SpatialData: an open and universal data framework for spatial omics

Marconato, L.; Palla, G.; Yamauchi, K. A.; Virshup, I.; Heidari, E.; Treis, T.; Toth, M.; Shrestha, R.; Vöhringer, H.; Huber, W.; Gerstung, M.; Moore, J.; Theis, F. J.; Stegle, O.

doi:10.1101/2023.05.05.539647

bioRxiv · 10.1101/2023.05.05.539647

SpatialData: an open and universal data framework for spatial omics

Marconato, L.·Palla, G.·Yamauchi, K. A.·Virshup, I.·Heidari, E.·Treis, T.·Toth, M.·Shrestha, R.·Vöhringer, H.·Huber, W.·Gerstung, M.·Moore, J.·Theis, F. J.·Stegle, O.

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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.

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Marconato, L., Palla, G., Yamauchi, K. A., Virshup, I., Heidari, E., Treis, T., Toth, M., Shrestha, R., Vöhringer, H., Huber, W., Gerstung, M., Moore, J., Theis, F. J., Stegle, O.. 2023-05-08. SpatialData: an open and universal data framework for spatial omics. https://doi.org/10.1101/2023.05.05.539647

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