Figure 2: Registration of images to the Allen Mouse CCF v.2 reference atlas. | Scientific Data

Figure 2: Registration of images to the Allen Mouse CCF v.2 reference atlas.

From: Brain-wide distribution of reporter expression in five transgenic tetracycline-transactivator mouse lines

Figure 2

Illustration of the principle used for spatial registration of microscopic mouse brain images to a three-dimensional reference atlas (a–d) and semi-quantitative scoring system used for analysis of labeling (e). (a) Image of a X-gal labeled horizontal section from the brain of a Pcp2-tTA mouse. (b) Slice from the Allen Mouse CCF v.2 reference atlas with position and angle of orientation matching the experimental section in (b). Insets indicate the virtual sectioning plane in coronal, sagittal, and horizontal views. (c) 3-D rendering of the Allen Mouse CCF v.2 atlas showing the virtual cutting plane used in (b) with delineations of major brain structures. This custom atlas diagram is superimposed and spatially aligned with the original section image (d). (e) A semi-quantitative grading scale from 0 to 4 is used to score the density of labeled elements in different brain regions (see methods section for details). Cb, cerebellum; Ctx, cerebral cortex; HF, hippocampal formation; Mb, midbrain. Scale bars, (a–e) 1 mm (e) 100 μm.

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