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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)

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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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Publication type Article: Journal article

Document type Scientific Article

Corresponding Author

Keywords Transcriptomic Cell-types; Gene-expression

ISSN (print) / ISBN 1548-7091

e-ISSN 1548-7105

Journal Nature Methods

Quellenangaben Volume: 22, Issue: 4, Pages: 813-823

Publisher Nature Publishing Group

Publishing Place New York, NY

Non-patent literature Publications

Reviewing status Peer reviewed

Institute(s) Institute of Computational Biology (ICB)
Institute for Tissue Engineering and Regenerative Medicine (ITERM)
Institute of Lung Health and Immunity (LHI)

Grants Bundesministerium fr Bildung und Forschung (Federal Ministry of Education and Research)