{"entity":{"id":"spatial-transcriptomics-platforms","kind":"term","name":"Spatial transcriptomics platforms (Visium HD, Xenium, MERFISH, CosMx, CODEX)","aka":["Visium","Visium HD","Xenium","MERFISH","CosMx","CODEX","PhenoCycler","spatial molecular imaging","in situ sequencing","spatial omics platform"],"tldr":"Spatial platforms measure RNA or protein while keeping each measurement's position on the tissue slide, so cell types and gene programmes can be mapped onto the tumour's architecture.","summary":"Spatial transcriptomics captures the positional context of transcription within intact tissue (Wikipedia). The platforms differ in what they trade: 10x Visium captures whole-transcriptome RNA on barcoded spots (55 micron spots originally, 2 micron bins in Visium HD); Xenium, MERFISH and CosMx image a targeted panel of hundreds to thousands of genes in situ at single-cell and subcellular resolution; CODEX (now PhenoCycler) cycles antibodies to image dozens of proteins. Public sections from 10x are CC BY 4.0 and are the usual first test for spatial models, and HTAN is assembling multi-platform tumour atlases.","asOf":"2026-09-24","wikipedia":"https://en.wikipedia.org/wiki/Spatial_transcriptomics","links":[{"label":"10x Genomics Visium HD","url":"https://www.10xgenomics.com/products/visium-hd-spatial-gene-expression"},{"label":"10x Genomics Xenium","url":"https://www.10xgenomics.com/platforms/xenium"},{"label":"Chen et al., MERFISH: spatially resolved, highly multiplexed RNA profiling in single cells (Science 2015)","url":"https://doi.org/10.1126/science.aaa6090"},{"label":"He et al., CosMx spatial molecular imager (Nature Biotechnology 2022)","url":"https://doi.org/10.1038/s41587-022-01483-z"},{"label":"Goltsev et al., CODEX multiplexed imaging (Cell 2018)","url":"https://doi.org/10.1016/j.cell.2018.07.010"},{"label":"Wikipedia","url":"https://en.wikipedia.org/wiki/Spatial_transcriptomics"}],"tags":["cansim-terms"],"related":["10x-genomics","cancer-ai-vocabulary"],"cancers":[],"sections":[],"technologies":["spatial-transcriptomics","spatial-biology-instruments","single-cell-spatial"],"targets":[],"drugs":[],"companies":[],"institutions":[],"pathways":[],"terms":["spatial-autocorrelation","single-cell-rna-seq"],"trials":[],"people":[],"bottlenecks":[],"keyPapers":[],"journals":[],"dependsOn":[],"notes":["Listed in the CanSim terms map 1.0.0 (docs/onco/terms.json, generated 2026-09-24), CC BY 4.0, attribution: CanSim project, an open, public-data-first cancer foundation-model programme; CanSim page path /terms/spatial-platforms."],"provenance":{"editedBy":"OnCo CanSim terms wave (Wikipedia summaries, standards and project pages, GDC and FDA pages, Europe PMC)","editedOn":"2026-09-24","note":"CanSim terms map 1.0.0 (docs/onco/terms.json, generated 2026-09-24), CC BY 4.0, attribution: CanSim project, an open, public-data-first cancer foundation-model programme"},"category":"Pathology"},"route":"/terms/spatial-transcriptomics-platforms/","neighbours":{"company":[{"id":"10x-genomics","kind":"company","name":"10x Genomics","route":"/companies/10x-genomics/"}],"term":[{"id":"cancer-ai-vocabulary","kind":"term","name":"Cancer AI vocabulary (CanSim terms map)","route":"/terms/cancer-ai-vocabulary/"},{"id":"single-cell-rna-seq","kind":"term","name":"Single-cell RNA sequencing (scRNA-seq, 10x Chromium)","route":"/terms/single-cell-rna-seq/"},{"id":"spatial-autocorrelation","kind":"term","name":"Spatial autocorrelation (Moran's I)","route":"/terms/spatial-autocorrelation/"},{"id":"spagcn","kind":"term","name":"Spatially aware clustering (SpaGCN, KNN smoothing)","route":"/terms/spagcn/"}],"technology":[{"id":"single-cell-spatial","kind":"technology","name":"Single-cell & spatial profiling","route":"/technologies/single-cell-spatial/"},{"id":"spatial-biology-instruments","kind":"technology","name":"Spatial biology instruments","route":"/technologies/spatial-biology-instruments/"},{"id":"spatial-transcriptomics","kind":"technology","name":"Spatial transcriptomics","route":"/technologies/spatial-transcriptomics/"}]}}