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Brain scans were co-registered to an annotated atlas (https://scalablebrainatlas.incf.org/mouse/ABA12#downloads/) using VINCI. Thresholding was achieved using the threshold function on VINCI by applying a value across all scans. Using the automated calculation function of VINCI, a mask was created from the ROIs in 3D, and the intensity profile of each region was determined using the VOI define function on VINCI. Representative images in the areas of interest were rendered using the Arivis software.

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