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

Installation requires Python 3.8 or greater.

pip install vitessce

To use the widget in Jupyer Notebook also run the following:

jupyter nbextension install --py --sys-prefix vitessce
jupyter nbextension enable --py --sys-prefix vitessce

To use the widget in JupyterLab also run the following:

jupyter labextension install @jupyter-widgets/jupyterlab-manager
jupyter labextension install vitessce-jupyter

Widget Compatibility

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

  • JupyterLab >=3.0.0

  • Jupyter Notebook (classic) >=1.0.0

Optional dependencies

The following dependencies are optional, and only required when using certain features.

  • jupyter-server-proxy>=1.5.2 - Required for using the widget through a proxy (e.g. a cloud notebook service like Binder). See widget parameter proxy.