This paper describes the use of a high-resolution flatbed scanner for neuroanatomical studies. Individual neurons that had been labeled using gold intensified diaminobenzidine (DAB) could be resolved in thionin-stained rat brain sections. One of the strengths of this method is that it permits the simultaneous visualization of labeled cells and their position relative to underlying cytoarchitectonic structures, allowing for highly accurate neuroanatomical analysis. High resolution maps of complete rat brains (similar to 100 sections spaced at 250 mum intervals) can be obtained in 10 h. Since much of this method can be automated, the scanning of brain sections is approximately 50% faster than conventional X-Y mapping, camera lucida, or photographic procedures. The method may have many other applications, particularly in evaluating the distribution of other types of labeled cells. For example, Fos immunoreactive neurons, cells labeled with reporter genes such as beta-galactosidase in brains from transgenic animals, and unique histological inclusions such as plaques found in Alzheimer's disease could all be directly imaged without a microscope. In addition, the exchange of primary data between labs via the Internet will provide additional opportunities for collaboration. (C) 2002 Elsevier Science B.V. All rights reserved.