From c288bb3051fb0f966d93c6fb62412cd58c6cd54f Mon Sep 17 00:00:00 2001 From: haesleinhuepf Date: Sun, 26 Nov 2023 12:07:15 +0000 Subject: [PATCH] deploy: 7843fecd473002811cb58697f416e22299ace45e --- 00_preparation/readme.html | 14 +++++++------- _sources/00_preparation/readme.md | 4 ++-- searchindex.js | 2 +- 3 files changed, 10 insertions(+), 10 deletions(-) diff --git a/00_preparation/readme.html b/00_preparation/readme.html index 5c64aad..109fc31 100644 --- a/00_preparation/readme.html +++ b/00_preparation/readme.html @@ -580,8 +580,8 @@

Contents

-
-

Step 1: Install Mambaforge#

-

Download and install mamba/conda. We recommend the distribution Mambaforge.

+
+

Step 1: Install Miniforge#

+

Download and install mamba/conda. We recommend the distribution Miniforge.

For ease-of-use, it is recommended to install it for your use only and to add Conda to the PATH variable during installation.

img.png

img.png

@@ -787,8 +787,8 @@

Troubleshooting: DLL load failed
  • - - Step 1: Install Mambaforge + + Step 1: Install Miniforge
  • diff --git a/_sources/00_preparation/readme.md b/_sources/00_preparation/readme.md index 966749b..11af320 100644 --- a/_sources/00_preparation/readme.md +++ b/_sources/00_preparation/readme.md @@ -14,8 +14,8 @@ See also * [Managing Scientific Python environments using Conda, Mamba and friends](https://focalplane.biologists.com/2022/12/08/managing-scientific-python-environments-using-conda-mamba-and-friends/) * [Scientific Data Analysis with Python](https://youtu.be/MOEPe9TGBK0) -## Step 1: Install Mambaforge -Download and install mamba/conda. We recommend the distribution [Mambaforge](https://github.com/conda-forge/miniforge#mambaforge). +## Step 1: Install Miniforge +Download and install mamba/conda. We recommend the distribution [Miniforge](https://github.com/conda-forge/miniforge#miniforge3). For ease-of-use, it is recommended to install it for your use only and to add Conda to the PATH variable during installation. diff --git a/searchindex.js b/searchindex.js index 1889f41..c90fa1d 100644 --- a/searchindex.js +++ b/searchindex.js @@ -1 +1 @@ -Search.setIndex({"docnames": ["00_preparation/readme", "01_scripting/napari_intro", "02_notebooks/napari-assistant", "02_notebooks/notebook_export", "03_supervised_machine_learning/interactive_object_classification/readme", "03_supervised_machine_learning/interactive_pixel_classification/readme", "04_unsupervised_machine_learning/interactive_clustering", "README", "imprint", "intro"], "filenames": ["00_preparation/readme.md", "01_scripting/napari_intro.ipynb", "02_notebooks/napari-assistant.md", "02_notebooks/notebook_export.md", "03_supervised_machine_learning/interactive_object_classification/readme.md", "03_supervised_machine_learning/interactive_pixel_classification/readme.md", "04_unsupervised_machine_learning/interactive_clustering.md", "README.md", "imprint.md", "intro.md"], "titles": ["Setting up your computer", "Scripting Napari using Python", "Interactive bioimage analysis workflow design", "Generating Jupyter Notebooks", "Interactive object classification", "Interactive pixel classification and object segmentation", "Interactive object clustering", "Napari Tutorial", "Imprint", "Napari Tutorial"], "terms": {"thi": [0, 1, 2, 3, 4, 5, 6, 7, 9], "chapter": 0, "provid": 0, "instruct": 0, "befor": [0, 5, 6], "tutori": [0, 2, 3], "when": [0, 1, 3, 4, 5], "work": [0, 1, 3, 5, 9], "we": [0, 1, 3, 4, 5, 6], "make": [0, 6], "us": [0, 2, 3, 4, 5, 6, 7], "mani": 0, "plugin": [0, 2, 4, 5, 6], "softwar": 0, "librari": 0, "which": [0, 1, 6], "need": [0, 4], "organ": 0, "One": 0, "wai": 0, "do": [0, 1, 2], "manag": 0, "A": [0, 5], "can": [0, 1, 2, 3, 4, 5, 6, 7, 9], "seen": [0, 1], "virtual": 0, "desktop": 0, "access": 0, "via": 0, "termin": [0, 4, 5, 6], "If": [0, 3, 4, 5, 9], "you": [0, 1, 2, 3, 4, 5, 6, 7, 9], "some": [0, 1, 4], "one": [0, 1, 4, 5, 9], "mai": [0, 3], "from": [0, 2, 3, 4, 5, 6, 7, 9], "anoth": [0, 1, 4], "break": 0, "e": [0, 3, 4, 8], "g": [0, 3, 4], "incompat": 0, "wa": [0, 1, 9], "just": [0, 1, 4, 5, 6], "new": [0, 1, 2, 4, 5], "start": [0, 2], "over": 0, "see": 0, "also": [0, 1, 2, 