3D Reconstruction of Mouse Brain from Allen Brain Atlas

Abstract

The paper describes a method for fully automatic 3D-reconstruction of mouse brain from a sequence of histological coronal 2D slices. The model is constructed via non-linear transformations between neighboring slices and further morphing for interpolation. We also use rigid-body transforms in preand post-processing stages for smoothing transitions. The bobtained 3D-model is then used for getting 2D-images of brain in arbitrary section-plane. We use this approach for automatic annotation of brain structures with the aid of Allen Brain Atlas which is available in electronic form.