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 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.

Installation

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.

Metadata

Release files for squidpy 1.1.2

For a detailed explanation of source distributions (sdists) and built distributions (wheels), please see the package formats documentation.

Source distribution (sdist)

Source distribution for squidpy 1.1.2
File	Size	Uploaded
squidpy-1.1.2.tar.gz	133.3 kB	Sep 10, 2021	Details

Built distribution (wheel)

Table of built distributions (wheels) for squidpy 1.1.2
File	Interpreter	ABI	Platform	Reset
squidpy-1.1.2-py3-none-any.whl 150.0 kB Sep 10, 2021	Python 3	none	any	Details

Total release size: 283.3 kB

Release files / squidpy-1.1.2.tar.gz

Download URL	squidpy-1.1.2.tar.gz
Size	133.3 kB
Tags	Source
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BLAKE2b-256 checksum How to use checksums	`fe99cb4f463ab818f6b6267247c70dc94bf333baf116548a953e1d3526514f1b`
Upload date	Sep 10, 2021
Uploaded using Trusted Publishing? What is trusted publishing?	No
Uploaded via	`twine/3.4.2 importlib_metadata/4.8.1 pkginfo/1.7.1 requests/2.26.0 requests-toolbelt/0.9.1 tqdm/4.62.2 CPython/3.9.7`

Release files / squidpy-1.1.2-py3-none-any.whl

Download URL	squidpy-1.1.2-py3-none-any.whl
Size	150.0 kB
Tags	Python 3
SHA-256 checksum How to use checksums	`0875bb4b5f9dfa8b2e3cabad80343df9a9d7022bdaa621c23d9c2c06e9f9d7ef`
BLAKE2b-256 checksum How to use checksums	`b8565402de970f1294e436eb211f494aa65ca2c82c60ea6780c788b67df170c3`
Upload date	Sep 10, 2021
Uploaded using Trusted Publishing? What is trusted publishing?	No
Uploaded via	`twine/3.4.2 importlib_metadata/4.8.1 pkginfo/1.7.1 requests/2.26.0 requests-toolbelt/0.9.1 tqdm/4.62.2 CPython/3.9.7`