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spatialdata-plot: rich static plotting from SpatialData objects

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The spatialdata-plot package extends spatialdata with a declarative plotting API that enables to quickly visualize spatialdata objects and their respective elements (i.e. images, labels, points and shapes).

SpatialData’s plotting capabilities allow to quickly visualise all contained modalities. The user can specify which elements should be rendered (images, labels, points, shapes) and specify certain parameters for each layer, such as for example the intent to color shapes by a gene’s expression profile or which color to use for which image channel. When the plot is then eventually displayed, all transformations, alignments and coordinate systems are internally processed to form the final visualisation. In concordance with the general SpatialData philosophy, all modalities of the major spatial technologies are supported out of the box.

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Getting started

For more information on the spatialdata-plot library, please refer to the documentation. In particular, the

Installation

You need to have Python 3.12 or newer installed on your system. If you don't have Python installed, we recommend installing Mambaforge.

There are several alternative options to install spatialdata-plot:

  1. Install the latest release of spatialdata-plot from PyPI <https://pypi.org/project/spatialdata-plot/>_:
pip install spatialdata-plot
  1. Install the latest development version:
pip install git+https://github.com/scverse/spatialdata-plot.git@main

Contact

For questions and help requests, you can reach out in the scverse discourse. If you found a bug, please use the issue tracker.

Citation

Marconato, L., Palla, G., Yamauchi, K.A. et al. SpatialData: an open and universal data framework for spatial omics. Nat Methods (2024). https://doi.org/10.1038/s41592-024-02212-x

spatialdata-plot is part of the scverse® project (website, governance) and is fiscally sponsored by NumFOCUS. If you like scverse® and want to support our mission, 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.

Project links

Data verified by PyPI on Aug 10, 2026
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Owner

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2 maintainers

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Avatar for kevin.yamauchi from gravatar.com kevin.yamauchi Avatar for LucaMarconato from gravatar.com LucaMarconato

Credits

Author: scverse

Maintainer: Tim Treis

GitHub Statistics

Data verified by PyPI on Aug 10, 2026
The GitHub source repository was provided by the project maintainers and verified by PyPI at the time of upload. Stars, forks, and open issues/PRs are derived from that repository and have not been independently verified.

License

BSD 3-Clause License

Requires

Python >=3.12

Provides Extra

interactive

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