Fig. 5
From: Enhanced and unified anatomical labeling for a common mouse brain atlas
Digitization of anatomical structures. a Example of our highly segmented FP based labels on the Allen CCF. Yellow arrows highlight the lateral subdivision of periaqueductal gray (PAG), Scale bar = 2 mm. b Exported delineation lines. c Digitization of labels with unique numerical ID for each anatomical structure. Different color of each structure pertains to different number. d SST-Cre:H2B-GFP showed distinct subregions in the PAG with different cell density level. Our labels (white font) divide the PAG into different subregions, as can be seen with the specific enrichment of SST neurons in the dorsolateral PAG (DLPAG) and the lateral PAG (LPAG, yellow arrow). Scale bar = 300 µm. e In contrast, the CCFv3 labels (color labels in the background) showed only 2 segmentations within the PAG (black font). f Hierarchical organization of anatomical labels based on the Allen ontology. Numerical IDs of individual structures assigned within parent structures for region-level and individual structure-level data analysis. For example, the PAG (shaded dark gray) is the parent structure of six subdivided structures (shaded light gray). Red font labels refer to structures further divided by the FP labels that are not present in the CCFv3 labels. Full name of abbreviations can be found in Supplementary Data 2
