick Usage
+
+!!! note
+
+    Using the CAVEclient with the MICrons dataset is required for the following examples.
+
+Here's a quick example of how to use NGLui to generate a Neuroglancer state from the [Microns cortical dataset](https://www.microns-explorer.org).
+
+```python
+import caveclient
+from nglui import statebuilder
+
+client = caveclient.CAVEclient('minnie65_public')
+
+# Get a root id of a specific neuron
+root_id = client.materialize.query_table(
+    'nucleus_detection_v0',
+    filter_equal_dict={'id': 255258}
+)['pt_root_id']
+
+statebuilder.helpers.make_neuron_neuroglancer_link(
+    client,
+    root_id,
+    show_inputs=True,
+    show_outputs=True,
+    ngl_url='https://spelunker.cave-explorer.org',
+)
+```
+
+This code will generate a link to produce a Neuroglancer state showing a neuron and its synapses.
\ No newline at end of file
diff --git a/docs/index.qmd b/docs/index.qmd
deleted file mode 100644
index b5e21cc..0000000
--- a/docs/index.qmd
+++ /dev/null
@@ -1,7 +0,0 @@
----
-title: "Docs"
----
-
-This is a Quarto website.
-
-To learn more about Quarto websites visit <https://quarto.org/docs/websites>.
diff --git a/docs/objects.json b/docs/objects.json
deleted file mode 100644
index 5d7b948..0000000
--- a/docs/objects.json
+++ /dev/null
@@ -1 +0,0 @@
-{"project": "nglui", "version": "0.0.9999", "count": 44, "items": [{"name": "nglui.statebuilder.ImageLayerConfig", "domain": "py", "role": "class", "priority": "1", "uri": "reference/statebuilder.ImageLayerConfig.html#nglui.statebuilder.ImageLayerConfig", "dispname": "-"}, {"name": "nglui.statebuilder.layers.ImageLayerConfig", "domain": "py", "role": "class", "priority": "1", "uri": "reference/statebuilder.ImageLayerConfig.html#nglui.statebuilder.ImageLayerConfig", "dispname": "nglui.statebuilder.ImageLayerConfig"}, {"name": "nglui.statebuilder.SegmentationLayerConfig", "domain": "py", "role": "class", "priority": "1", "uri": "reference/statebuilder.SegmentationLayerConfig.html#nglui.statebuilder.SegmentationLayerConfig", "dispname": "-"}, {"name": "nglui.statebuilder.layers.SegmentationLayerConfig", "domain": "py", "role": "class", "priority": "1", "uri": "reference/statebuilder.SegmentationLayerConfig.html#nglui.statebuilder.SegmentationLayerConfig", "dispname": "nglui.statebuilder.SegmentationLayerConfig"}, {"name": "nglui.statebuilder.AnnotationLayerConfig", "domain": "py", "role": "class", "priority": "1", "uri": "reference/statebuilder.AnnotationLayerConfig.html#nglui.statebuilder.AnnotationLayerConfig", "dispname": "-"}, {"name": "nglui.statebuilder.layers.AnnotationLayerConfig", "domain": "py", "role": "class", "priority": "1", "uri": "reference/statebuilder.AnnotationLayerConfig.html#nglui.statebuilder.AnnotationLayerConfig", "dispname": "nglui.statebuilder.AnnotationLayerConfig"}, {"name": "nglui.statebuilder.PointMapper", "domain": "py", "role": "class", "priority": "1", "uri": "reference/statebuilder.PointMapper.html#nglui.statebuilder.PointMapper", "dispname": "-"}, {"name": "nglui.statebuilder.mappers.PointMapper", "domain": "py", "role": "class", "priority": "1", "uri": "reference/statebuilder.PointMapper.html#nglui.statebuilder.PointMapper", "dispname": "nglui.statebuilder.PointMapper"}, {"name": "nglui.statebuilder.LineMapper", "domain": "py", "role": "class", "priority": "1", "uri": "reference/statebuilder.LineMapper.html#nglui.statebuilder.LineMapper", "dispname": "-"}, {"name": "nglui.statebuilder.mappers.LineMapper", "domain": "py", "role": "class", "priority": "1", "uri": "reference/statebuilder.LineMapper.html#nglui.statebuilder.LineMapper", "dispname": "nglui.statebuilder.LineMapper"}, {"name": "nglui.statebuilder.SphereMapper", "domain": "py", "role": "class", "priority": "1", "uri": "reference/statebuilder.SphereMapper.html#nglui.statebuilder.SphereMapper", "dispname": "-"}, {"name": "nglui.statebuilder.mappers.SphereMapper", "domain": "py", "role": "class", "priority": "1", "uri": "reference/statebuilder.SphereMapper.html#nglui.statebuilder.SphereMapper", "dispname": "nglui.statebuilder.SphereMapper"}, {"name": "nglui.statebuilder.BoundingBoxMapper", "domain": "py", "role": "class", "priority": "1", "uri": "reference/statebuilder.BoundingBoxMapper.html#nglui.statebuilder.BoundingBoxMapper", "dispname": "-"}, {"name": "nglui.statebuilder.mappers.BoundingBoxMapper", "domain": "py", "role": "class", "priority": "1", "uri": "reference/statebuilder.BoundingBoxMapper.html#nglui.statebuilder.BoundingBoxMapper", "dispname": "nglui.statebuilder.BoundingBoxMapper"}, {"name": "nglui.statebuilder.SplitPointMapper", "domain": "py", "role": "class", "priority": "1", "uri": "reference/statebuilder.SplitPointMapper.html#nglui.statebuilder.SplitPointMapper", "dispname": "-"}, {"name": "nglui.statebuilder.mappers.SplitPointMapper", "domain": "py", "role": "class", "priority": "1", "uri": "reference/statebuilder.SplitPointMapper.html#nglui.statebuilder.SplitPointMapper", "dispname": "nglui.statebuilder.SplitPointMapper"}, {"name": "nglui.statebuilder.StateBuilder", "domain": "py", "role": "class", "priority": "1", "uri": "reference/statebuilder.StateBuilder.html#nglui.statebuilder.StateBuilder", "dispname": "-"}, {"name": "nglui.statebuilder.statebuilder.StateBuilder", "domain": "py", "role": "class", "priority": "1", "uri": "reference/statebuilder.StateBuilder.html#nglui.statebuilder.StateBuilder", "dispname": "nglui.statebuilder.StateBuilder"}, {"name": "nglui.statebuilder.ChainedStateBuilder", "domain": "py", "role": "class", "priority": "1", "uri": "reference/statebuilder.ChainedStateBuilder.html#nglui.statebuilder.ChainedStateBuilder", "dispname": "-"}, {"name": "nglui.statebuilder.statebuilder.ChainedStateBuilder", "domain": "py", "role": "class", "priority": "1", "uri": "reference/statebuilder.ChainedStateBuilder.html#nglui.statebuilder.ChainedStateBuilder", "dispname": "nglui.statebuilder.ChainedStateBuilder"}, {"name": "nglui.statebuilder.helpers.from_client", "domain": "py", "role": "function", "priority": "1", "uri": "reference/statebuilder.helpers.from_client.html#nglui.statebuilder.helpers.from_client", "dispname": "-"}, {"name": "nglui.statebuilder.helpers.sort_dataframe_by_root_id", "domain": "py", "role": "function", "priority": "1", "uri": "reference/statebuilder.helpers.sort_dataframe_by_root_id.html#nglui.statebuilder.helpers.sort_dataframe_by_root_id", "dispname": "-"}, {"name": "nglui.statebuilder.helpers.make_line_statebuilder", "domain": "py", "role": "function", "priority": "1", "uri": "reference/statebuilder.helpers.make_line_statebuilder.html#nglui.statebuilder.helpers.make_line_statebuilder", "dispname": "-"}, {"name": "nglui.statebuilder.helpers.make_point_statebuilder", "domain": "py", "role": "function", "priority": "1", "uri": "reference/statebuilder.helpers.make_point_statebuilder.html#nglui.statebuilder.helpers.make_point_statebuilder", "dispname": "-"}, {"name": "nglui.statebuilder.helpers.make_pre_post_statebuilder", "domain": "py", "role": "function", "priority": "1", "uri": "reference/statebuilder.helpers.make_pre_post_statebuilder.html#nglui.statebuilder.helpers.make_pre_post_statebuilder", "dispname": "-"}, {"name": "nglui.statebuilder.helpers.make_state_url", "domain": "py", "role": "function", "priority": "1", "uri": "reference/statebuilder.helpers.make_state_url.html#nglui.statebuilder.helpers.make_state_url", "dispname": "-"}, {"name": "nglui.statebuilder.helpers.make_url_robust", "domain": "py", "role": "function", "priority": "1", "uri": "reference/statebuilder.helpers.make_url_robust.html#nglui.statebuilder.helpers.make_url_robust", "dispname": "-"}, {"name": "nglui.statebuilder.helpers.package_state", "domain": "py", "role": "function", "priority": "1", "uri": "reference/statebuilder.helpers.package_state.html#nglui.statebuilder.helpers.package_state", "dispname": "-"}, {"name": "nglui.statebuilder.helpers.make_synapse_neuroglancer_link", "domain": "py", "role": "function", "priority": "1", "uri": "reference/statebuilder.helpers.make_synapse_neuroglancer_link.html#nglui.statebuilder.helpers.make_synapse_neuroglancer_link", "dispname": "-"}, {"name": "nglui.statebuilder.helpers.make_neuron_neuroglancer_link", "domain": "py", "role": "function", "priority": "1", "uri": "reference/statebuilder.helpers.make_neuron_neuroglancer_link.html#nglui.statebuilder.helpers.make_neuron_neuroglancer_link", "dispname": "-"}, {"name": "nglui.parser.base.layer_names", "domain": "py", "role": "function", "priority": "1", "uri": "reference/parser.base.layer_names.html#nglui.parser.base.layer_names", "dispname": "-"}, {"name": "nglui.parser.base.image_layers", "domain": "py", "role": "function", "priority": "1", "uri": "reference/parser.base.image_layers.html#nglui.parser.base.image_layers", "dispname": "-"}, {"name": "nglui.parser.base.segmentation_layers", "domain": "py", "role": "function", "priority": "1", "uri": "reference/parser.base.segmentation_layers.html#nglui.parser.base.segmentation_layers", "dispname": "-"}, {"name": "nglui.parser.base.annotation_layers", "domain": "py", "role": "function", "priority": "1", "uri": "reference/parser.base.annotation_layers.html#nglui.parser.base.annotation_layers", "dispname": "-"}, {"name": "nglui.parser.base.tag_dictionary", "domain": "py", "role": "function", "priority": "1", "uri": "reference/parser.base.tag_dictionary.html#nglui.parser.base.tag_dictionary", "dispname": "-"}, {"name": "nglui.parser.base.get_layer", "domain": "py", "role": "function", "priority": "1", "uri": "reference/parser.base.get_layer.html#nglui.parser.base.get_layer", "dispname": "-"}, {"name": "nglui.parser.base.view_settings", "domain": "py", "role": "function", "priority": "1", "uri": "reference/parser.base.view_settings.html#nglui.parser.base.view_settings", "dispname": "-"}, {"name": "nglui.parser.base.get_selected_ids", "domain": "py", "role": "function", "priority": "1", "uri": "reference/parser.base.get_selected_ids.html#nglui.parser.base.get_selected_ids", "dispname": "-"}, {"name": "nglui.parser.base.point_annotations", "domain": "py", "role": "function", "priority": "1", "uri": "reference/parser.base.point_annotations.html#nglui.parser.base.point_annotations", "dispname": "-"}, {"name": "nglui.parser.base.line_annotations", "domain": "py", "role": "function", "priority": "1", "uri": "reference/parser.base.line_annotations.html#nglui.parser.base.line_annotations", "dispname": "-"}, {"name": "nglui.parser.base.sphere_annotations", "domain": "py", "role": "function", "priority": "1", "uri": "reference/parser.base.sphere_annotations.html#nglui.parser.base.sphere_annotations", "dispname": "-"}, {"name": "nglui.parser.base.group_annotations", "domain": "py", "role": "function", "priority": "1", "uri": "reference/parser.base.group_annotations.html#nglui.parser.base.group_annotations", "dispname": "-"}, {"name": "nglui.parser.base.extract_multicut", "domain": "py", "role": "function", "priority": "1", "uri": "reference/parser.base.extract_multicut.html#nglui.parser.base.extract_multicut", "dispname": "-"}, {"name": "nglui.parser.base.annotation_dataframe", "domain": "py", "role": "function", "priority": "1", "uri": "reference/parser.base.annotation_dataframe.html#nglui.parser.base.annotation_dataframe", "dispname": "-"}]}
\ No newline at end of file
diff --git a/docs/reference/AnnotationLayerConfig.qmd b/docs/reference/AnnotationLayerConfig.qmd
deleted file mode 100644
index eb07c64..0000000
--- a/docs/reference/AnnotationLayerConfig.qmd
+++ /dev/null
@@ -1,17 +0,0 @@
-# AnnotationLayerConfig { #nglui.statebuilder.layers.AnnotationLayerConfig }
-
-`statebuilder.layers.AnnotationLayerConfig(self, name=None, color=None, linked_segmentation_layer=None, mapping_rules=[], array_data=False, tags=None, active=True, filter_by_segmentation=False, brackets_show_segmentation=True, selection_shows_segmentation=True, filter_query=None, data_resolution=None)`
-
-Configuration class for annotation layers
-
-## Parameters
-
-| Name                        | Type                                                                                                                             | Description                                                                                                                                                                              | Default   |
-|-----------------------------|----------------------------------------------------------------------------------------------------------------------------------|------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|-----------|
-| `name`                      | str                                                                                                                              | Layer name. By default, 'annos'                                                                                                                                                          | `None`    |
-| `color`                     | str                                                                                                                              | Hex color code with an initial #. By default, None                                                                                                                                       | `None`    |
-| `linked_segmentation_layer` | str                                                                                                                              | Name of a linked segmentation layer for selected ids. By default, None                                                                                                                   | `None`    |
-| `mapping_rules`             | (nglui.statebuilder.mappers.PointMapper, nglui.statebuilder.mappers.LineMapper, nglui.statebuilder.mappers.SphereMapper or list) | One rule or a list of rules mapping data to annotations. By default, []                                                                                                                  | `[]`      |
-| `array_data`                | bool                                                                                                                             | If True, allows simple mapping where one or more arrays are passed instead of a dataframe. Only allows basic annotation creation, no tags, linked segmentations, or other rich features. | `False`   |
-| `tags`                      | list                                                                                                                             | List of tags for the layer.                                                                                                                                                              | `None`    |
-| `active`                    | bool                                                                                                                             | If True, makes the layer selected. Default is True (unlike for image/segmentation layers).                                                                                               | `True`    |
\ No newline at end of file
diff --git a/docs/reference/ChainedStateBuilder.qmd b/docs/reference/ChainedStateBuilder.qmd
deleted file mode 100644
index b9679aa..0000000
--- a/docs/reference/ChainedStateBuilder.qmd
+++ /dev/null
@@ -1,34 +0,0 @@
-# ChainedStateBuilder { #nglui.statebuilder.statebuilder.ChainedStateBuilder }
-
-`statebuilder.statebuilder.ChainedStateBuilder(self, statebuilders)`
-
-Builds a collection of states that sequentially add annotations based on a sequence of dataframes.
-
-## Parameters
-
-| Name            | Type   | Description                                                           | Default    |
-|-----------------|--------|-----------------------------------------------------------------------|------------|
-| `statebuilders` | list   | List of DataStateBuilders, in same order as dataframes will be passed | _required_ |
-
-## Methods
-
-| Name | Description |
-| --- | --- |
-| [render_state](#nglui.statebuilder.statebuilder.ChainedStateBuilder.render_state) | Generate a single neuroglancer state by addatively applying an ordered collection of |
-
-### render_state { #nglui.statebuilder.statebuilder.ChainedStateBuilder.render_state }
-
-`statebuilder.statebuilder.ChainedStateBuilder.render_state(data_list=None, base_state=None, return_as='url', url_prefix=default_neuroglancer_base, link_text='Neuroglancer Link', target_site=None)`
-
-Generate a single neuroglancer state by addatively applying an ordered collection of
-dataframes to an collection of StateBuilder renders.
-Parameters
-    data_list : Collection of DataFrame. The order must match the order of StateBuilders
-                contained in the class on creation.
-    base_state : JSON neuroglancer state (optional, default is None).
-                 Used as a base state for adding everything else to.
-    return_as: ['url', 'viewer', 'html', 'json']. optional, default='url'.
-               Sets how the state is returned. Note that if a viewer is returned,
-               the state is not reset to default.
-    url_prefix: string, optional (default is https://neuromancer-seung-import.appspot.com).
-                Overrides the default neuroglancer url for url generation.
\ No newline at end of file
diff --git a/docs/reference/ImageLayerConfig.qmd b/docs/reference/ImageLayerConfig.qmd
deleted file mode 100644
index d387a0d..0000000
--- a/docs/reference/ImageLayerConfig.qmd
+++ /dev/null
@@ -1,18 +0,0 @@
-# ImageLayerConfig { #nglui.statebuilder.layers.ImageLayerConfig }
-
-`statebuilder.layers.ImageLayerConfig(self, source, name=None, active=False, contrast_controls=False, black=0.0, white=1.0)`
-
-Image layer configuration class.
-
-This provides the rules for setting up an image layer in neuroglancer.
-
-## Parameters
-
-| Name                | Type   | Description                                                                                    | Default    |
-|---------------------|--------|------------------------------------------------------------------------------------------------|------------|
-| `source`            | str    | Cloudpath to an image source                                                                   | _required_ |
-| `name`              | str    | Name of the image layer. By default, 'img'.                                                    | `None`     |
-| `active`            | bool   | If True, makes the layer active in neuroglancer. Default is False.                             | `False`    |
-| `contrast_controls` | bool   | If True, gives the layer a user-controllable brightness and contrast shader. Default is False. | `False`    |
-| `black`             | float  | If contrast_controls is True, sets the default black level. Default is 0.0.                    | `0.0`      |
-| `white`             | float  | If contrast_controls is True, sets the default white level. Default is 1.0.                    | `1.0`      |
\ No newline at end of file
diff --git a/docs/reference/SegmentationLayerConfig.qmd b/docs/reference/SegmentationLayerConfig.qmd
deleted file mode 100644
index edda51b..0000000
--- a/docs/reference/SegmentationLayerConfig.qmd
+++ /dev/null
@@ -1,44 +0,0 @@
-# SegmentationLayerConfig { #nglui.statebuilder.layers.SegmentationLayerConfig }
-
-`statebuilder.layers.SegmentationLayerConfig(self, source, name=None, selected_ids_column=None, fixed_ids=None, fixed_id_colors=None, color_column=None, active=False, alpha_selected=0.3, alpha_3d=1, alpha_unselected=0, split_point_map=None, view_kws=None, timestamp=None, data_resolution=None)`
-
-Configuration class for segmentation layers
-
-## Parameters
-
-| Name                  | Type                         | Description                                                                                                                                                                                             | Default    |
-|-----------------------|------------------------------|---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|------------|
-| `source`              | str                          | Segmentation source                                                                                                                                                                                     | _required_ |
-| `name`                | (str, optional)              | Layer name.                                                                                                                                                                                             | `None`     |
-| `selected_ids_column` | str or list-like, optional.  | Column name (or list of column names) to use for selected ids.                                                                                                                                          | `None`     |
-| `fixed_ids`           | list-like, optional.         | List of root ids to select directly.                                                                                                                                                                    | `None`     |
-| `fixed_id_colors`     | list-like, optional.         | List of colors for fixed ids. Should be the same length as fixed_ids, although null entries can be padded with None values.                                                                             | `None`     |
-| `color_column`        | str, optional.               | # at the begining. Column to use for color values for selected objects. Values should be RGB hex strings with a                                                                                         | `None`     |
-| `active`              | bool, optional.              | If True, makes the layer selected. Default is False.                                                                                                                                                    | `False`    |
-| `alpha_selected`      |                              | Opacity of selected segmentations in the image layer. Optional, default is 0.3.                                                                                                                         | `0.3`      |
-| `alpha_3d`            |                              | Opacity of meshes. Optional, default is 1.                                                                                                                                                              | `1`        |
-| `alpha_unselected`    |                              | Opacity of unselected segments. Optional, default is 0.                                                                                                                                                 | `0`        |
-| `split_point_map`     |                              | If not None, provides an object to map the dataframe input to multicut points. Default is None.                                                                                                         | `None`     |
-| `view_kws`            | dict, optional.              | Keyword arguments for viewer.set_segmentation_view_options. Sets selected (and unselected) segmetation alpha values. Defaults to values in DEFAULT_SEGMENTATION_VIEW_KWS dict specified in this module. | `None`     |
-| `timestamp`           | float or datetime, optional. | Timestamp at which to fix the chunkedgraph in either unix epoch or datetime format. Optional, default is None.                                                                                          | `None`     |
-
-## Methods
-
-| Name | Description |
-| --- | --- |
-| [add_selection_map](#nglui.statebuilder.layers.SegmentationLayerConfig.add_selection_map) | Add rules for selecting active segment ids and their colors |
-
-### add_selection_map { #nglui.statebuilder.layers.SegmentationLayerConfig.add_selection_map }
-
-`statebuilder.layers.SegmentationLayerConfig.add_selection_map(selected_ids_column=None, fixed_ids=None, fixed_id_colors=None, color_column=None)`
-
-Add rules for selecting active segment ids and their colors
-
-#### Parameters
-
-| Name                  | Type        | Description                                                                                        | Default   |
-|-----------------------|-------------|----------------------------------------------------------------------------------------------------|-----------|
-| `selected_ids_column` | str         | Dataframe column to use for adding selected segment ids to the segmentation layer, by default None | `None`    |
-| `fixed_ids`           | int or list | Add one or more segment ids to be active, independent of the data, by default None                 | `None`    |
-| `fixed_id_colors`     | list        | Add a list of colors (hex, rgb, or CSS3 string) to assign to the fixed ids, by default None        | `None`    |
-| `color_column`        | str         | Dataframe column to use for adding selected segment colors, by default None                        | `None`    |
\ No newline at end of file
diff --git a/docs/reference/_api_index.qmd b/docs/reference/_api_index.qmd
deleted file mode 100644
index 0a1d945..0000000
--- a/docs/reference/_api_index.qmd
+++ /dev/null
@@ -1,74 +0,0 @@
-#  {.doc .doc-index}
-
-## StateBuilder Functions
-
-### Layers
-
-Instantiating types of layers
-
-| | |
-| --- | --- |
-| [statebuilder.ImageLayerConfig](statebuilder.ImageLayerConfig.qmd#nglui.statebuilder.ImageLayerConfig) | Image layer configuration class. |
-| [statebuilder.SegmentationLayerConfig](statebuilder.SegmentationLayerConfig.qmd#nglui.statebuilder.SegmentationLayerConfig) | Configuration class for segmentation layers |
-| [statebuilder.AnnotationLayerConfig](statebuilder.AnnotationLayerConfig.qmd#nglui.statebuilder.AnnotationLayerConfig) | Configuration class for annotation layers |
-
-### Mapping Rules
-
-Rules for mapping data to annotations
-
-| | |
-| --- | --- |
-| [statebuilder.PointMapper](statebuilder.PointMapper.qmd#nglui.statebuilder.PointMapper) | Sets rules to map dataframes to point annotations |
-| [statebuilder.LineMapper](statebuilder.LineMapper.qmd#nglui.statebuilder.LineMapper) | Sets rules to map dataframes to line annotations |
-| [statebuilder.SphereMapper](statebuilder.SphereMapper.qmd#nglui.statebuilder.SphereMapper) | Sets rules to map dataframes to sphere annotations |
-| [statebuilder.BoundingBoxMapper](statebuilder.BoundingBoxMapper.qmd#nglui.statebuilder.BoundingBoxMapper) | Sets rules to map dataframes to bounding box annotations |
-| [statebuilder.SplitPointMapper](statebuilder.SplitPointMapper.qmd#nglui.statebuilder.SplitPointMapper) | Mapper to create split points in a segmentation layer. |
-
-### StateBuilder Classes
-
-Tools for data-generated neuroglancer state creation
-
-| | |
-| --- | --- |
-| [statebuilder.StateBuilder](statebuilder.StateBuilder.qmd#nglui.statebuilder.StateBuilder) | A class for schematic mapping data frames into neuroglancer states. |
-| [statebuilder.ChainedStateBuilder](statebuilder.ChainedStateBuilder.qmd#nglui.statebuilder.ChainedStateBuilder) | Builds a collection of states that sequentially add annotations based on a sequence of dataframes. |
-
-### Helpers
-
-Tools for common types of states
-
-| | |
-| --- | --- |
-| [statebuilder.helpers.from_client](statebuilder.helpers.from_client.qmd#nglui.statebuilder.helpers.from_client) | Generate basic image and segmentation layers from a FrameworkClient |
-| [statebuilder.helpers.sort_dataframe_by_root_id](statebuilder.helpers.sort_dataframe_by_root_id.qmd#nglui.statebuilder.helpers.sort_dataframe_by_root_id) | Sort a dataframe so that rows belonging to the same root id are together, ordered by how many times the root id appears. |
-| [statebuilder.helpers.make_line_statebuilder](statebuilder.helpers.make_line_statebuilder.qmd#nglui.statebuilder.helpers.make_line_statebuilder) | Generate a state builder that puts points on a single column with a linked segmentaton id |
-| [statebuilder.helpers.make_point_statebuilder](statebuilder.helpers.make_point_statebuilder.qmd#nglui.statebuilder.helpers.make_point_statebuilder) | Generate a state builder that puts points on a single column with a linked segmentaton id |
-| [statebuilder.helpers.make_pre_post_statebuilder](statebuilder.helpers.make_pre_post_statebuilder.qmd#nglui.statebuilder.helpers.make_pre_post_statebuilder) | Function to generate ChainedStateBuilder with optional pre and post synaptic |
-| [statebuilder.helpers.make_state_url](statebuilder.helpers.make_state_url.qmd#nglui.statebuilder.helpers.make_state_url) | Generate a url from a neuroglancer state via a state server. |
-| [statebuilder.helpers.make_url_robust](statebuilder.helpers.make_url_robust.qmd#nglui.statebuilder.helpers.make_url_robust) | Generate a url from a neuroglancer state. If too long, return through state server, |
-| [statebuilder.helpers.package_state](statebuilder.helpers.package_state.qmd#nglui.statebuilder.helpers.package_state) | Automate creating a state from a statebuilder and |
-| [statebuilder.helpers.make_synapse_neuroglancer_link](statebuilder.helpers.make_synapse_neuroglancer_link.qmd#nglui.statebuilder.helpers.make_synapse_neuroglancer_link) | Generate a neuroglancer link from a synapse dataframe as returned from CAVEclient.materialize.synapse_query. |
-| [statebuilder.helpers.make_neuron_neuroglancer_link](statebuilder.helpers.make_neuron_neuroglancer_link.qmd#nglui.statebuilder.helpers.make_neuron_neuroglancer_link) | function to create a neuroglancer link view of a neuron, optionally including inputs and outputs |
-
-## Parser
-
-### Parser Tools
-
-Simple tools for parsing neuroglancer states
-
-| | |
-| --- | --- |
-| [parser.base.layer_names](parser.base.layer_names.qmd#nglui.parser.base.layer_names) | Get all layer names in the state |
-| [parser.base.image_layers](parser.base.image_layers.qmd#nglui.parser.base.image_layers) | Get all image layer names in the state |
-| [parser.base.segmentation_layers](parser.base.segmentation_layers.qmd#nglui.parser.base.segmentation_layers) | Get all segmentation layer names in the state |
-| [parser.base.annotation_layers](parser.base.annotation_layers.qmd#nglui.parser.base.annotation_layers) | Get all annotation layer names in the state |
-| [parser.base.tag_dictionary](parser.base.tag_dictionary.qmd#nglui.parser.base.tag_dictionary) | Get the tag id to string dictionary for a layer |
-| [parser.base.get_layer](parser.base.get_layer.qmd#nglui.parser.base.get_layer) | Gets the contents of the layer based on the layer name. |
-| [parser.base.view_settings](parser.base.view_settings.qmd#nglui.parser.base.view_settings) | Get all data about the view state in neuroglancer: position, |
-| [parser.base.get_selected_ids](parser.base.get_selected_ids.qmd#nglui.parser.base.get_selected_ids) | Get a list of selected ids in a segmentation layer |
-| [parser.base.point_annotations](parser.base.point_annotations.qmd#nglui.parser.base.point_annotations) | Get all point annotation points and other info from a layer. |
-| [parser.base.line_annotations](parser.base.line_annotations.qmd#nglui.parser.base.line_annotations) | Get all line annotation points and other info from a layer. |
-| [parser.base.sphere_annotations](parser.base.sphere_annotations.qmd#nglui.parser.base.sphere_annotations) | Get all sphere annotation points and other info from a layer. |
-| [parser.base.group_annotations](parser.base.group_annotations.qmd#nglui.parser.base.group_annotations) | All group annotations and their associated points |
-| [parser.base.extract_multicut](parser.base.extract_multicut.qmd#nglui.parser.base.extract_multicut) | Extract information entered into the multicut graph operation |
-| [parser.base.annotation_dataframe](parser.base.annotation_dataframe.qmd#nglui.parser.base.annotation_dataframe) | Return all annotations across all annotation layers in the state. |
\ No newline at end of file
diff --git a/docs/reference/easyviewer.md b/docs/reference/easyviewer.md
new file mode 100644
index 0000000..d5728fc
--- /dev/null
+++ b/docs/reference/easyviewer.md
@@ -0,0 +1,19 @@
+---
+title: EasyViewer
+---
+
+::: src.nglui.easyviewer.ev_base.base
+    options:
+        show_source: false
+        heading_level: 2
+
+
+::: src.nglui.easyviewer.ev_base.mainline
+    options:
+        show_source: false
+        heading_level: 2
+
+::: src.nglui.easyviewer.ev_base.seunglab
+    options:
+        show_source: false
+        heading_level: 2
\ No newline at end of file
diff --git a/docs/reference/get_object.qmd b/docs/reference/get_object.qmd
deleted file mode 100644
index 63d7643..0000000
--- a/docs/reference/get_object.qmd
+++ /dev/null
@@ -1,32 +0,0 @@
-# get_object { #quartodoc.get_object }
-
-`get_object(path, object_name=None, parser='numpy', load_aliases=True, dynamic=False, loader=None)`
-
-Fetch a griffe object.
-
-## Parameters
-
-| Name           | Type          | Description                                                                                                                                            | Default    |
-|----------------|---------------|--------------------------------------------------------------------------------------------------------------------------------------------------------|------------|
-| `path`         | str           | An import path to the object. This should have the form `path.to.module:object`. For example, `quartodoc:get_object` or `quartodoc:MdRenderer.render`. | _required_ |
-| `object_name`  | 'str \| None' | (Deprecated). A function name.                                                                                                                         | `None`     |
-| `parser`       | str           | A docstring parser to use.                                                                                                                             | `'numpy'`  |
-| `load_aliases` |               | For aliases that were imported from other modules, should we load that module?                                                                         | `True`     |
-| `dynamic`      |               | Whether to dynamically import object. Useful if docstring is not hard-coded, but was set on object by running python code.                             | `False`    |
-
-## See Also
-
-preview: print a user-friendly preview of a griffe object.
-
-## Examples
-
-```python
->>> get_function("quartodoc", "get_function")
-<Function('get_function', ...
-```
-
-## Returns
-
-| Type                                         | Description   |
-|----------------------------------------------|---------------|
-| griffe.dataclasses.griffe.dataclasses.Object | abc           |
\ No newline at end of file
diff --git a/docs/reference/index.qmd b/docs/reference/index.qmd
deleted file mode 100644
index 87a865c..0000000
--- a/docs/reference/index.qmd
+++ /dev/null
@@ -1,21 +0,0 @@
----
-name: function intro
-format:
-  html: 
-    grid:
-      sidebar-width: 300px
-      body-width: 900px
----
-
-# Function Intro
-This site provides basic documentation for the functions in `NGLui`.
-Please see the [tutorials](../tutorials/index.qmd) for more information about how to use them.
-
-Note that `nglui` spans two public submodules responsible for different tasks.
-
-- `StateBuilder` handles data-driven Neuroglancer state generation (hence the package name).
-- `Parser` extracts information from Neuroglancer states, as represented by dictionaries.
-
----
-
-{{< include /reference/_api_index.qmd >}}
\ No newline at end of file
diff --git a/docs/reference/layers.AnnotationLayerConfig.qmd b/docs/reference/layers.AnnotationLayerConfig.qmd
deleted file mode 100644
index f10fb43..0000000
--- a/docs/reference/layers.AnnotationLayerConfig.qmd
+++ /dev/null
@@ -1,17 +0,0 @@
-# layers.AnnotationLayerConfig { #nglui.statebuilder.layers.AnnotationLayerConfig }
-
-`statebuilder.layers.AnnotationLayerConfig(self, name=None, color=None, linked_segmentation_layer=None, mapping_rules=[], array_data=False, tags=None, active=True, filter_by_segmentation=False, brackets_show_segmentation=True, selection_shows_segmentation=True, filter_query=None, data_resolution=None)`
-
-Configuration class for annotation layers
-
-## Parameters
-
-| Name                        | Type                                                                                                                             | Description                                                                                                                                                                              | Default   |
-|-----------------------------|----------------------------------------------------------------------------------------------------------------------------------|------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|-----------|
-| `name`                      | str                                                                                                                              | Layer name. By default, 'annos'                                                                                                                                                          | `None`    |
-| `color`                     | str                                                                                                                              | Hex color code with an initial #. By default, None                                                                                                                                       | `None`    |
-| `linked_segmentation_layer` | str                                                                                                                              | Name of a linked segmentation layer for selected ids. By default, None                                                                                                                   | `None`    |
-| `mapping_rules`             | (nglui.statebuilder.mappers.PointMapper, nglui.statebuilder.mappers.LineMapper, nglui.statebuilder.mappers.SphereMapper or list) | One rule or a list of rules mapping data to annotations. By default, []                                                                                                                  | `[]`      |
-| `array_data`                | bool                                                                                                                             | If True, allows simple mapping where one or more arrays are passed instead of a dataframe. Only allows basic annotation creation, no tags, linked segmentations, or other rich features. | `False`   |
-| `tags`                      | list                                                                                                                             | List of tags for the layer.                                                                                                                                                              | `None`    |
-| `active`                    | bool                                                                                                                             | If True, makes the layer selected. Default is True (unlike for image/segmentation layers).                                                                                               | `True`    |
\ No newline at end of file
diff --git a/docs/reference/layers.ImageLayerConfig.qmd b/docs/reference/layers.ImageLayerConfig.qmd
deleted file mode 100644
index 837eb8b..0000000
--- a/docs/reference/layers.ImageLayerConfig.qmd
+++ /dev/null
@@ -1,18 +0,0 @@
-# layers.ImageLayerConfig { #nglui.statebuilder.layers.ImageLayerConfig }
-
-`statebuilder.layers.ImageLayerConfig(self, source, name=None, active=False, contrast_controls=False, black=0.0, white=1.0)`
-
-Image layer configuration class.
-
-This provides the rules for setting up an image layer in neuroglancer.
-
-## Parameters
-
-| Name                | Type   | Description                                                                                    | Default    |
-|---------------------|--------|------------------------------------------------------------------------------------------------|------------|
-| `source`            | str    | Cloudpath to an image source                                                                   | _required_ |
-| `name`              | str    | Name of the image layer. By default, 'img'.                                                    | `None`     |
-| `active`            | bool   | If True, makes the layer active in neuroglancer. Default is False.                             | `False`    |
-| `contrast_controls` | bool   | If True, gives the layer a user-controllable brightness and contrast shader. Default is False. | `False`    |
-| `black`             | float  | If contrast_controls is True, sets the default black level. Default is 0.0.                    | `0.0`      |
-| `white`             | float  | If contrast_controls is True, sets the default white level. Default is 1.0.                    | `1.0`      |
\ No newline at end of file
diff --git a/docs/reference/layers.SegmentationLayerConfig.qmd b/docs/reference/layers.SegmentationLayerConfig.qmd
deleted file mode 100644
index f5196f4..0000000
--- a/docs/reference/layers.SegmentationLayerConfig.qmd
+++ /dev/null
@@ -1,44 +0,0 @@
-# layers.SegmentationLayerConfig { #nglui.statebuilder.layers.SegmentationLayerConfig }
-
-`statebuilder.layers.SegmentationLayerConfig(self, source, name=None, selected_ids_column=None, fixed_ids=None, fixed_id_colors=None, color_column=None, active=False, alpha_selected=0.3, alpha_3d=1, alpha_unselected=0, split_point_map=None, view_kws=None, timestamp=None, data_resolution=None)`
-
-Configuration class for segmentation layers
-
-## Parameters
-
-| Name                  | Type                         | Description                                                                                                                                                                                             | Default    |
-|-----------------------|------------------------------|---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|------------|
-| `source`              | str                          | Segmentation source                                                                                                                                                                                     | _required_ |
-| `name`                | (str, optional)              | Layer name.                                                                                                                                                                                             | `None`     |
-| `selected_ids_column` | str or list-like, optional.  | Column name (or list of column names) to use for selected ids.                                                                                                                                          | `None`     |
-| `fixed_ids`           | list-like, optional.         | List of root ids to select directly.                                                                                                                                                                    | `None`     |
-| `fixed_id_colors`     | list-like, optional.         | List of colors for fixed ids. Should be the same length as fixed_ids, although null entries can be padded with None values.                                                                             | `None`     |
-| `color_column`        | str, optional.               | # at the begining. Column to use for color values for selected objects. Values should be RGB hex strings with a                                                                                         | `None`     |
-| `active`              | bool, optional.              | If True, makes the layer selected. Default is False.                                                                                                                                                    | `False`    |
-| `alpha_selected`      |                              | Opacity of selected segmentations in the image layer. Optional, default is 0.3.                                                                                                                         | `0.3`      |
-| `alpha_3d`            |                              | Opacity of meshes. Optional, default is 1.                                                                                                                                                              | `1`        |
-| `alpha_unselected`    |                              | Opacity of unselected segments. Optional, default is 0.                                                                                                                                                 | `0`        |
-| `split_point_map`     |                              | If not None, provides an object to map the dataframe input to multicut points. Default is None.                                                                                                         | `None`     |
-| `view_kws`            | dict, optional.              | Keyword arguments for viewer.set_segmentation_view_options. Sets selected (and unselected) segmetation alpha values. Defaults to values in DEFAULT_SEGMENTATION_VIEW_KWS dict specified in this module. | `None`     |
-| `timestamp`           | float or datetime, optional. | Timestamp at which to fix the chunkedgraph in either unix epoch or datetime format. Optional, default is None.                                                                                          | `None`     |
-
-## Methods
-
-| Name | Description |
-| --- | --- |
-| [add_selection_map](#nglui.statebuilder.layers.SegmentationLayerConfig.add_selection_map) | Add rules for selecting active segment ids and their colors |
-
-### add_selection_map { #nglui.statebuilder.layers.SegmentationLayerConfig.add_selection_map }
-
-`statebuilder.layers.SegmentationLayerConfig.add_selection_map(selected_ids_column=None, fixed_ids=None, fixed_id_colors=None, color_column=None)`
-
-Add rules for selecting active segment ids and their colors
-
-#### Parameters
-
-| Name                  | Type        | Description                                                                                        | Default   |
-|-----------------------|-------------|----------------------------------------------------------------------------------------------------|-----------|
-| `selected_ids_column` | str         | Dataframe column to use for adding selected segment ids to the segmentation layer, by default None | `None`    |
-| `fixed_ids`           | int or list | Add one or more segment ids to be active, independent of the data, by default None                 | `None`    |
-| `fixed_id_colors`     | list        | Add a list of colors (hex, rgb, or CSS3 string) to assign to the fixed ids, by default None        | `None`    |
-| `color_column`        | str         | Dataframe column to use for adding selected segment colors, by default None                        | `None`    |
\ No newline at end of file
diff --git a/docs/reference/layers.qmd b/docs/reference/layers.qmd
deleted file mode 100644
index 8e61ef7..0000000
--- a/docs/reference/layers.qmd
+++ /dev/null
@@ -1,112 +0,0 @@
-# layers { #nglui.statebuilder.layers }
-
-`statebuilder.layers`
-
-
-
-## Classes
-
-| Name | Description |
-| --- | --- |
-| [AnnotationLayerConfig](#nglui.statebuilder.layers.AnnotationLayerConfig) | Configuration class for annotation layers |
-| [ImageLayerConfig](#nglui.statebuilder.layers.ImageLayerConfig) | Image layer configuration class. |
-| [LayerConfigBase](#nglui.statebuilder.layers.LayerConfigBase) | Base class for configuring layers |
-| [SegmentationLayerConfig](#nglui.statebuilder.layers.SegmentationLayerConfig) | Configuration class for segmentation layers |
-
-## AnnotationLayerConfig { #nglui.statebuilder.layers.AnnotationLayerConfig }
-
-`statebuilder.layers.AnnotationLayerConfig(self, name=None, color=None, linked_segmentation_layer=None, mapping_rules=[], array_data=False, tags=None, active=True, filter_by_segmentation=False, brackets_show_segmentation=True, selection_shows_segmentation=True, filter_query=None, data_resolution=None)`
-
-Configuration class for annotation layers
-
-### Parameters
-
-| Name                        | Type                                                                                                                             | Description                                                                                                                                                                              | Default   |
-|-----------------------------|----------------------------------------------------------------------------------------------------------------------------------|------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|-----------|
-| `name`                      | str                                                                                                                              | Layer name. By default, 'annos'                                                                                                                                                          | `None`    |
-| `color`                     | str                                                                                                                              | Hex color code with an initial #. By default, None                                                                                                                                       | `None`    |
-| `linked_segmentation_layer` | str                                                                                                                              | Name of a linked segmentation layer for selected ids. By default, None                                                                                                                   | `None`    |
-| `mapping_rules`             | (nglui.statebuilder.mappers.PointMapper, nglui.statebuilder.mappers.LineMapper, nglui.statebuilder.mappers.SphereMapper or list) | One rule or a list of rules mapping data to annotations. By default, []                                                                                                                  | `[]`      |
-| `array_data`                | bool                                                                                                                             | If True, allows simple mapping where one or more arrays are passed instead of a dataframe. Only allows basic annotation creation, no tags, linked segmentations, or other rich features. | `False`   |
-| `tags`                      | list                                                                                                                             | List of tags for the layer.                                                                                                                                                              | `None`    |
-| `active`                    | bool                                                                                                                             | If True, makes the layer selected. Default is True (unlike for image/segmentation layers).                                                                                               | `True`    |
-
-## ImageLayerConfig { #nglui.statebuilder.layers.ImageLayerConfig }
-
-`statebuilder.layers.ImageLayerConfig(self, source, name=None, active=False, contrast_controls=False, black=0.0, white=1.0)`
-
-Image layer configuration class.
-
-This provides the rules for setting up an image layer in neuroglancer.
-
-### Parameters
-
-| Name                | Type   | Description                                                                                    | Default    |
-|---------------------|--------|------------------------------------------------------------------------------------------------|------------|
-| `source`            | str    | Cloudpath to an image source                                                                   | _required_ |
-| `name`              | str    | Name of the image layer. By default, 'img'.                                                    | `None`     |
-| `active`            | bool   | If True, makes the layer active in neuroglancer. Default is False.                             | `False`    |
-| `contrast_controls` | bool   | If True, gives the layer a user-controllable brightness and contrast shader. Default is False. | `False`    |
-| `black`             | float  | If contrast_controls is True, sets the default black level. Default is 0.0.                    | `0.0`      |
-| `white`             | float  | If contrast_controls is True, sets the default white level. Default is 1.0.                    | `1.0`      |
-
-## LayerConfigBase { #nglui.statebuilder.layers.LayerConfigBase }
-
-`statebuilder.layers.LayerConfigBase(self, name, type, source, color, active)`
-
-Base class for configuring layers
-
-### Parameters
-
-| Name     | Type   | Description                                 | Default    |
-|----------|--------|---------------------------------------------|------------|
-| `name`   | str    | Layer name for reference and display        | _required_ |
-| `type`   | str    | Layer type. Usually handled by the subclass | _required_ |
-| `source` | str    | Datasource for the layer                    | _required_ |
-| `color`  | str    | Hex string (with starting hash).            | _required_ |
-| `active` | (bool) | If True, becomes a selected layer.          | _required_ |
-
-## SegmentationLayerConfig { #nglui.statebuilder.layers.SegmentationLayerConfig }
-
-`statebuilder.layers.SegmentationLayerConfig(self, source, name=None, selected_ids_column=None, fixed_ids=None, fixed_id_colors=None, color_column=None, active=False, alpha_selected=0.3, alpha_3d=1, alpha_unselected=0, split_point_map=None, view_kws=None, timestamp=None, data_resolution=None)`
-
-Configuration class for segmentation layers
-
-### Parameters
-
-| Name                  | Type                         | Description                                                                                                                                                                                             | Default    |
-|-----------------------|------------------------------|---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|------------|
-| `source`              | str                          | Segmentation source                                                                                                                                                                                     | _required_ |
-| `name`                | (str, optional)              | Layer name.                                                                                                                                                                                             | `None`     |
-| `selected_ids_column` | str or list-like, optional.  | Column name (or list of column names) to use for selected ids.                                                                                                                                          | `None`     |
-| `fixed_ids`           | list-like, optional.         | List of root ids to select directly.                                                                                                                                                                    | `None`     |
-| `fixed_id_colors`     | list-like, optional.         | List of colors for fixed ids. Should be the same length as fixed_ids, although null entries can be padded with None values.                                                                             | `None`     |
-| `color_column`        | str, optional.               | # at the begining. Column to use for color values for selected objects. Values should be RGB hex strings with a                                                                                         | `None`     |
-| `active`              | bool, optional.              | If True, makes the layer selected. Default is False.                                                                                                                                                    | `False`    |
-| `alpha_selected`      |                              | Opacity of selected segmentations in the image layer. Optional, default is 0.3.                                                                                                                         | `0.3`      |
-| `alpha_3d`            |                              | Opacity of meshes. Optional, default is 1.                                                                                                                                                              | `1`        |
-| `alpha_unselected`    |                              | Opacity of unselected segments. Optional, default is 0.                                                                                                                                                 | `0`        |
-| `split_point_map`     |                              | If not None, provides an object to map the dataframe input to multicut points. Default is None.                                                                                                         | `None`     |
-| `view_kws`            | dict, optional.              | Keyword arguments for viewer.set_segmentation_view_options. Sets selected (and unselected) segmetation alpha values. Defaults to values in DEFAULT_SEGMENTATION_VIEW_KWS dict specified in this module. | `None`     |
-| `timestamp`           | float or datetime, optional. | Timestamp at which to fix the chunkedgraph in either unix epoch or datetime format. Optional, default is None.                                                                                          | `None`     |
-
-### Methods
-
-| Name | Description |
-| --- | --- |
-| [add_selection_map](#nglui.statebuilder.layers.SegmentationLayerConfig.add_selection_map) | Add rules for selecting active segment ids and their colors |
-
-#### add_selection_map { #nglui.statebuilder.layers.SegmentationLayerConfig.add_selection_map }
-
-`statebuilder.layers.SegmentationLayerConfig.add_selection_map(selected_ids_column=None, fixed_ids=None, fixed_id_colors=None, color_column=None)`
-
-Add rules for selecting active segment ids and their colors
-
-##### Parameters
-
-| Name                  | Type        | Description                                                                                        | Default   |
-|-----------------------|-------------|----------------------------------------------------------------------------------------------------|-----------|
-| `selected_ids_column` | str         | Dataframe column to use for adding selected segment ids to the segmentation layer, by default None | `None`    |
-| `fixed_ids`           | int or list | Add one or more segment ids to be active, independent of the data, by default None                 | `None`    |
-| `fixed_id_colors`     | list        | Add a list of colors (hex, rgb, or CSS3 string) to assign to the fixed ids, by default None        | `None`    |
-| `color_column`        | str         | Dataframe column to use for adding selected segment colors, by default None                        | `None`    |
\ No newline at end of file
diff --git a/docs/reference/nglui.statebuilder.layers.AnnotationLayerConfig.qmd b/docs/reference/nglui.statebuilder.layers.AnnotationLayerConfig.qmd
deleted file mode 100644
index eb07c64..0000000
--- a/docs/reference/nglui.statebuilder.layers.AnnotationLayerConfig.qmd
+++ /dev/null
@@ -1,17 +0,0 @@
-# AnnotationLayerConfig { #nglui.statebuilder.layers.AnnotationLayerConfig }
-
-`statebuilder.layers.AnnotationLayerConfig(self, name=None, color=None, linked_segmentation_layer=None, mapping_rules=[], array_data=False, tags=None, active=True, filter_by_segmentation=False, brackets_show_segmentation=True, selection_shows_segmentation=True, filter_query=None, data_resolution=None)`
-
-Configuration class for annotation layers
-
-## Parameters
-
-| Name                        | Type                                                                                                                             | Description                                                                                                                                                                              | Default   |
-|-----------------------------|----------------------------------------------------------------------------------------------------------------------------------|------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|-----------|
-| `name`                      | str                                                                                                                              | Layer name. By default, 'annos'                                                                                                                                                          | `None`    |
-| `color`                     | str                                                                                                                              | Hex color code with an initial #. By default, None                                                                                                                                       | `None`    |
-| `linked_segmentation_layer` | str                                                                                                                              | Name of a linked segmentation layer for selected ids. By default, None                                                                                                                   | `None`    |
-| `mapping_rules`             | (nglui.statebuilder.mappers.PointMapper, nglui.statebuilder.mappers.LineMapper, nglui.statebuilder.mappers.SphereMapper or list) | One rule or a list of rules mapping data to annotations. By default, []                                                                                                                  | `[]`      |
