SpatialData: an open and universal data framework for spatial omics

Luca Marconato, Giovanni Palla, Kevin A. Yamauchi, Isaac Virshup, Elyas Heidari, Tim Treis, Marcella Toth, Rahul B. Shrestha, Harald Vöhringer, Wolfgang Huber, Moritz Gerstung, Josh Moore, Fabian J. Theis, Oliver Stegle
bioRxiv (2023)


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.