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In the brain, neural stem and progenitor cells divide into restricted regions and their progenies migrate along complex trajectories to reach distant areas of the brain. Until now, the 3D organization of neurogenic zones and pathways of cell migration has remained undisclosed. In this study, we developed the new pipeline for 3D visualization and analysis of cell division and migration in the whole brain, based on whole-mount labeling dividing cells with 5-ethynyl-2'-deoxyuridine (EdU). Using this pipeline, we observed uneven distribution of EdU+ cells in the adult subventricular zone (SVZ) and found regions with high cell density forming three stripes, which merge into a rostral migration stream (RMS). Using an interval pulse labeling paradigm, we observed the displacement of the density of labeled cells from SVZ towards the olfactory bulb (OB). Three stripes in the V-SVZ were not visible clearly 2h after EdU injection and they appeared in 24 h. In 120 h after labeling, almost all EdU+ cells were located in OB. Thus, three stripes in SVZ correspond to three migration branches that have not been previously described. We also discovered two distinct segments of RMS with different proliferative potential - the anterior segment consisted of migrating but not dividing cells. Next, we visualized and analyzed patterns of dividing cells in the perinatal brain and found dynamics of cell migration differ from adults. Finally, we compared brain development of wt vs. autism model mice (16p11.2 df/+) and didn’t reveal a difference in 3D patterns and dynamics of proliferation in brain neurogenic zones.