Fig. 4: Examination of putative dorsal and ventral subregions of superior colliculus identified in the Allen 11 dataset using CellTransformer.
From: Data-driven fine-grained region discovery in the mouse brain with transformers
a Putative subregions of sensory layers of superior colliculus in tissue section 32 identified with k = 1300 CellTransformer domains. CCF registration is in the first column, with zonal (zo), superficial gray (sg), and optic (op) layers labeled by the color of their CellTransformer domain in third, fourth, and fifth columns. The second column shows all cells with color labels from their spatial domain from CellTransformer at k = 1300. The third, fourth, and fifth columns show the putative zo (gray-green), sg (purple), and op (red) domains. These columns also show the spatial distribution of one supertype level cell type in yellow across the section. b Sequential tissue sections (32: anterior, 31: posterior) shown similarly to (a) but visualizing subregions of the intermediate gray and intermediate white layers, which are indicated with black arrows in the CCF registered annotation image. c Proportions of different supertype level cell types for top-ten most abundant types in different spatial domains. Colors refer to the same spatial domain label in (a, b). Cell types visualized in (b) are denoted with a yellow asterisk. d Barplot of the percentage of cells of a given neurotransmitter class found in a given region (GABA GABAergic, Glut Glutamatergic, NN non-neuronal). e Number of unique cell types (at supertype level) found in each domain, grouped by neurotransmitter class.