-| `array_data`                | bool                                                                                                                             | If True, allows simple mapping where one or more arrays are passed instead of a dataframe. Only allows basic annotation creation, no tags, linked segmentations, or other rich features. | `False`   |
-| `tags`                      | list                                                                                                                             | List of tags for the layer.                                                                                                                                                              | `None`    |
-| `active`                    | bool                                                                                                                             | If True, makes the layer selected. Default is True (unlike for image/segmentation layers).                                                                                               | `True`    |
\ No newline at end of file
diff --git a/docs/reference/nglui.statebuilder.layers.ImageLayerConfig.qmd b/docs/reference/nglui.statebuilder.layers.ImageLayerConfig.qmd
deleted file mode 100644
index d387a0d..0000000
--- a/docs/reference/nglui.statebuilder.layers.ImageLayerConfig.qmd
+++ /dev/null
@@ -1,18 +0,0 @@
-# ImageLayerConfig { #nglui.statebuilder.layers.ImageLayerConfig }
-
-`statebuilder.layers.ImageLayerConfig(self, source, name=None, active=False, contrast_controls=False, black=0.0, white=1.0)`
-
-Image layer configuration class.
-
-This provides the rules for setting up an image layer in neuroglancer.
-
-## Parameters
-
-| Name                | Type   | Description                                                                                    | Default    |
-|---------------------|--------|------------------------------------------------------------------------------------------------|------------|
-| `source`            | str    | Cloudpath to an image source                                                                   | _required_ |
-| `name`              | str    | Name of the image layer. By default, 'img'.                                                    | `None`     |
-| `active`            | bool   | If True, makes the layer active in neuroglancer. Default is False.                             | `False`    |
-| `contrast_controls` | bool   | If True, gives the layer a user-controllable brightness and contrast shader. Default is False. | `False`    |
-| `black`             | float  | If contrast_controls is True, sets the default black level. Default is 0.0.                    | `0.0`      |
-| `white`             | float  | If contrast_controls is True, sets the default white level. Default is 1.0.                    | `1.0`      |
\ No newline at end of file
diff --git a/docs/reference/nglui.statebuilder.layers.LayerConfigBase.qmd b/docs/reference/nglui.statebuilder.layers.LayerConfigBase.qmd
deleted file mode 100644
index ca2b3ab..0000000
--- a/docs/reference/nglui.statebuilder.layers.LayerConfigBase.qmd
+++ /dev/null
@@ -1,15 +0,0 @@
-# LayerConfigBase { #nglui.statebuilder.layers.LayerConfigBase }
-
-`statebuilder.layers.LayerConfigBase(self, name, type, source, color, active)`
-
-Base class for configuring layers
-
-## Parameters
-
-| Name     | Type   | Description                                 | Default    |
-|----------|--------|---------------------------------------------|------------|
-| `name`   | str    | Layer name for reference and display        | _required_ |
-| `type`   | str    | Layer type. Usually handled by the subclass | _required_ |
-| `source` | str    | Datasource for the layer                    | _required_ |
-| `color`  | str    | Hex string (with starting hash).            | _required_ |
-| `active` | (bool) | If True, becomes a selected layer.          | _required_ |
\ No newline at end of file
diff --git a/docs/reference/nglui.statebuilder.layers.SegmentationLayerConfig.qmd b/docs/reference/nglui.statebuilder.layers.SegmentationLayerConfig.qmd
deleted file mode 100644
index edda51b..0000000
--- a/docs/reference/nglui.statebuilder.layers.SegmentationLayerConfig.qmd
+++ /dev/null
@@ -1,44 +0,0 @@
-# SegmentationLayerConfig { #nglui.statebuilder.layers.SegmentationLayerConfig }
-
-`statebuilder.layers.SegmentationLayerConfig(self, source, name=None, selected_ids_column=None, fixed_ids=None, fixed_id_colors=None, color_column=None, active=False, alpha_selected=0.3, alpha_3d=1, alpha_unselected=0, split_point_map=None, view_kws=None, timestamp=None, data_resolution=None)`
-
-Configuration class for segmentation layers
-
-## Parameters
-
-| Name                  | Type                         | Description                                                                                                                                                                                             | Default    |
-|-----------------------|------------------------------|---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|------------|
-| `source`              | str                          | Segmentation source                                                                                                                                                                                     | _required_ |
-| `name`                | (str, optional)              | Layer name.                                                                                                                                                                                             | `None`     |
-| `selected_ids_column` | str or list-like, optional.  | Column name (or list of column names) to use for selected ids.                                                                                                                                          | `None`     |
-| `fixed_ids`           | list-like, optional.         | List of root ids to select directly.                                                                                                                                                                    | `None`     |
-| `fixed_id_colors`     | list-like, optional.         | List of colors for fixed ids. Should be the same length as fixed_ids, although null entries can be padded with None values.                                                                             | `None`     |
-| `color_column`        | str, optional.               | # at the begining. Column to use for color values for selected objects. Values should be RGB hex strings with a                                                                                         | `None`     |
-| `active`              | bool, optional.              | If True, makes the layer selected. Default is False.                                                                                                                                                    | `False`    |
-| `alpha_selected`      |                              | Opacity of selected segmentations in the image layer. Optional, default is 0.3.                                                                                                                         | `0.3`      |
-| `alpha_3d`            |                              | Opacity of meshes. Optional, default is 1.                                                                                                                                                              | `1`        |
-| `alpha_unselected`    |                              | Opacity of unselected segments. Optional, default is 0.                                                                                                                                                 | `0`        |
-| `split_point_map`     |                              | If not None, provides an object to map the dataframe input to multicut points. Default is None.                                                                                                         | `None`     |
-| `view_kws`            | dict, optional.              | Keyword arguments for viewer.set_segmentation_view_options. Sets selected (and unselected) segmetation alpha values. Defaults to values in DEFAULT_SEGMENTATION_VIEW_KWS dict specified in this module. | `None`     |
-| `timestamp`           | float or datetime, optional. | Timestamp at which to fix the chunkedgraph in either unix epoch or datetime format. Optional, default is None.                                                                                          | `None`     |
-
-## Methods
-
-| Name | Description |
-| --- | --- |
-| [add_selection_map](#nglui.statebuilder.layers.SegmentationLayerConfig.add_selection_map) | Add rules for selecting active segment ids and their colors |
-
-### add_selection_map { #nglui.statebuilder.layers.SegmentationLayerConfig.add_selection_map }
-
-`statebuilder.layers.SegmentationLayerConfig.add_selection_map(selected_ids_column=None, fixed_ids=None, fixed_id_colors=None, color_column=None)`
-
-Add rules for selecting active segment ids and their colors
-
-#### Parameters
-
-| Name                  | Type        | Description                                                                                        | Default   |
-|-----------------------|-------------|----------------------------------------------------------------------------------------------------|-----------|
-| `selected_ids_column` | str         | Dataframe column to use for adding selected segment ids to the segmentation layer, by default None | `None`    |
-| `fixed_ids`           | int or list | Add one or more segment ids to be active, independent of the data, by default None                 | `None`    |
-| `fixed_id_colors`     | list        | Add a list of colors (hex, rgb, or CSS3 string) to assign to the fixed ids, by default None        | `None`    |
-| `color_column`        | str         | Dataframe column to use for adding selected segment colors, by default None                        | `None`    |
\ No newline at end of file
diff --git a/docs/reference/nglui.statebuilder.statebuilder.StateBuilder.initialize_state.qmd b/docs/reference/nglui.statebuilder.statebuilder.StateBuilder.initialize_state.qmd
deleted file mode 100644
index dc5e9e5..0000000
--- a/docs/reference/nglui.statebuilder.statebuilder.StateBuilder.initialize_state.qmd
+++ /dev/null
@@ -1,11 +0,0 @@
-# initialize_state { #nglui.statebuilder.statebuilder.StateBuilder.initialize_state }
-
-`statebuilder.statebuilder.StateBuilder.initialize_state(base_state=None, target_site=None)`
-
-Generate a new Neuroglancer state with layers as needed for the schema.
-
-## Parameters
-
-| Name         | Type   | Description                                                                 | Default   |
-|--------------|--------|-----------------------------------------------------------------------------|-----------|
-| `base_state` | str    | Optional initial state to build on, described by its JSON. By default None. | `None`    |
\ No newline at end of file
diff --git a/docs/reference/nglui.statebuilder.statebuilder.StateBuilder.render_state.qmd b/docs/reference/nglui.statebuilder.statebuilder.StateBuilder.render_state.qmd
deleted file mode 100644
index 5863fdb..0000000
--- a/docs/reference/nglui.statebuilder.statebuilder.StateBuilder.render_state.qmd
+++ /dev/null
@@ -1,21 +0,0 @@
-# render_state { #nglui.statebuilder.statebuilder.StateBuilder.render_state }
-
-`statebuilder.statebuilder.StateBuilder.render_state(data=None, base_state=None, return_as='url', url_prefix=None, link_text='Neuroglancer Link', target_site=None)`
-
-Build a Neuroglancer state out of a DataFrame.
-
-## Parameters
-
-| Name         | Type                                                                                   | Description                                                                                                                                                                                                                                                                                                                                                                                                  | Default               |
-|--------------|----------------------------------------------------------------------------------------|--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|-----------------------|
-| `data`       | pandas.pandas.DataFrame                                                                | DataFrame to use as a point source. By default None, for which it will return only the base_state and any fixed values.                                                                                                                                                                                                                                                                                      | `None`                |
-| `base_state` | dict                                                                                   | Initial state to build on, expressed as Neuroglancer JSON. By default None                                                                                                                                                                                                                                                                                                                                   | `None`                |
-| `return_as`  | \[url, nglui.statebuilder.statebuilder.StateBuilder.viewer, html, json, dict, shared\] | Choice of output types. Note that if a viewer is returned, the state is not reset.     url : Returns the raw url describing the state     viewer : Returns an EasyViewer object holding the state information     html : Returns an HTML link to the url, useful for notebooks.     json : Returns a JSON string describing the state.     dict : Returns a dict version of the JSON state. By default 'url' | `'url'`               |
-| `url_prefix` | str                                                                                    | Neuroglancer URL prefix to use. By default None, for which it will open with the class default.                                                                                                                                                                                                                                                                                                              | `None`                |
-| `link_text`  | str                                                                                    | Text to use for the link when returning as html, by default 'Neuroglancer Link'                                                                                                                                                                                                                                                                                                                              | `'Neuroglancer Link'` |
-
-## Returns
-
-| Type                                       | Description                                                                                                         |
-|--------------------------------------------|---------------------------------------------------------------------------------------------------------------------|
-| string or neuroglancer.neuroglancer.Viewer | A link to or viewer for a Neuroglancer state with layers, annotations, and selected objects determined by the data. |
\ No newline at end of file
diff --git a/docs/reference/parser.base.annotation_dataframe.qmd b/docs/reference/parser.base.annotation_dataframe.qmd
deleted file mode 100644
index 81d684d..0000000
--- a/docs/reference/parser.base.annotation_dataframe.qmd
+++ /dev/null
@@ -1,17 +0,0 @@
-# parser.base.annotation_dataframe { #nglui.parser.base.annotation_dataframe }
-
-`parser.base.annotation_dataframe(state)`
-
-Return all annotations across all annotation layers in the state.
-
-## Parameters
-
-| Name    | Type   | Description                   | Default    |
-|---------|--------|-------------------------------|------------|
-| `state` | dict   | Neuroglancer state dictionary | _required_ |
-
-## Returns
-
-| Type                    | Description                                                                                                        |
-|-------------------------|--------------------------------------------------------------------------------------------------------------------|
-| pandas.pandas.DataFrame | Dataframe with columns layer, anno_type, point, pointB, linked_segmentation, tags, anno_id, group_id, description. |
\ No newline at end of file
diff --git a/docs/reference/parser.base.annotation_layers.qmd b/docs/reference/parser.base.annotation_layers.qmd
deleted file mode 100644
index e8ec0d1..0000000
--- a/docs/reference/parser.base.annotation_layers.qmd
+++ /dev/null
@@ -1,17 +0,0 @@
-# parser.base.annotation_layers { #nglui.parser.base.annotation_layers }
-
-`parser.base.annotation_layers(state)`
-
-Get all annotation layer names in the state
-
-## Parameters
-
-| Name    | Type   | Description                       | Default    |
-|---------|--------|-----------------------------------|------------|
-| `state` | dict   | Neuroglancer state as a JSON dict | _required_ |
-
-## Returns
-
-| Type   | Description         |
-|--------|---------------------|
-| list   | List of layer names |
\ No newline at end of file
diff --git a/docs/reference/parser.base.extract_multicut.qmd b/docs/reference/parser.base.extract_multicut.qmd
deleted file mode 100644
index 46e8db0..0000000
--- a/docs/reference/parser.base.extract_multicut.qmd
+++ /dev/null
@@ -1,21 +0,0 @@
-# parser.base.extract_multicut { #nglui.parser.base.extract_multicut }
-
-`parser.base.extract_multicut(state, seg_layer=None)`
-
-Extract information entered into the multicut graph operation
-
-## Parameters
-
-| Name        | Type   | Description                                                                                                                                                                                                                 | Default    |
-|-------------|--------|-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|------------|
-| `state`     | dict   | Neuroglancer state                                                                                                                                                                                                          | _required_ |
-| `seg_layer` | str    | Name of a segmentation layer or None. If None, the function will check how many segmentation layers there are and, if only one exits, choose it. If more than one segmentation layer is present, it errors. By default None | `None`     |
-
-## Returns
-
-| Type              | Description                                                                                                           |
-|-------------------|-----------------------------------------------------------------------------------------------------------------------|
-| numpy.numpy.array | Nx3 array of points selected                                                                                          |
-| numpy.numpy.array | N array with 'source' or 'sink', depending on which side the point is on.                                             |
-| numpy.numpy.array | N array with selected supervoxel. If only points are selected (e.g. via clicking on the mesh), the value will be NaN. |
-| int               | Root id of the object to split                                                                                        |
\ No newline at end of file
diff --git a/docs/reference/parser.base.get_layer.qmd b/docs/reference/parser.base.get_layer.qmd
deleted file mode 100644
index 1646f20..0000000
--- a/docs/reference/parser.base.get_layer.qmd
+++ /dev/null
@@ -1,18 +0,0 @@
-# parser.base.get_layer { #nglui.parser.base.get_layer }
-
-`parser.base.get_layer(state, layer_name)`
-
-Gets the contents of the layer based on the layer name.
-
-## Parameters
-
-| Name         | Type   | Description                       | Default    |
-|--------------|--------|-----------------------------------|------------|
-| `state`      | dict   | Neuroglancer state as a JSON dict | _required_ |
-| `layer_name` | str    | Name of layer                     | _required_ |
-
-## Returns
-
-| Type   | Description         |
-|--------|---------------------|
-| dict   | Layer data contents |
\ No newline at end of file
diff --git a/docs/reference/parser.base.get_selected_ids.qmd b/docs/reference/parser.base.get_selected_ids.qmd
deleted file mode 100644
index eb596df..0000000
--- a/docs/reference/parser.base.get_selected_ids.qmd
+++ /dev/null
@@ -1,18 +0,0 @@
-# parser.base.get_selected_ids { #nglui.parser.base.get_selected_ids }
-
-`parser.base.get_selected_ids(state, layer=None)`
-
-Get a list of selected ids in a segmentation layer
-
-## Parameters
-
-| Name    | Type   | Description                                                                                                            | Default    |
-|---------|--------|------------------------------------------------------------------------------------------------------------------------|------------|
-| `state` | dict   | State dict                                                                                                             | _required_ |
-| `layer` | str    | Segmentation layer name, if needed. If None and only one segmentation layer is present, default to it. By default None | `None`     |
-
-## Returns
-
-| Type   | Description       |
-|--------|-------------------|
-| list   | List of root ids. |
\ No newline at end of file
diff --git a/docs/reference/parser.base.group_annotations.qmd b/docs/reference/parser.base.group_annotations.qmd
deleted file mode 100644
index 343e3cb..0000000
--- a/docs/reference/parser.base.group_annotations.qmd
+++ /dev/null
@@ -1,25 +0,0 @@
-# parser.base.group_annotations { #nglui.parser.base.group_annotations }
-
-`parser.base.group_annotations(state, layer_name, description=False, linked_segmentations=False, tags=False)`
-
-All group annotations and their associated points
-
-## Parameters
-
-| Name                   | Type   | Description                                                          | Default    |
-|------------------------|--------|----------------------------------------------------------------------|------------|
-| `state`                | dict   | Neuroglancer state as JSON dict                                      | _required_ |
-| `layer_name`           | str    | Annotation layer name                                                | _required_ |
-| `description`          | bool   | If True, also returns descriptions as well. By default False         | `False`    |
-| `linked_segmentations` | bool   | If True, also returns list of linked segmentations, by default False | `False`    |
-| `tags`                 | bool   | If True, also returns list of tags, by default False                 | `False`    |
-
-## Returns
-
-| Type   | Description                                                                |
-|--------|----------------------------------------------------------------------------|
-| list   | List of N 3-element points                                                 |
-| list   | List of N id strings for groups.                                           |
-| list   | List of N strings (or None), only returned if description=True.            |
-| list   | List of N lists of object ids. Only returned if linked_segmentations=True. |
-| list   | List of N lists of tag ids. Only returned if tags=True.                    |
\ No newline at end of file
diff --git a/docs/reference/parser.base.image_layers.qmd b/docs/reference/parser.base.image_layers.qmd
deleted file mode 100644
index 415b3da..0000000
--- a/docs/reference/parser.base.image_layers.qmd
+++ /dev/null
@@ -1,17 +0,0 @@
-# parser.base.image_layers { #nglui.parser.base.image_layers }
-
-`parser.base.image_layers(state)`
-
-Get all image layer names in the state
-
-## Parameters
-
-| Name    | Type   | Description                       | Default    |
-|---------|--------|-----------------------------------|------------|
-| `state` | dict   | Neuroglancer state as a JSON dict | _required_ |
-
-## Returns
-
-| Type   | Description         |
-|--------|---------------------|
-| list   | List of layer names |
\ No newline at end of file
diff --git a/docs/reference/parser.base.layer_names.qmd b/docs/reference/parser.base.layer_names.qmd
deleted file mode 100644
index 946a582..0000000
--- a/docs/reference/parser.base.layer_names.qmd
+++ /dev/null
@@ -1,17 +0,0 @@
-# parser.base.layer_names { #nglui.parser.base.layer_names }
-
-`parser.base.layer_names(state)`
-
-Get all layer names in the state
-
-## Parameters
-
-| Name    | Type   | Description                       | Default    |
-|---------|--------|-----------------------------------|------------|
-| `state` | dict   | Neuroglancer state as a JSON dict | _required_ |
-
-## Returns
-
-| Type   | Description         |
-|--------|---------------------|
-| list   | List of layer names |
\ No newline at end of file
diff --git a/docs/reference/parser.base.line_annotations.qmd b/docs/reference/parser.base.line_annotations.qmd
deleted file mode 100644
index 66ad684..0000000
--- a/docs/reference/parser.base.line_annotations.qmd
+++ /dev/null
@@ -1,26 +0,0 @@
-# parser.base.line_annotations { #nglui.parser.base.line_annotations }
-
-`parser.base.line_annotations(state, layer_name, description=False, linked_segmentations=False, tags=False, group=False)`
-
-Get all line annotation points and other info from a layer.
-
-## Parameters
-
-| Name                   | Type   | Description                                                          | Default    |
-|------------------------|--------|----------------------------------------------------------------------|------------|
-| `state`                | dict   | Neuroglancer state as JSON dict                                      | _required_ |
-| `layer_name`           | str    | Layer name                                                           | _required_ |
-| `description`          | bool   | If True, also returns descriptions as well. By default False         | `False`    |
-| `linked_segmentations` | bool   | If True, also returns list of linked segmentations, by default False | `False`    |
-| `tags`                 | bool   | If True, also returns list of tags, by default False                 | `False`    |
-
-## Returns
-
-| Type   | Description                                                                        |
-|--------|------------------------------------------------------------------------------------|
-| list   | List of N 3-element points (as list) of the first point in each line.              |
-| list   | List of N 3-element points (as list) of the second point in each line.             |
-| list   | List of N strings (or None), only returned if description=True.                    |
-| list   | List of N lists of object ids. Only returned if linked_segmentations=True.         |
-| list   | List of N lists of tag ids. Only returned if tags=True.                            |
-| list   | List of group ids (as string) or None for annotations. Only returned if group=True |
\ No newline at end of file
diff --git a/docs/reference/parser.base.point_annotations.qmd b/docs/reference/parser.base.point_annotations.qmd
deleted file mode 100644
index 6af753c..0000000
--- a/docs/reference/parser.base.point_annotations.qmd
+++ /dev/null
@@ -1,25 +0,0 @@
-# parser.base.point_annotations { #nglui.parser.base.point_annotations }
-
-`parser.base.point_annotations(state, layer_name, description=False, linked_segmentations=False, tags=False, group=False)`
-
-Get all point annotation points and other info from a layer.
-
-## Parameters
-
-| Name                   | Type   | Description                                                          | Default    |
-|------------------------|--------|----------------------------------------------------------------------|------------|
-| `state`                | dict   | Neuroglancer state as JSON dict                                      | _required_ |
-| `layer_name`           | str    | Layer name                                                           | _required_ |
-| `description`          | bool   | If True, also returns descriptions as well. By default False         | `False`    |
-| `linked_segmentations` | bool   | If True, also returns list of linked segmentations, by default False | `False`    |
-| `tags`                 | bool   | If True, also returns list of tags, by default False                 | `False`    |
-
-## Returns
-
-| Type   | Description                                                                        |
-|--------|------------------------------------------------------------------------------------|
-| list   | List of N 3-element points (as list)                                               |
-| list   | List of N strings (or None), only returned if description=True.                    |
-| list   | List of N lists of object ids. Only returned if linked_segmentations=True.         |
-| list   | List of N lists of tag ids. Only returned if tags=True.                            |
-| list   | List of group ids (as string) or None for annotations. Only returned if group=True |
\ No newline at end of file
diff --git a/docs/reference/parser.base.segmentation_layers.qmd b/docs/reference/parser.base.segmentation_layers.qmd
deleted file mode 100644
index 95dddb2..0000000
--- a/docs/reference/parser.base.segmentation_layers.qmd
+++ /dev/null
@@ -1,17 +0,0 @@
-# parser.base.segmentation_layers { #nglui.parser.base.segmentation_layers }
-
-`parser.base.segmentation_layers(state)`
-
-Get all segmentation layer names in the state
-
-## Parameters
-
-| Name    | Type   | Description                       | Default    |
-|---------|--------|-----------------------------------|------------|
-| `state` | dict   | Neuroglancer state as a JSON dict | _required_ |
-
-## Returns
-
-| Type   | Description         |
-|--------|---------------------|
-| list   | List of layer names |
\ No newline at end of file
diff --git a/docs/reference/parser.base.sphere_annotations.qmd b/docs/reference/parser.base.sphere_annotations.qmd
deleted file mode 100644
index 6911373..0000000
--- a/docs/reference/parser.base.sphere_annotations.qmd
+++ /dev/null
@@ -1,26 +0,0 @@
-# parser.base.sphere_annotations { #nglui.parser.base.sphere_annotations }
-
-`parser.base.sphere_annotations(state, layer_name, description=False, linked_segmentations=False, tags=False, group=False)`
-
-Get all sphere annotation points and other info from a layer.
-
-## Parameters
-
-| Name                   | Type   | Description                                                          | Default    |
-|------------------------|--------|----------------------------------------------------------------------|------------|
-| `state`                | dict   | Neuroglancer state as JSON dict                                      | _required_ |
-| `layer_name`           | str    | Layer name                                                           | _required_ |
-| `description`          | bool   | If True, also returns descriptions as well. By default False         | `False`    |
-| `linked_segmentations` | bool   | If True, also returns list of linked segmentations, by default False | `False`    |
-| `tags`                 | bool   | If True, also returns list of tags, by default False                 | `False`    |
-
-## Returns
-
-| Type   | Description                                                                        |
-|--------|------------------------------------------------------------------------------------|
-| list   | List of N 3-element center points (as list)                                        |
-| list   | List of N 3-element radii for each axis of the ellipsoid.                          |
-| list   | List of N strings (or None), only returned if description=True.                    |
-| list   | List of N lists of object ids. Only returned if linked_segmentations=True.         |
-| list   | List of N lists of tag ids. Only returned if tags=True.                            |
-| list   | List of group ids (as string) or None for annotations. Only returned if group=True |
\ No newline at end of file
diff --git a/docs/reference/parser.base.tag_dictionary.qmd b/docs/reference/parser.base.tag_dictionary.qmd
deleted file mode 100644
index 718d022..0000000
--- a/docs/reference/parser.base.tag_dictionary.qmd
+++ /dev/null
@@ -1,18 +0,0 @@
-# parser.base.tag_dictionary { #nglui.parser.base.tag_dictionary }
-
-`parser.base.tag_dictionary(state, layer_name)`
-
-Get the tag id to string dictionary for a layer
-
-## Parameters
-
-| Name         | Type     | Description   | Default    |
-|--------------|----------|---------------|------------|
-| `state`      | dict     |               | _required_ |
-| `layer_name` | \[type\] | [description] | _required_ |
-
-## Returns
-
-| Type     | Description   |
-|----------|---------------|
-| \[type\] | [description] |
\ No newline at end of file
diff --git a/docs/reference/parser.base.view_settings.qmd b/docs/reference/parser.base.view_settings.qmd
deleted file mode 100644
index f005eba..0000000
--- a/docs/reference/parser.base.view_settings.qmd
+++ /dev/null
@@ -1,18 +0,0 @@
-# parser.base.view_settings { #nglui.parser.base.view_settings }
-
-`parser.base.view_settings(state)`
-
-Get all data about the view state in neuroglancer: position,
-image zoom, orientation and zoom of the 3d view, and voxel size.
-
-## Parameters
-
-| Name    | Type   | Description                     | Default    |
-|---------|--------|---------------------------------|------------|
-| `state` | dict   | Neuroglancer state as JSON dict | _required_ |
-
-## Returns
-
-| Type   | Description                                                                                        |
-|--------|----------------------------------------------------------------------------------------------------|
-| dict   | Dictionary with keys: position, zoomFactor, perspectiveOrientation, perspectiveZoom, and voxelSize |
\ No newline at end of file
diff --git a/docs/reference/parser.md b/docs/reference/parser.md
new file mode 100644
index 0000000..81a99b4
--- /dev/null
+++ b/docs/reference/parser.md
@@ -0,0 +1,8 @@
+---
+title: State Parser
+---
+
+::: src.nglui.parser
+    options:
+        show_source: false
+        heading_level: 2
\ No newline at end of file
diff --git a/docs/reference/preview.qmd b/docs/reference/preview.qmd
deleted file mode 100644
index 7f58ab7..0000000
--- a/docs/reference/preview.qmd
+++ /dev/null
@@ -1,22 +0,0 @@
-# preview { #quartodoc.preview }
-
-`preview(ast, max_depth=999, compact=False, as_string=False)`
-
-Print a friendly representation of a griffe object (e.g. function, docstring)
-
-## Examples
-
-```python
->>> from quartodoc import get_object
->>> obj = get_object("quartodoc", "get_object")
-```
-
-```python
->>> preview(obj.docstring.parsed)
- ...
-```
-
-```python
->>> preview(obj)
- ...
-```
\ No newline at end of file
diff --git a/docs/reference/segprops.md b/docs/reference/segprops.md
new file mode 100644
index 0000000..fc56920
--- /dev/null
+++ b/docs/reference/segprops.md
@@ -0,0 +1,13 @@
+---
+title: Segment Properties
+---
+
+!!! note
+
+    Autogeneration of the function reference does not capture the full range of segment properties.
+    Please see the documentation for the individual segment types if you want to build segment properties manually.
+
+::: src.nglui.segmentprops.base
+    options:
+        show_source: false
+        heading_level: 2
diff --git a/docs/reference/statebuilder.AnnotationLayerConfig.qmd b/docs/reference/statebuilder.AnnotationLayerConfig.qmd
deleted file mode 100644
index 9bbc8fc..0000000
--- a/docs/reference/statebuilder.AnnotationLayerConfig.qmd
+++ /dev/null
@@ -1,17 +0,0 @@
-# statebuilder.AnnotationLayerConfig { #nglui.statebuilder.AnnotationLayerConfig }
-
-`statebuilder.AnnotationLayerConfig(self, name=None, color=None, linked_segmentation_layer=None, mapping_rules=[], array_data=False, tags=None, active=True, filter_by_segmentation=False, brackets_show_segmentation=True, selection_shows_segmentation=True, filter_query=None, data_resolution=None)`
-
-Configuration class for annotation layers
-
-## Parameters
-
-| Name                        | Type                                                                                                                             | Description                                                                                                                                                                              | Default   |
-|-----------------------------|----------------------------------------------------------------------------------------------------------------------------------|------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|-----------|
-| `name`                      | str                                                                                                                              | Layer name. By default, 'annos'                                                                                                                                                          | `None`    |
-| `color`                     | str                                                                                                                              | Hex color code with an initial #. By default, None                                                                                                                                       | `None`    |
-| `linked_segmentation_layer` | str                                                                                                                              | Name of a linked segmentation layer for selected ids. By default, None                                                                                                                   | `None`    |
-| `mapping_rules`             | (nglui.statebuilder.mappers.PointMapper, nglui.statebuilder.mappers.LineMapper, nglui.statebuilder.mappers.SphereMapper or list) | One rule or a list of rules mapping data to annotations. By default, []                                                                                                                  | `[]`      |
-| `array_data`                | bool                                                                                                                             | If True, allows simple mapping where one or more arrays are passed instead of a dataframe. Only allows basic annotation creation, no tags, linked segmentations, or other rich features. | `False`   |
-| `tags`                      | list                                                                                                                             | List of tags for the layer.                                                                                                                                                              | `None`    |
-| `active`                    | bool                                                                                                                             | If True, makes the layer selected. Default is True (unlike for image/segmentation layers).                                                                                               | `True`    |
\ No newline at end of file
diff --git a/docs/reference/statebuilder.BoundingBoxMapper.qmd b/docs/reference/statebuilder.BoundingBoxMapper.qmd
deleted file mode 100644
index 71df9bb..0000000
--- a/docs/reference/statebuilder.BoundingBoxMapper.qmd
+++ /dev/null
@@ -1,20 +0,0 @@
-# statebuilder.BoundingBoxMapper { #nglui.statebuilder.BoundingBoxMapper }
-
-`statebuilder.BoundingBoxMapper(self, point_column_a=None, point_column_b=None, description_column=None, linked_segmentation_column=None, tag_column=None, group_column=None, gather_linked_segmentations=True, share_linked_segmentations=False, set_position=True, multipoint=False, collapse_groups=False, split_positions=False, mapping_set=None)`
-
-Sets rules to map dataframes to bounding box annotations
-
-## Parameters
-
-| Name                         | Type   | Description                                                                                                                                                         | Default   |
-|------------------------------|--------|---------------------------------------------------------------------------------------------------------------------------------------------------------------------|-----------|
-| `point_column_a`             | str    | Column name with 3d position data for the first point of the bounding box. Must be set if array_data is False (the default)                                         | `None`    |
-| `point_column_b`             | str    | Column name with 3d position data for the second point of the bounding box. Must be set if array_data is False (the default)                                        | `None`    |
-| `description_column`         | str    | Column name with string data for annotation descriptions                                                                                                            | `None`    |
-| `linked_segmentation_column` | str    | Column name for root ids to link to annotations                                                                                                                     | `None`    |
-| `tag_column`                 | str    | Column name for categorical tag data. Tags must match those set in the annotation layer.                                                                            | `None`    |
-| `group_column`               | str    | Column name for grouping data. Data in this row should be numeric with possible NaNs. Rows with the same non-NaN value will be collected into a grouped annotation. | `None`    |
-| `set_position`               | bool   | If set to True, moves the position to center on the first point in the data (using point_column_a).                                                                 | `True`    |
-| `multipoint`                 |        | If True, permits multiple points in a given row, sharing data in other columns. Each point row must have the same number of points. Default is False.               | `False`   |
-| `collapse_groups`            |        | If True, groups are toggled closed in the annotation view.                                                                                                          | `False`   |
-| `mapping_set`                |        | If set, assumes data is passed as a dictionary and uses this string to as the key for the data to use.                                                              | `None`    |
\ No newline at end of file
diff --git a/docs/reference/statebuilder.ChainedStateBuilder.qmd b/docs/reference/statebuilder.ChainedStateBuilder.qmd
deleted file mode 100644
index d9fc296..0000000
--- a/docs/reference/statebuilder.ChainedStateBuilder.qmd
+++ /dev/null
@@ -1,11 +0,0 @@
-# statebuilder.ChainedStateBuilder { #nglui.statebuilder.ChainedStateBuilder }
-
-`statebuilder.ChainedStateBuilder(self, statebuilders)`
-
-Builds a collection of states that sequentially add annotations based on a sequence of dataframes.
-
-## Parameters
-
-| Name            | Type   | Description                                                           | Default    |
-|-----------------|--------|-----------------------------------------------------------------------|------------|
-| `statebuilders` | list   | List of DataStateBuilders, in same order as dataframes will be passed | _required_ |
\ No newline at end of file
diff --git a/docs/reference/statebuilder.ImageLayerConfig.qmd b/docs/reference/statebuilder.ImageLayerConfig.qmd
deleted file mode 100644
index 399e924..0000000
--- a/docs/reference/statebuilder.ImageLayerConfig.qmd
+++ /dev/null
@@ -1,18 +0,0 @@
-# statebuilder.ImageLayerConfig { #nglui.statebuilder.ImageLayerConfig }
-
-`statebuilder.ImageLayerConfig(self, source, name=None, active=False, contrast_controls=False, black=0.0, white=1.0)`
-
-Image layer configuration class.
-
-This provides the rules for setting up an image layer in neuroglancer.
-
-## Parameters
-
-| Name                | Type   | Description                                                                                    | Default    |
-|---------------------|--------|------------------------------------------------------------------------------------------------|------------|
-| `source`            | str    | Cloudpath to an image source                                                                   | _required_ |
-| `name`              | str    | Name of the image layer. By default, 'img'.                                                    | `None`     |
-| `active`            | bool   | If True, makes the layer active in neuroglancer. Default is False.                             | `False`    |
-| `contrast_controls` | bool   | If True, gives the layer a user-controllable brightness and contrast shader. Default is False. | `False`    |
-| `black`             | float  | If contrast_controls is True, sets the default black level. Default is 0.0.                    | `0.0`      |
-| `white`             | float  | If contrast_controls is True, sets the default white level. Default is 1.0.                    | `1.0`      |
\ No newline at end of file
diff --git a/docs/reference/statebuilder.LineMapper.qmd b/docs/reference/statebuilder.LineMapper.qmd
deleted file mode 100644
index 7d88e92..0000000
--- a/docs/reference/statebuilder.LineMapper.qmd
+++ /dev/null
@@ -1,20 +0,0 @@
-# statebuilder.LineMapper { #nglui.statebuilder.LineMapper }
-
-`statebuilder.LineMapper(self, point_column_a=None, point_column_b=None, description_column=None, linked_segmentation_column=None, tag_column=None, group_column=None, gather_linked_segmentations=True, share_linked_segmentations=False, set_position=True, multipoint=False, collapse_groups=False, split_positions=False, mapping_set=None)`
-
-Sets rules to map dataframes to line annotations
-
-## Parameters
-
-| Name                         | Type   | Description                                                                                                                                                         | Default   |
-|------------------------------|--------|---------------------------------------------------------------------------------------------------------------------------------------------------------------------|-----------|
-| `point_column_a`             | str    | Column name with 3d position data for the first point of the line. Must be set if array_data is False (the default)                                                 | `None`    |
-| `point_column_b`             | str    | Column name with 3d position data for the first point of the line. Must be set if array_data is False (the default)                                                 | `None`    |
-| `description_column`         | str    | Column name with string data for annotation descriptions                                                                                                            | `None`    |
-| `linked_segmentation_column` | str    | Column name for root ids to link to annotations                                                                                                                     | `None`    |
-| `tag_column`                 | str    | Column name for categorical tag data. Tags must match those set in the annotation layer.                                                                            | `None`    |
-| `group_column`               | str    | Column name for grouping data. Data in this row should be numeric with possible NaNs. Rows with the same non-NaN value will be collected into a grouped annotation. | `None`    |
-| `set_position`               | bool   | If set to True, moves the position to center on the first point in the data (using point_column_a).                                                                 | `True`    |
-| `multipoint`                 |        | If True, permits multiple points in a given row, sharing data in other columns. Each point row must have the same number of points. Default is False.               | `False`   |
-| `collapse_groups`            |        | If True, groups are toggled closed in the annotation view.                                                                                                          | `False`   |
-| `mapping_set`                |        | If set, assumes data is passed as a dictionary and uses this string to as the key for the data to use.                                                              | `None`    |
\ No newline at end of file
diff --git a/docs/reference/statebuilder.PointMapper.qmd b/docs/reference/statebuilder.PointMapper.qmd
deleted file mode 100644
index 71b1f12..0000000
--- a/docs/reference/statebuilder.PointMapper.qmd
+++ /dev/null
@@ -1,19 +0,0 @@
-# statebuilder.PointMapper { #nglui.statebuilder.PointMapper }
-
-`statebuilder.PointMapper(self, point_column=None, description_column=None, linked_segmentation_column=None, tag_column=None, group_column=None, gather_linked_segmentations=True, share_linked_segmentations=False, set_position=True, multipoint=False, collapse_groups=False, split_positions=False, mapping_set=None)`
-
-Sets rules to map dataframes to point annotations
-
-## Parameters
-
-| Name                         | Type   | Description                                                                                                                                                         | Default   |
-|------------------------------|--------|---------------------------------------------------------------------------------------------------------------------------------------------------------------------|-----------|
-| `point_column`               | str    | Column name with 3d position data                                                                                                                                   | `None`    |
-| `description_column`         | str    | Column name with string data for annotation descriptions                                                                                                            | `None`    |
-| `linked_segmentation_column` | str    | Column name for root ids to link to annotations                                                                                                                     | `None`    |
-| `tag_column`                 | str    | Column name for categorical tag data. Tags must match those set in the annotation layer.                                                                            | `None`    |
-| `group_column`               | str    | Column name for grouping data. Data in this row should be numeric with possible NaNs. Rows with the same non-NaN value will be collected into a grouped annotation. | `None`    |
-| `set_position`               | bool   | If set to True, moves the position to center on the first point in the data.                                                                                        | `True`    |
-| `multipoint`                 |        | If True, permits multiple points in a given row, sharing data in other columns. Default is False.                                                                   | `False`   |
-| `collapse_groups`            |        | If True, groups are toggled closed in the annotation view.                                                                                                          | `False`   |
-| `mapping_set`                |        | If given, assumes data is passed as a dictionary and uses this string to as the key for the data to use.                                                            | `None`    |
\ No newline at end of file
diff --git a/docs/reference/statebuilder.SegmentationLayerConfig.qmd b/docs/reference/statebuilder.SegmentationLayerConfig.qmd
deleted file mode 100644
index 2d3ed62..0000000
--- a/docs/reference/statebuilder.SegmentationLayerConfig.qmd
+++ /dev/null
@@ -1,23 +0,0 @@
-# statebuilder.SegmentationLayerConfig { #nglui.statebuilder.SegmentationLayerConfig }
-
-`statebuilder.SegmentationLayerConfig(self, source, name=None, selected_ids_column=None, fixed_ids=None, fixed_id_colors=None, color_column=None, active=False, alpha_selected=0.3, alpha_3d=1, alpha_unselected=0, split_point_map=None, view_kws=None, timestamp=None, data_resolution=None)`
-
-Configuration class for segmentation layers
-
-## Parameters
-
-| Name                  | Type                         | Description                                                                                                                                                                                             | Default    |
-|-----------------------|------------------------------|---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|------------|
-| `source`              | str                          | Segmentation source                                                                                                                                                                                     | _required_ |
-| `name`                | (str, optional)              | Layer name.                                                                                                                                                                                             | `None`     |
-| `selected_ids_column` | str or list-like, optional.  | Column name (or list of column names) to use for selected ids.                                                                                                                                          | `None`     |
-| `fixed_ids`           | list-like, optional.         | List of root ids to select directly.                                                                                                                                                                    | `None`     |
-| `fixed_id_colors`     | list-like, optional.         | List of colors for fixed ids. Should be the same length as fixed_ids, although null entries can be padded with None values.                                                                             | `None`     |
-| `color_column`        | str, optional.               | # at the begining. Column to use for color values for selected objects. Values should be RGB hex strings with a                                                                                         | `None`     |
-| `active`              | bool, optional.              | If True, makes the layer selected. Default is False.                                                                                                                                                    | `False`    |
-| `alpha_selected`      |                              | Opacity of selected segmentations in the image layer. Optional, default is 0.3.                                                                                                                         | `0.3`      |
-| `alpha_3d`            |                              | Opacity of meshes. Optional, default is 1.                                                                                                                                                              | `1`        |
-| `alpha_unselected`    |                              | Opacity of unselected segments. Optional, default is 0.                                                                                                                                                 | `0`        |
-| `split_point_map`     |                              | If not None, provides an object to map the dataframe input to multicut points. Default is None.                                                                                                         | `None`     |
-| `view_kws`            | dict, optional.              | Keyword arguments for viewer.set_segmentation_view_options. Sets selected (and unselected) segmetation alpha values. Defaults to values in DEFAULT_SEGMENTATION_VIEW_KWS dict specified in this module. | `None`     |
-| `timestamp`           | float or datetime, optional. | Timestamp at which to fix the chunkedgraph in either unix epoch or datetime format. Optional, default is None.                                                                                          | `None`     |
\ No newline at end of file
diff --git a/docs/reference/statebuilder.SphereMapper.qmd b/docs/reference/statebuilder.SphereMapper.qmd
deleted file mode 100644
index ca11e22..0000000
--- a/docs/reference/statebuilder.SphereMapper.qmd
+++ /dev/null
@@ -1,20 +0,0 @@
-# statebuilder.SphereMapper { #nglui.statebuilder.SphereMapper }
-
-`statebuilder.SphereMapper(self, center_column=None, radius_column=None, description_column=None, linked_segmentation_column=None, tag_column=None, group_column=None, gather_linked_segmentations=True, share_linked_segmentations=False, z_multiplier=0.1, set_position=True, multipoint=False, collapse_groups=False, split_positions=False, mapping_set=None)`
-
-Sets rules to map dataframes to sphere annotations
-
-## Parameters
-
-| Name                         | Type   | Description                                                                                                                                                         | Default   |
-|------------------------------|--------|---------------------------------------------------------------------------------------------------------------------------------------------------------------------|-----------|
-| `center_column`              | str    | Column name with 3d position data for the center of the sphere                                                                                                      | `None`    |
-| `radius_column`              | str    | Column name with a radius for the sphere (in nm)                                                                                                                    | `None`    |
-| `description_column`         | str    | Column name with string data for annotation descriptions                                                                                                            | `None`    |
-| `linked_segmentation_column` | str    | Column name for root ids to link to annotations                                                                                                                     | `None`    |
-| `tag_column`                 | str    | Column name for categorical tag data. Tags must match those set in the annotation layer.                                                                            | `None`    |
-| `group_column`               | str    | Column name for grouping data. Data in this row should be numeric with possible NaNs. Rows with the same non-NaN value will be collected into a grouped annotation. | `None`    |
-| `set_position`               | bool   | If set to True, moves the position to center on the first point in the data.                                                                                        | `True`    |
-| `multipoint`                 |        | If True, permits multiple points in a given row, sharing data in other columns. Each point row must have the same number of points. Default is False.               | `False`   |
-| `collapse_groups`            |        | If True, groups are toggled closed in the annotation view.                                                                                                          | `False`   |
-| `mapping_set`                |        | If set, assumes data is passed as a dictionary and uses this string to as the key for the data to use.                                                              | `None`    |
\ No newline at end of file
diff --git a/docs/reference/statebuilder.SplitPointMapper.qmd b/docs/reference/statebuilder.SplitPointMapper.qmd
deleted file mode 100644
index 84452b4..0000000
--- a/docs/reference/statebuilder.SplitPointMapper.qmd
+++ /dev/null
@@ -1,22 +0,0 @@
-# statebuilder.SplitPointMapper { #nglui.statebuilder.SplitPointMapper }
-
-`statebuilder.SplitPointMapper(self, id_column, point_column, team_column, team_names=['red', 'blue'], supervoxel_column=None, focus=True, mapping_set=None)`
-
-Mapper to create split points in a segmentation layer.
-
-## Parameters
-
-| Name                | Type        | Description                                                                                                                                    | Default           |
-|---------------------|-------------|------------------------------------------------------------------------------------------------------------------------------------------------|-------------------|
-| `id_column`         | str         | Column name for segment ids. The id column must contain the same id in all rows.                                                               | _required_        |
-| `point_column`      | str         | Name of the column containing points in space.                                                                                                 | _required_        |
-| `team_column`       | str         | Name of the column describing the team for the points. The contents of the column should have two values, by default "red" and "blue".         | _required_        |
-| `team_names`        | list        | List of two values for the team names used in the team column. The first is mapped to red points, the second blue. Default is ["red", "blue"]. | `['red', 'blue']` |
