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Marconato, L.* ; Palla, G. ; Yamauchi, K.A.* ; Virshup, I. ; Heidari, E.* ; Treis, T. ; Vierdag, W.M.* ; Toth, M. ; Stockhaus, S. ; Shrestha, R.B. ; Rombaut, B.* ; Pollaris, L.* ; Lehner, L. ; Vöhringer, H.* ; Kats, I.* ; Saeys, Y.* ; Saka, S.K.* ; Huber, W.* ; Gerstung, M.* ; Moore, J.* ; Theis, F.J. ; Stegle, O.*

SpatialData: An open and universal data framework for spatial omics.

Nat. Methods, DOI: 10.1038/s41592-024-02212-x (2024)
DOI PMC
Creative Commons Lizenzvertrag
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.
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Publication type Article: Journal article
Document type Scientific Article
Corresponding Author
Keywords Single-cell
ISSN (print) / ISBN 1548-7091
e-ISSN 1548-7105
Journal Nature Methods
Publisher Nature Publishing Group
Publishing Place New York, NY
Non-patent literature Publications
Reviewing status Peer reviewed
Institute(s) Institute of Computational Biology (ICB)
Grants Chan Zuckerberg Initiative DAF (advised fund of Silicon Valley Community Foundation)
FWO-EOS program
Research Foundation-Flanders
Flanders AI Research Program
Cellzome, a GSK company
DKFZ International PhD Programme
Personalized Health and Related Technologies Transition Postdoc Fellowship
Open Research Data Program of the ETH Board
Joachim Herz Foundation
Helmholtz Association under the joint research school Munich School for Data Science
European Molecular Biology Laboratory (EMBL)
BOF-GOA fund
BMBF grant (SIMONA)
Wellcome Leap as part of the triangleTissue Program
Helmholtz Association's Initiative and Networking Fund through Helmholtz AI
Deutsche Forschungsgemeinschaft (German Research Foundation)
Chan Zuckerberg Initiative DAF, an advised fund of Silicon Valley Community Foundation
European Molecular Biology Laboratory
EMBL International PhD Programme