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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.
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.
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.
Nothing in the corpus depends on this yet.
Dependencies are what this technology cannot be delivered without: manufacturing steps, instruments, software, upstream methods. See its full chain on the map.
Query for this technology: (TITLE:"Spatial transcriptomics" OR ABSTRACT:"Spatial transcriptomics") AND (cancer OR tumor OR tumour OR oncology OR carcinoma OR lymphoma OR leukemia OR leukaemia OR myeloma OR sarcoma OR melanoma OR glioma). Results are unfiltered search hits about Spatial transcriptomics, not a curated reading list.
Shares Navignostics, Vicinity Bio, Digital pathology & AI.
Shares Vicinity Bio, Digital pathology & AI.
Shares Spatial transcriptomics platforms (Visium HD, Xenium, MERFISH, CosMx, CODEX), Spatial biology instruments, Single-cell & spatial profiling.
Shares Single-cell & spatial profiling, Digital pathology & AI, RNA sequencing & expression profiling, Pancreatic ductal adenocarcinoma.
Shares Fibroblast subtypes in the pancreatic cancer stroma (myCAF, iCAF and apCAF), Single-cell & spatial profiling, Pancreatic ductal adenocarcinoma.
Shares Single-cell & spatial profiling, Digital pathology & AI, Pancreatic ductal adenocarcinoma.
Shares Spatial transcriptomics platforms (Visium HD, Xenium, MERFISH, CosMx, CODEX), Single-cell & spatial profiling.
Open-source projects that implement or serve this technology, from OnCo's own catalogue: licence and last activity as the repository reported them on the day of the fetch. Listing is not endorsement; check the licence before reuse and the validation before clinical use.
Spatial single-cell analysis in Python: neighbourhood graphs, spatial statistics and image features for spatial transcriptomics and multiplex imaging.
Maps cell types onto spatial transcriptomics spots with a Bayesian model, from the Sanger.
An R suite for spatial multi-omics analysis and visualisation.
Gustave Roussy's technology-agnostic pipeline for spatial omics: segmentation, annotation and visualisation for Xenium, MERSCOPE, CosMx and imaging.
A foundation model trained jointly on dissociated and spatial single-cell data from the Theis lab.
The portal of the Human Tumor Atlas Network, the NCI's single-cell and spatial atlases of tumour evolution.