Fig. 2: In situ cell-type identification, spatial mapping and projection mapping of individual cells in MOp by MERFISH.

a, Dendrogram showing the hierarchical relationship among the subclasses and clusters in the mouse MOp identified by MERFISH, coloured by the subclass each cluster belongs to. b, Left, spatial map of cell clusters identified in a coronal slice (bregma ~+0.9), with cells coloured by their cluster identity as shown in the colour index. Top right, zoomed-in map of the boxed region of the left panel. Bottom right, spatial localization of individual RNA molecules in the boxed region of the top right panel, coloured by their gene identity. The segmented cell boundaries are coloured according to the cell clusters they belong to. c, IT neurons in the same coronal slice as shown in b. The IT neurons are coloured by their cluster identity, as shown in the colour index, together with L6b cells in dark blue to mark the bottom border of the cortex. All other cells are shown in grey. d, Projection patterns of the MOp neurons into three other regions of the brain, MOs, SSp and TEa–ECT–PERI. Left, CTb was used as retrograde tracer and injected into these three regions. The CTb signals and the MERFISH gene panel were imaged in MOp to determine both the cluster identities and projection targets of individual cells. Projection of MOp neurons to the target regions are displayed as a dot plot, where the size of the dot represents the fraction of cells projecting to each indicated target among all CTb-positive, single-projecting cells in a cluster, and the colour represents the fraction of cells a target received from each indicated cluster. Data may be viewed at NeMO Analytics. OGC, oligodendrocyte; SMC, smooth muscle cell.