Skip to main content

Squidpy - Spatial Single Cell Analysis in Python

Project description

PyPI Downloads CI Notebooks CI Documentation Coverage

Squidpy - Spatial Single Cell Analysis in Python

Squidpy logo

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.

Squidpy title figure

Visit our documentation for installation, tutorials, examples and more.


Please see our manuscript Palla et al. (2022) in Nature Methods 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.

  • Interactively explore anndata and large tissue images in napari.


Install Squidpy via PyPI by running:

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

Contributing to Squidpy

We are happy about any contributions! Before you start, check out our contributing guide.

Project details

Download files

Download the file for your platform. If you're not sure which to choose, learn more about installing packages.

Source Distribution

squidpy-1.2.0.tar.gz (158.9 kB view hashes)

Uploaded source

Built Distribution

squidpy-1.2.0-py3-none-any.whl (179.2 kB view hashes)

Uploaded py3

Supported by

AWS AWS Cloud computing Datadog Datadog Monitoring Facebook / Instagram Facebook / Instagram PSF Sponsor Fastly Fastly CDN Google Google Object Storage and Download Analytics Huawei Huawei PSF Sponsor Microsoft Microsoft PSF Sponsor NVIDIA NVIDIA PSF Sponsor Pingdom Pingdom Monitoring Salesforce Salesforce PSF Sponsor Sentry Sentry Error logging StatusPage StatusPage Status page