Three-dimensional computerised atlas of the rat brain stem precerebellar system: approaches for mapping, visualization, and comparison of spatial distribution data

Comparisons of microscopical neuroanatomic data from different experiments and investigators are typically hampered by the use of different section pl anes and dissimilar techniques for data documentation. We have developed a framework for visualization and comparison of section-based, spatial distri bution data, in brain stem nuclei. This framework provides opportunities fo r harmonized data presentation in neuroinformatics databases. Three-dimensi onal computerized reconstructions of the rat brain stem and precerebellar n uclei served as a basis for establishing internal coordinate systems for th e pontine nuclei and the precerebellar divisions of the sensory trigeminal nuclei. Coordinate based diagrams were used for presentation of experimenta l data (spatial distribution of labelled neurons and axonal plexuses) from standard angles of view. Each nuclear coordinate system was based on a cubo id bounding box with a defined orientation. The bounding box was size-adjus ted to touch cyto- and myeloarchitectonically defined boundaries of the ind ividual nuclei, or easily identifiable nearby landmarks. We exemplify the u se of these internal coordinate systems with dual retrograde neural tracing data from pontocerebellar and trigeminocerebellar systems. The new experim ental data were combined, in the same coordinate based diagrams, with previ ously published data made available via a neuroinformatics data repository (www.nesys.uio.no/Database, see also www.cerebellum.org). Three-dimensional atlasing, internal nuclear coordinate systems, and consistent formats for presentation of neuroanatomic data in web-based data repositories, offer ne w opportunities for efficient analysis and re-analysis of neuroanatomic dat a.