|PyPI| |Downloads| |CI| |Notebooks| |Docs| |Coverage| |Discourse| |Zulip|
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<p align="center">
<a href="https://squidpy.readthedocs.io/en/stable/">
<img src="https://raw.githubusercontent.com/scverse/squidpy/main/docs/source/_static/img/squidpy_horizontal.png"
width="400px" alt="Squidpy logo">
</a>
</p>
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.
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<p align="center">
<a href="https://doi.org/10.1038/s41592-021-01358-2">
<img src="https://raw.githubusercontent.com/scverse/squidpy/main/docs/source/_static/img/figure1.png"
width="400px" alt="Squidpy title figure">
</a>
</p>
Visit our documentation
_ for installation, tutorials, examples and more.
Please see our manuscript Palla, Spitzer et al. (2022)
_ in Nature Methods to learn more.
skimage
_.anndata
and large tissue images in napari
.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
We are happy about any contributions! Before you start, check out our contributing guide <CONTRIBUTING.rst>
_.
.. |PyPI| image:: https://img.shields.io/pypi/v/squidpy.svg :target: https://pypi.org/project/squidpy/ :alt: PyPI
.. |CI| image:: https://img.shields.io/github/actions/workflow/status/scverse/squidpy/test.yml?branch=main :target: https://github.com/scverse/squidpy/actions :alt: CI
.. |Notebooks| image:: https://img.shields.io/github/actions/workflow/status/scverse/squidpy_notebooks/ci.yml?branch=main&label=notebooks :target: https://github.com/scverse/squidpy_notebooks/actions :alt: Notebooks CI
.. |Docs| image:: https://img.shields.io/readthedocs/squidpy :target: https://squidpy.readthedocs.io/en/stable/ :alt: Documentation
.. |Coverage| image:: https://codecov.io/gh/scverse/squidpy/branch/main/graph/badge.svg :target: https://codecov.io/gh/scverse/squidpy :alt: Coverage
.. |Downloads| image:: https://pepy.tech/badge/squidpy :target: https://pepy.tech/project/squidpy :alt: Downloads
.. |Discourse| image:: https://img.shields.io/discourse/posts?color=yellow&logo=discourse&server=https%3A%2F%2Fdiscourse.scverse.org :target: https://discourse.scverse.org/ :alt: Discourse
.. |Zulip| image:: https://img.shields.io/badge/zulip-join_chat-%2367b08f.svg :target: https://scverse.zulipchat.com :alt: Zulip
.. _Palla, Spitzer et al. (2022): https://doi.org/10.1038/s41592-021-01358-2 .. _scanpy: https://scanpy.readthedocs.io/en/stable/ .. _anndata: https://anndata.readthedocs.io/en/stable/ .. _napari: https://napari.org/ .. _skimage: https://scikit-image.org/ .. _documentation: https://squidpy.readthedocs.io/en/stable/