-| `supervoxel_column` | str or None | Name of a column providing supervoxel ids. If None (default), the supervoxel must be looked up on the server.                                  | `None`            |
-| `focus`             | bool        | If True, sets the focus on the split tool and sets the position to the center of split points. Default is True.                                | `True`            |
-
-## Returns
-
-| Type                                                       | Description   |
-|------------------------------------------------------------|---------------|
-| SplitPointMapper instance to pass to a segmentation layer. |               |
\ No newline at end of file
diff --git a/docs/reference/statebuilder.StateBuilder.qmd b/docs/reference/statebuilder.StateBuilder.qmd
deleted file mode 100644
index 9616dfb..0000000
--- a/docs/reference/statebuilder.StateBuilder.qmd
+++ /dev/null
@@ -1,17 +0,0 @@
-# statebuilder.StateBuilder { #nglui.statebuilder.StateBuilder }
-
-`statebuilder.StateBuilder(self, layers=[], base_state=None, url_prefix=None, state_server=None, resolution=None, view_kws={}, client=None, target_site=None)`
-
-A class for schematic mapping data frames into neuroglancer states.
-
-## Parameters
-
-| Name           | Type   | Description                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                         | Default   |
-|----------------|--------|---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|-----------|
-| `layers`       |        |                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                     | `[]`      |
-| `base_state`   |        |                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                     | `None`    |
-| `url_prefix`   |        | Defaults to None, which will use https://neuromancer-seung-import.appspot.com                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                       | `None`    |
-| `state_server` |        |                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                     | `None`    |
-| `resolution`   |        |                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                     | `None`    |
-| `view_kws`     |        | keys are: show_slices: Boolean     sets if slices are shown in the 3d view. Defaults to False. layout: str     `xy-3d`/`xz-3d`/`yz-3d` (sections plus 3d pane), `xy`/`yz`/`xz`/`3d` (only one pane), or `4panel` (all panes). Default is `xy-3d`. show_axis_lines: Boolean     determines if the axis lines are shown in the middle of each view. show_scale_bar: Boolean     toggles showing the scale bar. orthographic : Boolean     toggles orthographic view in the 3d pane. position* : 3-element vector     determines the centered location. zoom_image : float     Zoom level for the imagery in units of nm per voxel. Defaults to 8. zoom_3d : float     Zoom level for the 3d pane. Defaults to 2000. Smaller numbers are more zoomed in. background_color : str or list     Sets the background color of the 3d view. Arguments can be rgb values, hex colors, or named web colors. Defaults to black. | `{}`      |
-| `client`       |        |                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                     | `None`    |
\ No newline at end of file
diff --git a/docs/reference/statebuilder.helpers.from_client.qmd b/docs/reference/statebuilder.helpers.from_client.qmd
deleted file mode 100644
index 9bdbc7a..0000000
--- a/docs/reference/statebuilder.helpers.from_client.qmd
+++ /dev/null
@@ -1,21 +0,0 @@
-# statebuilder.helpers.from_client { #nglui.statebuilder.helpers.from_client }
-
-`statebuilder.helpers.from_client(client, image_name=None, segmentation_name=None, contrast=None)`
-
-Generate basic image and segmentation layers from a FrameworkClient
-
-## Parameters
-
-| Name                | Type                             | Description                                                                                                                      | Default    |
-|---------------------|----------------------------------|----------------------------------------------------------------------------------------------------------------------------------|------------|
-| `client`            | caveclient.caveclient.CAVEclient | A CAVEclient with a specified datastack                                                                                          | _required_ |
-| `image_name`        | str                              | Name for the image layer, by default None.                                                                                       | `None`     |
-| `segmentation_name` | str                              | Name for the segmentation layer, by default None                                                                                 | `None`     |
-| `contrast`          | list - like                      | Two elements specifying the black level and white level as floats between 0 and 1, by default None. If None, no contrast is set. | `None`     |
-
-## Returns
-
-| Type                                       | Description                                            |
-|--------------------------------------------|--------------------------------------------------------|
-| nglui.statebuilder.layers.ImageLayerConfig | Image layer with default values from the client        |
-| nglui.statebuilder.layers.ImageLayerConfig | Segmentation layer with default values from the client |
\ No newline at end of file
diff --git a/docs/reference/statebuilder.helpers.make_line_statebuilder.qmd b/docs/reference/statebuilder.helpers.make_line_statebuilder.qmd
deleted file mode 100644
index 5c61d9e..0000000
--- a/docs/reference/statebuilder.helpers.make_line_statebuilder.qmd
+++ /dev/null
@@ -1,26 +0,0 @@
-# statebuilder.helpers.make_line_statebuilder { #nglui.statebuilder.helpers.make_line_statebuilder }
-
-`statebuilder.helpers.make_line_statebuilder(client, point_column_a='pre_pt_position', point_column_b='post_pt_position', linked_seg_column='pt_root_id', description_column=None, tag_column=None, data_resolution=None, group_column=None, contrast=None, view_kws=None, point_layer_name='lines', color=None, split_positions=False)`
-
-Generate a state builder that puts points on a single column with a linked segmentaton id
-
-## Parameters
-
-| Name                 | Type                  | Description                                                                                                                      | Default              |
-|----------------------|-----------------------|----------------------------------------------------------------------------------------------------------------------------------|----------------------|
-| `client`             | caveclient.CAVEclient | CAVEclient configured for the datastack desired                                                                                  | _required_           |
-| `point_column_a`     | str                   | column in dataframe to pull points from. Defaults to "pre_pt_position".                                                          | `'pre_pt_position'`  |
-| `point_column_b`     | str                   | column in dataframe to pull points from. Defaults to "post_pt_position".                                                         | `'post_pt_position'` |
-| `linked_seg_column`  | str                   | column to link to segmentation, None for no column. Defaults to "pt_root_id".                                                    | `'pt_root_id'`       |
-| `group_column`       | str, or list          | column(s) to group annotations by, None for no grouping (default=None)                                                           | `None`               |
-| `tag_column`         | str                   | column to use for tags, None for no tags (default=None)                                                                          | `None`               |
-| `description_column` | str                   | column to use for descriptions, None for no descriptions (default=None)                                                          | `None`               |
-| `contrast`           | list                  | Two elements specifying the black level and white level as floats between 0 and 1, by default None. If None, no contrast is set. | `None`               |
-| `view_kws`           | dict                  | dictionary of view keywords to configure neuroglancer view                                                                       | `None`               |
-| `split_positions`    | bool                  | whether the position column into x,y,z columns. Defaults to False.                                                               | `False`              |
-
-## Returns
-
-| Type   | Description                                             |
-|--------|---------------------------------------------------------|
-|        | A statebuilder to make points with linked segmentations |
\ No newline at end of file
diff --git a/docs/reference/statebuilder.helpers.make_neuron_neuroglancer_link.qmd b/docs/reference/statebuilder.helpers.make_neuron_neuroglancer_link.qmd
deleted file mode 100644
index 2390c8c..0000000
--- a/docs/reference/statebuilder.helpers.make_neuron_neuroglancer_link.qmd
+++ /dev/null
@@ -1,43 +0,0 @@
-# statebuilder.helpers.make_neuron_neuroglancer_link { #nglui.statebuilder.helpers.make_neuron_neuroglancer_link }
-
-`statebuilder.helpers.make_neuron_neuroglancer_link(client, root_ids, return_as='html', shorten='always', show_inputs=False, show_outputs=False, sort_inputs=True, sort_outputs=True, sort_ascending=False, input_color=DEFAULT_POSTSYN_COLOR, output_color=DEFAULT_PRESYN_COLOR, contrast=None, timestamp=None, view_kws=None, point_column='ctr_pt_position', pre_pt_root_id_col='pre_pt_root_id', post_pt_root_id_col='post_pt_root_id', input_layer_name='syns_in', output_layer_name='syns_out', ngl_url=None, link_text='Neuroglancer Link', target_site=None)`
-
-function to create a neuroglancer link view of a neuron, optionally including inputs and outputs
-
-## Parameters
-
-| Name                  | Type                       | Description                                                                                                                                                                                                          | Default                 |
-|-----------------------|----------------------------|----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|-------------------------|
-| `client`              | caveclient.CAVEclient      | A CAVEclient configured for the datastack to visualize.                                                                                                                                                              | _required_              |
-| `root_ids`            | typing.Iterable\[int\]     | The root_ids to build the visualization around.                                                                                                                                                                      | _required_              |
-| `return_as`           | str                        | How to return the URL or state. Valid options are: - 'html': Returns an IPython HTML element. - 'json': Returns a dictionary representing the Neuroglancer state. - 'url': Returns a URL string. Defaults to 'html'. | `'html'`                |
-| `shorten`             | str                        | Whether to shorten the link. Valid options are: - 'always': Always shorten the link. - 'if_long': Shorten the link if it exceeds MAX_URL_LENGTH. - 'never': Never shorten the link. Defaults to 'if_long'.           | `'always'`              |
-| `show_inputs`         | bool                       | Whether to include input synapses. Defaults to False.                                                                                                                                                                | `False`                 |
-| `show_outputs`        | bool                       | Whether to include output synapses. Defaults to False.                                                                                                                                                               | `False`                 |
-| `sort_inputs`         | bool                       | Whether to sort input synapses by presynaptic root id, ordered by synapse count. Defaults to True.                                                                                                                   | `True`                  |
-| `sort_outputs`        | bool                       | Whether to sort output synapses by presynaptic root id, ordered by postsynaptic synapse count. Defaults to True.                                                                                                     | `True`                  |
-| `sort_ascending`      | bool                       | If sorting, whether to sort ascending (lowest synapse count to highest). Defaults to False.                                                                                                                          | `False`                 |
-| `input_color`         | list(float) or str         | Color of input synapse points as an RGB list [0, 1], hex string, or common name.                                                                                                                                     | `DEFAULT_POSTSYN_COLOR` |
-| `output_color`        | list(float) or str         | Color of output synapse points as an RGB list [0, 1], hex string, or common name.                                                                                                                                    | `DEFAULT_PRESYN_COLOR`  |
-| `contrast`            | list                       | List of two floats between 0 and 1, specifying the black and white levels. If None, no contrast is set.                                                                                                              | `None`                  |
-| `timestamp`           | datetime.datetime.datetime | Timestamp to use for the query. Defaults to None, which will use the materialized version.                                                                                                                           | `None`                  |
-| `view_kws`            | dict                       | Dictionary containing viewer settings for Neuroglancer. See nglui.StateBuilder for options. See the previous docstring for details on available keys.                                                                | `None`                  |
-| `point_column`        | str                        | Column to pull synapse positions from. Defaults to "ctr_pt_position".                                                                                                                                                | `'ctr_pt_position'`     |
-| `pre_pt_root_id_col`  | str                        | Column to pull presynaptic IDs for synapses from. Defaults to "pre_pt_root_id".                                                                                                                                      | `'pre_pt_root_id'`      |
-| `post_pt_root_id_col` | str                        | Column to pull postsynaptic IDs for synapses from. Defaults to "post_pt_root_id".                                                                                                                                    | `'post_pt_root_id'`     |
-| `input_layer_name`    | str                        | Name of the layer for input synapses. Defaults to "syns_in".                                                                                                                                                         | `'syns_in'`             |
-| `output_layer_name`   | str                        | Name of the layer for output synapses. Defaults to "syns_out".                                                                                                                                                       | `'syns_out'`            |
-| `ngl_url`             | str                        | URL of the Neuroglancer instance to use. Defaults to the default viewer set in the datastack.                                                                                                                        | `None`                  |
-| `link_text`           | str                        | Text to use for the HTML return. Defaults to 'Neuroglancer Link'.                                                                                                                                                    | `'Neuroglancer Link'`   |
-
-## Raises
-
-| Type       | Description                                                        |
-|------------|--------------------------------------------------------------------|
-| ValueError | If the specified point column is not present in the synapse table. |
-
-## Returns
-
-| Type                       | Description                                                                       |
-|----------------------------|-----------------------------------------------------------------------------------|
-| IPython.HTML, str, or dict | Representation of the Neuroglancer state, depending on the `return_as` parameter. |
\ No newline at end of file
diff --git a/docs/reference/statebuilder.helpers.make_point_statebuilder.qmd b/docs/reference/statebuilder.helpers.make_point_statebuilder.qmd
deleted file mode 100644
index fc4506e..0000000
--- a/docs/reference/statebuilder.helpers.make_point_statebuilder.qmd
+++ /dev/null
@@ -1,25 +0,0 @@
-# statebuilder.helpers.make_point_statebuilder { #nglui.statebuilder.helpers.make_point_statebuilder }
-
-`statebuilder.helpers.make_point_statebuilder(client, point_column='pt_position', linked_seg_column='pt_root_id', data_resolution=None, group_column=None, tag_column=None, description_column=None, contrast=None, view_kws=None, point_layer_name='pts', color=None, split_positions=False)`
-
-Generate a state builder that puts points on a single column with a linked segmentaton id
-
-## Parameters
-
-| Name                 | Type                  | Description                                                                                                                      | Default         |
-|----------------------|-----------------------|----------------------------------------------------------------------------------------------------------------------------------|-----------------|
-| `client`             | caveclient.CAVEclient | CAVEclient configured for the datastack desired                                                                                  | _required_      |
-| `point_column`       | str                   | Column in dataframe to pull points from. Defaults to "pt_position".                                                              | `'pt_position'` |
-| `linked_seg_column`  | str                   | column to link to segmentation, None for no column. Defaults to "pt_root_id".                                                    | `'pt_root_id'`  |
-| `group_column`       | str, or list          | column(s) to group annotations by, None for no grouping (default=None)                                                           | `None`          |
-| `tag_column`         | str, optional)        | column to use for tags, None for no tags (default=None)                                                                          | `None`          |
-| `description_column` | str                   | column to use for descriptions, None for no descriptions (default=None)                                                          | `None`          |
-| `contrast`           | list                  | Two elements specifying the black level and white level as floats between 0 and 1, by default None. If None, no contrast is set. | `None`          |
-| `view_kws`           | dict                  | dictionary of view keywords to configure neuroglancer view                                                                       | `None`          |
-| `split_positions`    | bool                  | whether the position column into x,y,z columns. Defaults to False.                                                               | `False`         |
-
-## Returns
-
-| Type   | Description                                             |
-|--------|---------------------------------------------------------|
-|        | A statebuilder to make points with linked segmentations |
\ No newline at end of file
diff --git a/docs/reference/statebuilder.helpers.make_pre_post_statebuilder.qmd b/docs/reference/statebuilder.helpers.make_pre_post_statebuilder.qmd
deleted file mode 100644
index 744b56a..0000000
--- a/docs/reference/statebuilder.helpers.make_pre_post_statebuilder.qmd
+++ /dev/null
@@ -1,28 +0,0 @@
-# statebuilder.helpers.make_pre_post_statebuilder { #nglui.statebuilder.helpers.make_pre_post_statebuilder }
-
-`statebuilder.helpers.make_pre_post_statebuilder(client, show_inputs=False, show_outputs=False, contrast=None, view_kws=None, point_column='ctr_pt_position', pre_pt_root_id_col='pre_pt_root_id', post_pt_root_id_col='post_pt_root_id', dataframe_resolution_pre=None, dataframe_resolution_post=None, input_layer_name='syns_in', output_layer_name='syns_out', input_layer_color=DEFAULT_POSTSYN_COLOR, output_layer_color=DEFAULT_PRESYN_COLOR, split_positions=False)`
-
-Function to generate ChainedStateBuilder with optional pre and post synaptic
-annotation layers
-
-## Parameters
-
-| Name                  | Type                  | Description                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                         | Default             |
-|-----------------------|-----------------------|-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|---------------------|
-| `client`              | caveclient.CAVEclient | a CAVEclient configured for datastack to visualize                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  | _required_          |
-| `show_inputs`         | bool                  | whether to show input synapses. Defaults to False.                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  | `False`             |
-| `show_outputs`        | bool                  | whether to show output synapses.. Defaults to False.                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                | `False`             |
-| `contrast`            | list                  | Two elements specifying the black level and white level as floats between 0 and 1, by default None. If None, no contrast is set.                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    | `None`              |
-| `view_kws`            | dict                  | view_kws to configure statebuilder, see nglui.StateBuilder. Defaults to None. keys are:     show_slices: Boolean         sets if slices are shown in the 3d view. Defaults to False.     layout: str         `xy-3d`/`xz-3d`/`yz-3d` (sections plus 3d pane), `xy`/`yz`/`xz`/`3d` (only one pane), or `4panel` (all panes). Default is `xy-3d`.     show_axis_lines: Boolean         determines if the axis lines are shown in the middle of each view.     show_scale_bar: Boolean         toggles showing the scale bar.     orthographic : Boolean         toggles orthographic view in the 3d pane.     position* : 3-element vector         determines the centered location.     zoom_image : float         Zoom level for the imagery in units of nm per voxel. Defaults to 8.     zoom_3d : float         Zoom level for the 3d pane. Defaults to 2000. Smaller numbers are more zoomed in. | `None`              |
-| `point_column`        | str                   | column to pull points for synapses from. Defaults to "ctr_pt_position".                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                             | `'ctr_pt_position'` |
-| `pre_pt_root_id_col`  | str                   | column to pull pre synaptic ids for synapses from. Defaults to "pre_pt_root_id".                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    | `'pre_pt_root_id'`  |
-| `post_pt_root_id_col` | str                   | column to pull post synaptic ids for synapses from. Defaults to "post_pt_root_id".                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  | `'post_pt_root_id'` |
-| `input_layer_name`    | str                   | name of layer for inputs. Defaults to "syns_in".                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    | `'syns_in'`         |
-| `output_layer_name`   | str                   | name of layer for outputs. Defaults to "syns_out".                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  | `'syns_out'`        |
-| `split_positions`     | bool                  | whether the position column is split into x,y,z columns. Defaults to False.                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                         | `False`             |
-
-## Returns
-
-| Type   | Description                                                                                                                                                                          |
-|--------|--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|
-|        | An instance of a ChainedStateBuilder configured to accept a list  starting with None followed by optionally synapse input dataframe followed by optionally synapse output dataframe. |
\ No newline at end of file
diff --git a/docs/reference/statebuilder.helpers.make_state_url.qmd b/docs/reference/statebuilder.helpers.make_state_url.qmd
deleted file mode 100644
index b49771d..0000000
--- a/docs/reference/statebuilder.helpers.make_state_url.qmd
+++ /dev/null
@@ -1,21 +0,0 @@
-# statebuilder.helpers.make_state_url { #nglui.statebuilder.helpers.make_state_url }
-
-`statebuilder.helpers.make_state_url(df, sb, client, ngl_url=None, target_site=None)`
-
-Generate a url from a neuroglancer state via a state server.
-
-## Parameters
-
-| Name          | Type                                                                         | Description                                                                                                                                                                                                                                                        | Default    |
-|---------------|------------------------------------------------------------------------------|--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|------------|
-| `df`          | pandas.pandas.DataFrame                                                      | Dataframe to pass through statebuilder                                                                                                                                                                                                                             | _required_ |
-| `sb`          | nglui.statebuilder.statebuilder.nglui.statebuilder.statebuilder.StateBuilder | Statebuilder to use to render data for link                                                                                                                                                                                                                        | _required_ |
-| `client`      | caveclient.CAVEclient                                                        | CAVEclient configured with a state server                                                                                                                                                                                                                          | _required_ |
-| `ngl_url`     | str                                                                          | Neuroglancer deployment URL, by default None                                                                                                                                                                                                                       | `None`     |
-| `target_site` | str                                                                          | Type of neuroglancer deployment to build link for, by default None. This value overrides automatic checking based on the provided url. Use `seunglab` for a Seung-lab branch and either `mainline` or `cave-explorer` for the Cave Explorer or main Google branch. | `None`     |
-
-## Returns
-
-| Type   | Description                             |
-|--------|-----------------------------------------|
-| str    | Url to the uploaded neuroglancer state. |
\ No newline at end of file
diff --git a/docs/reference/statebuilder.helpers.make_synapse_neuroglancer_link.qmd b/docs/reference/statebuilder.helpers.make_synapse_neuroglancer_link.qmd
deleted file mode 100644
index 768c03f..0000000
--- a/docs/reference/statebuilder.helpers.make_synapse_neuroglancer_link.qmd
+++ /dev/null
@@ -1,38 +0,0 @@
-# statebuilder.helpers.make_synapse_neuroglancer_link { #nglui.statebuilder.helpers.make_synapse_neuroglancer_link }
-
-`statebuilder.helpers.make_synapse_neuroglancer_link(synapse_df, client, return_as='html', shorten='always', contrast=None, point_column='ctr_pt_position', dataframe_resolution=None, group_connections=True, link_pre_and_post=True, ngl_url=None, view_kws=None, pre_post_columns=None, neuroglancer_link_text='Neuroglancer Link', color=None, split_positions=False, target_site=None)`
-
-Generate a neuroglancer link from a synapse dataframe as returned from CAVEclient.materialize.synapse_query.
-
-## Parameters
-
-| Name                     | Type                             | Description                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  | Default               |
-|--------------------------|----------------------------------|------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|-----------------------|
-| `synapse_df`             | pandas.pandas.DataFrame          | DataFrame where each row represents a synapse.                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               | _required_            |
-| `client`                 | caveclient.caveclient.CAVEclient | A CAVEclient instance.                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                       | _required_            |
-| `return_as`              | str                              | How to return the URL. Valid options are: - 'html': Returns an IPython HTML element. - 'url': Returns a URL string. - 'json': Returns a dictionary representing the Neuroglancer state. Defaults to 'html'.                                                                                                                                                                                                                                                                                                                                                                  | `'html'`              |
-| `shorten`                | str                              | Whether to shorten the link. Valid options are: - 'always': Always shorten the link. - 'if_long': Shorten the link if it exceeds MAX_URL_LENGTH. - 'never': Never shorten the link. Defaults to 'always'.                                                                                                                                                                                                                                                                                                                                                                    | `'always'`            |
-| `contrast`               | list                             | List of two floats between 0 and 1, specifying the black and white levels. If None, no contrast is set.                                                                                                                                                                                                                                                                                                                                                                                                                                                                      | `None`                |
-| `point_column`           | str                              | Column in the DataFrame containing synapse positions. Defaults to 'ctr_pt_position'.                                                                                                                                                                                                                                                                                                                                                                                                                                                                                         | `'ctr_pt_position'`   |
-| `dataframe_resolution`   | list                             | List of length 3, specifying the resolution units of the position column. If None, attempts to get the resolution from DataFrame metadata or client.info.viewer_resolution().                                                                                                                                                                                                                                                                                                                                                                                                | `None`                |
-| `group_connections`      | bool                             | Whether to group synapses within the same connection (between the same neurons). Defaults to True.                                                                                                                                                                                                                                                                                                                                                                                                                                                                           | `True`                |
-| `link_pre_and_post`      | bool                             | Whether to link the synapse annotations to the pre- and post-synaptic partners. Defaults to True.                                                                                                                                                                                                                                                                                                                                                                                                                                                                            | `True`                |
-| `ngl_url`                | str                              | URL of the Neuroglancer instance to use. Defaults to client.info.viewer_site() or DEFAULT_NGL.                                                                                                                                                                                                                                                                                                                                                                                                                                                                               | `None`                |
-| `view_kws`               | dict                             | Dictionary containing viewer settings for Neuroglancer. Available keys: - show_slices: Boolean, sets if slices are shown in the 3D view. - layout: str, specifies the viewer layout (e.g., 'xy-3d', '4panel'). - show_axis_lines: Boolean, determines if axis lines are shown. - show_scale_bar: Boolean, toggles the scale bar. - orthographic: Boolean, toggles orthographic view in the 3D pane. - position: 3-element vector, sets the centered location. - zoom_image: float, zoom level for the imagery in nm per voxel. - zoom_3d: float, zoom level for the 3D pane. | `None`                |
-| `pre_post_columns`       | list                             | List of two strings, specifying the column names for pre- and post-synaptic root_ids. Defaults to ['pre_pt_root_id', 'post_pt_root_id'].                                                                                                                                                                                                                                                                                                                                                                                                                                     | `None`                |
-| `neuroglancer_link_text` | str                              | Text to use in the returned HTML link. Defaults to 'Neuroglancer Link'.                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      | `'Neuroglancer Link'` |
-| `color`                  | list(float) or str               | Color of synapse points as an RGB list [0, 1], hex string, or common name.                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                   | `None`                |
-| `split_positions`        | bool                             | Whether the position column is split into x, y, and z columns.                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               | `False`               |
-| `target_site`            | str                              | Type of neuroglancer deployment to build link for, by default None. This value overrides automatic checking based on the provided url. Use `seunglab` for a Seung-lab branch and either `mainline` or `cave-explorer` for the Cave Explorer or main Google branch.                                                                                                                                                                                                                                                                                                           | `None`                |
-
-## Returns
-
-| Type                       | Description                                                                       |
-|----------------------------|-----------------------------------------------------------------------------------|
-| IPython.HTML, str, or dict | Representation of the Neuroglancer state, depending on the `return_as` parameter. |
-
-## Raises
-
-| Type       | Description                                                    |
-|------------|----------------------------------------------------------------|
-| ValueError | If the specified `point_column` is not found in the DataFrame. |
\ No newline at end of file
diff --git a/docs/reference/statebuilder.helpers.make_url_robust.qmd b/docs/reference/statebuilder.helpers.make_url_robust.qmd
deleted file mode 100644
index 5f4f7e5..0000000
--- a/docs/reference/statebuilder.helpers.make_url_robust.qmd
+++ /dev/null
@@ -1,24 +0,0 @@
-# statebuilder.helpers.make_url_robust { #nglui.statebuilder.helpers.make_url_robust }
-
-`statebuilder.helpers.make_url_robust(df, sb, client, shorten='if_long', ngl_url=None, max_url_length=MAX_URL_LENGTH, target_site=None)`
-
-Generate a url from a neuroglancer state. If too long, return through state server,
-othewise return a url containing the data directly.
-
-## Parameters
-
-| Name             | Type                                                                         | Description                                                                                                                                                                                                                                                                                                    | Default          |
-|------------------|------------------------------------------------------------------------------|----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|------------------|
-| `df`             | pandas.pandas.DataFrame                                                      | Dataframe to pass through statebuilder                                                                                                                                                                                                                                                                         | _required_       |
-| `sb`             | nglui.statebuilder.statebuilder.nglui.statebuilder.statebuilder.StateBuilder | Statebuilder to use to render data for link                                                                                                                                                                                                                                                                    | _required_       |
-| `client`         | caveclient.CAVEclient                                                        | CAVEclient configured with a state server                                                                                                                                                                                                                                                                      | _required_       |
-| `shorten`        | str                                                                          | How to shorten link. one of 'if_long', 'always', 'never'. 'if_long' will use the state server to shorten links longer than nglui.statebuilder.MAX_URL_LENGTH (set to 1,750,000). 'always' will always use the state server to shorten the url 'never' will always return the full url.  Defaults to "if_long". | `'if_long'`      |
-| `ngl_url`        | str                                                                          | Neuroglancer deployment URL, by default None                                                                                                                                                                                                                                                                   | `None`           |
-| `max_url_length` | int                                                                          | Maximum length of url to return directly, by default 1_750_000                                                                                                                                                                                                                                                 | `MAX_URL_LENGTH` |
-| `target_site`    | str                                                                          | Type of neuroglancer deployment to build link for, by default None. This value overrides automatic checking based on the provided url. Use `seunglab` for a Seung-lab branch and either `mainline` or `cave-explorer` for the Cave Explorer or main Google branch.                                             | `None`           |
-
-## Returns
-
-| Type   | Description                                           |
-|--------|-------------------------------------------------------|
-| str    | URL containing the state created by the statebuilder. |
\ No newline at end of file
diff --git a/docs/reference/statebuilder.helpers.package_state.qmd b/docs/reference/statebuilder.helpers.package_state.qmd
deleted file mode 100644
index 413ca0e..0000000
--- a/docs/reference/statebuilder.helpers.package_state.qmd
+++ /dev/null
@@ -1,27 +0,0 @@
-# statebuilder.helpers.package_state { #nglui.statebuilder.helpers.package_state }
-
-`statebuilder.helpers.package_state(df, sb, client, shorten='if_long', return_as='url', ngl_url=None, link_text='Neuroglancer Link', target_site=None)`
-
-Automate creating a state from a statebuilder and
-a dataframe, return it in the desired format, shortening if desired.
-
-# Convert below to numpydoc
-
-## Parameters
-
-| Name          | Type                                                                         | Description                                                                                                                                                                                                                                                                                                    | Default               |
-|---------------|------------------------------------------------------------------------------|----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|-----------------------|
-| `df`          | pandas.pandas.DataFrame                                                      | Dataframe to pass through statebuilder                                                                                                                                                                                                                                                                         | _required_            |
-| `sb`          | nglui.statebuilder.statebuilder.nglui.statebuilder.statebuilder.StateBuilder | Statebuilder to use to render data for link                                                                                                                                                                                                                                                                    | _required_            |
-| `client`      | caveclient.CAVEclient                                                        | CAVEclient configured with a state server                                                                                                                                                                                                                                                                      | _required_            |
-| `shorten`     | str                                                                          | How to shorten link. one of 'if_long', 'always', 'never'. 'if_long' will use the state server to shorten links longer than nglui.statebuilder.MAX_URL_LENGTH (set to 1,750,000). 'always' will always use the state server to shorten the url 'never' will always return the full url.  Defaults to "if_long". | `'if_long'`           |
-| `return_as`   | str                                                                          | How to return the state. one of 'html', 'url', 'json'. 'html' will return an ipython clickable link 'url' will return a string with the url 'json' will return the state as a dictionary                                                                                                                       | `'url'`               |
-| `ngl_url`     | str                                                                          | Neuroglancer deployment URL, by default None                                                                                                                                                                                                                                                                   | `None`                |
-| `link_text`   | str                                                                          | Text to use for the link, by default "Neuroglancer Link"                                                                                                                                                                                                                                                       | `'Neuroglancer Link'` |
-| `target_site` | str                                                                          | Type of neuroglancer deployment to build link for, by default None. This value overrides automatic checking based on the provided url. Use `seunglab` for a Seung-lab branch and either `mainline` or `cave-explorer` for the Cave Explorer or main Google branch.                                             | `None`                |
-
-## Returns
-
-| Type                                | Description                            |
-|-------------------------------------|----------------------------------------|
-| (IPython.display.HTML, str or dict) | state in format specified by return_as |
\ No newline at end of file
diff --git a/docs/reference/statebuilder.helpers.sort_dataframe_by_root_id.qmd b/docs/reference/statebuilder.helpers.sort_dataframe_by_root_id.qmd
deleted file mode 100644
index 4ab9139..0000000
--- a/docs/reference/statebuilder.helpers.sort_dataframe_by_root_id.qmd
+++ /dev/null
@@ -1,21 +0,0 @@
-# statebuilder.helpers.sort_dataframe_by_root_id { #nglui.statebuilder.helpers.sort_dataframe_by_root_id }
-
-`statebuilder.helpers.sort_dataframe_by_root_id(df, root_id_column, ascending=False, num_column='n_times', drop=False)`
-
-Sort a dataframe so that rows belonging to the same root id are together, ordered by how many times the root id appears.
-
-## Parameters
-
-| Name             | Type                    | Description                                                                  | Default     |
-|------------------|-------------------------|------------------------------------------------------------------------------|-------------|
-| `df`             | pandas.pandas.DataFrame | dataframe to sort                                                            | _required_  |
-| `root_id_column` | str                     | Column name to use for sorting root ids                                      | _required_  |
-| `ascending`      | bool                    | Whether to sort ascending (lowest count to highest) or not, by default False | `False`     |
-| `num_column`     | str                     | Temporary column name to use for count information, by default 'n_times'     | `'n_times'` |
-| `drop`           | bool                    | If True, drop the additional column when returning.                          | `False`     |
-
-## Returns
-
-| Type                    | Description   |
-|-------------------------|---------------|
-| pandas.pandas.DataFrame |               |
\ No newline at end of file
diff --git a/docs/reference/statebuilder.md b/docs/reference/statebuilder.md
new file mode 100644
index 0000000..1e5fcc3
--- /dev/null
+++ b/docs/reference/statebuilder.md
@@ -0,0 +1,23 @@
+---
+title: Statebuilder
+---
+
+::: src.nglui.statebuilder.statebuilder
+    options:
+        show_source: false
+        heading_level: 2
+
+::: src.nglui.statebuilder.layers
+    options:
+        show_source: false
+        heading_level: 2
+
+::: src.nglui.statebuilder.mappers
+    options:
+        show_source: false
+        heading_level: 2
+
+::: src.nglui.statebuilder.helpers
+    options:
+        show_source: false
+        heading_level: 2
\ No newline at end of file
diff --git a/docs/reference/statebuilder.qmd b/docs/reference/statebuilder.qmd
deleted file mode 100644
index c3e9364..0000000
--- a/docs/reference/statebuilder.qmd
+++ /dev/null
@@ -1,58 +0,0 @@
-# StateBuilder { #nglui.statebuilder.statebuilder.StateBuilder }
-
-`statebuilder.statebuilder.StateBuilder(self, layers=[], base_state=None, url_prefix=None, state_server=None, resolution=None, view_kws={}, client=None, target_site=None)`
-
-A class for schematic mapping data frames into neuroglancer states.
-
-## Parameters
-
-| Name           | Type   | Description                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                         | Default   |
-|----------------|--------|---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|-----------|
-| `layers`       |        |                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                     | `[]`      |
-| `base_state`   |        |                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                     | `None`    |
-| `url_prefix`   |        | Defaults to None, which will use https://neuromancer-seung-import.appspot.com                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                       | `None`    |
-| `state_server` |        |                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                     | `None`    |
-| `resolution`   |        |                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                     | `None`    |
-| `view_kws`     |        | keys are: show_slices: Boolean     sets if slices are shown in the 3d view. Defaults to False. layout: str     `xy-3d`/`xz-3d`/`yz-3d` (sections plus 3d pane), `xy`/`yz`/`xz`/`3d` (only one pane), or `4panel` (all panes). Default is `xy-3d`. show_axis_lines: Boolean     determines if the axis lines are shown in the middle of each view. show_scale_bar: Boolean     toggles showing the scale bar. orthographic : Boolean     toggles orthographic view in the 3d pane. position* : 3-element vector     determines the centered location. zoom_image : float     Zoom level for the imagery in units of nm per voxel. Defaults to 8. zoom_3d : float     Zoom level for the 3d pane. Defaults to 2000. Smaller numbers are more zoomed in. background_color : str or list     Sets the background color of the 3d view. Arguments can be rgb values, hex colors, or named web colors. Defaults to black. | `{}`      |
-| `client`       |        |                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                     | `None`    |
-
-## Methods
-
-| Name | Description |
-| --- | --- |
-| [initialize_state](#nglui.statebuilder.statebuilder.StateBuilder.initialize_state) | Generate a new Neuroglancer state with layers as needed for the schema. |
-| [render_state](#nglui.statebuilder.statebuilder.StateBuilder.render_state) | Build a Neuroglancer state out of a DataFrame. |
-
-### initialize_state { #nglui.statebuilder.statebuilder.StateBuilder.initialize_state }
-
-`statebuilder.statebuilder.StateBuilder.initialize_state(base_state=None, target_site=None)`
-
-Generate a new Neuroglancer state with layers as needed for the schema.
-
-#### Parameters
-
-| Name         | Type   | Description                                                                 | Default   |
-|--------------|--------|-----------------------------------------------------------------------------|-----------|
-| `base_state` | str    | Optional initial state to build on, described by its JSON. By default None. | `None`    |
-
-### render_state { #nglui.statebuilder.statebuilder.StateBuilder.render_state }
-
-`statebuilder.statebuilder.StateBuilder.render_state(data=None, base_state=None, return_as='url', url_prefix=None, link_text='Neuroglancer Link', target_site=None)`
-
-Build a Neuroglancer state out of a DataFrame.
-
-#### Parameters
-
-| Name         | Type                                                                                   | Description                                                                                                                                                                                                                                                                                                                                                                                                  | Default               |
-|--------------|----------------------------------------------------------------------------------------|--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|-----------------------|
-| `data`       | pandas.pandas.DataFrame                                                                | DataFrame to use as a point source. By default None, for which it will return only the base_state and any fixed values.                                                                                                                                                                                                                                                                                      | `None`                |
-| `base_state` | dict                                                                                   | Initial state to build on, expressed as Neuroglancer JSON. By default None                                                                                                                                                                                                                                                                                                                                   | `None`                |
-| `return_as`  | \[url, nglui.statebuilder.statebuilder.StateBuilder.viewer, html, json, dict, shared\] | Choice of output types. Note that if a viewer is returned, the state is not reset.     url : Returns the raw url describing the state     viewer : Returns an EasyViewer object holding the state information     html : Returns an HTML link to the url, useful for notebooks.     json : Returns a JSON string describing the state.     dict : Returns a dict version of the JSON state. By default 'url' | `'url'`               |
-| `url_prefix` | str                                                                                    | Neuroglancer URL prefix to use. By default None, for which it will open with the class default.                                                                                                                                                                                                                                                                                                              | `None`                |
-| `link_text`  | str                                                                                    | Text to use for the link when returning as html, by default 'Neuroglancer Link'                                                                                                                                                                                                                                                                                                                              | `'Neuroglancer Link'` |
-
-#### Returns
-
-| Type                                       | Description                                                                                                         |
-|--------------------------------------------|---------------------------------------------------------------------------------------------------------------------|
-| string or neuroglancer.neuroglancer.Viewer | A link to or viewer for a Neuroglancer state with layers, annotations, and selected objects determined by the data. |
\ No newline at end of file
diff --git a/docs/styles.css b/docs/styles.css
deleted file mode 100644
index 2ddf50c..0000000
--- a/docs/styles.css
+++ /dev/null
@@ -1 +0,0 @@
-/* css styles */
diff --git a/docs/tutorials/index.qmd b/docs/tutorials/index.qmd
deleted file mode 100644
index 1047f3e..0000000
--- a/docs/tutorials/index.qmd
+++ /dev/null
@@ -1,7 +0,0 @@
----
-name: Tutorials
----
-
-# Tutorials
-
-Do one thing, then another.
\ No newline at end of file
diff --git a/docs/tutorials/parser.qmd b/docs/tutorials/parser.qmd
deleted file mode 100644
index 99b322c..0000000
--- a/docs/tutorials/parser.qmd
+++ /dev/null
@@ -1,7 +0,0 @@
----
-name: Parser Tutorial
----
-
-# Parser Tutorial
-
-Basics of how to use `nglui` parser.
\ No newline at end of file
diff --git a/docs/tutorials/statebuilder.qmd b/docs/tutorials/statebuilder.qmd
deleted file mode 100644
index 48edc9c..0000000
--- a/docs/tutorials/statebuilder.qmd
+++ /dev/null
@@ -1,36 +0,0 @@
----
-title: "StateBuilder Tutorial"
-toc: true
-toc-location: left
----
-
-The StateBuilder module is designed to allow rules-based generation of Neuroglancer states based on DataFrames or numpy arrays.
-
-## Background
-
-[Neuroglancer](https://github.com/google/neuroglancer) is a web application for viewing large volumetric imagery and segmentation data, as well as meshes and annotations like points or lines.
-Data in Neuroglancer is organized into layers, where each layer is configured to show information like images, segmentation, or annotations.
-Each layer can show one type of data and has different properties associated with it.
-In addition, Neuroglancer also stores the exact view that the user sees — what location in the data is centered, the orientation and zoom level of the camera, and more.
-Collectively, the information underlying both layers and the user view is refered to as the "state," which is stored as a collection of key/value pairs.
-
-StateBuilder follows this model by defining a set of rules for initializing layers.
-For layers that contain properties like selected segment ids or annotations, this configuration involves specifying how to map DataFrame columns to selected segmentations or annotations such as synapses.
-The general pattern is that you build up a collection of configurations for individual layers, assemble them into a `StateBuilder` object, and then pass a dataframe through this object to render out a state.
-
-## Simple Layers and StateBuilder
-
-```python
-from nglui import statebuilder
-
-img = statebuilder.ImageLayerConfig(
-    source=client.info.image_source(),
-    contrast_controls=True, # this just puts in the code needed to manually adjust contrast
-)
-
-seg = statebuilder.SegmentationLayerConfig(
-    source=client.info.segmentation_source(),
-)
-```
-
-## Data-driven States
\ No newline at end of file
diff --git a/docs/usage/parser.md b/docs/usage/parser.md
new file mode 100644
index 0000000..8e96cb5
--- /dev/null
+++ b/docs/usage/parser.md
@@ -0,0 +1,3 @@
+---
+title: State Parser
+---
diff --git a/docs/usage/segprops.md b/docs/usage/segprops.md
new file mode 100644
index 0000000..66dda13
--- /dev/null
+++ b/docs/usage/segprops.md
@@ -0,0 +1,5 @@
+---
+title: Segment Properties
+---
+
+Segment properties are a method of organizing information about segment IDs in a Neuroglancer segment
\ No newline at end of file
diff --git a/docs/usage/statebuilder.md b/docs/usage/statebuilder.md
new file mode 100644
index 0000000..ef5e29e
--- /dev/null
+++ b/docs/usage/statebuilder.md
@@ -0,0 +1,3 @@
+---
+title: StateBuilder
+---
diff --git a/examples/dash_with_statebuilder.py b/examples/dash_with_statebuilder.py
index b3bbb74..d581eda 100644
--- a/examples/dash_with_statebuilder.py
+++ b/examples/dash_with_statebuilder.py
@@ -5,10 +5,10 @@
 github at https://github.com/AllenInstitute/DashDataFrame.
 '''
 
