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.

• spatialdata-io: load data from common spatial omics technologies into spatialdata (repository, documentation).

• spatialdata-plot: Static plotting library for spatialdata (repository, documentation).

• napari-spatialdata-repo: napari plugin for interactive exploration and annotation of spatialdata (repository, documentation).

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

Note

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.

Installation

Learn how to install spatialdata.

Tutorials

Learn how to use spatialdata with hands-on examples.

API

Find a detailed documentation of spatialdata.

Datasets

Example datasets from 8 different technologies.

Design document

Learn about the design approach behind spatialdata.

Contributing

Learn how to contribute to spatialdata.