3, 4, 5, 6], "get": [0, 1], "scientif": 0, "mamba": 0, "friend": 0, "data": [0, 1, 3, 8, 9], "analysi": [0, 7, 9], "download": [0, 9], "recommend": 0, "distribut": 0, "For": [0, 1, 5, 6], "eas": 0, "onli": [0, 2, 6], "add": [0, 1, 2, 3, 4, 5], "path": 0, "variabl": [0, 1], "dure": 0, "bioimag": 0, "command": [0, 1, 2, 5], "creat": [0, 1, 4], "name": [0, 6, 8], "env": [0, 2, 4, 5, 6], "9": 0, "pyqt": 0, "c": 0, "forg": 0, "tip": 0, "It": [0, 1, 7], "everi": 0, "project": [0, 9], "ar": [0, 1, 2, 4, 5, 6], "execut": [0, 3], "In": [0, 1, 3, 4, 5, 6], "tool": [0, 2, 4, 5, 6], "cannot": 0, "harm": 0, "each": [0, 5], "other": [0, 3, 4, 5, 6], "afterward": [0, 3, 4, 5, 6], "enter": 0, "whenev": 0, "want": [0, 3, 9], "same": [0, 7], "again": [0, 2, 3, 4, 6], "should": [0, 1, 3, 4, 5, 6], "line": [0, 2, 3, 4, 5], "activ": [0, 2, 4, 5, 6], "like": [0, 2, 3, 4, 6, 7], "naparia": 0, "And": 0, "window": [0, 1, 2, 4, 5, 6, 7], "open": [0, 2, 3, 4, 5, 6, 9], "close": [0, 2, 5, 6], "go": 0, "ahead": 0, "jupyt": [0, 7, 9], "lab": [0, 3, 7], "browser": 0, "show": [0, 1, 2, 5], "follow": [0, 1, 4, 5], "web": 0, "page": 0, "sectiojn": 0, "notebook": [0, 7, 9], "click": [0, 2, 3, 4, 5, 6], "ipykernel": 0, "first": [0, 1], "code": [0, 3], "cell": [0, 1, 2, 3], "print": 0, "hello": 0, "world": 0, "hit": 0, "shift": 0, "keyboard": 0, "everyth": 0, "properli": 0, "look": [0, 3, 6], "To": [0, 1, 6, 7], "import": [0, 1], "pyclesperanto_prototyp": 0, "cle": 0, "get_devic": 0, "case": [0, 3], "error": [0, 3], "messag": [0, 1, 3], "contain": [0, 6, 7, 9], "importerror": 0, "while": [0, 6], "cl": [0, 5], "The": [0, 1, 2, 3, 4, 5, 6, 7, 9], "specifi": 0, "procedur": [0, 4, 5], "could": 0, "found": 0, "clgetplatformid": 0, "platform_not_found_khr": 0, "pleas": [0, 9], "recent": 0, "opencl": 0, "devic": 0, "select": [0, 2, 3, 4, 5, 6], "right": [0, 5], "sourc": 0, "depend": 0, "hardwar": 0, "list": [0, 1, 2], "amd": 0, "nvidia": 0, "intel": 0, "gpu": 0, "http": [0, 7], "www": 0, "com": [0, 7], "content": [0, 7, 9], "en": 0, "726609": 0, "arc": 0, "dch": 0, "html": 0, "cpu": 0, "microsoft": 0, "support": [0, 6, 9], "sometim": [0, 6], "mac": 0, "user": [0, 4, 5], "ocl_icd_wrapper_appl": 0, "linux": 0, "ocl": 0, "icd": 0, "system": 0, "_get_win_folder_with_pywin32": 0, "win32com": 0, "shell": 0, "shellcon": 0, "try": 0, "within": [0, 2, 3, 5, 6, 9], "base": [0, 6], "pip": [0, 7], "upgrad": 0, "pywin32": 0, "228": 0, "an": [1, 2, 5, 8, 9], "interact": 1, "program": 1, "perform": 1, "them": 1, "skimag": [1, 6], "io": [1, 7], "imread": [1, 3], "filter": 1, "threshold_otsu": 1, "gaussian": 1, "order": [1, 3], "have": [1, 3, 5, 6, 9], "now": [1, 3], "separ": 1, "warn": 1, "abov": 1, "normal": 1, "let": 1, "s": [1, 3], "screenshot": 1, "here": 1, "pass": 1, "function": [1, 3], "util": [1, 2, 3], "nbscreenshot": [1, 3], "load": [1, 3, 4, 5], "exampl": [1, 2, 4, 5, 6], "3d": [1, 2], "mri": 1, "haase_mrt_tfl3d1": 1, "tif": [1, 3], "shape": [1, 4, 6], "192": 1, "256": 1, "add_imag": [1, 3], "0x24a2def79a0": 1, "bottom": 1, "left": 1, "screen": 1, "singl": [1, 2], "take": 1, "so": [1, 3, 4], "late": 1, "reproduc": [1, 3], "what": [1, 3], "re": 1, "how": 1, "view": [1, 2, 3], "ad": 1, "tune": 1, "contrast_limit": 1, "0": [1, 8, 9], "100": 1, "keep": [1, 3, 6], "modifi": [1, 2, 3], "afterwward": 1, "image_lay": 1, "200": 1, "colormap": 1, "viridi": 1, "second": [1, 4], "ha": [1, 5, 9], "index": 1, "1": [1, 4, 8], "Or": 1, "last": 1, "top": 1, "result": [1, 2, 3, 5, 6], "overlai": 1, "origin": [1, 2], "blur": 1, "sigma": [1, 2], "5": [1, 6], "binary_imag": 1, "add_label": 1, "outlin": 1, "labels_lay": 1, "contour": 1, "3": [1, 5], "mitosis_mod": 1, "folder": [1, 5, 7], "binar": [1, 2], "too": 1, "napari": [2, 3, 4, 6], "assist": [2, 3], "allow": 2, "imag": [2, 3, 4, 5, 6, 7, 9], "process": [2, 4, 5, 6], "avail": [2, 3, 7], "video": [2, 3, 4, 5], "mp4": [2, 3], "conda": [2, 4, 5, 6], "devbio": [2, 4, 5, 6], "menu": [2, 3, 4, 5, 6], "file": [2, 3, 4, 5, 6], "sampl": [2, 3, 4, 5, 6], "2ch": 2, "explor": 2, "dataset": [2, 4, 5, 6], "2d": 2, "button": [2, 3, 5, 6], "na": 2, "panel": [2, 3], "remov": 2, "nois": 2, "ey": 2, "layer": [2, 