Spatially resolved omics technologies are transforming our understanding of biological tissues. However, the handling of uni- and multimodal spatial omics datasets remains a challenge owing to large data volumes, heterogeneity of data types and the lack of flexible, spatially aware data structures. Here we introduce SpatialData, a framework that establishes a unified and extensible multiplatform 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 in the context of multiple vignettes, including integrative analysis on a multimodal Xenium and Visium breast cancer study.
CITATION STYLE
Marconato, L., Palla, G., Yamauchi, K. A., Virshup, I., Heidari, E., Treis, T., … Stegle, O. (2024). SpatialData: an open and universal data framework for spatial omics. Nature Methods. https://doi.org/10.1038/s41592-024-02212-x
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