Journal Article

DKFZ-2024-00579

http://join2-wiki.gsi.de/foswiki/pub/Main/Artwork/join2_logo100x88.png SpatialData: an open and universal data framework for spatial omics.

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

2025
Nature Publishing Group London [u.a.]

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Please use a persistent id in citations: doi:10.1038/s41592-024-02212-x

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.

Note: #EA:B260#LA:B260# / 2025 Jan;22(1):58-62

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Contributing Institute(s):

1. B260 Bioinformatik der Genomik und Systemgenetik (B260)
2. Künstl. Intelligenz in der Onkologie (B450)

Research Program(s):

1. 312 - Funktionelle und strukturelle Genomforschung (POF4-312) (POF4-312)

Appears in the scientific report 2024

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Database coverage:
; BIOSIS Previews ; Biological Abstracts ; Clarivate Analytics Master Journal List ; Current Contents - Life Sciences ; DEAL Nature ; Ebsco Academic Search ; Essential Science Indicators ; IF >= 40 ; JCR ; Nationallizenz ; SCOPUS ; Science Citation Index Expanded ; Web of Science Core Collection

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