We describe here an automated system that accurately maps tissue sections stained by immunocytochemistry for an inducible nuclear protein. The sections are scanned with a computer-controlled microscope setup hooked to a CCD camera. Raw images captured at high resolution are filtered using highly selective criteria for the recognition of labeled cell nuclei. The total population of recognized labeled nuclei is then divided into separate bins, according to their labeling intensities. Finally, information about both the position and labeling intensity of labeled nuclei is represented in average density maps. The system was optimized for the quantitative mapping of neuronal cells expressing the inducible gene ZENK in the brain of songbirds, in response to stimulation with song, but should be of general applicability for the mapping of inducible nuclear proteins.