scverse/spatialdata

An open and interoperable data framework for spatial omics data

What it solves

It provides a universal framework, schema, and serialization format for handling uni- and multi-modal spatial omics datasets, allowing researchers to process and analyze complex biological data across different software libraries and languages.

How it works

SpatialData acts as a core data framework built on top of the OME-NGFF specification. It establishes a standardized way to store and serialize spatial omics data, which is then supported by a suite of ecosystem libraries for loading data (spatialdata-io), static plotting (spatialdata-plot), and interactive exploration (napari-spatialdata), with implementations available in Python, R, and JavaScript.

Who it’s for

Scientists and developers working with spatial omics data who need a consistent way to organize, manipulate, and analyze multi-modal biological datasets.

Highlights

  • Universal schema and serialization format for spatial omics.
  • Multi-language support including Python, R, and JavaScript.
  • Integration with the OME-NGFF specification.
  • Part of the scverse ecosystem with dedicated tools for interactive exploration and data loading.

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