Figure 9.

Orientation and tiled area of STPT-imaged adult mouse brain

(A) All three panels consist of STPT-captured and stitched images of a 50 μm-thick coronal section of an adult mouse brain with grid overlay. Each grid square represents a single 700 μm tile, which extends in both X- and Y-directions for calculating the size of the brain and setting the total tile area for image acquisition. From top to bottom: anterior portion of the brain with olfactory bulbs and prefrontal cortex; mid-coronal brain section with view of isocortical layers and subcortical regions; posterior portion of the brain with the cerebellum and brainstem.

(B) The image display here shows the midline or center of the brainstem, as indicated by the magenta-colored arrow, with a part of the cerebellum at the bottom of the screen. This anatomical landmark is identified to familiarize users with the orientation of the 700 μm-sized tile currently being viewed. Users can point to this landmark as a reference while moving the stage during the sample setup process.