Figure 2. Automated acquisition and analysis of whole-brain tracing data.
(A) A schematic of the brain clearing, imaging, and analysis pipeline used to acquire data from brains labeled using the injection schematics outlined in Figure 1A and Figure 1G. (B) A graphical explanation of the image acquisition and stitching process. Whole brains were imaged horizontally, from the dorsal (orange arrow) and ventral (purple arrow) sides and these images were stitched and combined to create a whole brain image. An example brain expressing tdTomato under the control of genetically encoded Vglut2-Cre is shown. (C) An example of a horizontal optical section acquired as described in A, B. Boxes indicate the locations of inset panels. Bar indicates 2 mm. (D) The automatically generated segmentation of C, with each labeled cell being represented by a single pixel. Bar indicates 2 mm. (E–H) Insets displaying raw images and automatically generated segmentations from the indicated regions (cortex, striatum, midbrain, and cerebellum). Bars indicate 200 μm.