Shape and volume of manually detected brain cell nuclei varies between red blood cells (RBCs) and motor neurons (n = 20 cells each) (A, B). The mean elongation was 1.9, 1.3, and 1.1 for RBCs, motor neurons, and brain nuclei, respectively. The mean volume was 99, 102, and 13 µm3 for RBCs, motor neurons, and brain nuclei, respectively. These releative values are consistent with what is visually apparent in both histology (C1 and C3) and histotomography (C2 and C4). Volumes of motor neuron and erythrocytes include both nuclei and cytoplasm. Differences in the distribution of brain nuclei were also observed. Cell nuclei were also identified across whole zebrafish samples via a manually trained classifier and segregated by registering brain regions for five five dpf samples (D). The regions identified through anatomical landmarks include olfactory epithelium, telencephalon, diencephalon, mesencephalon, metencephalon, myelencephalon, hypothalamus, spinal cord, and white matter. The proportion of cells per brain region as percentage of total cell counts, agree in rank order between samples (E). Computed elongation and volumes showed no significant difference between individual fish (F, G).