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 repository contains 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.
• spatialdata-plot: Static plotting library for spatialdata.
• napari-spatialdata: napari plugin for interactive exploration and annotation of spatialdata.

• The library is currently under review. We expect there to be changes as the community provides feedback.
• To get involved in the discussion, or if you need help to get started, you are welcome to join our scverse Zulip chat and our scverse discourse forum.
• The SpatialData storage format is built on top of the OME-NGFF specification.

Please refer to the documentation. In particular:

• API documentation.
• Design doc.
• Example notebooks.

Check out the docs for more complete installation instructions. To get started with the "batteries included" installation, you can install via pip:

pip install "spatialdata[extra]"

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

L Marconato*, G Palla*, KA Yamauchi*, I Virshup*, E Heidari, T Treis, M Toth, R Shrestha, H Vöhringer, W Huber, M Gerstung, J Moore, FJ Theis, O Stegle, bioRxiv, 2023. * = equal contribution

The spatialdata project is supported by the EMBL International PhD Programme and the Chan Zuckerberg Initiative.

The scverse project uses a consensus based governance model and is fiscally sponsored by NumFOCUS. Consider making a tax-deductible donation to help the project pay for developer time, professional services, travel, workshops, and a variety of other needs.