-import os
 import dash
 import pandas as pd
 from dashdataframe import configure_app
+
 from nglui import statebuilder
 
 FLASK_PORT = 8880
diff --git a/mkdocs.yml b/mkdocs.yml
new file mode 100644
index 0000000..c5d2e41
--- /dev/null
+++ b/mkdocs.yml
@@ -0,0 +1,87 @@
+site_name: NGLui Documentation
+site_url: https://caveconnectome.github.io/nglui/
+repo_url: https://github.com/CAVEconnectome/nglui/
+repo_name: CAVEconnectome/NGLui
+
+nav:
+- About: index.md
+- Usage:
+    - usage/parser.md
+    - usage/segprops.md
+    - usage/statebuilder.md
+- Function Reference:
+    - reference/parser.md
+    - reference/segprops.md
+    - reference/statebuilder.md
+    - reference/easyviewer.md
+- Changelog: changelog.md
+
+  
+theme:
+  name: material
+  language: en
+  palette:
+    primary: blue grey
+    accent: deep orange
+  font:
+    text: Bitter
+    code: Inconsolata
+  icon:
+    repo: fontawesome/brands/github
+  features:
+    - navigation.indexes
+    - navigation.instant
+    # - navigation.footer
+    # - navigation.path
+    - navigation.prune
+    # - navigation.sections # toggle to have sections in side nav
+    - navigation.tabs # toggle to mainly use top nav
+    - navigation.tabs.sticky
+    - toc.follow
+    - toc.integrate # whether to include the toc in the main nav bar to the left
+    - navigation.top
+    - search.suggest
+    - search.highlight
+    - search.share
+    - content.code.copy
+    - header.autohide
+    
+markdown_extensions:
+  - admonition
+
+plugins:
+  - mkdocstrings:
+      default_handler: python
+      handlers:
+        python:
+          import:
+            - https://docs.python.org/3/objects.inv
+            - https://numpy.org/doc/stable/objects.inv
+            - https://pandas.pydata.org/pandas-docs/stable/objects.inv
+          paths: [.]
+          options:
+            show_source: false
+            docstring_style: numpy
+            docstring_section_style: list # list, table, spacy
+            docstring_options:
+              ignore_init_summary: false
+            merge_init_into_class: true
+            allow_section_blank_line: false
+            show_root_heading: false
+            show_root_toc_entry: false
+            show_object_full_path: false
+            show_symbol_type_heading: false # whether to show "meth/func/etc" in the page
+            show_symbol_type_toc: false # whether to show "meth/func/etc" in the toc
+            signature_crossrefs: true # https://mkdocstrings.github.io/python/usage/configuration/signatures/#signature_crossrefs
+            members_order: alphabetical # can be source
+            group_by_category: true  # order is attributes, classes, functions, modules
+            summary: true
+            show_if_no_docstring: false
+            show_docstring_attributes: false
+            annotations_path: brief # https://mkdocstrings.github.io/python/usage/configuration/signatures/#annotations_path
+            show_signature: true
+            separate_signature: false
+            show_signature_annotations: false
+            unwrap_annotated: false # https://mkdocstrings.github.io/python/usage/configuration/signatures/#unwrap_annotated
+            heading_level: 2
+            inherited_members: true
diff --git a/pyproject.toml b/pyproject.toml
new file mode 100644
index 0000000..bd42a9a
--- /dev/null
+++ b/pyproject.toml
@@ -0,0 +1,53 @@
+[build-system]
+requires = ["hatchling"]
+build-backend = "hatchling.build"
+
+[project]
+name = "nglui"
+dynamic = ["version"]
+description = "Framework for data-driven generation of neuroglancer states."
+readme = "README.md"
+license = "MIT"
+authors = [
+    { name = "Derrick Brittain", email = "caseysm@gmail.com" },
+    { name = "Casey Schneider-Mizell" },
+    { name = "Forrest Collman" },
+]
+dependencies = [
+    "caveclient>=5.14.0",
+    "ipython",
+    "neuroglancer",
+    "numpy>=1.11.0",
+    "pandas>=1.0.0",
+    "requests",
+    "six",
+    "tables",
+    "webcolors",
+]
+classifiers = [
+    "License :: OSI Approved :: MIT License",
+]
+
+[project.urls]
+Homepage = "https://github.com/seung-lab/NeuroglancerAnnotationUI"
+
+[tool.hatch.version]
+path = "src/nglui/__init__.py"
+
+[tool.hatch.build.targets.sdist]
+include = [
+    "/src",
+]
+
+[[tool.hatch.envs.hatch-test.matrix]]
+python = ["3.9", "3.10", "3.11", "3.12"]
+
+[tool.hatch.envs.docs]
+dependencies = [
+  "mkdocs",
+  "mkdocs-material",
+  "mkdocstrings[python]",
+]
+[tool.hatch.envs.docs.scripts]
+build = "mkdocs build --clean --strict"
+serve = "mkdocs serve --dev-addr localhost:8000"
diff --git a/setup.py b/setup.py
index 8b4da53..da4b965 100644
--- a/setup.py
+++ b/setup.py
@@ -1,8 +1,8 @@
-from setuptools import setup
-import re
-import os
 import codecs
-from setuptools import find_packages
+import os
+import re
+
+from setuptools import find_packages, setup
 
