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

Marco Salas S, Kuemmerle LB, Mattsson-Langseth C, Tismeyer S, Avenel C, Hu T, Rehman H, Grillo M, Czarnewski P, Helgadottir S, Tiklova K, Andersson A, Rafati N, Chatzinikolaou M, Theis FJ, Luecken MD, Wählby C, Ishaque N, Nilsson M

Nat. Methods 22 (4) 813-823 [2025-04-00; online 2025-03-13]

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.

Bioinformatics (NBIS) [Collaborative]

Bioinformatics Support and Infrastructure [Collaborative]

Bioinformatics Support, Infrastructure and Training [Collaborative]

PubMed 40082609

DOI 10.1038/s41592-025-02617-2

Crossref 10.1038/s41592-025-02617-2

pmc: PMC11978515
pii: 10.1038/s41592-025-02617-2