Installation

Squidpy requires Python version >= 3.11 to run.

PyPI

Install Squidpy by running::

pip install squidpy

Conda

Install Squidpy via Conda as::

conda install -c conda-forge squidpy

Development version

To install Squidpy from GitHub, run::

pip install git+https://github.com/scverse/squidpy@main

Interactive visualization

For interactive visualization with napari, please use napari-spatialdata. The original napari plugin from Squidpy has been deprecated and replaced by napari-spatialdata, which offers improved functionality and support for the SpatialData ecosystem.

Install napari-spatialdata with::

pip install napari-spatialdata