# Spatial transcriptomics

Source: https://onco.cc/technologies/spatial-transcriptomics/  
OnCo record `spatial-transcriptomics` (Technology). Data CC BY-NC 4.0, attribute "Data from OnCo (onco.cc)"; commercial use needs a licence.

## TL;DR

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.

## Fields

- Kind: Technology
- Status: emerging
- Last checked: 2026-09-04
- 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

## Sources

- Wikipedia: https://en.wikipedia.org/wiki/Spatial_transcriptomics
- Wikipedia: https://en.wikipedia.org/wiki/Spatial_transcriptomics

## Connected records

- fronts: [Diagnostics & Biomarkers](https://onco.cc/fronts/diagnostics/), [Drug Discovery Platforms](https://onco.cc/fronts/drug-discovery/)
- technologies: [Digital pathology & AI](https://onco.cc/technologies/digital-pathology-ai/), [Single-cell & spatial profiling](https://onco.cc/technologies/single-cell-spatial/)

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