squidpy

Spatial Single Cell Analysis in Python

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Project description

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.

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.

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.

Project details

These details have not been verified by PyPI

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Release history Release notifications | RSS feed

1.6.2

Nov 12, 2024

1.6.1

Sep 2, 2024

1.6.0

Jul 23, 2024

1.5.0

May 27, 2024

1.4.1

Feb 6, 2024

This version

1.4.0

Feb 6, 2024

1.3.1

Oct 9, 2023

1.3.0

Jun 16, 2023

1.2.3

Oct 18, 2022

1.2.2

May 17, 2022

1.2.1

May 14, 2022

1.2.0

Apr 19, 2022

1.1.2

Sep 10, 2021

1.1.1

Aug 16, 2021

1.1.0

Jul 2, 2021

1.0.1

Jun 13, 2021

1.0.0

Feb 20, 2021

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