squidpy · Python Simple Repository Browser

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Author: Giovanni Palla, Michal Klein, Hannah Spitzer

Maintainer: Giovanni Palla, Michal Klein, Tim Treis

Requires Python: >=3.10

Classifiers

Development Status

5 - Production/Stable

Environment

Console

Framework

Jupyter

Intended Audience

Science/Research

License

OSI Approved :: BSD License

Natural Language

English

Operating System

MacOS :: MacOS X
POSIX :: Linux

Programming Language

Python :: 3
Python :: 3.10
Python :: 3.11
Python :: 3.12

Topic

Scientific/Engineering :: Bio-Informatics
Scientific/Engineering :: Visualization

Typing

Typed

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.

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

Manuscript

Please see our manuscript Palla, Spitzer 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.

Installation

Install Squidpy via PyPI by running:

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

or via Conda as:

conda install -c conda-forge squidpy

Contributing to Squidpy

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

Squidpy is part of the scverse® project (website, governance) and is fiscally sponsored by NumFOCUS. Please consider making a tax-deductible donation to help the project pay for developer time, professional services, travel, workshops, and a variety of other needs.