Fig. 3: Comparison of CellTransformer domain sets identified in the Allen 11 dataset with k = 1300 with a comprehensive region set found in Ding et al.34, reproduced with permission from Elsevier.
From: Data-driven fine-grained region discovery in the mouse brain with transformers
a Representative images reproduced from Ding et al. of region boundaries in prosubiculum (PS), subiculum (SUB), and hippocampal-amygdala (HA) particularly along the dorsal-ventral axis. Polymorphic and pyramidal layers of the dorsal subiculum (SUBd) and ventral prosubiclum are indicated. b Images from hippocampal formation across 4 sequential tissue sections (anterior to posterior) roughly aligned to sections presented in Ding et al. Each dot is a cell colored using domain labels with k = 1300. c Same as (b) but only showing cells inside PS, SUB, and HA. Putative regional annotations are indicated and grouped by dorsal or ventral region within PS and SUB. d Gene expression patterns visualized at the corresponding tissue section, where only cells within PS/SUB/HA are shown. Units are in log2 probe counts. e Gene expression heatmap of identified subregions, with putative anatomical annotation. Dendrogram from hierarchical clustering in gene expression space is shown to the right. Genes visualized in (d) are bolded and denoted with a pink asterisk. Colored brackets indicate the genes which are differentially expressed with respect to the domain (colors match those shown on the left of the heatmap). Two genes per domain are shown and each gene is expressed with at least log-fold change greater than 1 relative to the other domains. Abbreviations: PS-mo prosubiculum molecular layer, PS-py pyramidal layer of subiculum, SUBv-py ventral subiculum, pyramidal layer, HA-py hippocampal-amygdaloid transition area, pyramidal layer, HA-po hippocampal-amygdaloid transition area, polymorphic layer, SUB-mo subiculum, molecular layer, PSd-po dorsal prosubiculum, polymorphic layer, PSv-po ventral prosubiculum, polymorphic layer, PSd-py dorsal prosubiculum, pyramidal layer, SUBd-py dorsal subiculum, pyramidal layer, SUBv-py ventral subiculum, pyramidal layer, PSv-po ventral prosubiculum, polymorphic layer, PSd-po dorsal prosubiculum, polymorphic layer.