 here = os.path.abspath(os.path.dirname(__file__))
 
@@ -21,10 +21,10 @@ def find_version(*file_paths):
     raise RuntimeError("Unable to find version string.")
 
 
-with open('requirements.txt', 'r') as f:
+with open('requirements.txt') as f:
     required = f.read().splitlines()
 
-with open('test_requirements.txt', 'r') as f:
+with open('test_requirements.txt') as f:
     test_required = f.read().splitlines()
 
 setup(
@@ -38,8 +38,7 @@ def find_version(*file_paths):
     url="https://github.com/seung-lab/NeuroglancerAnnotationUI",
     packages=find_packages('src'),
     package_dir={'': 'src'},
-    setup_requires=['pytest-runner'],
     tests_require=test_required,
     include_package_data=True,
-    install_requires=[required],  # external packages as dependencies
+    install_requires=required,  # external packages as dependencies
 )
diff --git a/src/nglui/__init__.py b/src/nglui/__init__.py
index 1a21507..67d58ad 100644
--- a/src/nglui/__init__.py
+++ b/src/nglui/__init__.py
@@ -2,5 +2,6 @@
 
 from . import statebuilder
 from . import parser
+from . import segmentprops
 
-__version__ = "3.1.0"
+__version__ = "3.2.0"
diff --git a/src/nglui/easyviewer/__init__.py b/src/nglui/easyviewer/__init__.py
index 3d45cdd..817da1f 100644
--- a/src/nglui/easyviewer/__init__.py
+++ b/src/nglui/easyviewer/__init__.py
@@ -1,11 +1,18 @@
-from .ev_base import EasyViewerSeunglab, EasyViewerMainline
+from .ev_base import EasyViewerMainline, EasyViewerSeunglab
+
 
 def EasyViewer(
-    target_site='seunglab',
+    target_site="seunglab",
 ):
-    if target_site == 'seunglab' or target_site is None:
+    if target_site == "seunglab" or target_site is None:
         return EasyViewerSeunglab()
-    elif target_site == 'mainline' or target_site == 'cave-explorer':
+    elif (
+        target_site == "mainline"
+        or target_site == "cave-explorer"
+        or target_site == "spelunker"
+    ):
         return EasyViewerMainline()
     else:
-        raise ValueError(f'Unknown target: {target_site}. Must be one of "seunglab" or "mainline"/"cave-explorer"')
+        raise ValueError(
+            f'Unknown target: {target_site}. Must be one of "seunglab" or "spelunker/mainline"/"cave-explorer"'
+        )
diff --git a/src/nglui/easyviewer/ev_base/__init__.py b/src/nglui/easyviewer/ev_base/__init__.py
index 4bf9211..3d1e81c 100644
--- a/src/nglui/easyviewer/ev_base/__init__.py
+++ b/src/nglui/easyviewer/ev_base/__init__.py
@@ -1,2 +1,2 @@
 from .mainline import EasyViewerMainline
-from .seunglab import EasyViewerSeunglab
\ No newline at end of file
+from .seunglab import EasyViewerSeunglab
diff --git a/src/nglui/easyviewer/ev_base/annotation_compatibility.py b/src/nglui/easyviewer/ev_base/annotation_compatibility.py
index fcabc2a..d8cc1bc 100644
--- a/src/nglui/easyviewer/ev_base/annotation_compatibility.py
+++ b/src/nglui/easyviewer/ev_base/annotation_compatibility.py
@@ -1,8 +1,8 @@
 from neuroglancer import (
+    AxisAlignedBoundingBoxAnnotation,
+    EllipsoidAnnotation,
     LineAnnotation,
     PointAnnotation,
-    EllipsoidAnnotation,
-    AxisAlignedBoundingBoxAnnotation,
 )
 
 
diff --git a/src/nglui/easyviewer/ev_base/base.py b/src/nglui/easyviewer/ev_base/base.py
index 5796f65..1f198f2 100644
--- a/src/nglui/easyviewer/ev_base/base.py
+++ b/src/nglui/easyviewer/ev_base/base.py
@@ -1,18 +1,18 @@
-from . import utils
-from typing import Union, List, Dict, Tuple, Optional
-
 from abc import ABC, abstractmethod
+from typing import Dict, List, Optional, Tuple, Union
+
+from . import utils
 
 SEGMENTATION_LAYER_TYPES = ["segmentation", "segmentation_with_graph"]
 
+
 class EasyViewerBase(ABC):
     def __init__(self):
         self._default_viewer_url = None
-        pass
 
     def __repr__(self):
         return self.as_url()
-    
+
     def __repr_html__(self):
         return f'<a href="{self.as_url()}" target="_blank">Viewer</a>'
 
@@ -29,12 +29,12 @@ def add_layers(
     ) -> None:
         self.set_resolution(resolution)
         with self.txn() as s:
-                for ln, kws in image_layers.items():
-                    s.layers[ln] = self._ImageLayer(**kws)
-                for ln, kws in segmentation_layers.items():
-                    self._SegmentationLayer(s, **kws)
-                for ln, kws in annotation_layers.items():
-                    s.layers[ln] = self._AnnotationLayer(**kws)
+            for ln, kws in image_layers.items():
+                s.layers[ln] = self._ImageLayer(**kws)
+            for ln, kws in segmentation_layers.items():
+                self._SegmentationLayer(s, **kws)
+            for ln, kws in annotation_layers.items():
+                s.layers[ln] = self._AnnotationLayer(**kws)
 
     @abstractmethod
     def _ImageLayer(self, source, **kwargs):
@@ -56,19 +56,22 @@ def add_segmentation_layer(self, layer_name, source, **kwargs):
             source (str): source of neuroglancer segment layer
         """
         with self.txn() as s:
-            s.layers[layer_name] = self._SegmentationLayer(
-                source=source, **kwargs
-            )
-    
-    def add_image_layer(self, layer_name, source, **kwargs):
+            s.layers[layer_name] = self._SegmentationLayer(source=source, **kwargs)
+
+    def add_image_layer(self, layer_name, source, contrast_range=None, **kwargs):
         """Add segmentation layer to viewer instance.
 
