Systematic benchmarking of imaging spatial transcriptomics platforms in FFPE tissues
Emerging imaging spatial transcriptomics (iST) platforms and coupled analytical methods can recover cell-to-cell interactions, groups of spatially covarying genes, and gene signatures associated with pathological features, and are thus particularly well-suited for applications in formalin fixed paraffin embedded (FFPE) tissues. Here, we benchmark the performance of three commercial iST platforms-10X Xenium, Vizgen MERSCOPE, and Nanostring CosMx-on serial sections from tissue microarrays (TMAs) containing 17 tumor and 16 normal tissue types for both relative technical and biological performance. On matched genes, we find that Xenium consistently generates higher transcript counts per gene without sacrificing specificity. Xenium and CosMx measure RNA transcripts in concordance with orthogonal single-cell transcriptomics. All three platforms can perform spatially resolved cell typing with varying degrees of sub-clustering capabilities, with Xenium and CosMx finding slightly more clusters than MERSCOPE, albeit with different false discovery rates and cell segmentation error frequencies. Taken together, our analyses provide a comprehensive benchmark to guide the choice of iST method as researchers design studies with precious samples in this rapidly evolving field.
Authors
- Sachi Krishna (ORCID: https://orcid.org/0000-0002-7457-9700)
- Anna Yeaton (ORCID: https://orcid.org/0000-0002-7654-371X)
- Ruixu Huang (ORCID: https://orcid.org/0009-0007-7133-0436)
- Ce Gao (ORCID: https://orcid.org/0000-0002-3775-790X)
- Kristen D. Felt (ORCID: https://orcid.org/0000-0001-7063-8374)
- Jack Nelson
- Kevin Wei (ORCID: https://orcid.org/0000-0002-1821-167X)
- Teri Bowman
- Scott J. Rodig (ORCID: https://orcid.org/0000-0003-1761-9769)
- Brittany A. Goods (ORCID: https://orcid.org/0000-0002-5962-9570)
- Kathleen L. Pfaff (ORCID: https://orcid.org/0000-0003-3311-5384)
- Samouil L. Farhi (ORCID: https://orcid.org/0000-0003-1359-4568)
- Huan Wang (ORCID: https://orcid.org/0000-0001-6773-8382)
- Miles Tran (ORCID: https://orcid.org/0009-0005-9330-9297)
Institutions
- Broad Institute (US)
- Dartmouth College (US)
- Brigham and Women's Hospital (US)
- Immunai (United States) (US)
- Dana-Farber Cancer Institute (US)
- Dana-Farber Brigham Cancer Center (US)
Publication Details
- Journal
- Nature Communications
- Published
- 2025-11-20
- DOI
- https://doi.org/10.1038/s41467-025-64990-y
- Citations
- 6
- Primary Topic
- Single-cell and spatial transcriptomics
- Type
- article
- Field-Weighted Citation Impact
- 4.84
Funders
- Brigham and Women's Hospital
- Dartmouth College
- Broad Institute
- Scheme for Promotion of Academic and Research Collaboration
- National Institutes of Health
- Audrey and Theodor Geisel School of Medicine at Dartmouth
- National Institute of General Medical Sciences
- National Institute of Arthritis and Musculoskeletal and Skin Diseases