3, 4, 5, 6], "hide": [2, 4, 6], "step": 2, "gener": [2, 6], "binari": 2, "current": [2, 3], "toggl": 2, "visibl": 2, "after": [2, 3, 4], "switch": 2, "back": [2, 5], "label": [2, 4, 5, 6], "choos": [2, 6], "oper": 2, "connect": [2, 5], "compon": [2, 5], "clesperanto": [2, 4, 5, 6], "gaussian_blur": 2, "its": [2, 6], "paramet": 2, "note": 2, "subsequ": 2, "threshold": 2, "otsu": [2, 4, 6], "updat": 2, "grid": 2, "all": [2, 6, 9], "continu": 2, "except": 2, "nuclei": [2, 3, 6], "membran": 2, "turn": 2, "gridview": 2, "time": [2, 4], "chang": [2, 5], "spot_sigma": 2, "instead": 2, "inspect": [2, 3], "set": [3, 6], "up": [3, 4, 5, 6], "workflow": 3, "export": 3, "python": [3, 7], "export_notebook": 3, "ask": 3, "kernel": 3, "default": [3, 6], "option": 3, "appear": [3, 4], "scroll": 3, "down": 3, "end": 3, "read": 3, "didn": [3, 5], "t": [3, 5], "scoll": 3, "disc": 3, "don": 3, "save": [3, 5], "alreadi": 3, "rerun": 3, "viewer": 3, "background": [3, 5], "shown": [3, 4, 5], "raw": 3, "togeth": [3, 6], "segment": [3, 4], "your": [3, 4, 5, 6], "image0_n": 3, "manual": 3, "At": 3, "voila": 3, "document": 3, "share": 3, "human_mitosi": 3, "builtin": [3, 5, 6], "human": [3, 5, 6], "mitosi": [3, 5, 6], "design": 3, "train": [4, 5], "random": [4, 5], "forest": [4, 5], "classifi": [4, 5], "acceler": [4, 5], "pixel": 4, "environ": [4, 5, 6], "blob": [4, 5], "imagej": [4, 5], "furthermor": 4, "earlier": 4, "gauss": [4, 6], "our": 4, "point": 4, "renam": 4, "class": [4, 6], "annot": [4, 5], "mix": 4, "brush": [4, 5], "put": 4, "small": [4, 5, 6], "dot": 4, "roundish": 4, "purpos": 4, "realli": 4, "smaller": [4, 5], "ones": 4, "increas": [4, 5], "2": [4, 5, 6], "draw": [4, 5], "throught": 4, "larger": 4, "elong": 4, "center": [4, 8, 9], "post": [4, 6], "apoc": [4, 5], "interfac": [4, 5], "checkbox": [4, 6], "run": [4, 6, 7], "brown": 4, "blue": 4, "round": [4, 6], "unintention": 4, "newli": 4, "more": 4, "happi": 4, "copi": 4, "safe": 4, "place": 4, "next": 4, "might": [4, 6], "overwritten": 4, "retrain": 4, "differenti": 4, "three": 4, "differ": 4, "larg": 4, "convert": 5, "instanc": 5, "under": [5, 9], "hood": 5, "size": [5, 6], "number": [5, 9], "paint": 5, "region": [5, 6], "where": [5, 6], "drawn": 5, "interest": [5, 6], "closer": 5, "two": [5, 6], "degre": 5, "freedom": 5, "comput": 5, "optim": 5, "model": 5, "later": 5, "channel": 5, "well": 5, "consid": 5, "objectsegment": 5, "been": [5, 9], "locat": 5, "find": [5, 9], "plotter": 6, "group": 6, "properti": 6, "regionprop": 6, "icon": 6, "widget": 6, "intens": 6, "tabl": 6, "scikit": 6, "nsr": 6, "sure": 6, "tick": 6, "both": 6, "pop": 6, "umap": 6, "did": 6, "method": 6, "untick": 6, "bbox_area": 6, "local_centroid1": 6, "ctrl": 6, "kei": 6, "wait": 6, "minut": 6, "ncp": 6, "plai": 6, "bit": 6, "column": 6, "eventu": 6, "umap_0": 6, "umap_2": 6, "ax": 6, "releas": 6, "mous": 6, "drag": 6, "repeat": 6, "hold": 6, "multipl": 6, "relat": 6, "hypothesi": 6, "area": 6, "manual_cluster_id": 6, "unselect": 6, "aspect_ratio": 6, "becaus": 6, "inf": 6, "valu": 6, "algorithm": 6, "umap_1": 6, "compress": 6, "inform": 6, "about": 6, "k": 6, "mean": 6, "standard": 6, "autom": 6, "kmeans_cluster_id": 6, "give": 6, "approxim": 6, "repositori": [7, 9], "collect": 7, "demonstr": [7, 9], "bio": [7, 9], "scad": [7, 9], "github": [7, 9], "2023": 7, "maintain": 7, "build": 7, "book": [7, 9], "edit": 7, "instal": 7, "depenc": 7, "jupyterlab": 7, "spellcheck": 7, "git": 7, "clone": 7, "cd": 7, "bat": 7, "dr": 8, "rer": 8, "medic": 8, "robert": 8, "haas": 8, "scienc": 8, "uni": 8, "leipzig": [8, 9], "l\u00f6hr": 8, "carr\u00e9": 8, "humboldtstra\u00df": 8, "25": 8, "04105": 8, "telefon": 8, "49": 8, "351": 8, "463": 8, "40315": 8, "mail": 8, "de": 8, "die": 8, "unser": 8, "seiten": 8, "wurden": 8, "mit": 8, "gr\u00f6\u00dfter": 8, "sorgfalt": 8, "erstellt": 8, "richtigkeit": 8, "vollst\u00e4ndigkeit": 8, "und": [8, 9], "aktualit\u00e4t": 8, "der": 8, "k\u00f6nnen": 8, "wir": 8, "jedoch": 8, "kein": 8, "gew\u00e4hr": 8, "\u00fcbernehmen": 8, "al": 8, "diensteanbiet": 8, "sind": 8, "7": 8, "eigen": 8, "auf": 8, "diesen": 8, "allgemeinen": 8, "gesetzen": 