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Plate IV.102 · Publications

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

Article in Nature Methods, 13 March 2025.

Open accessSpatial, Omics Data

  1. Sergio Marco Salas
  2. Louis B. Kuemmerle
  3. Christoffer Mattsson-Langseth
  4. Sebastian Tismeyer
  5. Christophe Avenel
  6. Taobo Hu
  7. Habib Rehman
  8. Marco Grillo
  9. Paulo Czarnewski
  10. Saga Helgadottir
  11. Katarina Tiklova
  12. Axel Andersson
  13. Nima Rafati
  14. Maria Chatzinikolaou
  15. Fabian J. Theis
  16. Malte D. Luecken
  17. Carolina Wählby
  18. Naveed Ishaque
  19. Mats Nilsson

Abstract

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.

Versions2

  1. PublishedNature Methods10.1038/s41592-025-02617-2
  2. PreprintbioRxiv10.1101/2023.02.13.528102

Cite

@article{marcosalas2025optimizing,
  title = {{Optimizing Xenium In Situ data utility by quality assessment and best-practice analysis workflows}},
  author = {Marco Salas, Sergio and Kuemmerle, Louis B. and Mattsson-Langseth, Christoffer and Tismeyer, Sebastian and Avenel, Christophe and Hu, Taobo and Rehman, Habib and Grillo, Marco and Czarnewski, Paulo and Helgadottir, Saga and Tiklova, Katarina and Andersson, Axel and Rafati, Nima and Chatzinikolaou, Maria and Theis, Fabian J. and Luecken, Malte D. and Wählby, Carolina and Ishaque, Naveed and Nilsson, Mats},
  journal = {Nature Methods},
  publisher = {Springer Science and Business Media LLC},
  year = {2025},
  month = mar,
  doi = {10.1038/s41592-025-02617-2},
  url = {https://doi.org/10.1038/s41592-025-02617-2},
  pmid = {40082609},
  pmcid = {PMC11978515}
}
.bib file