Transcriptome

Neuroscience

Organic chemistry

Cortex (anatomy)

Visual cortex

Evolutionary biology

In situ hybridization

Biology

Gene

Gene expression

Somatosensory system

Spatial organization

Chemistry

In situ

Computational biology

Genetics

Nature Methods

Global efforts to create a molecular census of the brain using single-cell transcriptomics are producing a large catalog of molecularly defined cell types. However, spatial information is lacking and new methods are needed to map a large number of cell type–specific markers simultaneously on large tissue areas. Here, we describe a cyclic single-molecule fluorescence in situ hybridization methodology and define the cellular organization of the somatosensory cortex. osmFISH applies automated cycles of single-molecule fluorescence in situ hybridization without barcoding to provide spatial gene expression in tissue sections at high sensitivity, accuracy and throughput.

Spatial organization of the somatosensory cortex revealed by osmFISH