Vitessce is a visual integration tool for exploration of spatial single-cell experiments. To learn more about the features of Vitessce, please visit our core docs.

Getting Started

The vitessce Python package includes:

  • Vitessce as a Jupyter Widget

    • Use Vitessce directly within Jupyter Notebook or Jupyter Lab as an interactive widget

  • View config API

    • Create and edit Vitessce configurations using Python object-oriented syntax

  • Data preparation

    • Use our data conversion wrapper classes to process data stored in common single-cell file types including AnnData and SnapATAC.


Installation requires Python 3.9 or greater. Install from PyPI:

pip install vitessce[all]

Widget Compatibility

The Vitessce widget is compatible with the following interactive Python platforms:

  • JupyterLab >=3.0.0

  • Jupyter Notebook (classic) >=1.0.0

Indices and tables