To determine what fraction of total brain cells are retained in a single cell suspension, we compared estimates of total cell number from stereological counts of tissue to cell totals in suspension. For suspension assays, we estimated cell totals from a single 400 μm coronal slab of either Frontal Cortex or dorsal Striatum. Stereological assays were performed on a series of thinner, paraformaldehyde-fixed tissue from the same anterior-posterior location (40 μm; see IHC section for fixation procedure). To get total counts, densities were multiplied by volume estimates calculated using a thickness of 400 μm and surface area calculated from slide scans of the same tissue sections (Olympus VS110). A 10% shrinkage factor due to fixation was taken into account. We aided cell counting by using a double transgenic mouse (male, P59–60) carrying a Nestin-Cre driver (Jackson Labs, 003771) and lox-stop-lox (lsl) ZsGreen Cre-reporter (Jackson Labs, 007906). ZsGreen aids in the identification of single-cells as it is sequestered in the soma and proximal processes of cells. Specifically, confocal stacks were obtained with a 40× objective using the FV1200 (Olympus). ZsGreen+ and