         Attributes:
             layer_name (str): name of layer to be displayed in neuroglancer ui.
             source (str): source of neuroglancer image layer
+            contrast_range = (float, float): contrast range for image layer either in 0-1 (floats) or 0-255 (ints).
         """
         with self.txn() as s:
             s.layers[layer_name] = self._ImageLayer(source=source, **kwargs)
+        if contrast_range is not None:
+            self.add_contrast_shader(
+                layer_name, black=contrast_range[0], white=contrast_range[1]
+            )
 
     @abstractmethod
     def set_resolution(self, resolution) -> None:
@@ -76,9 +79,9 @@ def set_resolution(self, resolution) -> None:
 
     def add_contrast_shader(self, layer_name, black=0.0, white=1.0):
         shader_text = f"#uicontrol float black slider(min=0, max=1, default={black})\n#uicontrol float white slider(min=0, max=1, default={white})\nfloat rescale(float value) {{\n  return (value - black) / (white - black);\n}}\nvoid main() {{\n  float val = toNormalized(getDataValue());\n  if (val < black) {{\n    emitRGB(vec3(0,0,0));\n  }} else if (val > white) {{\n    emitRGB(vec3(1.0, 1.0, 1.0));\n  }} else {{\n    emitGrayscale(rescale(val));\n  }}\n}}\n"
-        self._update_layer_shader(layer_name, shader_text)
+        self.update_shader(layer_name, shader_text)
 
-    def _update_layer_shader(self, layer_name, shader_text):
+    def update_shader(self, layer_name, shader_text):
         with self.txn() as s:
             s.layers[layer_name]._json_data["shader"] = shader_text
 
@@ -113,24 +116,24 @@ def clear_annotation_layers(self, layer_names):
                 s.layers[ln].annotations._data = []
 
     def add_annotations(
-            self,
-            layer_name: str,
-            annotations: List,
-        ):
+        self,
+        layer_name: str,
+        annotations: List,
+    ):
         with self.txn() as s:
             s.layers[layer_name].annotations.extend(annotations)
 
     def add_multilayer_annotations(
-            self,
-            layer_anno_dict: Dict[str, List],
-        ):
+        self,
+        layer_anno_dict: Dict[str, List],
+    ):
         """
         layer_anno_dict is a layer_name to annotation list dict.
         """
         with self.txn() as s:
             for ln, annos in layer_anno_dict.items():
                 if annos is None:
-                    continue 
+                    continue
                 s.layers[ln].annotations.extend(annos)
 
     def remove_annotations(self, layer_name, anno_ids):
@@ -149,7 +152,6 @@ def remove_annotations(self, layer_name, anno_ids):
         except:
             self.update_message("Could not remove annotation")
 
-
     @abstractmethod
     def add_annotation_tags(self, layer_name, tags):
         pass
@@ -178,13 +180,13 @@ def select_annotation(self, layer_name, anno_id):
     @property
     def layer_names(self):
         return [l.name for l in self.state.layers]
-    
+
     def selected_objects(self, segmentation_layer):
         return list(self.state.layers[segmentation_layer].segments)
 
     @abstractmethod
     def add_selected_objects(
-        self, 
+        self,
         segmentation_layer: str,
         oids: List[int],
         colors: Optional[Union[List, Dict]] = None,
@@ -195,7 +197,7 @@ def add_selected_objects(
     def set_view_options(
         self,
         show_slices: Optional[bool] = None,
-        layout: Optional[str]=None,
+        layout: Optional[str] = None,
         show_axis_lines: Optional[bool] = None,
         show_scale_bar: Optional[bool] = None,
         orthographic: Optional[bool] = None,
@@ -203,7 +205,7 @@ def set_view_options(
         zoom_image: Optional[float] = None,
         zoom_3d: Optional[float] = None,
         background_color: Optional[Tuple[float]] = None,
-    )->None:
+    ) -> None:
         pass
 
     @abstractmethod
@@ -211,7 +213,7 @@ def set_segmentation_view_options(
         self,
         layer_name: str,
         alpha_selected: Optional[float] = None,
-        alpha_3d: Optional[float] =None,
+        alpha_3d: Optional[float] = None,
         alpha_unselected: Optional[float] = None,
         **kwargs,
     ):
@@ -236,7 +238,6 @@ def assign_colors(self, layer_name, seg_colors):
         seg_colors : dict
             dict with root ids as keys and colors as values.
         """
-        pass
 
     @abstractmethod
     def set_multicut_points(
@@ -250,7 +251,7 @@ def set_multicut_points(
         focus=True,
     ):
         pass
-    
+
     @staticmethod
     @abstractmethod
     def point_annotation(
@@ -316,4 +317,3 @@ def group_annotations(
         children_visible=True,
     ):
         pass
-
diff --git a/src/nglui/easyviewer/ev_base/mainline.py b/src/nglui/easyviewer/ev_base/mainline.py
index 37ee24d..17b4d2c 100644
--- a/src/nglui/easyviewer/ev_base/mainline.py
+++ b/src/nglui/easyviewer/ev_base/mainline.py
@@ -10,12 +10,14 @@
     use_ngl = False
 else:
     use_ngl = True
+from typing import Dict, List, Optional, Tuple, Union
+from warnings import warn
+
+from numpy import integer, issubdtype
+
 from . import utils
+from .base import SEGMENTATION_LAYER_TYPES, EasyViewerBase
 
-from warnings import warn
-from .base import EasyViewerBase, SEGMENTATION_LAYER_TYPES
-from typing import Union, List, Dict, Tuple, Optional
-from numpy import issubdtype, integer
 
 def nanometer_dimension(resolution):
     return neuroglancer.CoordinateSpace(
@@ -24,14 +26,18 @@ def nanometer_dimension(resolution):
         units="nm",
     )
 
+
 class UnservedViewer(neuroglancer.viewer_base.UnsynchronizedViewerBase):
     def __init__(self, **kwargs):
         super().__init__(**kwargs)
-        self._default_viewer_url = kwargs.pop('default_viewer_url', utils.default_mainline_neuroglancer_base)
+        self._default_viewer_url = kwargs.pop(
+            "default_viewer_url", utils.default_mainline_neuroglancer_base
+        )
 
     def get_server_url(self):
         return self._default_viewer_url
 
+
 class EasyViewerMainline(UnservedViewer, EasyViewerBase):
     def __init__(self, **kwargs):
         super(UnservedViewer, self).__init__(**kwargs)
@@ -44,11 +50,14 @@ def load_url(self, url) -> None:
 
     def _ImageLayer(self, source, **kwargs):
         return neuroglancer.viewer_state.ImageLayer(source=source, **kwargs)
-    
+
     def _SegmentationLayer(self, source, **kwargs):
-        source = utils.parse_graphene_header(source, target='mainline')
+        if isinstance(source, str):
+            source = utils.parse_graphene_header(source, target="mainline")
+        elif isinstance(source, list):
+            source = [utils.parse_graphene_header(s, target="mainline") for s in source]
         return neuroglancer.viewer_state.SegmentationLayer(source=source, **kwargs)
-    
+
     def _AnnotationLayer(self, *args, **kwargs):
         return neuroglancer.viewer_state.LocalAnnotationLayer(*args, **kwargs)
 
@@ -57,8 +66,7 @@ def set_resolution(self, resolution) -> None:
             s.dimensions = nanometer_dimension(resolution)
 
     def set_state_server(self, state_server) -> None:
-        Warning('State server is set by neuroglancer deployment for this viewer type.')
-        pass
+        Warning("State server is set by neuroglancer deployment for this viewer type.")
 
     def add_annotation_layer(
         self,
@@ -71,17 +79,17 @@ def add_annotation_layer(
         tags=None,
     ) -> None:
         if layer_name is None:
-            layer_name = 'annos'
+            layer_name = "annos"
         if layer_name in [l.name for l in self.state.layers]:
-            raise ValueError("Layer name already exists")        
+            raise ValueError("Layer name already exists")
 
         if filter_by_segmentation:
-            filter_by_segmentation = ['segments']
+            filter_by_segmentation = ["segments"]
         else:
             filter_by_segmentation = []
 
         if linked_segmentation_layer is not None:
-            linked_segmentation_layer = {'segments': linked_segmentation_layer}
+            linked_segmentation_layer = {"segments": linked_segmentation_layer}
         else:
             linked_segmentation_layer = {}
 
@@ -96,10 +104,10 @@ def add_annotation_layer(
                 s.layers[layer_name].annotationColor = utils.parse_color(color)
 
         if tags is not None:
-            warn('Tags are not supported by this viewer type.')
-        
+            warn("Tags are not supported by this viewer type.")
+
     def add_annotation_tags(self, layer_name, tags):
-        warn('Annotation tags are not supported by this viewer type.')
+        warn("Annotation tags are not supported by this viewer type.")
 
     def as_url(
         self,
@@ -111,32 +119,47 @@ def as_url(
             prefix = utils.default_mainline_neuroglancer_base
         ngl_url = neuroglancer.to_url(self.state, prefix=prefix)
         if as_html:
-            return '<a href="{}" target="_blank">{}</a>'.format(ngl_url, link_text)
+            return f'<a href="{ngl_url}" target="_blank">{link_text}</a>'
         else:
             return ngl_url
 
     def set_selected_layer(self, layer_name):
         with self.txn() as s:
-            s.selected_layer = neuroglancer.SelectedLayerState({'visible': True, 'layer': layer_name}) 
+            s.selected_layer = neuroglancer.SelectedLayerState(
+                {"visible": True, "layer": layer_name}
+            )
+
+    def add_contrast_shader(self, layer_name, black=0, white=255):
+        if isinstance(black, float) and black < 1:
+            black = int(black * 255)
+        if isinstance(white, float) and white < 1:
+            white = int(white * 255)
+        with self.txn() as s:
+            s.layers[
+                layer_name
+            ].shader_controls = neuroglancer.viewer_state.ShaderControls(
+                {"normalized": {"range": [black, white]}}
+            )
 
     def select_annotation(self, layer_name, annotation_id):
         # self.set_selected_layer(layer_name)
-        raise Warning('Annotation selection is not supported by this viewer type.')
+        raise Warning("Annotation selection is not supported by this viewer type.")
 
     def assign_colors(self, layer_name, seg_colors):
         with self.txn() as s:
             s.layers[layer_name].segmentColors = seg_colors
 
     def add_selected_objects(
-            self,
-            segmentation_layer: str,
-            oids: List[int],
-            colors: Optional[Union[List,  Dict]] = None
-        ) -> None:
+        self,
+        segmentation_layer: str,
+        oids: List[int],
+        colors: Optional[Union[List, Dict]] = None,
+    ) -> None:
         if issubdtype(type(oids), integer):
             oids = [oids]
         with self.txn() as s:
-            s.layers[segmentation_layer].segments.update(oids)
+            for oid in oids:
+                s.layers[segmentation_layer].segments.add(oid)
         if colors is not None:
             if isinstance(colors, dict):
                 self.assign_colors(segmentation_layer, colors)
@@ -144,10 +167,38 @@ def add_selected_objects(
                 seg_colors = {oid: clr for oid, clr in zip(oids, colors)}
                 self.assign_colors(segmentation_layer, seg_colors)
 
+    def add_segmentation_layer(self, layer_name, source, **kwargs):
+        """Add segmentation layer to viewer instance.
+
+        Attributes:
+            layer_name (str): name of layer to be displayed in neuroglancer ui.
+            source (str): source of neuroglancer segment layer
+        """
+        with self.txn() as s:
+            s.layers[layer_name] = self._SegmentationLayer(source=source, **kwargs)
+
+    def append_source_to_segmentation_layer(self, layer_name, source):
+        """Append source or sources to an existing segmentation layer.
+
+        Parameters
+        ----------
+        layer_name : str
+            Name of an existing layer
+        source : str or list of str
+            Source or sources to add to the layer
+        """
+        if isinstance(source, str):
+            source = [source]
+        source = [utils.parse_graphene_header(s, target="mainline") for s in source]
+
+        with self.txn() as s:
+            for src in source:
+                s.layers[layer_name].source.append({"url": src})
+
     def set_view_options(
         self,
         show_slices: Optional[bool] = None,
-        layout: Optional[str]=None,
+        layout: Optional[str] = None,
         show_axis_lines: Optional[bool] = None,
         show_scale_bar: Optional[bool] = None,
         orthographic: Optional[bool] = None,
@@ -155,7 +206,7 @@ def set_view_options(
         zoom_image: Optional[float] = None,
         zoom_3d: Optional[float] = None,
         background_color: Optional[Tuple[float]] = None,
-    )->None:
+    ) -> None:
         with self.txn() as s:
             if show_slices is not None:
                 s.showSlices = show_slices
@@ -164,9 +215,9 @@ def set_view_options(
             if show_axis_lines is not None:
                 s.showAxisLines = show_axis_lines
             if show_scale_bar is not None:
-                s.showScaleBar  = show_scale_bar
+                s.showScaleBar = show_scale_bar
             if orthographic is not None:
-                s.layout.orthographic_projection = orthographic 
+                s.layout.orthographic_projection = orthographic
             if position is not None:
                 s.position = position
             if zoom_image is not None:
@@ -176,12 +227,11 @@ def set_view_options(
             if background_color is not None:
                 s.perspectiveViewBackgroundColor = utils.parse_color(background_color)
 
-
     def set_segmentation_view_options(
         self,
         layer_name: str,
         alpha_selected: Optional[float] = None,
-        alpha_3d: Optional[float] =None,
+        alpha_3d: Optional[float] = None,
         alpha_unselected: Optional[float] = None,
         silhouette_value: Optional[float] = None,
         **kwargs,
@@ -198,7 +248,6 @@ def set_segmentation_view_options(
                 l.notSelectedAlpha = alpha_unselected
             if silhouette_value is not None:
                 l.meshSilhouetteRendering = silhouette_value
-            
 
     def set_timestamp(
         self,
@@ -207,7 +256,6 @@ def set_timestamp(
     ):
         if timestamp is not None:
             warn("Timestamp setting is not yet enabled for this viewer type.")
-        pass
 
     def set_multicut_points(
         self,
@@ -219,7 +267,7 @@ def set_multicut_points(
         supervoxels_blue=None,
         focus=True,
     ):
-        Warning('Setting multicut is not yet enabled for this viewer type')
+        Warning("Setting multicut is not yet enabled for this viewer type")
 
     @staticmethod
     def point_annotation(
@@ -238,7 +286,7 @@ def point_annotation(
             description=description,
             segments=[[int(x) for x in segments]],
         )
-    
+
     @staticmethod
     def line_annotation(
         pointA,
@@ -278,7 +326,7 @@ def ellipsoid_annotation(
             description=description,
             segments=[[int(x) for x in segments]],
         )
-    
+
     @staticmethod
     def bounding_box_annotation(
         pointA,
@@ -310,7 +358,4 @@ def group_annotations(
         children_visible=True,
         **kwargs,
     ):
-        Warning(
-            'Annotation groups are not yet supported by this viewer type.'
-        )
-        pass
\ No newline at end of file
+        Warning("Annotation groups are not yet supported by this viewer type.")
diff --git a/src/nglui/easyviewer/ev_base/nglite/__init__.py b/src/nglui/easyviewer/ev_base/nglite/__init__.py
index e775346..f4ba20d 100644
--- a/src/nglui/easyviewer/ev_base/nglite/__init__.py
+++ b/src/nglui/easyviewer/ev_base/nglite/__init__.py
@@ -19,4 +19,4 @@
 from .equivalence_map import EquivalenceMap
 from .url_state import to_url, parse_url
 from . import skeleton
-from .annotation import *
\ No newline at end of file
+from .annotation import *
diff --git a/src/nglui/easyviewer/ev_base/nglite/equivalence_map.py b/src/nglui/easyviewer/ev_base/nglite/equivalence_map.py
index 4420014..2bef24f 100644
--- a/src/nglui/easyviewer/ev_base/nglite/equivalence_map.py
+++ b/src/nglui/easyviewer/ev_base/nglite/equivalence_map.py
@@ -12,14 +12,13 @@
 # See the License for the specific language governing permissions and
 # limitations under the License.
 
-from __future__ import absolute_import
 
 import copy
 
 import six
 
 
-class EquivalenceMap(object):
+class EquivalenceMap:
     """Union-find data structure"""
 
     supports_readonly = True
diff --git a/src/nglui/easyviewer/ev_base/nglite/json_utils.py b/src/nglui/easyviewer/ev_base/nglite/json_utils.py
index 3d0b068..3f64713 100644
--- a/src/nglui/easyviewer/ev_base/nglite/json_utils.py
+++ b/src/nglui/easyviewer/ev_base/nglite/json_utils.py
@@ -12,7 +12,6 @@
 # See the License for the specific language governing permissions and
 # limitations under the License.
 
-from __future__ import absolute_import
 
 import collections
 import json
@@ -34,9 +33,7 @@ def json_encoder_default(obj):
         return str(obj)
     elif isinstance(obj, np.floating):
         return float(obj)
-    elif isinstance(obj, np.ndarray):
-        return list(obj)
-    elif isinstance(obj, (set, frozenset)):
+    elif isinstance(obj, (frozenset, np.ndarray, set)):
         return list(obj)
     raise TypeError
 
diff --git a/src/nglui/easyviewer/ev_base/nglite/json_wrappers.py b/src/nglui/easyviewer/ev_base/nglite/json_wrappers.py
index bad4340..f1cd28b 100644
--- a/src/nglui/easyviewer/ev_base/nglite/json_wrappers.py
+++ b/src/nglui/easyviewer/ev_base/nglite/json_wrappers.py
@@ -13,7 +13,6 @@
 # limitations under the License.
 """Facilities for converting JSON <-> Python objects"""
 
-from __future__ import absolute_import
 
 import collections
 import copy
@@ -24,8 +23,6 @@
 import numpy as np
 import six
 
-from six.moves import range
-
 from .json_utils import encode_json_for_repr
 
 
@@ -39,7 +36,7 @@ def to_json(value):
     return method()
 
 
-class JsonObjectWrapper(object):
+class JsonObjectWrapper:
     supports_readonly = True
 
     __slots__ = ("_json_data", "_cached_wrappers", "_lock", "_readonly")
@@ -75,7 +72,7 @@ def __deepcopy__(self, memo):
         return type(self)(copy.deepcopy(self.to_json(), memo))
 
     def __repr__(self):
-        return u"%s(%s)" % (type(self).__name__, encode_json_for_repr(self.to_json()))
+        return "%s(%s)" % (type(self).__name__, encode_json_for_repr(self.to_json()))
 
     def _get_wrapped(self, key, wrapped_type):
         with self._lock:
@@ -167,7 +164,7 @@ def modified_wrapper(value, **kwargs):
     return modified_wrapper
 
 
-class MapBase(object):
+class MapBase:
     pass
 
 
@@ -257,7 +254,7 @@ def wrapper(x, _readonly=False):
 def typed_list(wrapped_type, validator=None):
     validator = _normalize_validator(wrapped_type, validator)
 
-    class TypedList(object):
+    class TypedList:
         supports_readonly = True
         supports_validation = True
 
diff --git a/src/nglui/easyviewer/ev_base/nglite/skeleton.py b/src/nglui/easyviewer/ev_base/nglite/skeleton.py
index 8d15b37..2284656 100644
--- a/src/nglui/easyviewer/ev_base/nglite/skeleton.py
+++ b/src/nglui/easyviewer/ev_base/nglite/skeleton.py
@@ -12,7 +12,6 @@
 # See the License for the specific language governing permissions and
 # limitations under the License.
 
-from __future__ import absolute_import
 
 import collections
 import io
@@ -22,7 +21,7 @@
 import six
 
 
-class Skeleton(object):
+class Skeleton:
     def __init__(self, vertex_positions, edges, vertex_attributes=None):
         self.vertex_positions = np.array(vertex_positions, dtype="<f4")
         self.edges = np.array(edges, dtype="<u4")
@@ -59,7 +58,7 @@ def encode(self, source):
 )
 
 
-class SkeletonSource(object):
+class SkeletonSource:
     def __init__(self):
         self.vertex_attributes = collections.OrderedDict()
 
diff --git a/src/nglui/easyviewer/ev_base/nglite/trackable_state.py b/src/nglui/easyviewer/ev_base/nglite/trackable_state.py
index f8b1f03..40c567d 100644
--- a/src/nglui/easyviewer/ev_base/nglite/trackable_state.py
+++ b/src/nglui/easyviewer/ev_base/nglite/trackable_state.py
@@ -12,7 +12,6 @@
 # See the License for the specific language governing permissions and
 # limitations under the License.
 
-from __future__ import absolute_import
 
 import contextlib
 import copy
@@ -25,7 +24,7 @@ class ConcurrentModificationError(RuntimeError):
     pass
 
 
-class ChangeNotifier(object):
+class ChangeNotifier:
     def __init__(self):
         self.__changed_callbacks = set()
         self.change_count = 0
@@ -142,4 +141,4 @@ def retry_txn(self, func, retries=10):
                 raise
 
     def __repr__(self):
-        return u"%s(%r)" % (type(self).__name__, self.state)
+        return "%s(%r)" % (type(self).__name__, self.state)
diff --git a/src/nglui/easyviewer/ev_base/nglite/url_state.py b/src/nglui/easyviewer/ev_base/nglite/url_state.py
index 8a0f761..9443c08 100644
--- a/src/nglui/easyviewer/ev_base/nglite/url_state.py
+++ b/src/nglui/easyviewer/ev_base/nglite/url_state.py
@@ -12,7 +12,6 @@
 # See the License for the specific language governing permissions and
 # limitations under the License.
 
-from __future__ import absolute_import
 
 import collections
 import json
@@ -24,18 +23,18 @@
 from .json_utils import json_encoder_default
 from .json_wrappers import to_json
 
-SINGLE_QUOTE_STRING_PATTERN = u"('(?:[^'\\\\]|(?:\\\\.))*')"
-DOUBLE_QUOTE_STRING_PATTERN = u'("(?:[^\'\\\\]|(?:\\\\.))*")'
+SINGLE_QUOTE_STRING_PATTERN = "('(?:[^'\\\\]|(?:\\\\.))*')"
+DOUBLE_QUOTE_STRING_PATTERN = '("(?:[^\'\\\\]|(?:\\\\.))*")'
 SINGLE_OR_DOUBLE_QUOTE_STRING_PATTERN = (
-    SINGLE_QUOTE_STRING_PATTERN + u"|" + DOUBLE_QUOTE_STRING_PATTERN
+    SINGLE_QUOTE_STRING_PATTERN + "|" + DOUBLE_QUOTE_STRING_PATTERN
 )
 DOUBLE_OR_SINGLE_QUOTE_STRING_PATTERN = (
-    DOUBLE_QUOTE_STRING_PATTERN + u"|" + SINGLE_QUOTE_STRING_PATTERN
+    DOUBLE_QUOTE_STRING_PATTERN + "|" + SINGLE_QUOTE_STRING_PATTERN
 )
 
 
-DOUBLE_QUOTE_PATTERN = u'^((?:[^"\'\\\\]|(?:\\\\.))*)"'
-SINGLE_QUOTE_PATTERN = u"^((?:[^\"'\\\\]|(?:\\\\.))*)'"
+DOUBLE_QUOTE_PATTERN = '^((?:[^"\'\\\\]|(?:\\\\.))*)"'
+SINGLE_QUOTE_PATTERN = "^((?:[^\"'\\\\]|(?:\\\\.))*)'"
 
 
 def _convert_string_literal(x, quote_initial, quote_replace, quote_search):
@@ -48,7 +47,7 @@ def _convert_string_literal(x, quote_initial, quote_replace, quote_search):
                 s += inner
                 break
             s += m.group(1)
-            s += u"\\"
+            s += "\\"
             s += quote_replace
             inner = inner[m.end() :]
         s += quote_replace
@@ -57,22 +56,22 @@ def _convert_string_literal(x, quote_initial, quote_replace, quote_search):
 
 
 def _convert_json_helper(x, desired_comma_char, desired_quote_char):
-    comma_search = u"[&_,]"
-    if desired_quote_char == u'"':
-        quote_initial = u"'"
+    comma_search = "[&_,]"
+    if desired_quote_char == '"':
+        quote_initial = "'"
         quote_search = DOUBLE_QUOTE_PATTERN
         string_literal_pattern = SINGLE_OR_DOUBLE_QUOTE_STRING_PATTERN
     else:
-        quote_initial = u'"'
+        quote_initial = '"'
         quote_search = SINGLE_QUOTE_PATTERN
         string_literal_pattern = DOUBLE_OR_SINGLE_QUOTE_STRING_PATTERN
-    s = u""
+    s = ""
     while x:
         m = re.search(string_literal_pattern, x)
         if m is None:
             before = x
-            x = u""
-            replacement = u""
+            x = ""
+            replacement = ""
         else:
             before = x[: m.start()]
             x = x[m.end() :]
@@ -89,11 +88,11 @@ def _convert_json_helper(x, desired_comma_char, desired_quote_char):
 
 
 def url_safe_to_json(x):
-    return _convert_json_helper(x, u",", u'"')
+    return _convert_json_helper(x, ",", '"')
 
 
 def json_to_url_safe(x):
-    return _convert_json_helper(x, u"_", u"'")
+    return _convert_json_helper(x, "_", "'")
 
 
 def url_fragment_to_json(fragment_value):
@@ -117,13 +116,13 @@ def parse_url(url):
 
 def to_url_fragment(state):
     json_string = json.dumps(
-        to_json(state), separators=(u",", u":"), default=json_encoder_default
+        to_json(state), separators=(",", ":"), default=json_encoder_default
     )
-    return urllib.parse.quote(json_string, safe=u"~@#$&()*!+=:;,.?/'")
+    return urllib.parse.quote(json_string, safe="~@#$&()*!+=:;,.?/'")
 
 
-default_neuroglancer_url = u"https://neuromancer-seung-import.appspot.com"
+default_neuroglancer_url = "https://neuromancer-seung-import.appspot.com"
 
 
 def to_url(state, prefix=default_neuroglancer_url):
-    return u"%s#!%s" % (prefix, to_url_fragment(state))
+    return "%s#!%s" % (prefix, to_url_fragment(state))
diff --git a/src/nglui/easyviewer/ev_base/nglite/viewer.py b/src/nglui/easyviewer/ev_base/nglite/viewer.py
index f8fe5d4..151f712 100644
--- a/src/nglui/easyviewer/ev_base/nglite/viewer.py
+++ b/src/nglui/easyviewer/ev_base/nglite/viewer.py
@@ -12,12 +12,11 @@
 # See the License for the specific language governing permissions and
 # limitations under the License.
 
-from __future__ import absolute_import
 
-from . import url_state, viewer_base
+from . import viewer_base
 
 
-class _ViewerHelper(object):
+class _ViewerHelper:
     """Mixin for implementing viewers based on the built-in server [kept for compatibility]."""
 
     def __init__(self):
diff --git a/src/nglui/easyviewer/ev_base/nglite/viewer_base.py b/src/nglui/easyviewer/ev_base/nglite/viewer_base.py
index b573f84..82d1305 100644
--- a/src/nglui/easyviewer/ev_base/nglite/viewer_base.py
+++ b/src/nglui/easyviewer/ev_base/nglite/viewer_base.py
@@ -12,7 +12,6 @@
 # See the License for the specific language governing permissions and
 # limitations under the License.
 
-from __future__ import absolute_import
 
 import contextlib
 import json
@@ -56,7 +55,7 @@ def update(self, json_str):
             self._dispatch_changed_callbacks()
 
 
-class ViewerCommonBase(object):
+class ViewerCommonBase:
     def __init__(self):
         self.token = make_random_token()
         self.config_state = trackable_state.TrackableState(
diff --git a/src/nglui/easyviewer/ev_base/nglite/viewer_config_state.py b/src/nglui/easyviewer/ev_base/nglite/viewer_config_state.py
index b30d215..d3a3570 100644
--- a/src/nglui/easyviewer/ev_base/nglite/viewer_config_state.py
+++ b/src/nglui/easyviewer/ev_base/nglite/viewer_config_state.py
@@ -12,7 +12,6 @@
 # See the License for the specific language governing permissions and
 # limitations under the License.
 
-from __future__ import absolute_import
 
 import base64
 import collections
@@ -77,7 +76,7 @@ class ActionState(JsonObjectWrapper):
     screenshot = wrapped_property("screenshot", optional(ScreenshotReply))
 
 
-class Actions(object):
+class Actions:
     def __init__(self, set_config):
         self._action_handlers = dict()
         self._set_config = set_config
diff --git a/src/nglui/easyviewer/ev_base/nglite/viewer_state.py b/src/nglui/easyviewer/ev_base/nglite/viewer_state.py
index 6461747..7fddadb 100644
--- a/src/nglui/easyviewer/ev_base/nglite/viewer_state.py
+++ b/src/nglui/easyviewer/ev_base/nglite/viewer_state.py
@@ -13,7 +13,6 @@
 # limitations under the License.
 """Wrappers for representing the Neuroglancer viewer state."""
 
