SpatialData specifications#
SpatialData is an open framework for working with uni- and multi-modal spatial omics datasets. It defines a common data model and storage format, supported by software libraries for accessing, manipulating and analyzing spatial omics data in languages including Python, R and JavaScript.
This site provides the normative, language-independent specifications of the SpatialData abstract data model and storage format.
What a SpatialData dataset is: elements, coordinate systems, instances and annotation tables.
How datasets are stored on disk: Zarr and Parquet, building on OME-NGFF.
The storage format implements the data model on disk, and its version identifies the data model version: storage format 0.1–0.4 all implement data model 1.0 (version history).
Background and contributing#
The SpatialData specifications were developed from the design and implementation of the original
Python spatialdata package (see the SpatialData Python documentation
for installation, tutorials and API reference). Their initial release formalized abstract data model 1.0
and storage format 0.4; earlier storage formats (0.1–0.3) are also specified, with the corresponding
spatialdata releases listed in the version history.
The specifications are now maintained and developed in the open, independently of any particular implementation, and contributions are welcome. Found something unclear, incomplete or inconsistent? Open a GitHub issue or submit a pull request. Substantial changes and new features can be proposed through an RFC; see Contributing for details.
To cite SpatialData, please see our publication.
Funding#
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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