3-D Mouse Brain Model Reconstruction from a Sequence of 2-D Slices in Application to Allen Brain Atlas

  • Anton Osokin
  • Dmitry Vetrov
  • Dmitry Kropotov
Conference paper
Part of the Lecture Notes in Computer Science book series (LNCS, volume 6160)


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 high-resolution anatomic 3D-model of a mouse brain using well-known Allen Brain Atlas which is publicly available.


3D-Reconstruction neuroimaging morphing elastic deformations image registration B-splines 


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Copyright information

© Springer-Verlag Berlin Heidelberg 2010

Authors and Affiliations

  • Anton Osokin
    • 1
  • Dmitry Vetrov
    • 1
  • Dmitry Kropotov
    • 2
  1. 1.Computational Mathematics and Cybernetics DepartmentMoscow State UniversityRussia
  2. 2.Dorodnicyn Computing Center of the Russian Academy of SciencesRussia

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