Inspecting the resulting cell-type distribution maps, we found reassuringly that the automatically assigned locations corresponded well with the known source of the cells. For example, cortical and hippocampal projection neurons were assigned to the cortex and hippocampus as expected (Figure S5). But the spatial maps provided much more detail: for example, the distinction between CA1 and CA3 pyramidal cells was clear (Figure S5, right), and cortical pyramidal cells could be assigned highly specific distributions across the cortical surface (Figure S5, left) and layers. Interestingly, the spatial distribution of cortical pyramidal neurons correlated with their molecular similarity. For example, pyramidal neurons of the piriform and entorhinal cortex, as well as the subiculum, were molecularly closely related (shown by their forming a separate subtree of the dendrogram), as well as spatially aligned. Similarly, the pyramidal cells of the neocortex were arranged by molecular similarity in layer order (i.e., layers 2/3, layer 4, layer 5, layers 6/6b). Notably, this also corresponds with their order of development during embryogenesis.
