Single-Cell and Spatial Data Visualization with Vitessce

Welcome! Here you will find the source material for the Vitessce tutorial.

An overview of the content can be found at notebooks/Index.ipynb

Run the Tutorial

If you have a Google/Gmail account, you can Run this tutorial from your browser using Colab: .

Molab

If colab is not working, you can try Molab instead:

• 01-Single-Spatial-View.ipynb
• 02-Multiple-Views.ipynb
• 03-Available-View-Types.ipynb
• 04-Coordinated-Multiple-Views.ipynb

Additional materials

Prior tutorial materials can be found in https://github.com/vitessce/vitessce-python-tutorial-2023.

Acknowledgements

The format and structure of these tutorial materials are inspired heavily by the Gosling Tutorial created by Sehi L'Yi, Trevor Manz, Qianwen Wang, and Nils Gehlenborg.

Local usage

To use these notebooks locally, clone the repository:

git clone https://github.com/vitessce/vitessce-python-tutorial-2026.git
cd vitessce-python-tutorial-2026

We recommend using uv.

Create the virtual environment:

uv venv --python 3.12

Activate the virtual environment:

source .venv/bin/activate

Install:

uv add --requirements requirements.txt

Run the notebooks

uv run jupyter lab

When running the notebooks locally, ignore (i.e., do not run) the !pip install lines in the notebooks. Your virtual environment already contains these packages since they are listed in requirements.txt.

Troubleshooting

If you see an anndata error that mentions allow_write_nullable_strings, run the following code:

import anndata
anndata.settings.allow_write_nullable_strings = True

If you see errors related to missing data, try renaming the output file path and re-running the data writing code:

- zarr_path = join("data", "pbmc68k.adata.zarr")
+ zarr_path = join("data", "pbmc68k_v2.adata.zarr")