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Plate IV.152 · Publications

SpatialData: an open and universal data framework for spatial omics

Article in Nature Methods, 20 March 2024.

Open accessSpatial, Omics Data

  1. Luca Marconato
  2. Giovanni Palla
  3. Kevin A. Yamauchi
  4. Isaac Virshup
  5. Elyas Heidari
  6. Tim Treis
  7. Wouter-Michiel Vierdag
  8. Marcella Toth
  9. Sonja Stockhaus
  10. Rahul B. Shrestha
  11. Benjamin Rombaut
  12. Lotte Pollaris
  13. Laurens Lehner
  14. Harald Vöhringer
  15. Ilia Kats
  16. Yvan Saeys
  17. Sinem K. Saka
  18. Wolfgang Huber
  19. Moritz Gerstung
  20. Josh Moore
  21. Fabian J. Theis
  22. Oliver Stegle

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.

Versions2

  1. PublishedNature Methods10.1038/s41592-024-02212-x
  2. PreprintbioRxiv10.1101/2023.05.05.539647

Cite

@article{marconato2024spatialdata,
  title = {{SpatialData: an open and universal data framework for spatial omics}},
  author = {Marconato, Luca and Palla, Giovanni and Yamauchi, Kevin A. and Virshup, Isaac and Heidari, Elyas and Treis, Tim and Vierdag, Wouter-Michiel and Toth, Marcella and Stockhaus, Sonja and Shrestha, Rahul B. and Rombaut, Benjamin and Pollaris, Lotte and Lehner, Laurens and Vöhringer, Harald and Kats, Ilia and Saeys, Yvan and Saka, Sinem K. and Huber, Wolfgang and Gerstung, Moritz and Moore, Josh and Theis, Fabian J. and Stegle, Oliver},
  journal = {Nature Methods},
  publisher = {Springer Science and Business Media LLC},
  year = {2024},
  month = mar,
  doi = {10.1038/s41592-024-02212-x},
  url = {https://doi.org/10.1038/s41592-024-02212-x},
  pmid = {38509327},
  pmcid = {PMC11725494}
}
.bib file