SpatialData is a data framework, a schema and a serialization format for uni- and multi-modal spatial omics datasets. It is supported by a growing suite of software libraries for performant access, manipulation and analysis in multiple languages, including Python, R and JavaScript.
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 spatial data.
- SpatialData (R): R implementation of the SpatialData framework.
- SpatialData.js: JavaScript/TypeScript implementation of the SpatialData framework.
spatialdata 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.
The spatialdata project also received support by the Chan Zuckerberg Initiative.
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- The SpatialData data model and storage format are defined by the SpatialData specifications; the storage format is built on top of the OME-NGFF specification.
Please refer to the documentation. In particular:
- API documentation.
- Design doc (historical; superseded by the SpatialData specifications).
- Example notebooks.
Another useful resource to get started is the source code of the spatialdata-io package, which shows example of how to read data from common technologies.
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]"or via conda:
Update Feb 2025: spatialdata cannot be currently be installed via conda because some dependencies of our dependencies are not updated in conda-forge and we are still waiting for an update. Please install from pip; the latest versions of the spatialdata libraries are always available via PyPI.
mamba install -c conda-forge spatialdata napari-spatialdata spatialdata-io spatialdata-plot
To get involved in the discussion, or if you need help to get started, you are welcome to use the following options.
- Chat via
scverseZulip (public or 1 to 1). - Forum post in the scverse discourse forum.
- Bug report/feature request via the GitHub issue tracker.
- Zoom call as part of the SpatialData Community Meetings, held every 2 weeks on Thursday, schedule here <--- new link!.
Finally, especially relevant for for developers that are building a library upon spatialdata, please follow this channel for:
- Announcements on new features and important changes Zulip.
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