1. SpatialData: an open and universal data framework for spatial omics.
- Author
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Marconato L, Palla G, Yamauchi KA, Virshup I, Heidari E, Treis T, Vierdag WM, Toth M, Stockhaus S, Shrestha RB, Rombaut B, Pollaris L, Lehner L, Vöhringer H, Kats I, Saeys Y, Saka SK, Huber W, Gerstung M, Moore J, Theis FJ, and Stegle O
- Subjects
- Humans, Software, Genomics methods, Computational Biology methods, Female, Algorithms, Breast Neoplasms genetics
- Abstract
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., Competing Interests: Competing interests: 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 and has ownership interest in Dermagnostix GmbH and Cellarity. O.S. is a paid consultant of Insitro, Inc., S.K.S. is a consulting scientific cofounder for Digital Biology, Inc. The remaining authors declare no competing interests., (© 2024. The Author(s).)
- Published
- 2025
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