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High-plex Multiomic Analysis in FFPE at Subcellular Level by Spatial Molecular Imaging

Shanshan HeiD, Ruchir Bhatt, Carl Brown, Emily A. BrowniD, Derek L. Buhr, Kan Chantranuvatana, Patrick J. DanaheriD, Dwayne L. Dunaway, Ryan G. Garrison, Gary K. GeissiD, Mark GregoryiD, Margaret L. HoangiD, Rustem Khafizov, Emily E. KillingbeckiD, Dae Joon KimiD, Tae Kyoung KimiD, Youngmi KimiD, Andrew Klock, Mithra KorukondaiD, Alecksandr J. Kutchma, Zachary LewisiD, Yan LiangiD, Jeffrey S. Nelson, Giang T. OngiD, Evan P. PerilloiD, , Joseph BeechemiD

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Abstract

The Spatial Molecular Imaging platform (CosMxTM SMI, NanoString Technologies, Seattle, WA) utilizes high-plex in-situ imaging chemistry for both RNA and protein detection. This automated instrument provides 1000s of plex, at high sensitivity (1 to 2 copies/cell), very low error rate (0.0092 false calls/cell) and background ([~]0.04 counts/cell). The imaging system generates three-dimensional super-resolution localization of analytes at [~]2 million cells per sample, four samples per run. Cell segmentation is morphology-based using antibodies, compatible with FFPE samples. Multiomic data (980 RNAs, 108 proteins) were measured at subcellular resolution using FFPE tissues (non-small cell lung (NSCLC) and breast cancer) and allowed identification of over 18 distinct cell types, 10 unique tumor microenvironments, and 100 pairwise ligand-receptor interactions. Over 800,000 single cells and [~]260 million transcripts data are released into the public domain allowing extended data analysis by the entire spatial biology research community.

Abstract summary

Claude Opus 5.5 · xhigh effort · 18 Oct 2026 · from the abstract

An automated in-situ imaging platform reads 980 RNAs and 108 proteins in FFPE tissue at subcellular resolution, with 0.0092 false calls per cell; 800,000-plus cells released publicly.

CosMx SMI applies thousand-plex in-situ chemistry to both RNA and protein in FFPE tissue, with three-dimensional super-resolution localisation and antibody-based morphological cell segmentation. The abstract reports per-cell sensitivity and error figures, about two million cells per sample, and a public release of the resulting single-cell data.

Key results

  1. SuggestedThe instrument reports single-copy-level sensitivity with a low per-cell error floor, at roughly two million cells per sample.

    Sensitivity of 1 to 2 copies/cell, 0.0092 false calls/cell, background ~0.04 counts/cell, with three-dimensional super-resolution localisation across ~2 million cells per sample and four samples per run; how these figures were measured is not described. · Abstract

  2. SuggestedJoint RNA and protein readout on FFPE tumour tissue supported cell typing, niche definition and interaction analysis.

    980 RNAs and 108 proteins measured at subcellular resolution in FFPE non-small cell lung (NSCLC) and breast cancer tissue, yielding more than 18 cell types, 10 separate tumor microenvironments and 100 pairwise ligand-receptor interactions. · Abstract

  3. ClaimedThe resulting single-cell data are stated to be released for public reuse.

    Over 800,000 single cells and ~260 million transcripts described as placed in the public domain; no repository, accession or URL is given in the text. · Abstract

Methods, data and reproducibility

CosMx SMI is an automated instrument that applies high-plex in-situ chemistry to detect RNA and protein in the same FFPE tissue, localising analytes in three dimensions at super-resolution and segmenting cells by morphology using antibodies. It was run on non-small cell lung and breast cancer tissue with a panel of 980 RNAs and 108 proteins.

  • FFPE non-small cell lung cancer (NSCLC) tissue profiled with the RNA and protein panel
  • FFPE breast cancer tissue profiled on the same platform
  • Single-cell and transcript data stated to be released into the public domain · n = over 800,000 single cells; ~260 million transcripts
Methods & tools
CosMx SMI (Spatial Molecular Imaging), NanoString Technologies
Reproducibility gaps
The cell and transcript data are described as public, but no repository, accession or URL is printed, and no analysis code is mentioned.
Limitations (2)
  • Sensitivity, false-call rate and background are quoted without saying how they were measured or what platform they are benchmarked against, so they cannot be compared with other spatial assays. · noted in this summary
  • Only two tumour types were profiled, and the counts of cell types, microenvironments and ligand-receptor pairs are reported without the clustering or interaction thresholds that produced them. · noted in this summary

Read this if you plan spatial RNA and protein profiling on archival FFPE blocks and want the reported plex, error rate and per-run throughput before committing to a platform.

Citations
72

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