Computer assisted three-dimensional reconstruction of brain regions from serial section digitized images. Application to the organization of striato-nigral relationships in the rat

We have developed a software which allows the three-dimensional reconstruction of brain regions from serial section digitized images. This software, which generates wire-frame three dimensional models, requires at least a 486 PC microcomputer running Microsoft Windows(R) (3.x or 95). Mosaics of high resolution images, covering large brain areas, digitized by means of a camera fitted on a microscope equipped with a motorized stage, are handled by our software as single high resolution images. Serial sets of such images may be segmented and manually aligned. We have utilized this software to study the organization of striatal efferences within the substantia nigra pars reticulata, as well as the distribution of neuronal cell bodies within the substantia nigra pars compacta after micro-ionophoretic application of wheat germ agglutinin conjugated to horseradish peroxidase into the orofacial sensorimotor region of the striatum. The three dimensional representation of anterogradely labeled striatal efferences confirmed and determined the lamellar organization previously postulated from serial plane section micrographs. The distribution in the rat brain of retrogradely labeled nigro-striatal cell bodies, which had not yet been studied after injection of tracer into functionally identified regions of the striatum, revealed two subpopulations: a first one rather dense, located in the anterior half of the substantia nigra pars compacta, which was in close register with the striatal efferences, and a second one, much more scattered and less numerous, located in the posterior part of the structure which extended far from the substantia nigra along the medio-lateral axis. Our three dimensional reconstruction software will now be used to study the neuronal connectivity within the basal ganglia and other brain regions.