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‎.github/workflows/book.yml‎

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name: deploy-book
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on:
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push:
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branches:
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- main
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jobs:
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deploy-book:
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runs-on: ubuntu-latest
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steps:
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- uses: actions/checkout@v3
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- uses: actions/setup-python@v4
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with:
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python-version: '3.10'
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- name: Install dependencies
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run: |
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pip install -r requirements.txt
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- name: Build the book
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run: |
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jupyter-book build .
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- name: GitHub Pages action
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uses: peaceiris/actions-gh-pages@v3
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with:
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github_token: ${{ secrets.GITHUB_TOKEN }}
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publish_dir: ./_build/html

‎.gitignore‎

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__pycache__/
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_build/
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.ipynb_checkpoints/
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*.bed
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.DS_Store

‎LICENSE‎

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MIT License
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Copyright (c) 2026 Vitessce Developers
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Permission is hereby granted, free of charge, to any person obtaining a copy
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of this software and associated documentation files (the "Software"), to deal
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in the Software without restriction, including without limitation the rights
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to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
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copies of the Software, and to permit persons to whom the Software is
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furnished to do so, subject to the following conditions:
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The above copyright notice and this permission notice shall be included in all
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copies or substantial portions of the Software.
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THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
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IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
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FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
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AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
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LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
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OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
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SOFTWARE.
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‎README.md‎

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# vitessce-python-tutorial-2026
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# Single-Cell and Spatial Data Visualization with Vitessce
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![vitessce examples](https://user-images.githubusercontent.com/9922882/109852545-e05f3400-7c22-11eb-90f3-7371e4ddeb42.png)
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Welcome! Here you will find the source material for the Vitessce tutorial, presented at ISMB 2026.
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An overview of the content can be found at [notebooks/Index.ipynb](notebooks/Index.ipynb)
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## Run the Tutorial
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If you have a Google/Gmail account, you can Run this tutorial from your browser using Colab: [![Open In Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/vitessce/vitessce-python-tutorial-2026/blob/main/notebooks/Index.ipynb).

‎_config.yml‎

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title: Vitessce Tutorial
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author: Mark Keller, Eric Moerth, Nils Gehlenborg
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logo: 'images/vitessce-logo.png'
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html:
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favicon: "images/favicon.ico"
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repository:
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url: "https://github.com/vitessce/vitessce-python-tutorial-2026"

‎_toc.yml‎

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format: jb-article
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root: README
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sections:
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- file: notebooks/Index
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- file: notebooks/01-Single-Spatial-View
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- file: notebooks/02-Multiple-Views
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- file: notebooks/03-Available-View-Types
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- file: notebooks/04-Coordinated-Multiple-Views

‎images/vitessce-logo.png‎

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‎notebooks/Index.ipynb‎

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{
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"cells": [
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{
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"cell_type": "markdown",
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"metadata": {},
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"source": [
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"# Outline\n",
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"\n",
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"These notebooks contain an introduction to exploratory single-cell and spatial data visualization with [Vitessce](https://github.com/vitessce/vitessce), presented at ISMB 2026.\n",
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"\n",
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"Our tutorial will start with several introductory slides about single-cell data visualization and the Vitessce framework, followed by four hands-on practical sessions using the [Vitessce](https://github.com/vitessce/vitessce-python) and [EasyVitessce](https://github.com/vitessce/easy_vitessce) Python packages.\n",
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"\n",
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"## 1. Single Spatial View\n",
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"\n",
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"Configure Vitessce for 2D/3D spatial and imaging data.\n",
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"\n",
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"- [01-Single-Spatial-View.ipynb](01-Single-Spatial-View.ipynb)\n",
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"\n",
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"## 2. Multiple Views\n",
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"\n",
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"Configure Vitessce with additional views, including for non-spatial data.\n",
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"\n",
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"- [02-Multiple-Views.ipynb](02-Multiple-Views.ipynb)\n",
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"\n",
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"## 3. Available View Types\n",
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"\n",
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"Learn more of the view types available in Vitessce, such as statistical plots.\n",
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"\n",
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"- [03-Available-View-Types.ipynb](03-Available-View-Types.ipynb)\n",
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"\n",
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"## 4. Coordinated Multiple Views\n",
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"\n",
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"Compose multiple views with coordinated interactions.\n",
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"\n",
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"- [04-Coordinated-Multiple-Views.ipynb](04-Coordinated-Multiple-Views.ipynb)\n",
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" "
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]
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},
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{
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"cell_type": "code",
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"execution_count": null,
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"metadata": {},
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"outputs": [],
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"source": []
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}
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],
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"metadata": {
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"kernelspec": {
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"display_name": "Python 3 (ipykernel)",
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"language": "python",
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"name": "python3"
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},
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"language_info": {
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"codemirror_mode": {
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"name": "ipython",
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"version": 3
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},
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"file_extension": ".py",
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"mimetype": "text/x-python",
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"name": "python",
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"nbconvert_exporter": "python",
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"pygments_lexer": "ipython3",
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"version": "3.9.12"
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},
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"nteract": {
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"version": "0.23.1"
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}
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},
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"nbformat": 4,
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"nbformat_minor": 4
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}

‎requirements.txt‎

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jupyter-book==0.13.0
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pandas
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vitessce[all]==3.9.0

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