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.

Manuscript¶
Please see our manuscript [Palla et al., 2022] in Nature Methods to learn more.
Squidpy’s key applications¶
Getting started with Squidpy¶
Contributing to Squidpy¶
We are happy about any contributions! Before you start, check out our contributing guide.