Neuroinformatics web applications for 3-D analysis of brain connectivity: anatomical organization of subcortical projections from whisker and forelimb regions of the rat somatosensory cortex

Subcortical re-entrant projection systems connecting cerebral cortical areas with the basal ganglia and cerebellum contribute to regulation of movement and other behaviour. The striatum and pontine nuclei receive direct cortical input, and are thought to play an important role in the gating of signals to the basal ganglia and cerebellum, respectively. As the topographical arrangement of axonal projections provides an anatomical substrate for function, comparison of corticostriatal and corticopontine projections may shed light on the functional properties of these circuits. While presence of somatotopically organized projections from the primary somatosensory cortex (SI) to the striatum and pontine nuclei are well known, little is known about differences in the organization of these two major projection systems. We here present a neuroinformatics-based approach aimed at a quantitative comparison of corticostriatal and corticopontine axonal projections. Utilizing our recent histological atlas of SI-efferent projections (http://www.rbwb.org/, select Whole Brain Connectivity Atlas), high-resolution microscopic images of sections showing the detailed distribution of SI-forelimb and -whisker projections to the striatum and pontine nuclei have been mapped into a common spatial framework. Image analysis tools are used to derive simplified representations of labelled axonal terminals. These simplified representations are visualized and analyzed for the purpose of 1) identifying relative differences in the amount of labelling across regions, 2) comparing principles of the topographical organization, and 3) determining degrees of overlap and segregation between forelimb and whisker projections in each of the two target regions. To validate our approach, we also utilize another database containing an extensive material of more than seventy detailed three-dimensional reconstructions of SI-pontine axonal projections (http://www.rbwb.org/, select FACCS application). We conclude that this 3-D atlasing approach facilitates visualization and analysis of the anatomical organization of major projection systems in the brain.