BRAIN: Software Tools for Primate Brain Reconstruction from Histological Sections

Funded by: University of ParmaReference: BRAIN
Start: 2001-01-01Duration: 6 months
Coordinator: CRS4Italy


We have developed software for 3-D reconstruction and visualization of architectonic, neurophysiological and tract tracing data of primate cerebral cortex. Our emphasis is on providing interactive solutions to reconstruction and analysis problems by harnessing the power of new generation commodity graphics accelerators. We take as input data acquired in serially collected individual sections, in which the locations of outer and inner cortical boundaries, architectonic borders, electrode tracks, and labeled neurons are coded in X-Y coordinates. Linear and non-linear local transformations are interactively applied to sections for aligning them and minimizing distortions introduced by sectioning and histological procedures. Cortical surfaces are incrementally reconstructed during section manipulation using both direct triangulation and functional techniques. Using multipass rendering techniques, the system interactively generates realistic 3-D views that present in the same image the location of architectonic areas and the spatial location, density and cortical depth of the introduced data. The reconstructed brain can be resliced according to arbitrary planes and virtually dissected for showing sulcal banks without distortion. Application of this software to the analysis of data from our previous studies showed that this integrated system is a powerful tool for anatomo-functional correlation in highly convoluted brains and for comparing data from brains cut along different sectioning plans. The availability of low-cost, high performance graphics PC platforms makes this approach practical for everyday laboratory work.

Related information


[1] Fabio Bettio, Sergio Demelio, Enrico Gobbetti, Giuseppe Luppino, and Massimo Matelli. Interactive 3-D Reconstruction and Visualization of Primates Cerebral Cortex. In Society for Neuroscience 31st Annual Meeting, October 2001.
[2] Sergio Demelio, Fabio Bettio, Enrico Gobbetti, and Giuseppe Luppino. Three-dimensional Reconstruction and Visualization of the Cerebral Cortex in Primates. In David Ebert, Jean Favre, and Ronny Peikert, editors, Data Visualization 2001, Springer Verlag, New York, NY, USA, May 2001. Proceedings of the Joint Eurographics and IEEE TCVG Symposium on Visualization, Ascona, Switzerland, May 28-30, 2001.