3-D mouse brain model reconstruction from a sequence of 2-D slices in application to Allen brain atlas

Authors:
Anton Osokin;Dmitry Vetrov;Dmitry Kropotov
Affiliations:
Moscow State University, Computational Mathematics and Cybernetics Department, Moscow, Russia;Moscow State University, Computational Mathematics and Cybernetics Department, Moscow, Russia;Dorodnicyn Computing Center, Russian Academy of Sciences, Moscow, Russia
Venue:
CIBB'09 Proceedings of the 6th international conference on Computational intelligence methods for bioinformatics and biostatistics
Year:
2009

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Abstract

The paper describes a method of fully automatic 3D-reconstruction of a mouse brain from a sequence of histological coronal 2D slices. The model is constructed via non-linear transformations between the neighboring slices and further morphing. We also use rigid-body transforms in the preprocessing stage to align the slices. Afterwards, the obtained 3D-model is used to generate virtual 2D-images of the brain in arbitrary section-plane. We use this approach to construct a highresolution anatomic 3D-model of a mouse brain using well-known Allen Brain Atlas which is publicly available.