To evaluate representations at the level of cell type and subtypes, we used smFISH labeling combined with whole-slide imaging to quantify neuron populations in situ. We sampled the frontal cortex of n=3 p60 male mice by performing smFISH on every 5th cryosection (18 sections per animal) followed by whole-slide imaging on a Zeiss Axioscan z1 at 20× magnification. For quantification, images were down sampled (Zoom factor × 4) and converted to TIFF via the Zeiss CZItoTiffBatchConverter (CZI to Tiff Converter Suite software by Zeiss). Regions of interest that approximated the regions microdissected as inputs for Drop-seq experiments (i.e. frontal cortex) were defined by hand using a custom ROI pipeline in CellProfiler 2.1.1 (Carpenter et al., 2006) and subsequently input into a custom CellProfiler cell-counting pipeline. To evaluate cell type comparisons, we assessed inhibitory/excitatory ratios, using cocktails of smFISH probes to label GABAergic (Gad1/Gad2) and glutamatergic (Slc17a6/Slc17a7/Slc17a8) populations (Advanced Cell Diagnostic Biosystems). We counted a total of 487,003 glutamatergic and GABAergic neurons total from n=3 mice using a custom pipeline in CellProfiler. To evaluate representations at the level of subtypes, we