8, "8": 8, "bi": 8, "10": 8, "nicht": 8, "verpflichtet": 8, "\u00fcbermittelt": 8, "oder": 8, "gespeichert": 8, "fremd": 8, "informationen": 8, "zu": 8, "\u00fcberwachen": 8, "umst\u00e4nden": 8, "forschen": 8, "ein": 8, "rechtswidrig": 8, "t\u00e4tigkeit": 8, "hinweisen": 8, "verpflichtungen": 8, "zur": 8, "entfernung": 8, "sperrung": 8, "nutzung": 8, "von": 8, "bleiben": 8, "hiervon": 8, "unber\u00fchrt": 8, "diesbez\u00fcglich": 8, "ist": 8, "erst": 8, "dem": 8, "zeitpunkt": 8, "kenntni": 8, "einer": 8, "konkreten": 8, "rechtsverletzung": 8, "m\u00f6glich": 8, "bei": 8, "bekanntwerden": 8, "entsprechenden": 8, "rechtsverletzungen": 8, "werden": 8, "dies": 8, "umgehend": 8, "entfernen": 8, "angebot": 8, "enth\u00e4lt": 8, "externen": 8, "webseiten": 8, "dritter": 8, "deren": 8, "keinen": 8, "einfluss": 8, "haben": 8, "deshalb": 8, "fremden": 8, "auch": 8, "verlinkten": 8, "stet": 8, "jeweilig": 8, "anbiet": 8, "betreib": 8, "zum": 8, "verlinkung": 8, "rechtsverst\u00f6\u00df": 8, "\u00fcberpr\u00fcft": 8, "waren": 8, "erkennbar": 8, "permanent": 8, "inhaltlich": 8, "kontrol": 8, "ohn": 8, "konkret": 8, "anhaltspunkt": 8, "zumutbar": 8, "derartig": 8, "durch": 8, "seitenbetreib": 8, "erstellten": 8, "werk": 8, "unterliegen": 8, "deutschen": 8, "vervielf\u00e4ltigung": 8, "bearbeitung": 8, "verbreitung": 8, "jede": 8, "art": 8, "verwertung": 8, "au\u00dferhalb": 8, "grenzen": 8, "gestattet": 8, "unter": 8, "einhaltung": 8, "lizenzbedingungen": 8, "creativ": 8, "common": 8, "cc": [8, 9], "BY": [8, 9], "4": [8, 9], "lizenz": 8, "soweit": 8, "dieser": 8, "seit": 8, "vom": 8, "beachtet": 8, "insbesonder": 8, "solch": 8, "gekennzeichnet": 8, "sollten": 8, "sie": 8, "trotzdem": 8, "urheberrechtsverletzung": 8, "aufmerksam": 8, "bitten": 8, "um": 8, "einen": 8, "hinwei": 8, "webseit": 8, "regel": 8, "angab": 8, "personenbezogen": 8, "daten": 8, "unseren": 8, "beispielsweis": 8, "anschrift": 8, "email": 8, "adressen": 8, "erhoben": 8, "erfolgt": 8, "di": 8, "freiwillig": 8, "basi": 8, "ihr": 8, "ausdr\u00fccklich": 8, "zustimmung": 8, "dritt": 8, "weitergegeben": 8, "weisen": 8, "darauf": 8, "hin": 8, "dass": 8, "daten\u00fcbertragung": 8, "im": 8, "internet": 8, "z": 8, "b": 8, "kommunik": 8, "per": 8, "sicherheitsl\u00fccken": 8, "aufweisen": 8, "kann": 8, "l\u00fcckenlos": 8, "schutz": 8, "vor": 8, "zugriff": 8, "rahmen": 8, "impressumspflicht": 8, "ver\u00f6ffentlichten": 8, "kontaktdaten": 8, "\u00fcbersendung": 8, "angefordert": 8, "werbung": 8, "informationsmaterialien": 8, "wird": 8, "hiermit": 8, "widersprochen": 8, "behalten": 8, "sich": 8, "rechtlich": 8, "schritt": 8, "fall": 8, "unverlangten": 8, "zusendung": 8, "werbeinformationen": 8, "etwa": 8, "spam": 8, "zenodo": 9, "short": 9, "version": 9, "adapt": 9, "onlin": 9, "discuss": 9, "lesson": 9, "feedback": 9, "suggest": 9, "thread": 9, "sc": 9, "tag": 9, "haesleinhuepf": 9, "author": 9, "financi": 9, "feder": 9, "ministri": 9, "educ": 9, "research": 9, "germani": 9, "s\u00e4chsisch": 9, "staatsministerium": 9, "f\u00fcr": 9, "wissenschaft": 9, "kultur": 9, "tourismu": 9, "programm": 9, "excel": 9, "ai": 9, "scalabl": 9, "analyt": 9, "artifici": 9, "intellig": 9, "dresden": 9, "identif": 9, "fund": 9, "german": 9, "compet": 9, "bmbf": 9, "01is18026b": 9, "made": 9, "possibl": 9, "part": 9, "grant": 9, "2021": 9, "240341": 9, "2022": 9, "252520": 9, "chan": 9, "zuckerberg": 9, "initi": 9, "daf": 9, "advis": 9, "silicon": 9, "vallei": 9, "commun": 9, "foundat": 9, "correspond": 9, "reus": 9, "term": 9, "unless": 9, "mention": 9, "otherwis": 9}, "objects": {}, "objtypes": {}, "objnames": {}, "titleterms": {"set": 0, "up": 0, "your": 0, "comput": 0, "python": [0, 1], "conda": 0, "environ": 0, "step": 0, "1": 0, "instal": 0, "mambaforg": 0, "2": [0, 8], "devbio": 0, "napari": [0, 1, 5, 7, 9], "3": 0, "test": 0, "troubleshoot": 0, "graphic": 0, "card": 0, "driver": 0, "dll": 0, "load": 0, "fail": 0, "script": 1, "us": 1, "open": 1, "viewer": 1, "imag": 1, "from": 1, "notebook": [1, 3], "visual": [1, 6], "configur": 1, "remov": 1, "layer": 1, "segment": [1, 5, 6], "exercis": [1, 3, 4, 5, 6], "interact": [2, 4, 5, 6], "bioimag": 