-from __future__ import absolute_import
 
 import collections
 import copy
@@ -189,7 +188,7 @@ def volume_source(x):
     return text_type(x)
 
 
-class _AnnotationLayerOptions(object):
+class _AnnotationLayerOptions:
     __slots__ = ()
     annotation_color = annotationColor = wrapped_property(
         "annotationColor", optional(text_type)
@@ -515,7 +514,7 @@ def __deepcopy__(self, memo):
 
 
 @export
-class Layers(object):
+class Layers:
     __slots__ = ("_layers", "_readonly")
     supports_readonly = True
 
@@ -568,18 +567,17 @@ def __setitem__(self, k, v):
                 self._layers.append(v)
             else:
                 self._layers[i] = v
-        else:
-            if isinstance(k, slice):
-                values = []
-                for x in v:
-                    if not isinstance(v, ManagedLayer):
-                        raise TypeError
-                    values.append(x)
-                self._layers[k] = values
-            else:
+        elif isinstance(k, slice):
+            values = []
+            for x in v:
                 if not isinstance(v, ManagedLayer):
                     raise TypeError
-                self._layers[k] = v
+                values.append(x)
+            self._layers[k] = values
+        else:
+            if not isinstance(v, ManagedLayer):
+                raise TypeError
+            self._layers[k] = v
 
     def clear(self):
         """Clears the list of layers."""
diff --git a/src/nglui/easyviewer/ev_base/nglite_compatibility/__init__.py b/src/nglui/easyviewer/ev_base/nglite_compatibility/__init__.py
index 5484023..fdce4d3 100644
--- a/src/nglui/easyviewer/ev_base/nglite_compatibility/__init__.py
+++ b/src/nglui/easyviewer/ev_base/nglite_compatibility/__init__.py
@@ -1,6 +1,6 @@
+from neuroglancer.url_state import *
 from neuroglancer.viewer_base import UnsynchronizedViewerBase
 from neuroglancer.viewer_state import *
-from neuroglancer.url_state import *
 
 
 class Viewer(UnsynchronizedViewerBase):
diff --git a/src/nglui/easyviewer/ev_base/nglite_compatibility/base.py b/src/nglui/easyviewer/ev_base/nglite_compatibility/base.py
index 80e1950..139597f 100644
--- a/src/nglui/easyviewer/ev_base/nglite_compatibility/base.py
+++ b/src/nglui/easyviewer/ev_base/nglite_compatibility/base.py
@@ -1,5 +1,2 @@
-from . import Viewer
-from ..annotation_compatibility import convert_annotation
-import neuroglancer
 
 
diff --git a/src/nglui/easyviewer/ev_base/seunglab.py b/src/nglui/easyviewer/ev_base/seunglab.py
index 8867082..16aebad 100644
--- a/src/nglui/easyviewer/ev_base/seunglab.py
+++ b/src/nglui/easyviewer/ev_base/seunglab.py
@@ -1,12 +1,15 @@
 # Seung lab branch of easyviewer
 
-from .base import EasyViewerBase, SEGMENTATION_LAYER_TYPES
-from . import utils
 import re
-from . import nglite as neuroglancer
-from typing import Union, List, Dict, Tuple, Optional
-from numpy import issubdtype, integer, uint64, vstack
 from collections import OrderedDict
+from typing import Dict, List, Optional, Tuple, Union
+from warnings import warn
+
+from numpy import integer, issubdtype, uint64, vstack
+
+from . import nglite as neuroglancer
+from . import utils
+from .base import SEGMENTATION_LAYER_TYPES, EasyViewerBase
 
 
 class EasyViewerSeunglab(neuroglancer.UnsynchronizedViewer, EasyViewerBase):
@@ -44,6 +47,18 @@ def set_state_server(self, state_server) -> None:
         with self.txn() as s:
             s._json_data["jsonStateServer"] = state_server
 
+    def add_segmentation_layer(self, layer_name, source, **kwargs):
+        """Add segmentation layer to viewer instance.
+
+        Attributes:
+            layer_name (str): name of layer to be displayed in neuroglancer ui.
+            source (str): source of neuroglancer segment layer
+        """
+        if type(source) is not str:
+            source = source[0]
+            warn("Only using first source in list for seung-lab segmentation layer")
+        super().add_segmentation_layer(layer_name, source, **kwargs)
+
     def add_annotation_layer(
         self,
         layer_name=None,
@@ -100,7 +115,7 @@ def as_url(
         )  # 'seunglab' hard-coded because of file.
         ngl_url = neuroglancer.to_url(self.state, prefix=prefix)
         if as_html:
-            return '<a href="{}" target="_blank">{}</a>'.format(ngl_url, link_text)
+            return f'<a href="{ngl_url}" target="_blank">{link_text}</a>'
         else:
             return ngl_url
 
diff --git a/src/nglui/easyviewer/ev_base/utils.py b/src/nglui/easyviewer/ev_base/utils.py
index 096e4a1..ace1e71 100644
--- a/src/nglui/easyviewer/ev_base/utils.py
+++ b/src/nglui/easyviewer/ev_base/utils.py
@@ -1,12 +1,15 @@
+import numbers
+import re
+from urllib.parse import urlparse
+
 import numpy as np
 import pandas as pd
 import webcolors
-import re
-import numbers
-from urllib.parse import urlparse
 
 default_seunglab_neuroglancer_base = "https://neuromancer-seung-import.appspot.com/"
 default_mainline_neuroglancer_base = "https://ngl.cave-explorer.org/"
+MAINLINE_NAMES = ["mainline", "cave-explorer", "spelunker"]
+
 
 def omit_nones(seg_list):
     if seg_list is None or np.all(pd.isna(seg_list)):
@@ -18,6 +21,7 @@ def omit_nones(seg_list):
     else:
         return seg_list
 
+
 def parse_color(clr):
     if clr is None:
         return None
@@ -34,36 +38,42 @@ def parse_color(clr):
     else:
         return webcolors.rgb_to_hex([int(255 * x) for x in clr])
 
+
 def parse_graphene_header(source, target):
     qry = urlparse(source)
-    if qry.scheme=='graphene':
-        if target == 'seunglab':
+    if qry.scheme == "graphene":
+        if target == "seunglab":
             return _parse_to_seunglab(qry)
-        elif target == 'mainline' or target == 'cave-explorer':
+        elif target == "mainline" or target == "cave-explorer":
             return _parse_to_mainline(qry)
     else:
         return source
 
+
 def _parse_to_seunglab(qry):
     return f"{qry.scheme}://https:{qry.path}"
 
+
 def _parse_to_mainline(qry):
-    if 'https' in qry.netloc:
+    if "https" in qry.netloc:
         return f"{qry.scheme}://middleauth+https:{qry.path}"
     else:
         return f"{qry.scheme}://middleauth+http:{qry.path}"
-    
+
+
 def neuroglancer_url(url, target_site):
     """
     Check neuroglancer info to determine which kind of site a neuroglancer URL is.
     """
     if url is not None:
         return url
-    elif target_site == 'seunglab':
+    elif target_site is None:
+        return None
+    elif target_site == "seunglab":
         return default_seunglab_neuroglancer_base
-    elif target_site == 'mainline' or target_site == 'cave-explorer':
+    elif target_site in MAINLINE_NAMES:
         return default_mainline_neuroglancer_base
     else:
-        raise ValueError("Must specify either a URL or a target site (one of 'seunglab' or 'mainline'/'cave-explorer')")
-
-    
\ No newline at end of file
+        raise ValueError(
+            f"Must specify either a URL or a target site (either 'seunglab' or one of {MAINLINE_NAMES})"
+        )
diff --git a/src/nglui/parser/base.py b/src/nglui/parser/base.py
index d3a4d65..57499f0 100644
--- a/src/nglui/parser/base.py
+++ b/src/nglui/parser/base.py
@@ -1,6 +1,6 @@
+
 import numpy as np
 import pandas as pd
-from itertools import chain
 
 from ..easyviewer.ev_base.base import SEGMENTATION_LAYER_TYPES
 
diff --git a/src/nglui/parser/info.py b/src/nglui/parser/info.py
index 1619ef8..e4eeaa6 100644
--- a/src/nglui/parser/info.py
+++ b/src/nglui/parser/info.py
@@ -13,4 +13,4 @@ def get_ngl_info(ngl_url):
         return r.json()
     except Exception as e:
         print(f"Error getting neuroglancer version: {e}")
-        return None
\ No newline at end of file
+        return None
diff --git a/src/nglui/segmentprops/__init__.py b/src/nglui/segmentprops/__init__.py
new file mode 100644
index 0000000..7094649
--- /dev/null
+++ b/src/nglui/segmentprops/__init__.py
@@ -0,0 +1,7 @@
+from .base import (
+    LabelProperty,
+    NumberProperty,
+    SegmentProperties,
+    StringProperty,
+    TagProperty,
+)
diff --git a/src/nglui/segmentprops/base.py b/src/nglui/segmentprops/base.py
new file mode 100644
index 0000000..b6b521b
--- /dev/null
+++ b/src/nglui/segmentprops/base.py
@@ -0,0 +1,432 @@
+from functools import partial
+from itertools import chain
+from typing import Optional, Union
+
+import attrs
+import numpy as np
+import pandas as pd
+
+"""
+Options and validation for neuroglancer segment properties based on the segment properties spec:
+https://github.com/google/neuroglancer/blob/master/src/datasource/precomputed/segment_properties.md
+"""
+
+
+class SegmentPropertyBase:
+    pass
+
+
+ALLOWED_NUMBER_DATA_TYPES = [
+    "uint8",
+    "int8",
+    "uint16",
+    "int16",
+    "uint32",
+    "int32",
+    "float32",
+]
+NONE_ATTR_FILTERS = ["tag_descriptions", "description"]
+
+
+def list_of_strings(x: list) -> list:
+    return [str(v) for v in x]
+
+
+def space_to_underscore(x: list) -> list:
+    return [str(y).replace(" ", "_") for y in x]
+
+
+def sort_tag_arrays(x: list) -> list:
+    return [sorted(y) for y in x]
+
+
+@attrs.define
+class InlineProperties:
+    ids = attrs.field(type=list[int], converter=list_of_strings, kw_only=True)
+    properties = attrs.field(type=list[SegmentPropertyBase], default=[], kw_only=True)
+
+    def __len__(self):
+        return len(self.ids)
+
+    def __attrs_post_init__(self):
+        if len(self.properties) > 0:
+            _validate_properties(self.ids, self.properties)
+
+
+@attrs.define
+class LabelProperty(SegmentPropertyBase):
+    id = attrs.field(default="label", type=str, kw_only=True)
+    type = attrs.field(init=False, default="label", type=str)
+    values = attrs.field(type=list, converter=list_of_strings, kw_only=True)
+    description = attrs.field(type=Optional[str], default=None, kw_only=True)
+
+    def __len__(self):
+        return len(self.values)
+
+
+@attrs.define
+class DescriptionProperty(SegmentPropertyBase):
+    id = attrs.field(default="description", type=str, kw_only=True)
+    type = attrs.field(init=False, default="description", type=str)
+    values = attrs.field(type=list, converter=list_of_strings, kw_only=True)
+    description = attrs.field(type=Optional[str], default=None, kw_only=True)
+
+    def __len__(self):
+        return len(self.values)
+
+
+@attrs.define
+class StringProperty(SegmentPropertyBase):
+    id = attrs.field(type=str, kw_only=True)
+    type = attrs.field(init=False, default="string", type=str)
+    values = attrs.field(type=list, converter=list_of_strings, kw_only=True)
+    description = attrs.field(type=Optional[str], default=None, kw_only=True)
+
+    def __len__(self):
+        return len(self.values)
+
+
+@attrs.define
+class NumberProperty(SegmentPropertyBase):
+    id = attrs.field(type=str, kw_only=True)
+    type = attrs.field(init=False, default="number", type=str)
+    values = attrs.field(type=list, kw_only=True)
+    description = attrs.field(type=Optional[str], default=None, kw_only=True)
+    data_type = attrs.field(
+        type=str,
+        kw_only=True,
+        validator=attrs.validators.in_(ALLOWED_NUMBER_DATA_TYPES),
+    )
+
+    def __attrs_post_init__(self):
+        prop_dtype = np.dtype(self.data_type)
+        self.values = (
+            np.array(self.values).astype(prop_dtype, casting="same_kind").tolist()
+        )
+
+    def __len__(self):
+        return len(self.values)
+
+
+@attrs.define
+class TagProperty(SegmentPropertyBase):
+    id = attrs.field(type=str, kw_only=True, default="tags")
+    type = attrs.field(init=False, type=str, default="tags")
+    tags = attrs.field(
+        type=list[str],
+        converter=space_to_underscore,
+        validator=attrs.validators.not_(attrs.validators.matches_re(r"^\#")),
+        kw_only=True,
+    )
+    tag_descriptions = attrs.field(
+        type=list[str],
+        default=None,
+        kw_only=True,
+    )
+    values = attrs.field(
+        type=list[list[int]],
+        converter=sort_tag_arrays,
+        kw_only=True,
+    )
+
+    def __len__(self):
+        return len(self.values)
+
+
+def prop_filter(attr, value):
+    "Filters out None for optional attributes for use in 'attrs.asdict' conversion"
+    return value is not None or attr.name not in NONE_ATTR_FILTERS
+
+
+prop_to_dict = partial(attrs.asdict, filter=prop_filter)
+
+
+def _validate_properties(
+    ids,
+    properties,
+):
+    n_ids = len(ids)
+    for prop in properties:
+        if len(prop) != n_ids:
+            msg = f"Property {prop} does not have the same number of entries as the id list."
+            raise ValueError(msg)
+
+
+def build_segment_properties(
+    ids: list[int],
+    properties: list,
+):
+    return {
+        "@type": "neuroglancer_segment_properties",
+        "inline": prop_to_dict(InlineProperties(ids=ids, properties=properties)),
+    }
+
+
+def _find_column_dtype(column):
+    "Get data type string from a dataframe column"
+    if column.dtype in ALLOWED_NUMBER_DATA_TYPES:
+        return str(column.dtype)
+    elif column.dtype == "int64":
+        return "int32"
+    elif column.dtype == "float64":
+        return "float32"
+    elif column.dtype == "object":
+        try:
+            column.astype("float32")
+        except Exception:
+            raise ValueError(
+                f"Column {column} has an unsupported data type {column.dtype}"
+            )
+    else:
+        raise ValueError(f"Column {column} has an unsupported data type {column.dtype}")
+
+
+def _tag_descriptions(tags, tag_descriptions):
+    if tag_descriptions is None:
+        return None
+    else:
+        return [tag_descriptions.get(tag, tag) for tag in tags]
+
+
+def _make_tag_property(df, value_columns, bool_columns, tag_descriptions, name="tags"):
+    if value_columns is None:
+        value_columns = []
+    if bool_columns is None:
+        bool_columns = []
+    tags = []
+    for col in value_columns:
+        unique_tags = df[col].unique()
+        # df.unique works differently for categorical dtype columns and does not return an ndarray so we have to check
+        if isinstance(unique_tags, np.ndarray):
+            unique_tags = sorted([x for x in unique_tags.tolist() if x is not None])
+        else:
+            unique_tags = unique_tags.sort_values().tolist()
+        if np.any(np.isin(tags, unique_tags)):
+            raise ValueError("Tags across columns are not unique")
+        tags.extend(unique_tags)
+    tags.extend(bool_columns)
+    tag_map = {tag: i for i, tag in enumerate(tags) if tag is not None}
+    tag_values = []
+    for _, row in df.iterrows():
+        tag_values.append(
+            [tag_map[tag] for tag in row[value_columns] if tag is not None]
+        )
+    for tv in bool_columns:
+        for loc in np.flatnonzero(df[tv]):
+            tag_values[loc].append(tag_map[tv])
+    return TagProperty(
+        id=name,
+        tags=tags,
+        values=tag_values,
+        tag_descriptions=_tag_descriptions(tags, tag_descriptions),
+    )
+
+
+class SegmentProperties:
+    def __init__(
+        self,
+        ids: list[int],
+        label_property: Optional[LabelProperty] = None,
+        description_property: Optional[DescriptionProperty] = None,
+        tag_properties: Optional[TagProperty] = None,
+        string_properties: Optional[Union[StringProperty, list[StringProperty]]] = None,
+        number_properties: Optional[Union[NumberProperty, list[NumberProperty]]] = None,
+    ):
+        self.ids = ids
+        self.label_property = label_property
+        self.description_property = description_property
+        self.tag_properties = tag_properties
+
+        if isinstance(string_properties, StringProperty):
+            string_properties = [string_properties]
+        self.string_properties = string_properties
+
+        if isinstance(number_properties, NumberProperty):
+            number_properties = [number_properties]
+        self.number_properties = number_properties
+
+    def __len__(self):
+        return len(self.ids)
+
+    def _property_list(self):
+        single_prop_list = [
+            prop
+            for prop in [
+                self.label_property,
+                self.description_property,
+                self.tag_properties,
+            ]
+            if prop is not None
+        ]
+        multi_prop_list = list(
+            chain.from_iterable(
+                [
+                    prop
+                    for prop in [
+                        self.string_properties,
+                        self.number_properties,
+                    ]
+                    if prop is not None
+                ]
+            )
+        )
+        return single_prop_list + multi_prop_list
+
+    def __repr__(self):
+        return f"SegmentProperties ({len(self.ids)} segments, {len(self._property_list())} properties)"
+
+    def __str__(self):
+        return self.__repr__()
+
+    def property_description(self):
+        return [(prop.id, prop.type, len(prop)) for prop in self._property_list()]
+
+    def to_dict(self):
+        "Converts the segment properties to a dictionary for use in neuroglancer"
+        return build_segment_properties(
+            self.ids,
+            self._property_list(),
+        )
+
+    @classmethod
+    def from_dataframe(
+        cls,
+        df: pd.DataFrame,
+        id_col: str = "pt_root_id",
+        label_col: Optional[str] = None,
+        description_col: Optional[str] = None,
+        string_cols: Optional[Union[str, list[str]]] = None,
+        number_cols: Optional[Union[str, list[str]]] = None,
+        tag_value_cols: Optional[Union[str, list[str]]] = None,
+        tag_bool_cols: Optional[list[str]] = None,
+        tag_descriptions: Optional[dict] = None,
+    ):
+        """Generate a segment property object from a pandas dataframe based on column
+
+        Parameters
+        ----------
+        df : pd.DataFrame
+            Dataframe containing propeties
+        id_col : str, optional
+            Name of the column with object ids, by default "pt_root_id"
+        label_col : Optional[str], optional
+            Name of column to use for producing labels, by default None
+        description_col : Optional[str], optional
+            Name of column to use for producing descriptions, by default None
+        string_cols : Optional[Union[str, list[str]]], optional
+            Column (or list of columns) to use for string properties, by default None.
+            WARNING: Neuroglancer does not currently display these properties.
+        number_cols : Optional[Union[str, list[str]]], optional
+            Column (or list of columns) to use for numeric properties, by default None.
+        tag_value_cols : Optional[list[str]], optional
+            Column (or list of columns) to generate tags based on unique values.
+            Each column produces one tag per row based on the value, by default None
+        tag_bool_cols : Optional[list[str]], optional
+            List of columns to generate tags based on boolean values where each column is a tag, and each id gets the tag if it has a True in its row.
+            By default None.
+        tag_descriptions : Optional[dict], optional
+            Dictionary of tag values to long-form tag descriptions, by default None.
+            Tags without a key/value are passed through directly.
+
+        Returns
+        -------
+        SegmentProperties
+            Segment properties object
+        """
+        ids = df[id_col].tolist()
+        properties = {}
+        if label_col:
+            properties["label_property"] = LabelProperty(values=df[label_col].tolist())
+        if description_col:
+            properties["description_property"] = DescriptionProperty(
+                values=df[description_col].tolist()
+            )
+        if string_cols:
+            if isinstance(string_cols, str):
+                string_cols = [string_cols]
+            properties["string_properties"] = [
+                StringProperty(id=col, values=df[col].tolist()) for col in string_cols
+            ]
+        if number_cols:
+            if isinstance(number_cols, str):
+                number_cols = [number_cols]
+            properties["number_properties"] = [
+                NumberProperty(
+                    id=col,
+                    values=df[col].tolist(),
+                    data_type=_find_column_dtype(df[col]),
+                )
+                for col in number_cols
+            ]
+        if tag_value_cols or tag_bool_cols:
+            if isinstance(tag_value_cols, str):
+                tag_value_cols = [tag_value_cols]
+            if isinstance(tag_bool_cols, str):
+                tag_bool_cols = [tag_bool_cols]
+            properties["tag_properties"] = _make_tag_property(
+                df,
+                tag_value_cols,
+                tag_bool_cols,
+                tag_descriptions,
+            )
+        return cls(ids, **properties)
+
+    @classmethod
+    def from_dict(
+        cls,
+        seg_prop_dict: dict,
+    ):
+        """Generate a segment property object from a segment property dictionary
+
+        Parameters
+        ----------
+        seg_prop_dict : dict
+            Segment property dictionary, as imported from the json.
+
+        Returns
+        -------
+        SegmentProperties
+            Segment properties object
+        """
+        ids = seg_prop_dict["inline"]["ids"]
+        props = seg_prop_dict["inline"]["properties"]
+        prop_classes = {}
+        for prop in props:
+            if prop["type"] == "label":
+                prop_classes["label_property"] = LabelProperty(
+                    values=prop["values"],
+                    description=prop.get("description"),
+                )
+            elif prop["type"] == "description":
+                prop_classes["description_property"] = DescriptionProperty(
+                    values=prop["values"],
+                    description=prop.get("description"),
+                )
+            elif prop["type"] == "string":
+                if "string_properties" not in prop_classes:
+                    prop_classes["string_properties"] = []
+                prop_classes["string_properties"].append(
+                    StringProperty(
+                        id=prop["id"],
+                        values=prop["values"],
+                        description=prop.get("description"),
+                    )
+                )
+            elif prop["type"] == "number":
+                if "number_properties" not in prop_classes:
+                    prop_classes["number_properties"] = []
+                prop_classes["number_properties"].append(
+                    NumberProperty(
+                        id=prop["id"],
+                        values=prop["values"],
+                        data_type=prop["data_type"],
+                        description=prop.get("description"),
+                    )
+                )
+            elif prop["type"] == "tags":
+                prop_classes["tag_properties"] = TagProperty(
+                    tags=prop["tags"],
+                    values=prop["values"],
+                    tag_descriptions=prop.get("tag_descriptions"),
+                )
+        return cls(ids, **prop_classes)
diff --git a/src/nglui/statebuilder/helpers.py b/src/nglui/statebuilder/helpers.py
index 51edc9f..85651fe 100644
--- a/src/nglui/statebuilder/helpers.py
+++ b/src/nglui/statebuilder/helpers.py
@@ -1,16 +1,17 @@
 from typing import Iterable
+
+import pandas as pd
+from caveclient import CAVEclient
+from caveclient.endpoints import fallback_ngl_endpoint
+from IPython.display import HTML
+
 from .layers import (
+    AnnotationLayerConfig,
     ImageLayerConfig,
     SegmentationLayerConfig,
-    AnnotationLayerConfig,
-    PointMapper,
-    LineMapper,
 )
+from .mappers import LineMapper, PointMapper
 from .statebuilder import ChainedStateBuilder, StateBuilder
-from caveclient import CAVEclient
-from caveclient.endpoints import fallback_ngl_endpoint
-import pandas as pd
-from IPython.display import HTML
 
 DEFAULT_POSTSYN_COLOR = (0.25098039, 0.87843137, 0.81568627)  # CSS3 color turquise
 DEFAULT_PRESYN_COLOR = (1.0, 0.38823529, 0.27843137)  # CSS3 color tomato
@@ -20,7 +21,12 @@
         "contrast_controls": True,
         "black": 0.35,
         "white": 0.70,
-    }
+    },
+    "minnie65_public": {
+        "contrast_controls": True,
+        "black": 0.35,
+        "white": 0.70,
+    },
 }
 MAX_URL_LENGTH = 1_750_000
 DEFAULT_NGL = fallback_ngl_endpoint
@@ -106,7 +112,10 @@ def make_line_statebuilder(
         dictionary of view keywords to configure neuroglancer view
     split_positions : bool, optional
         whether the position column into x,y,z columns. Defaults to False.
-
+    ngl_url : str, optional
+        URL of the Neuroglancer instance to use. Defaults to client.info.viewer_site() or DEFAULT_NGL.
+    target_site : str, optional
+        Category of Neuroglancer deployment to build link for. Defaults to None.
     Returns
     -------
     StateBuilder:
@@ -284,8 +293,8 @@ def make_pre_post_statebuilder(
 
     if view_kws is None:
         view_kws = {}
-    sb1 = StateBuilder(layers=[img_layer, seg_layer], client=client, view_kws=view_kws)
 
+    sb1 = StateBuilder(layers=[img_layer, seg_layer], client=client, view_kws=view_kws)
     state_builders = [sb1]
     if show_inputs:
         # First state builder
@@ -350,7 +359,9 @@ def make_state_url(df, sb, client, ngl_url=None, target_site=None):
         ngl_url = client.info.viewer_site()
         if ngl_url is None:
             ngl_url = DEFAULT_NGL
-    url = client.state.build_neuroglancer_url(state_id, ngl_url=ngl_url)
+    url = client.state.build_neuroglancer_url(
+        state_id, ngl_url=ngl_url, target_site=target_site
+    )
     return url
 
 
@@ -404,7 +415,7 @@ def make_url_robust(
                 df, sb, client, ngl_url=ngl_url, target_site=target_site
             )
     elif shorten == "always":
-        url = make_state_url(df, sb, client, target_site=target_site)
+        url = make_state_url(df, sb, client, ngl_url=ngl_url, target_site=target_site)
     elif shorten == "never":
         url = sb.render_state(
             df, return_as="url", url_prefix=ngl_url, target_site=target_site
@@ -476,7 +487,9 @@ def package_state(
         else:
             return url
     elif return_as == "json":
-        return sb.render_state(df, return_as=return_as, target_site=target_site)
+        return sb.render_state(
+            df, return_as=return_as, ngl_url=ngl_url, target_site=target_site
+        )
     else:
         raise (
             ValueError(
@@ -756,16 +769,17 @@ def make_neuron_neuroglancer_link(
         dataframe_resolution_post=data_resolution_post,
         split_positions=True,
     )
-    return package_state(
-        dataframes,
-        sb,
-        client,
-        shorten,
-        return_as,
-        ngl_url,
-        link_text,
-        target_site=target_site,
-    )
+    return sb, dataframes
+    # return package_state(
+    #     dataframes,
+    #     sb,
+    #     client,
+    #     shorten,
+    #     return_as,
+    #     ngl_url,
+    #     link_text,
+    #     target_site=target_site,
+    # )
 
 
 def from_client(client, image_name=None, segmentation_name=None, contrast=None):
@@ -797,8 +811,16 @@ def from_client(client, image_name=None, segmentation_name=None, contrast=None):
         )
     else:
         config = {"contrast_controls": True, "black": contrast[0], "white": contrast[1]}
-    img_layer = ImageLayerConfig(client.info.image_source(), name=image_name, **config)
-    seg_layer = SegmentationLayerConfig(
-        client.info.segmentation_source(), name=segmentation_name
-    )
+    if image_name is not False:
+        img_layer = ImageLayerConfig(
+            client.info.image_source(), name=image_name, **config
+        )
+    else:
+        img_layer = None
+    if segmentation_name is not False:
+        seg_layer = SegmentationLayerConfig(
+            client.info.segmentation_source(), name=segmentation_name
+        )
+    else:
+        seg_layer = None
     return img_layer, seg_layer
diff --git a/src/nglui/statebuilder/layers.py b/src/nglui/statebuilder/layers.py
index de4fd88..c61f639 100644
--- a/src/nglui/statebuilder/layers.py
+++ b/src/nglui/statebuilder/layers.py
@@ -1,14 +1,16 @@
+import numbers
+from datetime import datetime
+from typing import Optional, Union
+from warnings import warn
+
+import numpy as np
+
+from ..easyviewer import EasyViewerMainline
+from ..segmentprops.base import SegmentProperties
 from .mappers import (
-    SelectionMapper,
     AnnotationMapperBase,
-    PointMapper,
-    LineMapper,
-    SphereMapper,
-    BoundingBoxMapper,
+    SelectionMapper,
 )
-from datetime import datetime
-import numpy as np
-import numbers
 
 DEFAULT_IMAGE_LAYER = "img"
 DEFAULT_SEG_LAYER = "seg"
@@ -21,7 +23,7 @@
 }
 
 
-class LayerConfigBase(object):
+class LayerConfigBase:
     """Base class for configuring layers
 
     Parameters
@@ -91,7 +93,7 @@ def active(self, val):
         self._config["active"] = val
 
     def _render_layer(
-        self, viewer, data, viewer_resolution=None, return_annos=False
+        self, viewer, data, viewer_resolution=None, return_annos=False, client=None
     ):
         """Applies rendering rules"""
         annos = self._specific_rendering(
@@ -99,6 +101,7 @@ def _render_layer(
             data,
             viewer_resolution=viewer_resolution,
             return_annos=return_annos,
+            client=client,
         )
         if self.active:
             viewer.set_selected_layer(self.name)
@@ -107,21 +110,21 @@ def _render_layer(
         else:
             pass
 
-    def _add_layer(
-            self, viewer
-    ):
+    def _add_layer(self, viewer):
         "Subclass implements layer addition rules"
-        pass
 
     def _set_view_options(self, *args, **kwargs):
         "Subclass implements own rules"
-        pass
 
     def _specific_rendering(
-        self, viewer, data, viewer_resolution=None, return_annos=False,
+        self,
+        viewer,
+        data,
+        viewer_resolution=None,
+        return_annos=False,
+        client=None,
     ):
         """Subclasses implement specific rendering rules"""
-        pass
 
 
 class ImageLayerConfig(LayerConfigBase):
@@ -167,7 +170,12 @@ def _add_layer(self, viewer):
         viewer.add_image_layer(self.name, self.source)
 
     def _specific_rendering(
-        self, viewer, data, viewer_resolution=None, return_annos=False,
+        self,
+        viewer,
+        data,
+        viewer_resolution=None,
+        return_annos=False,
+        client=None,
     ):
         if self._contrast_controls:
             viewer.add_contrast_shader(self.name, black=self._black, white=self._white)
@@ -205,6 +213,10 @@ class SegmentationLayerConfig(LayerConfigBase):
         Keyword arguments for viewer.set_segmentation_view_options. Sets selected (and unselected) segmetation alpha values. Defaults to values in DEFAULT_SEGMENTATION_VIEW_KWS dict specified in this module.
     timestamp : float or datetime, optional.
         Timestamp at which to fix the chunkedgraph in either unix epoch or datetime format. Optional, default is None.
+    mapping_set : str, optional.
+        Name of the mapping set, the key in the data dictionary for statebuilder. Optional, default is None.
+    segment_properties: str, optional
+        Location of a segment properties file. Optional, default is None.
     """
 
     def __init__(
@@ -223,6 +235,8 @@ def __init__(
         view_kws=None,
         timestamp=None,
         data_resolution=None,
+        mapping_set=None,
+        segment_properties=None,
     ):
         if name is None:
             name = DEFAULT_SEG_LAYER
@@ -231,6 +245,7 @@ def __init__(
             name=name, type="segmentation", source=source, color=None, active=active
         )
         self._config["data_resolution"] = data_resolution
+        self._config["segment_properties"] = segment_properties
 
         if selected_ids_column is not None or fixed_ids is not None:
             self._selection_map = SelectionMapper(
@@ -238,6 +253,7 @@ def __init__(
                 fixed_ids=fixed_ids,
                 fixed_id_colors=fixed_id_colors,
                 color_column=color_column,
+                mapping_set=mapping_set,
             )
         else:
             self._selection_map = None
@@ -257,17 +273,114 @@ def __init__(
             }
         base_seg_kws.update(view_kws)
         self._view_kws = view_kws
+        self._segment_property_map = None
 
     @property
     def data_resolution(self):
         return self._config.get("data_resolution", None)
 
+    @property
+    def segment_properties(self):
+        if isinstance(self._config.get("segment_properties"), str):
+            return [self._config.get("segment_properties")]
+        else:
+            return self._config.get("segment_properties", [])
+
+    @property
+    def source(self):
+        if self.segment_properties:
+            seg_prop_url = self.segment_properties
+        else:
+            seg_prop_url = []
+        if self._config.get("source"):
+            if isinstance(self._config.get("source"), str):
+                source = [self._config.get("source")]
+            else:
+                source = self._config.get("source")
+        else:
+            source = []
+        out = source + seg_prop_url
+        if len(out) == 1:
+            return out[0]
+        else:
+            return out
+
+    def add_segment_propeties(
+        self,
+        segment_property: str,
+    ):
+        self._config["segment_properties"] = segment_property
+
+    def add_segment_properties_map(
+        self,
+        id_col: str = "pt_root_id",
+        label_col: Optional[str] = None,
+        description_col: Optional[str] = None,
+        string_cols: Optional[Union[str, list[str]]] = None,
+        number_cols: Optional[Union[str, list[str]]] = None,
+        tag_value_cols: Optional[Union[str, list[str]]] = None,
+        tag_bool_cols: Optional[list[str]] = None,
+        tag_descriptions: Optional[dict] = None,
+        mapping_set: Optional[str] = None,
+    ):
+        segment_property_map = {
+            "id_col": id_col,
+            "label_col": label_col,
+            "description_col": description_col,
+            "string_cols": string_cols,
+            "number_cols": number_cols,
+            "tag_value_cols": tag_value_cols,
+            "tag_bool_cols": tag_bool_cols,
+            "tag_descriptions": tag_descriptions,
+        }
+        if mapping_set:
+            if not isinstance(self._segment_property_map, dict):
+                self._segment_property_map = {}
+            self._segment_property_map[mapping_set] = segment_property_map
+        else:
+            self._segment_property_map = segment_property_map
+
+    def _render_single_segment_prop(self, data, seg_prop_map, client):
+        props = SegmentProperties.from_dataframe(data, **seg_prop_map)
+        pid = client.state.upload_property_json(props.to_dict())
+        return client.state.build_neuroglancer_url(
+            pid,
+            target_site="cave-explorer",
+            format_propeties=True,
+        )
+
+    def _render_segment_property_map(self, data, client, target_site=None):
+        if target_site == "seunglab":
+            warn("Cannot render segment properties for seunglab")
+            return None
+        if client is None:
+            raise ValueError(
+                "Client must be provided to dynamically render segment properties"
+            )
+        seg_prop_urls = []
+        if isinstance(data, dict):
+            for k, v in data.items():
+                if k in self._segment_property_map:
+                    seg_prop_urls.append(
+                        self._render_single_segment_prop(
+                            v, self._segment_property_map.get(k), client
+                        )
+                    )
+        else:
+            seg_prop_urls.append(
+                self._render_single_segment_prop(
+                    data, self._segment_property_map, client
+                )
+            )
+        return seg_prop_urls
+
     def add_selection_map(
         self,
         selected_ids_column=None,
         fixed_ids=None,
         fixed_id_colors=None,
         color_column=None,
+        mapping_set=None,
     ):
         """Add rules for selecting active segment ids and their colors
 
