Figure 2

Schematic illustration of the full procedure for sampling and analysis of the SVZ. (A) Representative picture of a P10 mouse brain prior to cutting. (B) Representative micrographs show a subsampled series of counterstained brain sections (Dapi) covering the full rostro-caudal extent of the LV. Sections are collected/subsampled in series according to the experimental question (here for illustration a subsampling of 1 section out of 12). (C,E) Schematic illustration of virtual contours of serial brain sections (C), which are used for the generation of 3D reconstructions of the brain (bright grey) and LVs (dark grey; E). (D) Schematic illustration of the definition of the ROI (here lSVZ in green) and the automatic distribution of probes for OD measurements of the investigated marker. Probes width are defined by the user (in this study 50 µm), while the height is calculated by “FlashMap”. (F) The software generates automatically 2D heatmaps of SVZ thickness and OD values along the rostro-caudal axis of the ROI (here lSVZ). Values (here SVZ thickness) are represented by a relative colour code (deep blue = 0 to deep red = 1 = highest value). (G) Heatmaps can be presented in 3D, by superimposing those onto a 3D reconstruction of the ventricular system (here complete heatmap of SVZ thickness). Scale bars: (A) = 5 mm; (B, C) = 1 mm. Abbreviations: SVZ, subventricular zone; 2D, two dimensional; 3D, three dimensional; OD, optical density; ROI, region of interest; LV, lateral ventricle.