2, "analysi": 2, "workflow": 2, "design": 2, "gener": 3, "jupyt": 3, "object": [4, 5, 6], "classif": [4, 5], "get": [4, 5], "start": [4, 5, 6], "extra": 4, "pixel": 5, "cluster": 6, "point": 6, "featur": 6, "extract": 6, "dimension": 6, "reduct": 6, "plot": 6, "measur": 6, "manual": 6, "automat": 6, "tutori": [7, 9], "imprint": 8, "impressum": 8, "angaben": 8, "gem\u00e4\u00df": 8, "5": 8, "tmg": 8, "kontakt": 8, "verantwortlich": 8, "f\u00fcr": 8, "den": 8, "inhalt": 8, "nach": 8, "55": 8, "ab": 8, "rstv": 8, "haftungsausschluss": 8, "haftung": 8, "link": 8, "urheberrecht": 8, "datenschutz": 8, "slide": 9, "other": 9, "question": 9, "answer": 9, "acknowledg": 9, "licens": 9}, "envversion": {"sphinx.domains.c": 2, "sphinx.domains.changeset": 1, "sphinx.domains.citation": 1, "sphinx.domains.cpp": 6, "sphinx.domains.index": 1, "sphinx.domains.javascript": 2, "sphinx.domains.math": 2, "sphinx.domains.python": 3, "sphinx.domains.rst": 2, "sphinx.domains.std": 2, "sphinx.ext.intersphinx": 1, "sphinx": 56}}) \ No newline at end of file +Search.setIndex({"docnames": ["00_preparation/readme", "01_scripting/napari_intro", "02_notebooks/napari-assistant", "02_notebooks/notebook_export", "03_supervised_machine_learning/interactive_object_classification/readme", "03_supervised_machine_learning/interactive_pixel_classification/readme", "04_unsupervised_machine_learning/interactive_clustering", "README", "imprint", "intro"], "filenames": ["00_preparation/readme.md", "01_scripting/napari_intro.ipynb", "02_notebooks/napari-assistant.md", "02_notebooks/notebook_export.md", "03_supervised_machine_learning/interactive_object_classification/readme.md", "03_supervised_machine_learning/interactive_pixel_classification/readme.md", "04_unsupervised_machine_learning/interactive_clustering.md", "README.md", "imprint.md", "intro.md"], "titles": ["Setting up your computer", "Scripting Napari using Python", "Interactive bioimage analysis workflow design", "Generating Jupyter Notebooks", "Interactive object classification", "Interactive pixel classification and object segmentation", "Interactive object clustering", "Napari Tutorial", "Imprint", "Napari Tutorial"], "terms": {"thi": [0, 1, 2, 3, 4, 5, 6, 7, 9], "chapter": 0, "provid": 0, "instruct": 0, "befor": [0, 5, 6], "tutori": [0, 2, 3], "when": [0, 1, 3, 4, 5], "work": [0, 1, 3, 5, 9], "we": [0, 1, 3, 4, 5, 6], "make": [0, 6], "us": [0, 2, 3, 4, 5, 6, 7], "mani": 0, "plugin": [0, 2, 4, 5, 6], "softwar": 0, "librari": 0, "which": [0, 1, 6], "need": [0, 4], "organ": 0, "One": 0, "wai": 0, "do": [0, 1, 2], "manag": 0, "A": [0, 5], "can": [0, 1, 2, 3, 4, 5, 6, 7, 9], "seen": [0, 1], "virtual": 0, "desktop": 0, "access": 0, "via": 0, "termin": [0, 4, 5, 6], "If": [0, 3, 4, 5, 9], "you": [0, 1, 2, 3, 4, 5, 6, 7, 9], "some": [0, 1, 4], "one": [0, 1, 4, 5, 9], "mai": [0, 3], "from": [0, 2, 3, 4, 5, 6, 7, 9], "anoth": [0, 1, 4], "break": 0, "e": [0, 3, 4, 8], "g": [0, 3, 4], "incompat": 0, "wa": [0, 1, 9], "just": [0, 1, 4, 5, 6], "new": [0, 1, 2, 4, 5], "start": [0, 2], "over": 0, "see": 0, "also": [0, 1, 2, 3, 4, 5, 6], "get": [0, 1], "mambaforg": 0, "scientif": 0, "mamba": 0, "friend": 0, "data": [0, 1, 3, 8, 9], "analysi": [0, 7, 9], "download": [0, 9], "recommend": 0, "distribut": 0, "For": [0, 1, 5, 6], "eas": 0, "onli": [0, 2, 6], "add": [0, 1, 2, 3, 4, 5], "path": 0, "variabl": [0, 1], "dure": 0, "bioimag": 0, "command": [0, 1, 2, 5], "creat": [0, 1, 4], "name": [0, 6, 8], "env": [0, 2, 4, 5, 6], "9": 0, "pyqt": 0, "c": 0, "forg": 0, "tip": 0, "It": [0, 1, 7], "everi": 0, "project": [0, 9], "ar": [0, 1, 2, 4, 5, 6], "execut": [0, 3], "In": [0, 1, 3, 4, 5, 6], "tool": [0, 2, 4, 5, 6], "cannot": 0, "harm": 0, "each": [0, 5], "other": [0, 3, 4, 5, 6], "afterward": [0, 3, 4, 5, 6], "enter": 0, "whenev": 0, "want": [0, 3, 9], "same": [0, 7], "again": [0, 2, 3, 4, 6], "should": [0, 1, 3, 4, 5, 6], "line": [0, 2, 3, 4, 5], "activ": [0, 2, 4, 5, 6], "like": [0, 2, 3, 4, 6, 7], "naparia": 0, "And": 0, "window": [0, 1, 2, 4, 5, 6, 7], "open": [0, 2, 3, 4, 5, 6, 9], "close": [0, 2, 5, 6], "go": 0, "ahead": 0, "jupyt": [0, 7, 9], "lab": [0, 3, 7], "browser": 