@@ -281,6 +394,8 @@ def add_selection_map(
             Add a list of colors (hex, rgb, or CSS3 string) to assign to the fixed ids, by default None
         color_column : str, optional
             Dataframe column to use for adding selected segment colors, by default None
+        mapping_set : str, optional
+            Name of the mapping set, the key in the data dictionary for statebuilder, by default None
         """
         if self._selection_map is not None:
             if isinstance(selected_ids_column, str):
@@ -327,19 +442,34 @@ def add_selection_map(
             fixed_ids=new_fixed_ids,
             fixed_id_colors=new_fixed_id_colors,
             color_column=color_column,
+            mapping_set=mapping_set,
         )
 
     def _add_layer(self, viewer):
         viewer.add_segmentation_layer(self.name, self.source)
 
     def _specific_rendering(
-        self, viewer, data, viewer_resolution=None, return_annos=False,
+        self,
+        viewer,
+        data,
+        viewer_resolution=None,
+        return_annos=False,
+        client=None,
     ):
         if self._selection_map is not None:
             selected_ids = self._selection_map.selected_ids(data)
             colors = self._selection_map.seg_colors(data)
             viewer.add_selected_objects(self.name, selected_ids, colors)
 
+        if self._segment_property_map is not None:
+            if isinstance(viewer, EasyViewerMainline):
+                target_site = "cave-explorer"
+            else:
+                target_site = "seunglab"
+            seg_prop_urls = self._render_segment_property_map(data, client, target_site)
+            for seg_prop_url in seg_prop_urls:
+                viewer.append_source_to_segmentation_layer(self.name, seg_prop_url)
+
         if self._split_point_map is not None:
             (
                 seg_id,
@@ -365,7 +495,6 @@ def _specific_rendering(
 
         viewer.set_timestamp(self.name, self.timestamp)
         viewer.set_segmentation_view_options(self.name, **self._view_kws)
-        pass
 
 
 class AnnotationLayerConfig(LayerConfigBase):
@@ -471,19 +600,22 @@ def _set_view_options(self, viewer, data, viewer_resolution=None):
                 data = data.query(self.filter_query)
             for rule in self._annotation_map_rules:
                 pos = rule._get_position(
-                        data,
-                        data_resolution=self.data_resolution,
-                        viewer_resolution=viewer_resolution,
-                    )
-                viewer.set_view_options(
-                    position=pos
+                    data,
+                    data_resolution=self.data_resolution,
+                    viewer_resolution=viewer_resolution,
                 )
+                viewer.set_view_options(position=pos)
                 if pos is not None:
                     break
         return pos
 
     def _specific_rendering(
-        self, viewer, data, viewer_resolution=None, return_annos=False,
+        self,
+        viewer,
+        data,
+        viewer_resolution=None,
+        return_annos=False,
+        client=None,
     ):
         annos = []
         for rule in self._annotation_map_rules:
@@ -504,4 +636,3 @@ def _specific_rendering(
             return annos
         else:
             viewer.add_annotations(self.name, annos)
-            pass
diff --git a/src/nglui/statebuilder/mappers.py b/src/nglui/statebuilder/mappers.py
index fd5e141..d321881 100644
--- a/src/nglui/statebuilder/mappers.py
+++ b/src/nglui/statebuilder/mappers.py
@@ -1,9 +1,12 @@
-import numpy as np
-import pandas as pd
 from collections.abc import Collection
 from itertools import chain
+
+import numpy as np
+import pandas as pd
+
 from .utils import is_split_position, split_position_columns
 
+
 def _multipoint_transform(row, pt_columns, squeeze_cols):
     """Reshape dataframe to accomodate multiple points in a single row"""
     pts = {pcol: np.atleast_2d(row[pcol]) for pcol in pt_columns}
@@ -22,12 +25,13 @@ def _multipoint_transform(row, pt_columns, squeeze_cols):
                 r[col] = row[col]
     return rows
 
+
 def _multipoint_transform_split(df, multi_columns=[]):
     col_data = {}
     for col in df.columns:
         col_data[col] = []
     for _, row in df.iterrows():
-        if len(multi_columns)>0:
+        if len(multi_columns) > 0:
             n_pts = len(row[multi_columns[0]])
         else:
             n_pts = 1
@@ -35,7 +39,7 @@ def _multipoint_transform_split(df, multi_columns=[]):
             if col in multi_columns:
                 col_data[col].extend(row[col])
             else:
-                col_data[col].extend(n_pts*[row[col]])
+                col_data[col].extend(n_pts * [row[col]])
     return pd.DataFrame(col_data)
 
 
@@ -47,7 +51,7 @@ def _data_scaler(data_resolution, viewer_resolution):
     return (np.array(data_resolution) / np.array(viewer_resolution)).reshape((1, 3))
 
 
-class SelectionMapper(object):
+class SelectionMapper:
     """Class for configuring object selections based on root id
 
     Parameters
@@ -67,7 +71,12 @@ class SelectionMapper(object):
     """
 
     def __init__(
-        self, data_columns=None, fixed_ids=None, fixed_id_colors=None, color_column=None, mapping_set=None,
+        self,
+        data_columns=None,
+        fixed_ids=None,
+        fixed_id_colors=None,
+        color_column=None,
+        mapping_set=None,
     ):
         if isinstance(data_columns, str):
             data_columns = [data_columns]
@@ -114,7 +123,6 @@ def color_column(self):
     def mapping_set(self):
         return self._config.get("mapping_set", None)
 
-
     def selected_ids(self, data):
         """Uses the rules to generate a list of ids from a dataframe."""
         if self.mapping_set is not None:
@@ -129,6 +137,9 @@ def selected_ids(self, data):
         return np.concatenate(selected_ids)
 
     def seg_colors(self, data):
+        if self.mapping_set is not None:
+            data = data.get(self.mapping_set)
+
         colors = {}
         if len(self.fixed_id_colors) == len(self.fixed_ids):
             for ii, oid in enumerate(self.fixed_ids):
@@ -143,7 +154,7 @@ def seg_colors(self, data):
         return colors
 
 
-class AnnotationMapperBase(object):
+class AnnotationMapperBase:
     def __init__(
         self,
         type,
@@ -160,7 +171,6 @@ def __init__(
         split_positions=None,
         mapping_set=None,
     ):
-
         self._config = dict(
             type=type,
             data_columns=data_columns,
@@ -226,28 +236,27 @@ def collapse_groups(self):
     def multipoint_reshape(self, data, pt_columns, squeeze_cols=[]):
         if data is None or len(data) == 0:
             return data
+        elif not self.split_positions:
+            rows = data.apply(
+                lambda x: _multipoint_transform(
+                    x, pt_columns=pt_columns, squeeze_cols=squeeze_cols
+                ),
+                axis=1,
+            ).tolist()
+            return pd.DataFrame.from_records([r for r in chain.from_iterable(rows)])
         else:
-            if not self.split_positions:
-                rows = data.apply(
-                    lambda x: _multipoint_transform(
-                        x, pt_columns=pt_columns, squeeze_cols=squeeze_cols
-                    ),
-                    axis=1,
-                ).tolist()
-                return pd.DataFrame.from_records([r for r in chain.from_iterable(rows)])
-            else:
-                split_cols = []
-                for pt_col in pt_columns:
-                    split_cols.extend(split_position_columns(pt_col))
-                return _multipoint_transform_split(data, split_cols)
+            split_cols = []
+            for pt_col in pt_columns:
+                split_cols.extend(split_position_columns(pt_col))
+            return _multipoint_transform_split(data, split_cols)
 
     @property
     def split_positions(self):
-        return self._config.get('split_positions')
+        return self._config.get("split_positions")
 
     @property
     def mapping_set(self):
-        return self._config.get('mapping_set', None)
+        return self._config.get("mapping_set", None)
 
     @property
     def tag_map(self):
@@ -292,25 +301,28 @@ def _assign_tags(self, data):
             anno_tags = [[None] for x in range(len(data))]
         return anno_tags
 
-
     def _parse_data(self, data, first=False):
         if self.mapping_set is not None:
             if not isinstance(data, dict):
-                raise ValueError('If mapping sets are used, dataframes must be provided as values in a dictionary')
+                raise ValueError(
+                    "If mapping sets are used, dataframes must be provided as values in a dictionary"
+                )
             data = data.get(self.mapping_set)
         if first and data is not None:
             if len(data) > 0:
                 if isinstance(data, pd.DataFrame):
                     data = data.iloc[[0]]
                 else:
-                    data = np.array(data)[0].reshape(1,-1)
+                    data = np.array(data)[0].reshape(1, -1)
         return data
 
     def _process_columns(self, data, skip_columns=[]):
         if self.split_positions is not None:
             split_positions = self.split_positions
         else:
-            is_split = np.bool([is_split_position(col, data) for col in self.data_columns])
+            is_split = np.bool(
+                [is_split_position(col, data) for col in self.data_columns]
+            )
             if np.all(~is_split):
                 split_positions = False
             if np.any(is_split):
@@ -319,13 +331,13 @@ def _process_columns(self, data, skip_columns=[]):
                 for col, spl in zip(self.data_columns, is_split):
                     if spl:
                         skip_columns.append(col)
-            
+
         if split_positions and not self.array_data:
             data = data.copy()
             for col in self.data_columns:
                 if col in skip_columns:
                     continue
-                split_cols = [f'{col}_{suf}' for suf in ["x", "y", "z"]]
+                split_cols = [f"{col}_{suf}" for suf in ["x", "y", "z"]]
                 data[col] = np.vstack(data[split_cols].values).tolist()
             return data
         else:
@@ -391,10 +403,11 @@ def _add_groups(self, data, annos, viewer):
         annos.extend([g for g in group_annos if g is not None])
         return annos
 
-
     def _get_position(self, data, data_resolution=None, viewer_resolution=None):
         # Parse data because get_position is called by the layer, not the render_annotation function.
-        data = self._preprocess_data(data, skip_columns=self.data_columns[1:], first=True)
+        data = self._preprocess_data(
+            data, skip_columns=self.data_columns[1:], first=True
+        )
         if data is None:
             return None
 
@@ -434,6 +447,7 @@ class PointMapper(AnnotationMapperBase):
     mapping_set: str, optional
         If given, assumes data is passed as a dictionary and uses this string to as the key for the data to use.
     """
+
     def __init__(
         self,
         point_column=None,
@@ -530,6 +544,7 @@ class LineMapper(AnnotationMapperBase):
     mapping_set: str, optional
         If set, assumes data is passed as a dictionary and uses this string to as the key for the data to use.
     """
+
     def __init__(
         self,
         point_column_a=None,
@@ -675,7 +690,7 @@ def _render_data(self, data, data_resolution, viewer_resolution, viewer):
         "Transforms data to neuroglancer annotations"
         col_ctr, col_rad = self.data_columns
 
-        data = self._preprocess_data(data, skip_columns=['rad'], squeeze_cols=[col_rad])
+        data = self._preprocess_data(data, skip_columns=["rad"], squeeze_cols=[col_rad])
         if data is None:
             return []
 
@@ -741,6 +756,7 @@ class BoundingBoxMapper(AnnotationMapperBase):
     mapping_set: str, optional
         If set, assumes data is passed as a dictionary and uses this string to as the key for the data to use.
     """
+
     def __init__(
         self,
         point_column_a=None,
@@ -782,7 +798,7 @@ def _process_array_data(self, data):
                 data={"pt_a": data[0].tolist(), "pt_b": data[1].tolist()}
             )
         return data
-    
+
     def _render_data(self, data, data_resolution, viewer_resolution, viewer):
         "Transforms data to neuroglancer annotations"
         data = self._preprocess_data(data)
@@ -812,7 +828,7 @@ def _render_data(self, data, data_resolution, viewer_resolution, viewer):
         return annos
 
 
-class SplitPointMapper(object):
+class SplitPointMapper:
     """Mapper to create split points in a segmentation layer.
 
     Parameters
diff --git a/src/nglui/statebuilder/statebuilder.py b/src/nglui/statebuilder/statebuilder.py
index be85223..95a0b4b 100644
--- a/src/nglui/statebuilder/statebuilder.py
+++ b/src/nglui/statebuilder/statebuilder.py
@@ -1,10 +1,18 @@
+from warnings import warn
+
+from IPython.display import HTML
+
 from nglui.easyviewer import EasyViewer
-from ..easyviewer.ev_base.utils import neuroglancer_url, default_seunglab_neuroglancer_base
 from nglui.easyviewer.ev_base.nglite.json_utils import encode_json
-from IPython.display import HTML
+
+from ..easyviewer.ev_base.utils import (
+    default_seunglab_neuroglancer_base,
+    neuroglancer_url,
+)
 from .utils import check_target_site
 
-DEFAULT_TARGET_SITE = 'seunglab'
+DEFAULT_TARGET_SITE = "seunglab"
+DEFAULT_URL = default_seunglab_neuroglancer_base
 
 DEFAULT_VIEW_KWS = {
     "layout": "xy-3d",
@@ -13,39 +21,57 @@
     "zoom_3d": 2000,
 }
 
+
 class StateBuilder:
     """A class for schematic mapping data frames into neuroglancer states.
 
     Parameters
     ----------
-    layers (list, optional): list of nglui.statebuilder.layers.LayerConfigBase to add. Defaults to [].
-    base_state (dict, optional): json state to add to. Defaults to None.
-    url_prefix (str, optional): http(s) path to neuroglancer deployment to use. 
-        Defaults to None, which will use https://neuromancer-seung-import.appspot.com
-    state_server (str, optional): state server to post links to. Defaults to None.
-    resolution (list, optional): 3 element vector controlling the viewer resolution. Defaults to None. If None and a client is set, uses the client viewer resolution.
-    view_kws (dict, optional): dictionary controlling view parameters. Defaults to {}.
-        keys are:
-        show_slices: Boolean
-            sets if slices are shown in the 3d view. Defaults to False.
-        layout: str
-            `xy-3d`/`xz-3d`/`yz-3d` (sections plus 3d pane), `xy`/`yz`/`xz`/`3d` (only one pane), or `4panel` (all panes). Default is `xy-3d`.
-        show_axis_lines: Boolean
-            determines if the axis lines are shown in the middle of each view.
-        show_scale_bar: Boolean
-            toggles showing the scale bar.
-        orthographic : Boolean
-            toggles orthographic view in the 3d pane.
-        position* : 3-element vector
-            determines the centered location.
-        zoom_image : float
-            Zoom level for the imagery in units of nm per voxel. Defaults to 8.
-        zoom_3d : float
-            Zoom level for the 3d pane. Defaults to 2000. Smaller numbers are more zoomed in.
-        background_color : str or list
-            Sets the background color of the 3d view. Arguments can be rgb values, hex colors, or named web colors. Defaults to black.
-    client (caveclient.CAVEclient, optional): a caveclient to get defaults from. Defaults to None.
+    layers : list of nglui.statebuilder.layers.LayerConfigBase, optional
+        List of layers to add. Defaults to [].
+    base_state : dict, optional
+        JSON state to add to. Defaults to None.
+    url_prefix : str, optional
+        http(s) path to Neuroglancer deployment to use. Defaults to None,
+        which will use https://neuromancer-seung-import.appspot.com
+    state_server : str, optional
+        State server to post links to. Defaults to None.
+    resolution : list of float, optional
+        3-element vector controlling the viewer resolution. Defaults to None.
+        If None and a client is set, uses the client viewer resolution.
+    view_kws : dict, optional
+        Dictionary controlling view parameters. Defaults to {}.
+
+        Keys are:
+            show_slices : bool, optional
+                Sets if slices are shown in the 3d view. Defaults to False.
+            layout : str, optional
+                `xy-3d`/`xz-3d`/`yz-3d` (sections plus 3d pane),
+                `xy`/`yz`/`xz`/`3d` (only one pane), or `4panel` (all panes).
+                Default is `xy-3d`.
+            show_axis_lines : bool, optional
+                Determines if the axis lines are shown in the middle of each view.
+            show_scale_bar : bool, optional
+                Toggles showing the scale bar.
+            orthographic : bool, optional
+                Toggles orthographic view in the 3d pane.
+            position : list of float, optional (length-3)
+                Determines the centered location.
+            zoom_image : float, optional
+                Zoom level for the imagery in units of nm per voxel. Defaults to 8.
+            zoom_3d : float, optional
+                Zoom level for the 3d pane. Defaults to 2000. Smaller numbers are
+                more zoomed in.
+            background_color : str or list of float, optional
+                Sets the background color of the 3d view. Arguments can be rgb
+                values, hex colors, or named web colors. Defaults to black.
+    client : caveclient.CAVEclient, optional
+        A caveclient to get defaults from. Defaults to None.
+    target_site : str, optional
+        Target Neuroglancer category: either "seunglab" or "mainline"/"cave-explorer"/"spelunker". Defaults to None.
+        Will be looked up automatically based on ngl_url, if used.
     """
+
     def __init__(
         self,
         layers=[],
@@ -66,8 +92,7 @@ def __init__(
                 resolution = client.info.viewer_resolution().tolist()
             if target_site is None:
                 target_site = check_target_site(url_prefix, client)
-        if url_prefix is None and target_site is None:
-            target_site = DEFAULT_TARGET_SITE
+        self._client = client
         url_prefix = neuroglancer_url(url_prefix, target_site)
 
         self._base_state = base_state
@@ -112,10 +137,11 @@ def initialize_state(self, base_state=None, target_site=None):
 
     def handle_positions(self, data):
         for l in self._layers[::-1]:
-            pos = l._set_view_options(self._temp_viewer, data, viewer_resolution=self._resolution)
+            pos = l._set_view_options(
+                self._temp_viewer, data, viewer_resolution=self._resolution
+            )
             if pos is not None:
                 break
-        pass
 
     def render_state(
         self,
@@ -156,19 +182,26 @@ class default.
         if base_state is None:
             base_state = self._base_state
         if target_site is None:
-            if self._target_site is not None:
-                target_site = self._target_site        
+            target_site = self._target_site
+        if url_prefix is None:
+            url_prefix = self._url_prefix
+        if target_site is None and url_prefix is not None:
+            if self._client is not None:
+                target_site = check_target_site(url_prefix, self._client)
+        elif target_site is None and url_prefix is None:
+            target_site = DEFAULT_TARGET_SITE
+            url_prefix = DEFAULT_URL
+            warn(
+                'Deprecation warning: No target site or url prefix set, using default "seunglab" site. This will switch to "spelunker" in the future.'
+            )
 
-        self.initialize_state(
-            base_state=base_state, target_site=target_site
-        )
+        self.initialize_state(base_state=base_state, target_site=target_site)
         self.handle_positions(data)
 
         self._render_layers(
             data,
         )
 
-
         if url_prefix is None:
             url_prefix = self._url_prefix
 
@@ -176,27 +209,26 @@ class default.
             return self.viewer
         elif return_as == "url":
             url = self._temp_viewer.as_url(prefix=url_prefix)
-            self.initialize_state()
             return url
         elif return_as == "html":
             out = self._temp_viewer.as_url(
                 prefix=url_prefix, as_html=True, link_text=link_text
             )
             out = HTML(out)
-            self.initialize_state()
             return out
         elif return_as == "dict":
             out = self._temp_viewer.state.to_json()
-            self.initialize_state()
             return out
         elif return_as == "json":
             out = self._temp_viewer.state.to_json()
-            self.initialize_state()
             return encode_json(out)
         else:
             raise ValueError("No appropriate return type selected")
 
-    def _render_layers(self, data,):
+    def _render_layers(
+        self,
+        data,
+    ):
         # Inactivate all layers except last.
         found_active = False
         for l in self._layers[::-1]:
@@ -211,6 +243,7 @@ def _render_layers(self, data,):
                 data,
                 viewer_resolution=self._resolution,
                 return_annos=True,
+                client=self._client,
             )
         self._temp_viewer.add_multilayer_annotations(anno_dict)
 
@@ -227,6 +260,7 @@ class ChainedStateBuilder:
     statebuilders : list
         List of DataStateBuilders, in same order as dataframes will be passed
     """
+
     def __init__(self, statebuilders):
         self._statebuilders = statebuilders
         if len(self._statebuilders) == 0:
@@ -267,7 +301,8 @@ def render_state(
                 data=data,
                 base_state=temp_state,
                 return_as="dict",
-                target_site=target_site
+                url_prefix=url_prefix,
+                target_site=target_site,
             )
         last_builder = self._statebuilders[-1]
         return last_builder.render_state(
diff --git a/src/nglui/statebuilder/utils.py b/src/nglui/statebuilder/utils.py
index 8bbe428..8a66c6c 100644
--- a/src/nglui/statebuilder/utils.py
+++ b/src/nglui/statebuilder/utils.py
@@ -1,7 +1,7 @@
+import re
 from collections.abc import Iterable
-from dataclasses import dataclass
+
 import numpy as np
-import re
 
 FALLBACK_SEUNGLAB_NGL_URL = "https://neuroglancer.neuvue.io"
 FALLBACK_MAINLINE_NGL_URL = "https://ngl.cave-explorer.org"
@@ -29,16 +29,14 @@ def bucket_of_values(col, data, item_is_array=False, array_width=3):
                 return np.vstack(dataseries.values)
             else:
                 return dataseries.values[0].reshape(1, -1)
+        elif len(data) > 1:
+            return np.vstack(dataseries.map(np.vstack)).reshape(-1, array_width)
         else:
-            if len(data) > 1:
-                return np.vstack(dataseries.map(np.vstack)).reshape(-1, array_width)
-            else:
-                return np.vstack(dataseries).reshape(1, -1)
+            return np.vstack(dataseries).reshape(1, -1)
+    elif isinstance(dataseries.iloc[0], Iterable):
+        return np.concatenate(dataseries.values)
     else:
-        if isinstance(dataseries.iloc[0], Iterable):
-            return np.concatenate(dataseries.values)
-        else:
-            return dataseries.values
+        return dataseries.values
 
 
 def is_split_position(pt_col, df, suffixes=SPLIT_SUFFIXES):
@@ -59,7 +57,7 @@ def is_split_split_position(pt_col, df, suffixes=SPLIT_SUFFIXES):
         expected_name = '_'.join(split_name[:-1]) + f'_{suf}_{split_name[-1]}'
         is_split_split.append(expected_name in df.columns)
     return np.all(is_split_split)
-    
+
 def assemble_split_points(pt_col, df, suffixes=SPLIT_SUFFIXES):
     cols = split_position_columns(pt_col, suffixes)
     return np.vstack(df[cols].values)
@@ -79,4 +77,3 @@ def check_target_site(ngl_url, client):
         return 'seunglab'
     else:
         return "cave-explorer"
-    
\ No newline at end of file
diff --git a/tests/conftest.py b/tests/conftest.py
index 54eddc1..93f9f86 100644
--- a/tests/conftest.py
+++ b/tests/conftest.py
@@ -1,17 +1,21 @@
+import json
+
+import numpy as np
+import pandas as pd
 import pytest
+
 from nglui import EasyViewer
-import pandas as pd
-import numpy as np
-import json
 
 
 @pytest.fixture(scope="session")
 def viewer():
-    return EasyViewer(target_site='seunglab')
+    return EasyViewer(target_site="seunglab")
+
 
 @pytest.fixture(scope="session")
 def viewer_cave_explorer():
-    return EasyViewer(target_site='mainline')
+    return EasyViewer(target_site="mainline")
+
 
 @pytest.fixture(scope="session")
 def img_path():
@@ -42,7 +46,7 @@ def soma_df():
 def soma_df_Int64():
     df = pd.read_hdf("tests/testdata/test_data.h5", "soma").head(5)
     df["pt_root_id"] = df["pt_root_id"].astype("Int64")
-    df["pt_root_id"].iloc[0] = np.nan
+    df.loc[0, "pt_root_id"] = np.nan
     return df.head()
 
 
@@ -58,7 +62,7 @@ def post_syn_df():
 
 @pytest.fixture(scope="session")
 def test_state():
-    with open("tests/testdata/test_state.json", "r") as f:
+    with open("tests/testdata/test_state.json") as f:
         state = json.load(f)
     return state
 
@@ -87,4 +91,4 @@ def split_point_df():
         }
     )
 
-    return pd.concat((red_df, blue_df))
\ No newline at end of file
+    return pd.concat((red_df, blue_df))
diff --git a/tests/test_parser.py b/tests/test_parser.py
index 22f7ad4..595699c 100644
--- a/tests/test_parser.py
+++ b/tests/test_parser.py
@@ -1,6 +1,6 @@
-import pytest
 import numpy as np
 import pandas as pd
+
 from nglui import parser
 
 
diff --git a/tests/test_segment_props.py b/tests/test_segment_props.py
new file mode 100644
index 0000000..9b2c3e9
--- /dev/null
+++ b/tests/test_segment_props.py
@@ -0,0 +1,40 @@
+import numpy as np
+import pandas as pd
+import pytest
+
+from nglui.segmentprops import SegmentProperties
+
+
+@pytest.fixture
+def test_df():
+    return pd.DataFrame(
+        {
+            "seg_id": np.arange(0, 100),
+            "cell_type": 30 * ["ct_a"] + 30 * ["ct_b"] + 40 * ["ct_c"],
+            "category": 50 * ["cat_1"] + 40 * ["cat_2"] + 10 * [None],
+            "number_int": np.arange(300, 400),
+            "number_float": np.arange(300, 400) + 0.1,
+            "tag_a": 90 * [False] + 10 * [True],
+            "tag_b": 95 * [True] + 5 * [False],
+        }
+    )
+
+
+def test_segment_props(test_df):
+    props = SegmentProperties.from_dataframe(
+        test_df,
+        id_col="seg_id",
+        label_col="seg_id",
+        number_cols=["number_int", "number_float"],
+        tag_value_cols="cell_type",
+        tag_bool_cols=["tag_a", "tag_b"],
+        tag_descriptions={"tag_a": "The first tag", "tag_b": "The second tag"},
+    )
+
+    assert len(props) == 100
+    assert len(props.property_description()) == 4
+    p_dict = props.to_dict()
+    assert p_dict["inline"]["properties"][2]["data_type"] == "int32"
+
+    rh_props = SegmentProperties.from_dict(p_dict)
+    assert len(rh_props) == 100
diff --git a/tests/test_statebuilder.py b/tests/test_statebuilder.py
index 4ab1a49..b9d0945 100644
--- a/tests/test_statebuilder.py
+++ b/tests/test_statebuilder.py
@@ -1,16 +1,18 @@
-import pytest
-import numpy as np
 from collections import OrderedDict
+
+import numpy as np
+import pytest
+
 from nglui.statebuilder import (
-    ImageLayerConfig,
-    SegmentationLayerConfig,
     AnnotationLayerConfig,
-    StateBuilder,
-    PointMapper,
+    ChainedStateBuilder,
+    ImageLayerConfig,
     LineMapper,
+    PointMapper,
+    SegmentationLayerConfig,
     SphereMapper,
     SplitPointMapper,
-    ChainedStateBuilder,
+    StateBuilder,
 )
 
 
@@ -68,7 +70,7 @@ def test_basic_cave_explorer(image_layer, seg_layer_basic, anno_layer_basic):
     assert state.data == f'<a href="{state_url}" target="_blank">Neuroglancer Link</a>'
 
     state = sb.render_state(return_as="dict")
-    assert isinstance(state, OrderedDict)
+    assert isinstance(state, (OrderedDict, dict))  # Cave-explorer uses dict
 
     state = sb.render_state(return_as="json")
     assert type(state) is str
@@ -89,8 +91,15 @@ def test_segmentation_layer(soma_df, seg_path_precomputed, target_site):
     sb = StateBuilder(layers=[seg_layer], target_site=target_site)
     state = sb.render_state(soma_df, return_as="dict")
     print(state["layers"])
-    assert 648518346349538466 in state["layers"][0]["segments"]
-    assert 1000 in state["layers"][0]["segments"]
+    assert (
+        648518346349538466 in state["layers"][0]["segments"]
+        or "648518346349538466"
+        in state["layers"][0]["segments"]  # Cave-explorer uses strings for ids
+    )
+    assert (
+        1000 in state["layers"][0]["segments"]
+        or "1000" in state["layers"][0]["segments"]
+    )
 
 
 @pytest.mark.parametrize("target_site", [None, "seunglab", "cave-explorer"])
@@ -188,6 +197,7 @@ def test_annotations_linked(soma_df, soma_df_Int64, seg_path_precomputed, target
     )
 
     state = sb.render_state(soma_df_Int64, return_as="dict")
+    print("TYPE IS", state["layers"][1]["annotations"][0]["segments"])
     assert len(np.squeeze(state["layers"][1]["annotations"][0]["segments"])) == 0
 
 
diff --git a/tests/test_viewer.py b/tests/test_viewer.py
index 4b63268..4b1781f 100644
--- a/tests/test_viewer.py
+++ b/tests/test_viewer.py
@@ -1,4 +1,3 @@
-import pytest
 # from nglui import annotation
 import numpy as np