An open and universal framework for processing spatial omics data.

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An open and universal framework for processing spatial omics data.#

SpatialData is a data framework that comprises a FAIR storage format and a collection of python libraries for performant access, alignment, and processing of uni- and multi-modal spatial omics datasets. This page provides documentation on how to install, use, and extend the core spatialdata library. See the links below to learn more about other packages in the SpatialData ecosystem.

Please see our preprint [Marconato et al., 2023] for citation and to learn more.


This library is currently under active development. We may make changes to the API between versions as the community provides feedback. To ensure reproducibility, please make note of the version you are developing against.


Learn how to install spatialdata.


Learn how to use spatialdata with hands-on examples.


Find a detailed documentation of spatialdata.


Example datasets from 8 different technologies.

Design document

Learn about the design approach behind spatialdata.


Learn how to contribute to spatialdata.