ArticleNature communications2025
Systematic benchmarking of imaging spatial transcriptomics platforms in FFPE tissues.
Article in Nature communications, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 82 papers.
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Who cites it
82 citing papers in PubMed.
- STiLE: automated tissue microarray dearraying for spatial transcriptomics.Bioinformatics (Oxford, England) · 2026Article
- STAT3D as a new image-tailored Xenium-based spatial transcriptomics tool for accurately dissecting the tumor microenvironment.Nucleic acids research · 2026Article
- CoexpressDeconvolve enables reference-free single-cell-resolution deconvolution from spot-based spatial transcriptomics.iScience · 2026Article
- RNA-aware tissue preservation workflows for high-quality spatial transcriptomics.bioRxiv : the preprint server for biology · 2026Article
- Review
- Iron-catalyzed oxidative stress reveals an exposome-related ferroptosis-resistant karyomegalic niche in BRCA1-linked renal carcinogenesis.Redox biology · 2026Article
- Next-generation kidney tissue analysis - spatial omics and digital pathology.Nature reviews. Nephrology · 2026Review
- Amplification bias in sequencing-based spatial transcriptomics: sources, mechanisms, impacts, and mitigation strategies.Briefings in bioinformatics · 2026Review
- Spatial analysis reveals cellular microenvironments and mechanisms of inflammation and injury in acute interstitial nephritis.Nature communications · 2026Article
- Spatiotemporal heterogeneity in non-small cell lung cancer: A paradigm shift from characterization to dynamic management (Review).Oncology letters · 2026Review
- Prediction of single cell expression from low-plex immunofluorescence images for guiding precision oncology.NPJ precision oncology · 2026Article
- Review
- Single-cell spatial transcriptomics of formalin-fixed, paraffin-embedded biopsies reveals colitis-associated cell networks.The Journal of clinical investigation · 2026Article
- Spatial Transcriptomics for Dissecting Cellular and Molecular Heterogeneity in the Aging and Diseased Brain.International journal of molecular sciences · 2026Review
- Article
- NanoCellAnnotator: Formalizing Expert Cell Type Annotation with Large Language Models.bioRxiv : the preprint server for biology · 2026Article
- Correcting spatial transcriptomics data affected by a prevalent transcript leakage problem across platforms, species, and tissues.bioRxiv : the preprint server for biology · 2026Article
- KLF6 activation marks an angiogenic and apoptosis resistant endothelial phenotype in pulmonary arterial hypertension.Communications biology · 2026Article
- Chromogenic in situ HCR as a targeted translational interface for routine molecular histology.Histochemistry and cell biology · 2026Article
- HyperNiche: Learning Heterophilic Cellular Niches with Hypergraph Neural Networks.bioRxiv : the preprint server for biology · 2026Article
22 more citing papers are in PubMed but not listed here.
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Abstract
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.
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