Easy Vitessce

🪄 Configure Vitessce with a single line of code!

Turn your static Scanpy and SpatialData plots into interactive Vitessce visualizations simply by importing the easy_vitessce package!

Supported Functions

• sc.pl.umap
• sc.pl.tsne
• sc.pl.pca
• sc.pl.embedding
• sc.pl.spatial
• sc.pl.violin
• sc.pl.dotplot
• sc.pl.heatmap
• sdata.pl (.render_images, .render_labels, and .render_shapes)

See the documentation for further details.

Installation

Install package using pip:

pip install easy_vitessce

How to Use

Importing Easy Vitessce

import easy_vitessce as ev

🪄 By default, interactive plots are enabled via this import statement.

Deactivating Interactive Plots:

ev.configure_plots(disable_plots = ["embedding", "violin", "spatialdata-plot"])

Reactivating Interactive Plots:

ev.configure_plots(enable_plots = ["spatialdata-plot"])

Development

Set up environment

uv sync --extra dev --extra docs

This command should also be run after updating dependencies in pyproject.toml.

Run tests

# uv sync --extra dev
uv run pytest

Make documentation

uv run make html # on mac/linux
# uv run make.bat html # on windows
open docs/_build/html/index.html

Launch Jupyter notebook or lab

# uv sync --extra dev
uv run jupyter notebook --notebook-dir .
# or
uv run jupyter lab --notebook-dir .

Citation

To cite EasyVitessce in your work, please use:

@article{luo2025easyvitessce,
  title = {{EasyVitessce: auto-magically adding interactivity to Scverse single-cell and spatial biology plots}},
  author = {Luo, Selena and Keller, Mark S. and Kakar, Tabassum and Choy, Lisa and Gehlenborg, Nils},
  journal = {arXiv},
  year = {2025},
  month = oct,
  doi = {10.48550/arXiv.2510.19532}
}

To cite Vitessce in your work, please use:

@article{keller2024vitessce,
  title = {{Vitessce: integrative visualization of multimodal and spatially resolved single-cell data}},
  author = {Keller, Mark S. and Gold, Ilan and McCallum, Chuck and Manz, Trevor and Kharchenko, Peter V. and Gehlenborg, Nils},
  journal = {Nature Methods},
  year = {2024},
  month = sep,
  doi = {10.1038/s41592-024-02436-x}
}

If you use the image rendering functionality, please additionally cite Viv:

@article{manz2022viv,
  title = {{Viv: multiscale visualization of high-resolution multiplexed bioimaging data on the web}},
  author = {Manz, Trevor and Gold, Ilan and Patterson, Nathan Heath and McCallum, Chuck and Keller, Mark S. and Herr, II, Bruce W. and Börner, Kay and Spraggins, Jeffrey M. and Gehlenborg, Nils},
  journal = {Nature Methods},
  year = {2022},
  month = may,
  doi = {10.1038/s41592-022-01482-7}
}