The latest developments in computer-based stereology build upon the similarities of classical stereology and computer microscopy to provide refined and effective spatial analyses that also permit mapping of anatomical regions. Classical stereology and computer microscopy have developed along independent pathways as methodologies to provide a quantitative understanding of the structure of the brain. They approach brain morphology and brain morphometry from different points of view. On one hand, stereology has concentrated upon the unbiased numerical estimation of parameters, such as length, area, volume, and population size that characterize entire regions of the brain, e.g. hippocampus, as well as individual elements within them, e.g. cell volume. On the other hand, computer microscopy has concentrated upon providing accurate three-dimensional maps of the morphology of entire regions of the brain as well as of individual elements within them, e.g. neuronal dendrite and axon systems. The differences in point of view are not so extensive as to keep the two methodologies separate. They share, after all, a similar manner of controlling microscope data input and analyzing the images the microscope provides. The incorporation of data archiving permits easier access to previous studies, as well as the sharing of stereological findings and their related maps throughout the scientific community. Some of the stereological systems now integrate spatial mapping with stereological analyses to provide more comprehensive methods to analyze brain tissue.