0, "show": [0, 1, 2, 5], "follow": [0, 1, 4, 5], "web": 0, "page": 0, "sectiojn": 0, "notebook": [0, 7, 9], "click": [0, 2, 3, 4, 5, 6], "ipykernel": 0, "first": [0, 1], "code": [0, 3], "cell": [0, 1, 2, 3], "print": 0, "hello": 0, "world": 0, "hit": 0, "shift": 0, "keyboard": 0, "everyth": 0, "properli": 0, "look": [0, 3, 6], "To": [0, 1, 6, 7], "import": [0, 1], "pyclesperanto_prototyp": 0, "cle": 0, "get_devic": 0, "case": [0, 3], "error": [0, 3], "messag": [0, 1, 3], "contain": [0, 6, 7, 9], "importerror": 0, "while": [0, 6], "cl": [0, 5], "The": [0, 1, 2, 3, 4, 5, 6, 7, 9], "specifi": 0, "procedur": [0, 4, 5], "could": 0, "found": 0, "clgetplatformid": 0, "platform_not_found_khr": 0, "pleas": [0, 9], "recent": 0, "opencl": 0, "devic": 0, "select": [0, 2, 3, 4, 5, 6], "right": [0, 5], "sourc": 0, "depend": 0, "hardwar": 0, "list": [0, 1, 2], "amd": 0, "nvidia": 0, "intel": 0, "gpu": 0, "http": [0, 7], "www": 0, "com": [0, 7], "content": [0, 7, 9], "en": 0, "726609": 0, "arc": 0, "dch": 0, "html": 0, "cpu": 0, "microsoft": 0, "support": [0, 6, 9], "sometim": [0, 6], "mac": 0, "user": [0, 4, 5], "ocl_icd_wrapper_appl": 0, "linux": 0, "ocl": 0, "icd": 0, "system": 0, "_get_win_folder_with_pywin32": 0, "win32com": 0, "shell": 0, "shellcon": 0, "try": 0, "within": [0, 2, 3, 5, 6, 9], "base": [0, 6], "pip": [0, 7], "upgrad": 0, "pywin32": 0, "228": 0, "an": [1, 2, 5, 8, 9], "interact": 1, "program": 1, "perform": 1, "them": 1, "skimag": [1, 6], "io": [1, 7], "imread": [1, 3], "filter": 1, "threshold_otsu": 1, "gaussian": 1, "order": [1, 3], "have": [1, 3, 5, 6, 9], "now": [1, 3], "separ": 1, "warn": 1, "abov": 1, "normal": 1, "let": 1, "s": [1, 3], "screenshot": 1, "here": 1, "pass": 1, "function": [1, 3], "util": [1, 2, 3], "nbscreenshot": [1, 3], "load": [1, 3, 4, 5], "exampl": [1, 2, 4, 5, 6], "3d": [1, 2], "mri": 1, "haase_mrt_tfl3d1": 1, "tif": [1, 3], "shape": [1, 4, 6], "192": 1, "256": 1, "add_imag": [1, 3], "0x24a2def79a0": 1, "bottom": 1, "left": 1, "screen": 1, "singl": [1, 2], "take": 1, "so": [1, 3, 4], "late": 1, "reproduc": [1, 3], "what": [1, 3], "re": 1, "how": 1, "view": [1, 2, 3], "ad": 1, "tune": 1, "contrast_limit": 1, "0": [1, 8, 9], "100": 1, "keep": [1, 3, 6], "modifi": [1, 2, 3], "afterwward": 1, "image_lay": 1, "200": 1, "colormap": 1, "viridi": 1, "second": [1, 4], "ha": [1, 5, 9], "index": 1, "1": [1, 4, 8], "Or": 1, "last": 1, "top": 1, "result": [1, 2, 3, 5, 6], "overlai": 1, "origin": [1, 2], "blur": 1, "sigma": [1, 2], "5": [1, 6], "binary_imag": 1, "add_label": 1, "outlin": 1, "labels_lay": 1, "contour": 1, "3": [1, 5], "mitosis_mod": 1, "folder": [1, 5, 7], "binar": [1, 2], "too": 1, "napari": [2, 3, 4, 6], "assist": [2, 3], "allow": 2, "imag": [2, 3, 4, 5, 6, 7, 9], "process": [2, 4, 5, 6], "avail": [2, 3, 7], "video": [2, 3, 4, 5], "mp4": [2, 3], "conda": [2, 4, 5, 6], "devbio": [2, 4, 5, 6], "menu": [2, 3, 4, 5, 6], "file": [2, 3, 4, 5, 6], "sampl": [2, 3, 4, 5, 6], "2ch": 2, "explor": 2, "dataset": [2, 4, 5, 6], "2d": 2, "button": [2, 3, 5, 6], "na": 2, "panel": [2, 3], "remov": 2, "nois": 2, "ey": 2, "layer": [2, 3, 4, 5, 6], "hide": [2, 4, 6], "step": 2, "gener": [2, 6], "binari": 2, "current": [2, 3], "toggl": 2, "visibl": 2, "after": [2, 3, 4], "switch": 2, "back": [2, 5], "label": [2, 4, 5, 6], "choos": [2, 6], "oper": 2, "connect": [2, 5], "compon": [2, 5], "clesperanto": [2, 4, 5, 6], "gaussian_blur": 2, "its": [2, 6], "paramet": 2, "note": 2, "subsequ": 2, "threshold": 2, "otsu": [2, 4, 6], "updat": 2, "grid": 2, "all": [2, 6, 9], "continu": 2, "except": 2, "nuclei": [2, 3, 6], "membran": 2, "turn": 2, "gridview": 2, "time": [2, 4], "chang": [2, 5], "spot_sigma": 2, "instead": 2, "inspect": [2, 3], "set": [3, 6], "up": [3, 4, 5, 6], "workflow": 3, "export": 3, "python": [3, 7], "export_notebook": 3, "ask": 3, "kernel": 3, "default": [3, 6], "option": 3, "appear": [3, 4], "scroll": 3, "down": 3, "end": 3, "read": 3, "didn": [3, 5], "t": [3, 5], "scoll": 3, "disc": 3, "don": 3, "save": [3, 5], "alreadi": 3, "rerun": 3, "viewer": 3, "background": [3, 5], "shown": [3, 4, 5], "raw": 3, "togeth": [3, 6], "segment": [3, 4], "your": [3, 