Spatial Comparison Studies

Putting our Xenium platform to the test in
8 independent comparison studies

 
 
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Over the past 16 months, eight independent studies have been completed that compare Xenium single cell spatial imaging with Nanostring CosMx and/or Vizgen MERSCOPE. We’d argue that we came out on top but, in science, seeing is believing—so we've taken the liberty of compiling these articles for you, so you can see how the Xenium platform was able to:

  • Identify a greater number of cell types
  • Reliably capture rare/difficult cell types
  • Reflect the ground truth of, and correlate well with, single cell sequencing methods

Article Citation

Direct Link

Mennillo E, et al. Single-cell spatial transcriptomics of fixed, paraffin-embedded biopsies reveals colitis-associated cell networks. bioRvix (2024). doi: 10.1101/2024.11.11.623014

https://www.biorxiv.org/content/10.1101/2024.11.11.623014v1

Lermi NO, et al. Comparison of imaging-based single-cell resolution spatial transcriptomics profiling platforms using formalin-fixed, paraffin-embedded tumor samples. bioRxiv (2024). doi: 10.1101/2024.12.13.628390

https://www.biorxiv.org/content/10.1101/2024.12.13.628390v1

Ren P, et al. Systematic benchmarking of high-throughput subcellular spatial transcriptomics platforms. bioRxiv (2024) doi: 10.1101/2024.12.23.630033

https://www.biorxiv.org/content/10.1101/2024.12.23.630033v1

Wang H, et al. Systematic benchmarking of imaging spatial transcriptomics platforms in FFPE tissues. bioRxiv (2023). doi: 10.1101/2023.12.07.570603

https://www.biorxiv.org/content/10.1101/2023.12.07.570603v1

Cook D, et al. A Comparative analysis of imaging-based spatial transcriptomics platforms. bioRxiv (2023). doi: 10.1101/2023.12.13.571385

https://www.biorxiv.org/content/10.1101/2023.12.13.571385v1

Cervilla S, et al. Comparison of spatial transcriptomics technologies across six cancer types. bioRxiv (2024). doi: 10.1101/2024.05.21.593407

https://www.biorxiv.org/content/10.1101/2024.05.21.593407v1

Hartman A and Satija R. Comparative analysis of multiplexed in situ gene expression profiling technologies. bioRxiv (2024). doi: 10.1101/2024.01.11.575135

https://www.biorxiv.org/content/10.1101/2024.01.11.575135v2

Willis A, et al. Single cell approaches define neural stem cell niches and identify microglial ligands that can enhance precursor-mediated oligodendrogenesis. Cell Reports (2025). doi: 10.1016/j.celrep.2024.115194

https://doi.org/10.1016/j.celrep.2024.115194

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