Squidpy - Spatial Single Cell Analysis in Python

Squidpy is a tool for the analysis and visualization of spatial molecular data. It builds on top of scanpy and anndata, from which it inherits modularity and scalability. It provides analysis tools that leverages the spatial coordinates of the data, as well as tissue images if available.



Please see our preprint on bioRxiv to learn more.

Squidpy's key applications

  • Build and analyze the neighborhood graph from spatial coordinates.
  • Compute spatial statistics for cell-types and genes.
  • Efficiently store, analyze and visualize large tissue images, leveraging skimage.
  • Explore anndata and the large tissue image in napari.


Install Squidpy via PyPI by running:

pip install squidpy
# or with napari included
pip install 'squidpy[interactive]'