Stitcher: A Surface Reconstruction Tool for Highly Gyrified Brains.

Abstract

Brain reconstruction, specially of the cerebral cortex, is a challenging task and even more so when it comes to highly gyrified brained animals. Here, we present Stitcher, a novel tool capable of generating such surfaces utilizing MRI data and manual segmentation. Stitcher makes a triangulation between consecutive brain slice segmentations by recursively adding edges that minimize the total length and simultaneously avoid self-intersection. We applied this new method to build the cortical surfaces of two dolphins: Guiana dolphin (Sotalia guianensis), Franciscana dolphin (Pontoporia blainvillei); and one pinniped: Steller sea lion (Eumetopias jubatus). Specifically in the case of P. blainvillei, two reconstructions at two different resolutions were made. Additionally, we also performed reconstructions for sub and non-cortical structures of Guiana dolphin. All our cortical mesh results show remarkable resemblance with the real anatomy of the brains, except P. blainvillei with low-resolution data. Sub and non-cortical meshes were also properly reconstructed and the spatial positioning of structures was preserved with respect to S. guianensis cerebral cortex. In a comparative perspective between methods, Stitcher presents compatible results for volumetric measurements when contrasted with other anatomical standard tools. In this way, Stitcher seems to be a viable pipeline for new neuroanatomical analysis, enhancing visualization and descriptions of non-primates species, and broadening the scope of compared neuroanatomy.