4, 5, 6], "image0_n": 3, "manual": 3, "At": 3, "voila": 3, "document": 3, "share": 3, "human_mitosi": 3, "builtin": [3, 5, 6], "human": [3, 5, 6], "mitosi": [3, 5, 6], "design": 3, "train": [4, 5], "random": [4, 5], "forest": [4, 5], "classifi": [4, 5], "acceler": [4, 5], "pixel": 4, "environ": [4, 5, 6], "blob": [4, 5], "imagej": [4, 5], "furthermor": 4, "earlier": 4, "gauss": [4, 6], "our": 4, "point": 4, "renam": 4, "class": [4, 6], "annot": [4, 5], "mix": 4, "brush": [4, 5], "put": 4, "small": [4, 5, 6], "dot": 4, "roundish": 4, "purpos": 4, "realli": 4, "smaller": [4, 5], "ones": 4, "increas": [4, 5], "2": [4, 5, 6], "draw": [4, 5], "throught": 4, "larger": 4, "elong": 4, "center": [4, 8, 9], "post": [4, 6], "apoc": [4, 5], "interfac": [4, 5], "checkbox": [4, 6], "run": [4, 6, 7], "brown": 4, "blue": 4, "round": [4, 6], "unintention": 4, "newli": 4, "more": 4, "happi": 4, "copi": 4, "safe": 4, "place": 4, "next": 4, "might": [4, 6], "overwritten": 4, "retrain": 4, "differenti": 4, "three": 4, "differ": 4, "larg": 4, "convert": 5, "instanc": 5, "under": [5, 9], "hood": 5, "size": [5, 6], "number": [5, 9], "paint": 5, "region": [5, 6], "where": [5, 6], "drawn": 5, "interest": [5, 6], "closer": 5, "two": [5, 6], "degre": 5, "freedom": 5, "comput": 5, "optim": 5, "model": 5, "later": 5, "channel": 5, "well": 5, "consid": 5, "objectsegment": 5, "been": [5, 9], "locat": 5, "find": [5, 9], "plotter": 6, "group": 6, "properti": 6, "regionprop": 6, "icon": 6, "widget": 6, "intens": 6, "tabl": 6, "scikit": 6, "nsr": 6, "sure": 6, "tick": 6, "both": 6, "pop": 6, "umap": 6, "did": 6, "method": 6, "untick": 6, "bbox_area": 6, "local_centroid1": 6, "ctrl": 6, "kei": 6, "wait": 6, "minut": 6, "ncp": 6, "plai": 6, "bit": 6, "column": 6, "eventu": 6, "umap_0": 6, "umap_2": 6, "ax": 6, "releas": 6, "mous": 6, "drag": 6, "repeat": 6, "hold": 6, "multipl": 6, "relat": 6, "hypothesi": 6, "area": 6, "manual_cluster_id": 6, "unselect": 6, "aspect_ratio": 6, "becaus": 6, "inf": 6, "valu": 6, "algorithm": 6, "umap_1": 6, "compress": 6, "inform": 6, "about": 6, "k": 6, "mean": 6, "standard": 6, "autom": 6, "kmeans_cluster_id": 6, "give": 6, "approxim": 6, "repositori": [7, 9], "collect": 7, "demonstr": [7, 9], "bio": [7, 9], "scad": [7, 9], "github": [7, 9], "2023": 7, "maintain": 7, "build": 7, "book": [7, 9], "edit": 7, "instal": 7, "depenc": 7, "jupyterlab": 7, "spellcheck": 7, "git": 7, "clone": 7, "cd": 7, "bat": 7, "dr": 8, "rer": 8, "medic": 8, "robert": 8, "haas": 8, "scienc": 8, "uni": 8, "leipzig": [8, 9], "l\u00f6hr": 8, "carr\u00e9": 8, "humboldtstra\u00df": 8, "25": 8, "04105": 8, "telefon": 8, "49": 8, "351": 8, "463": 8, "40315": 8, "mail": 8, "de": 8, "die": 8, "unser": 8, "seiten": 8, "wurden": 8, "mit": 8, "gr\u00f6\u00dfter": 8, "sorgfalt": 8, "erstellt": 8, "richtigkeit": 8, "vollst\u00e4ndigkeit": 8, "und": [8, 9], "aktualit\u00e4t": 8, "der": 8, "k\u00f6nnen": 8, "wir": 8, "jedoch": 8, "kein": 8, "gew\u00e4hr": 8, "\u00fcbernehmen": 8, "al": 8, "diensteanbiet": 8, "sind": 8, "7": 8, "eigen": 8, "auf": 8, "diesen": 8, "allgemeinen": 8, "gesetzen": 8, "8": 8, "bi": 8, "10": 8, "nicht": 8, "verpflichtet": 8, "\u00fcbermittelt": 8, "oder": 8, "gespeichert": 8, "fremd": 8, "informationen": 8, "zu": 8, "\u00fcberwachen": 8, "umst\u00e4nden": 8, "forschen": 8, "ein": 8, "rechtswidrig": 8, "t\u00e4tigkeit": 8, "hinweisen": 8, "verpflichtungen": 8, "zur": 8, "entfernung": 8, "sperrung": 8, "nutzung": 8, "von": 8, "bleiben": 8, "hiervon": 8, "unber\u00fchrt": 8, "diesbez\u00fcglich": 8, "ist": 8, "erst": 8, "dem": 8, "zeitpunkt": 8, "kenntni": 8, "einer": 8, "konkreten": 8, "rechtsverletzung": 8, "m\u00f6glich": 8, "bei": 8, "bekanntwerden": 8, "entsprechenden": 8, "rechtsverletzungen": 8, "werden": 8, "dies": 8, "umgehend": 8, "entfernen": 8, "angebot": 8, "enth\u00e4lt": 8, "externen": 8, "webseiten": 8, "dritter": 8, "deren": 8, "keinen": 8, "einfluss": 8, "haben": 8, "deshalb": 8, "fremden": 8, "auch": 8, "verlinkten": 8, "stet": 8, "jeweilig": 8, "anbiet": 8, "betreib": 8, "zum": 8, "verlinkung": 8, "rechtsverst\u00f6\u00df": 8, "\u00fcberpr\u00fcft": 8, "waren": 8, "erkennbar": 