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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)
Verlagsversion DOI PMC
Open Access Hybrid
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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Publikationstyp Artikel: Journalartikel
Dokumenttyp Wissenschaftlicher Artikel
Schlagwörter Single-cell
Sprache englisch
Veröffentlichungsjahr 2024
HGF-Berichtsjahr 2024
ISSN (print) / ISBN 1548-7091
e-ISSN 1548-7105
Zeitschrift Nature Methods
Verlag Nature Publishing Group
Verlagsort New York, NY
Begutachtungsstatus Peer reviewed
Institut(e) Institute of Computational Biology (ICB)
POF Topic(s) 30205 - Bioengineering and Digital Health
Forschungsfeld(er) Enabling and Novel Technologies
PSP-Element(e) G-503800-001
G-503800-004
Förderungen 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
DOI 10.1038/s41592-024-02212-x
WOS ID 001188190200002
Scopus ID 85188181242
PubMed ID 38509327
Erfassungsdatum 2024-05-13
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