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 publication [Marconato et al., 2024] 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.

Installation
Tutorials

Learn how to use spatialdata with hands-on examples.

Tutorials
API

Find a detailed documentation of spatialdata.

API
Datasets

Example datasets from 8 different technologies.

Obtaining the datasets
Design document

Learn about the design approach behind spatialdata.

Design document for SpatialData
Contributing

Learn how to contribute to spatialdata.

Contributing guide