Update v030 release folder

mobie · Nov 15, 2022 · 86e2179 · 86e2179
1 parent 0727dd1
commit 86e2179
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Showing 51 changed files with 435 additions and 175 deletions.
diff --git a/scripts/make_release.py b/scripts/make_release.py
@@ -0,0 +1,33 @@
+# script to copy all the relevant files to a release folder
+
+import argparse
+import os
+from shutil import copytree, copyfile
+
+parser = argparse.ArgumentParser()
+parser.add_argument("version")
+args = parser.parse_args()
+version = args.version
+if not version.startswith("v"):
+    version = f"v{version}"
+
+folder = os.path.join("..", version)
+os.makedirs(folder, exist_ok=True)
+
+copyfile("../index.md", os.path.join(folder, "index.md"))
+copytree(
+    "../schema",
+    os.path.join(folder, "schema")
+)
+copytree(
+    "../tutorials",
+    os.path.join(folder, "tutorials")
+)
+copytree(
+    "../specs",
+    os.path.join(folder, "specs")
+)
+copytree(
+    "../use-cases",
+    os.path.join(folder, "use-cases")
+)
diff --git a/v030/index.md b/v030/index.md
@@ -22,10 +22,11 @@ views, images and tables for your colleagues to explore
 - [Getting Started](./tutorials/explore_a_project.md)
 - [Exploring segmentations and tables](./tutorials/exploring_segmentations.md)
 - [Locations and views](./tutorials/views_and_locations.md)
-- [Importign and exporting tables](./tutorials/importing_and_exporting_tables.md)
+- [Importing and exporting tables](./tutorials/importing_and_exporting_tables.md)
 - [Creating your own views](./tutorials/creating_your_own_views.md)
 - [Annotation tutorial](./tutorials/annotation_tutorial.md)
 - [Grid views & image region tables](./tutorials/image_grids_and_tables.md)
+- [More features](./tutorials/more_features.md)
 
 ## Advanced usage
 - [Opening projects from branches and with credentials](./tutorials/branches_and_credentials.md)
@@ -40,8 +41,8 @@ views, images and tables for your colleagues to explore
 
 ## Use-cases and example projects
 
-Most of the examples used in the tutorial come from the publication [Whole-body integration of gene expression and single-cell morphology](https://www.sciencedirect.com/science/article/pii/S009286742100876X). In this work MoBIE was used to visualize a electron microscopy volume showing a *Platynereis dumerilii* larva, as well as derived segmentations and genetic data that was imaged in light microscopy and registered to the EM.
-Besides this application MoBIE supports several other data modalities and combining them together in a project, for example:
+Most of the examples in the tutorial are from [Whole-body integration of gene expression and single-cell morphology](https://www.sciencedirect.com/science/article/pii/S009286742100876X), where MoBIE is used to visualize a EM volume of a *Platynereis dumerilii* larva, derived segmentations and gene expression profiles.
+MoBIE supports several other data modalities and combinations thereof, for example:
 
 - [Correlative light and electron microscopy](./use-cases/clem.md)
 - [High-throughput microscopy](./use-cases/htm.md)
@@ -56,6 +57,7 @@ The MoBIE functionality is also demonstrated in a series of videos:
 - [Image Registration in MoBIE](https://youtu.be/jKlM68lrhso)
 - [Interactive user annotation](https://youtu.be/M-QUE-Qh97w)
 - [Timeseries in MoBIE](https://youtu.be/Md4PbK50NE0)
+- [Spatial Transcriptomics data in MoBIE](https://youtu.be/1dDaxOAZ9Sg)
 
 There is also a [NeuBIAS BigData Seminar](https://youtu.be/CZpaTCuSQao?t=2868) introducing MoBIE.
 

diff --git a/v030/specs/examples/advanced_fig2c.json b/v030/specs/examples/advanced_fig2c.json
@@ -4,7 +4,7 @@
     "sourceDisplays": [
       {
         "imageDisplay": {
-          "blendingMode": "sumOccluding",
+          "blendingMode": "alpha",
           "color": "r=255,g=255,b=255,a=255",
           "contrastLimits": [
             150.0,
@@ -21,7 +21,7 @@
       },
       {
         "imageDisplay": {
-          "blendingMode": "sumOccluding",
+          "blendingMode": "alpha",
           "color": "r=255,g=255,b=255,a=255",
           "contrastLimits": [
             30000,
@@ -36,7 +36,7 @@
       },
       {
         "imageDisplay": {
-          "blendingMode": "sumOccluding",
+          "blendingMode": "alpha",
           "color": "white",
           "contrastLimits": [
             70.0,
@@ -116,14 +116,7 @@
               "tomo_38_lm"
             ]
           },
-          "tableData": {
-            "tsv": {
-              "relativePath": "tables/lm-tomogram-table"
-            }
-          },
-          "tables": [
-            "default.tsv"
-          ]
+          "tableSource": "lm-tomogram-table" 
         }
       },
       {
@@ -139,14 +132,7 @@
               "tomo_38_hm"
             ]
           },
-          "tableData": {
-            "tsv": {
-              "relativePath": "tables/highmag_tomos"
-            }
-          },
-          "tables": [
-            "default.tsv"
-          ]
+          "tableSource": "highmag_tomos"
         }
       }
     ],

diff --git a/v030/specs/examples/grid_view.json b/v030/specs/examples/grid_view.json
@@ -4,7 +4,7 @@
     "sourceDisplays": [
       {
         "imageDisplay": {
-          "blendingMode": "sumOccluding",
+          "blendingMode": "alpha",
           "color": "r=255,g=255,b=255,a=255",
           "contrastLimits": [
             30,
@@ -47,14 +47,7 @@
               "tomo_54_hm"
             ]
           },
-          "tableData": {
-            "tsv": {
-              "relativePath": "tables/highmag_tomos"
-            }
-          },
-          "tables": [
-            "default.tsv"
-          ]
+          "tableSource": "highmag_tomos"
         }
       }
     ],