Abstract
Spatially resolved omics technologies are transforming our understanding of biological tissues. However, handling uni- and multi-modal spatial omics datasets remains a challenge owing to large volumes of data, heterogeneous data types and the lack of unified spatially-aware data structures. Here, we introduce SpatialData, a framework that establishes a unified and extensible multi-platform file-format, lazy representation of larger-than-memory data, transformations, and alignment to common coordinate systems. SpatialData facilitates spatial annotations and cross-modal aggregation and analysis, the utility of which is illustrated via multiple vignettes, including integrative analysis on a multi-modal Xenium and Visium breast cancer study.
Competing Interest Statement
J.M. holds equity in Glencoe Software which builds products based on OME-NGFF. F.J.T. consults for Immunai Inc., Singularity Bio B.V., CytoReason Ltd, Cellarity, and Omniscope Ltd, and has ownership interest in Dermagnostix GmbH and Cellarity.