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Salas, S.M. ; Kuemmerle, L. ; Mattsson-Langseth, C.* ; Tismeyer, S.* ; Avenel, C.* ; Hu, T.* ; Rehmann, H. ; Grillo, M.* ; Czarnewski, P.* ; Helgadottir, S.* ; Tiklova, K.* ; Andersson, A.* ; Rafati, N.* ; Chatzinikolaou, M.* ; Theis, F.J. ; Luecken, M. ; Wählby, C.* ; Ishaque, N.* ; Nilsson, M.*

Optimizing Xenium In Situ data utility by quality assessment and best-practice analysis workflows.

Nat. Methods 22, 813-823 (2025)
Verlagsversion Forschungsdaten DOI PMC
Open Access Hybrid
Creative Commons Lizenzvertrag
The Xenium In Situ platform is a new spatial transcriptomics product commercialized by 10x Genomics, capable of mapping hundreds of genes in situ at subcellular resolution. Given the multitude of commercially available spatial transcriptomics technologies, recommendations in choice of platform and analysis guidelines are increasingly important. Herein, we explore 25 Xenium datasets generated from multiple tissues and species, comparing scalability, resolution, data quality, capacities and limitations with eight other spatially resolved transcriptomics technologies and commercial platforms. In addition, we benchmark the performance of multiple open-source computational tools, when applied to Xenium datasets, in tasks including preprocessing, cell segmentation, selection of spatially variable features and domain identification. This study serves as an independent analysis of the performance of Xenium, and provides best practices and recommendations for analysis of such datasets.
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Publikationstyp Artikel: Journalartikel
Dokumenttyp Wissenschaftlicher Artikel
Schlagwörter Transcriptomic Cell-types; Gene-expression
Sprache englisch
Veröffentlichungsjahr 2025
HGF-Berichtsjahr 2025
ISSN (print) / ISBN 1548-7091
e-ISSN 1548-7105
Zeitschrift Nature Methods
Quellenangaben Band: 22, Heft: 4, Seiten: 813-823 Artikelnummer: , Supplement: ,
Verlag Nature Publishing Group
Verlagsort New York, NY
Begutachtungsstatus Peer reviewed
Institut(e) Institute of Computational Biology (ICB)
Institute for Tissue Engineering and Regenerative Medicine (ITERM)
Institute of Lung Health and Immunity (LHI)
POF Topic(s) 30205 - Bioengineering and Digital Health
80000 - German Center for Lung Research
Forschungsfeld(er) Enabling and Novel Technologies
Lung Research
PSP-Element(e) G-503800-001
G-505800-001
G-501800-833
Förderungen Bundesministerium fr Bildung und Forschung (Federal Ministry of Education and Research)
DOI 10.1038/s41592-025-02617-2
WOS ID 001444358900001
PubMed ID 40082609
Erfassungsdatum 2025-05-08
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