8, "permanent": 8, "inhaltlich": 8, "kontrol": 8, "ohn": 8, "konkret": 8, "anhaltspunkt": 8, "zumutbar": 8, "derartig": 8, "durch": 8, "seitenbetreib": 8, "erstellten": 8, "werk": 8, "unterliegen": 8, "deutschen": 8, "vervielf\u00e4ltigung": 8, "bearbeitung": 8, "verbreitung": 8, "jede": 8, "art": 8, "verwertung": 8, "au\u00dferhalb": 8, "grenzen": 8, "gestattet": 8, "unter": 8, "einhaltung": 8, "lizenzbedingungen": 8, "creativ": 8, "common": 8, "cc": [8, 9], "BY": [8, 9], "4": [8, 9], "lizenz": 8, "soweit": 8, "dieser": 8, "seit": 8, "vom": 8, "beachtet": 8, "insbesonder": 8, "solch": 8, "gekennzeichnet": 8, "sollten": 8, "sie": 8, "trotzdem": 8, "urheberrechtsverletzung": 8, "aufmerksam": 8, "bitten": 8, "um": 8, "einen": 8, "hinwei": 8, "webseit": 8, "regel": 8, "angab": 8, "personenbezogen": 8, "daten": 8, "unseren": 8, "beispielsweis": 8, "anschrift": 8, "email": 8, "adressen": 8, "erhoben": 8, "erfolgt": 8, "di": 8, "freiwillig": 8, "basi": 8, "ihr": 8, "ausdr\u00fccklich": 8, "zustimmung": 8, "dritt": 8, "weitergegeben": 8, "weisen": 8, "darauf": 8, "hin": 8, "dass": 8, "daten\u00fcbertragung": 8, "im": 8, "internet": 8, "z": 8, "b": 8, "kommunik": 8, "per": 8, "sicherheitsl\u00fccken": 8, "aufweisen": 8, "kann": 8, "l\u00fcckenlos": 8, "schutz": 8, "vor": 8, "zugriff": 8, "rahmen": 8, "impressumspflicht": 8, "ver\u00f6ffentlichten": 8, "kontaktdaten": 8, "\u00fcbersendung": 8, "angefordert": 8, "werbung": 8, "informationsmaterialien": 8, "wird": 8, "hiermit": 8, "widersprochen": 8, "behalten": 8, "sich": 8, "rechtlich": 8, "schritt": 8, "fall": 8, "unverlangten": 8, "zusendung": 8, "werbeinformationen": 8, "etwa": 8, "spam": 8, "zenodo": 9, "short": 9, "version": 9, "adapt": 9, "onlin": 9, "discuss": 9, "lesson": 9, "feedback": 9, "suggest": 9, "thread": 9, "sc": 9, "tag": 9, "haesleinhuepf": 9, "author": 9, "financi": 9, "feder": 9, "ministri": 9, "educ": 9, "research": 9, "germani": 9, "s\u00e4chsisch": 9, "staatsministerium": 9, "f\u00fcr": 9, "wissenschaft": 9, "kultur": 9, "tourismu": 9, "programm": 9, "excel": 9, "ai": 9, "scalabl": 9, "analyt": 9, "artifici": 9, "intellig": 9, "dresden": 9, "identif": 9, "fund": 9, "german": 9, "compet": 9, "bmbf": 9, "01is18026b": 9, "made": 9, "possibl": 9, "part": 9, "grant": 9, "2021": 9, "240341": 9, "2022": 9, "252520": 9, "chan": 9, "zuckerberg": 9, "initi": 9, "daf": 9, "advis": 9, "silicon": 9, "vallei": 9, "commun": 9, "foundat": 9, "correspond": 9, "reus": 9, "term": 9, "unless": 9, "mention": 9, "otherwis": 9}, "objects": {}, "objtypes": {}, "objnames": {}, "titleterms": {"set": 0, "up": 0, "your": 0, "comput": 0, "python": [0, 1], "conda": 0, "environ": 0, "step": 0, "1": 0, "instal": 0, "miniforg": 0, "2": [0, 8], "devbio": 0, "napari": [0, 1, 5, 7, 9], "3": 0, "test": 0, "troubleshoot": 0, "graphic": 0, "card": 0, "driver": 0, "dll": 0, "load": 0, "fail": 0, "script": 1, "us": 1, "open": 1, "viewer": 1, "imag": 1, "from": 1, "notebook": [1, 3], "visual": [1, 6], "configur": 1, "remov": 1, "layer": 1, "segment": [1, 5, 6], "exercis": [1, 3, 4, 5, 6], "interact": [2, 4, 5, 6], "bioimag": 2, "analysi": 2, "workflow": 2, "design": 2, "gener": 3, "jupyt": 3, "object": [4, 5, 6], "classif": [4, 5], "get": [4, 5], "start": [4, 5, 6], "extra": 4, "pixel": 5, "cluster": 6, "point": 6, "featur": 6, "extract": 6, "dimension": 6, "reduct": 6, "plot": 6, "measur": 6, "manual": 6, "automat": 6, "tutori": [7, 9], "imprint": 8, "impressum": 8, "angaben": 8, "gem\u00e4\u00df": 8, "5": 8, "tmg": 8, "kontakt": 8, "verantwortlich": 8, "f\u00fcr": 8, "den": 8, "inhalt": 8, "nach": 8, "55": 8, "ab": 8, "rstv": 8, "haftungsausschluss": 8, "haftung": 8, "link": 8, "urheberrecht": 8, "datenschutz": 8, "slide": 9, "other": 9, "question": 9, "answer": 9, "acknowledg": 9, "licens": 9}, "envversion": {"sphinx.domains.c": 2, "sphinx.domains.changeset": 1, "sphinx.domains.citation": 1, "sphinx.domains.cpp": 6, "sphinx.domains.index": 1, "sphinx.domains.javascript": 2, "sphinx.domains.math": 2, "sphinx.domains.python": 3, "sphinx.domains.rst": 2, "sphinx.domains.std": 2, "sphinx.ext.intersphinx": 1, "sphinx": 56}}) \ No newline at end of file