Fig. 6

Comparison between the Allen CCFv3, the ARA, and our labels. First column: Our highly segmented FP based labels on the Allen CCF. Scale bar = 2 mm, second column; our labels (white lines) with marker brain background, third column: comparison between our labels and the CCFv3 labels (colored background), fourth column: comparisons between our labels and the ARA labels (colored background). b–p Anatomical names in black and white are from the Allen CCF and our labels, respectively. b–d PV-Cre:H2B-GFP (b) to identify subregions in the zona incerta (ZI). Scale bar = 300 µm. Low in dorsal and high in ventral parts (ZID and ZIV, respectively) in our labels while the CCFv3 and the ARA labels have a single combined structure for ZI. f–h (f) Virtual overlay of Chat-Cre:Ai75 (red) and SST-Cre:H2B-GFP (green) to compare basal forebrain regions. Scale bar = 300 µm. g, h Our labels further segregate the single structure defined as the substantia innominate (SI, Allen) into the ventral pallidum (VP) and the extended amygdala (EA). Yellow arrow highlights the border between the basal forebrain and the hypothalamus. j–l Disagreeing borders between the somatosensory and the motor cortices. Yellow arrow highlights border between the somatosensory and motor cortices. j Virtual overlay of pseudo colored Cux2:Ai75 (L2/3, green), Rbp4:Ai75 (L5, magenta), Ntsr1:Ai75 (L6, yellow), and Ctgf:Ai75 (L6b, red). Scale bar = 200 µm. Note the lack of Cux2:Ai75 and Rbp4:Ai75 signal in layer 4 of the somatosensory cortex. n–p The BST is divided into several subregions in our labels compared to a single BST structure in the CCFv3 labels, despite the original ARA version with finer delineations for this structure. n SST-Cre:H2B-GFP used to identify subdivisions of BST. Scale bar = 300 µm. Note the higher degree of segmentations in our labels compared to the CCFv3 and the ARA (a–d, e–h, m–p), and inconsistencies in anatomical delineations of the same structures between the atlases (i–l). See Supplementary Data 2 for abbreviations