Spatial transcriptomics (ST) has revolutionised transcriptomic analysis by preserving tissue architecture, allowing researchers to study gene expression within its spatial context. Understanding a cell’s position relative to its neighbours and extracellular structures provides crucial insights into cellular phenotype, function, and disease progression, particularly in cancer, where the tumour microenvironment (TME) influences processes such as chemoresistance.
The commercialisation of ST platforms has enabled broad access to these techniques, earning ST the title of “Method of the Year 2020” by Nature Methods.

Imaging-based fluorescence in situ hybridisation (FISH) technologies, such as 10x Genomics Xenium (figure above) and the NanoString CosMx SMI, provide high-multiplex, subcellular-resolution transcript information across hundreds of thousands of cells, with high sensitivity and specificity. These advances facilitate the exploration of cell atlases, cell–cell interactions, and tumour microenvironment phenotypes. While transcriptomic techniques have existed for decades, the combined integration of spatial transcriptomics remains in its early stages. Beyond transcriptomics, spatial omics technologies, including spatial proteomics, chromatin accessibility assays, and spatial genomics are further expanding the field.