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. 2016 Mar 23;5:e13925. doi: 10.7554/eLife.13925

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© 2016, Sugar et al

This article is distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use and redistribution provided that the original author and source are credited.

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Figure 1. — (A) The location of the center of each injection was normalized to a standard 3D atlas of the rat brain (Waxholm space; Papp et al., 2014; See video 1 and 2). Lateral (A1), dorsal (A2) and para-caudal view (A3) of the 3D atlas brain with the center of each injection (colored spheres). The injections are color-coded according to age (see color code bottom left). Injections were performed in either the left or right hemisphere but to ease visualization, all injections were plotted in the right hemisphere. Dentate gyrus (DG), CA3-1, subiculum (SUB), fasciola cinereum (FC), pre- and parasubiculum (PrS and PaS), medial- and lateral entorhinal cortex (MEC and LEC), A35-36 and postrhinal cortex (POR) are color coded, while the rest of the brain is colored green. (B) Midsagital view of the center of the injections projected to the pial surface. The laminar position is disregarded to allow the injections to be plotted in 2D. Light blue, light red and grey line depict respectively the dorsal border of A30, the border between A29 and A30 and the ventral border of A29. Injections are color coded according to age. Triangle explained in C. (C) One example, as shown in B, of the algorithm used for calculating normalized 2D coordinates of the injections. The pial surface area of A29 and A30 was divided into triangles (grey area). The shortest vector (black line) between the injection (red sphere) and the cortical surface was calculated. Thereafter, we calculated the coordinate of the intersection of the vector and the plane within the triangle (yellow dot) which represented the 'transposed' location of the injection. The normalized dorsoventral coordinate of each injection was defined by calculating the shortest vector from the transposed injection to dorsal ( $d_{d o r s a l}$ ) and ventral border of A29 or A30 ( $d_{v e n t r a l}$ ). The normalized rostrocaudal coordinate was obtained by first calculating a line along the rostrocaudal extend of A29 and A30, positioned equally distant from the dorsal and ventral borders (magenta line). Next, we calculated the shortest vector between the injection and this line (red line) and found the intersection between the two. The rostrocaudal coordinate was obtained by calculating the cumulative distance from the cross section to the rostral ( $d_{r o s t r a l}$ ) and caudal end of RSC ( $d_{c a u d a l}$ ). (D) Normalized flatmap of the injections. The 3D RSC is converted to a 2D normalized flatmap to obtain relative rostrocaudal and dorsoventral positions of the injections. The figure is oriented with rostral RSC (left), caudal RSC (right), dorsal RSC (top) ventral RSC (bottom) to each of the sides of the rectangle. Grey line depicts the border between A29 and A30 in RSC. In all figures, each injection is color coded according to the bottom left color scheme; light grey colored injections represent injections in pups aged P1, green colored injections represent injections in pups aged P8 while cyan colored injections represent injections in pups aged close to P15. Grey injections represent injections in pups older than P15.

DOI: http://dx.doi.org/10.7554/eLife.13925.003