Fig. 6. Brain region-specific features of cell types.
a, Heat map showing the CCFv3 region distribution (y axis) in each subclass (x axis) for MERFISH cells. Bar graphs on the left show the broad CCFv3 regions, proportion of neuronal versus glial cells per region of interest (ROI), and proportion of neurotransmitter types per ROI. Bar graphs on the right show broad CCFv3 regions, Shannon diversity per subclass and supertype, and number of cells per ROI. Bar graphs on the top show number of cells per subclass, Gini coefficient and class assignment. Bar graphs on the bottom show subclass and class annotations. b, Scatter plot showing the number of neuronal clusters identified per major brain region versus the number of neuronal cells profiled by scRNA-seq in the corresponding region. Each neuronal cluster is assigned to the most dominant region. c, As in b, except numbers of clusters and profiled cells are normalized by the region volume. d, Distribution of the number of DEGs (identified in scRNA-seq data) between every pair of neuronal clusters within each major brain region, split into indicated quantiles. The curves show the spread of the number of DEGs between more similar types at 0.1 quantile versus the more distinct types at 0.9 quantile. e, Scatter plot showing the number of cells mapped to a given neuronal cluster versus the span (as measured by IQR) of their 3D coordinates along the anteroposterior, dorsoventral and mediolateral axes based on the MERFISH dataset, stratified by the major brain regions. Note that both axes are in log scales. The plot shows how localized the clusters are within each region along each spatial axis. IQR, inter-quantile range (the difference between 75% quantile and 25% quantile). Pall, pallium.