Skip to main content

Spatial Single Cell Analysis in Python

Project description

PyPI Downloads CI Documentation Coverage Discourse Zulip NumFOCUS

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.

https://raw.githubusercontent.com/numfocus/templates/master/images/numfocus-logo.png

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-1.6.5.tar.gz (5.9 MB view details)

Uploaded Source

Built Distribution

squidpy-1.6.5-py3-none-any.whl (161.3 kB view details)

Uploaded Python 3

File details

Details for the file squidpy-1.6.5.tar.gz.

File metadata

  • Download URL: squidpy-1.6.5.tar.gz
  • Upload date:
  • Size: 5.9 MB
  • Tags: Source
  • Uploaded using Trusted Publishing? No
  • Uploaded via: twine/6.1.0 CPython/3.12.9

File hashes

Hashes for squidpy-1.6.5.tar.gz
Algorithm Hash digest
SHA256 c5f9449cde5829c2d916f56c210a62e110fea44d4839951007aa2abb59c4ca21
MD5 d0f3e155181ac9134b9c3f84e7829c2e
BLAKE2b-256 a04dc45cff096c0b4811f9e55708f0a20e0f43fca9438c85c2cbfe001e0cb08c

See more details on using hashes here.

File details

Details for the file squidpy-1.6.5-py3-none-any.whl.

File metadata

  • Download URL: squidpy-1.6.5-py3-none-any.whl
  • Upload date:
  • Size: 161.3 kB
  • Tags: Python 3
  • Uploaded using Trusted Publishing? No
  • Uploaded via: twine/6.1.0 CPython/3.12.9

File hashes

Hashes for squidpy-1.6.5-py3-none-any.whl
Algorithm Hash digest
SHA256 bb2e94c6ecef4ff39b68dc0696a33cf81f3cee46be53ad4a371cb467aa173f8d
MD5 b754b400315c439b4041a3331f52c1d5
BLAKE2b-256 4ad9419c241e27ec311793bdb2980d7261f5383eadaed56354161865a65b102b

See more details on using hashes here.

Supported by

AWS Cloud computing and Security Sponsor Datadog Monitoring Fastly CDN Google Download Analytics Pingdom Monitoring Sentry Error logging StatusPage Status page