{"entity":{"id":"spatial-transcriptomics","kind":"technology","name":"Spatial transcriptomics","aka":[],"tldr":"Methods that read which genes are switched on in each spot or cell of a tumour slice while keeping the tissue's geography, so scientists can see how cancer, immune and stromal cells sit next to one another.","summary":"Spatial transcriptomics measures gene expression across a tissue section without losing position. Sequencing-based platforms capture RNA on barcoded spots (10x Genomics Visium), while imaging-based platforms read hundreds to thousands of RNA species in place at single-cell resolution (MERFISH, 10x Xenium, NanoString CosMx). In oncology it maps the tumour microenvironment, immune exclusion and clonal territories, and it underpins atlases such as the Human Tumor Atlas Network.","status":"emerging","asOf":"2026-09-04","wikipedia":"https://en.wikipedia.org/wiki/Spatial_transcriptomics","links":[{"label":"Wikipedia","url":"https://en.wikipedia.org/wiki/Spatial_transcriptomics"}],"tags":[],"related":[],"cancers":[],"sections":["diagnostics","drug-discovery"],"technologies":["single-cell-spatial","digital-pathology-ai"],"targets":[],"drugs":[],"companies":["navignostics","vicinity-bio"],"institutions":[],"pathways":[],"terms":[],"trials":[],"people":[],"bottlenecks":[],"keyPapers":[],"journals":[],"dependsOn":["spatial-biology-instruments","rna-seq"],"notes":[],"principle":"Tissue sections are either overlaid on barcoded capture arrays whose oligonucleotides record position before sequencing, or hybridised with fluorescent probes read out over many imaging rounds with combinatorial barcodes.","strengths":["Keeps position, which single-cell sequencing discards","Reveals immune exclusion, niches and cell neighbourhoods","Works on archived formalin-fixed tissue on newer platforms"],"limitations":["Costly and data-heavy, mostly research use","Spot-based methods mix several cells per spot","No agreed clinical assay yet"]},"route":"/technologies/spatial-transcriptomics/","neighbours":{"section":[{"id":"diagnostics","kind":"section","name":"Diagnostics & Biomarkers","route":"/fronts/diagnostics/"},{"id":"drug-discovery","kind":"section","name":"Drug Discovery Platforms","route":"/fronts/drug-discovery/"}],"technology":[{"id":"digital-pathology-ai","kind":"technology","name":"Digital pathology & AI","route":"/technologies/digital-pathology-ai/"},{"id":"rna-seq","kind":"technology","name":"RNA sequencing & expression profiling","route":"/technologies/rna-seq/"},{"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/"}],"company":[{"id":"navignostics","kind":"company","name":"Navignostics","route":"/companies/navignostics/"},{"id":"vicinity-bio","kind":"company","name":"Vicinity Bio","route":"/companies/vicinity-bio/"}],"cancer":[{"id":"pancreatic","kind":"cancer","name":"Pancreatic ductal adenocarcinoma","route":"/cancers/pancreatic/"}],"paper":[{"id":"paper-grunwald-subtme-pancreatic-cell-2021","kind":"paper","name":"Spatially confined sub-tumor microenvironments in pancreatic cancer","route":"/key-papers/paper-grunwald-subtme-pancreatic-cell-2021/"}],"term":[{"id":"caf-subtypes-pancreatic","kind":"term","name":"Fibroblast subtypes in the pancreatic cancer stroma (myCAF, iCAF and apCAF)","route":"/terms/caf-subtypes-pancreatic/"},{"id":"spatial-autocorrelation","kind":"term","name":"Spatial autocorrelation (Moran's I)","route":"/terms/spatial-autocorrelation/"},{"id":"spatial-transcriptomics-platforms","kind":"term","name":"Spatial transcriptomics platforms (Visium HD, Xenium, MERFISH, CosMx, CODEX)","route":"/terms/spatial-transcriptomics-platforms/"},{"id":"spagcn","kind":"term","name":"Spatially aware clustering (SpaGCN, KNN smoothing)","route":"/terms/spagcn/"},{"id":"tertiary-lymphoid-structures","kind":"term","name":"Tertiary lymphoid structures (TLS)","route":"/terms/tertiary-lymphoid-structures/"}]}}