scverse/spatialdata

An open and interoperable data framework for spatial omics data

What it solves

SpatialData provides a universal framework for handling spatial omics data. It addresses the challenge of managing uni- and multi-modal datasets that combine biological information with spatial coordinates, ensuring these datasets can be processed and analyzed consistently across different software libraries and programming languages.

How it works

It functions as a combined data framework, schema, and serialization format. The storage format is built on top of the OME-NGFF specification, allowing for performant access and manipulation. The ecosystem includes specialized libraries for loading data (spatialdata-io), static plotting (spatialdata-plot), and interactive exploration via a napari plugin.

Who it’s for

Researchers and developers working with spatial omics data who need a standardized way to store, manipulate, and analyze complex biological datasets across Python, R, and JavaScript.

Highlights

  • Universal schema and serialization format for spatial omics.
  • Multi-modal data support.
  • Cross-language compatibility with implementations in Python, R, and JavaScript.
  • Integration with the OME-NGFF specification for efficient data storage.

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