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An Interactive Method of Anatomical Segmentation and Gene Expression Estimation for an Experimental Mouse Brain Slice

  • Anton Osokin
  • Dmitry Vetrov
  • Alexey Lebedev
  • Vladimir Galatenko
  • Dmitry Kropotov
  • Konstantin Anokhin
Part of the Lecture Notes in Computer Science book series (LNCS, volume 6685)

Abstract

We consider the problem of statistical analysis of gene expression in a mouse brain during cognitive processes. In particular we focus on the problems of anatomical segmentation of a histological brain slice and estimation of slice’s gene expression level. The first problem is solved by interactive registration of an experimental brain slice into 3D brain model constructed using Allen Brain Atlas. The second problem is solved by special image filtering and further smart resolution reduction. We also describe the procedure of non-linear correction of atlas slices which improves the quality of the 3D-model significantly.

Keywords

mouse brain studies gene expression detection image segmentation morphing Allen Brain Atlas 

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Copyright information

© Springer-Verlag Berlin Heidelberg 2011

Authors and Affiliations

  • Anton Osokin
    • 1
  • Dmitry Vetrov
    • 1
    • 2
  • Alexey Lebedev
    • 1
  • Vladimir Galatenko
    • 1
  • Dmitry Kropotov
    • 2
  • Konstantin Anokhin
    • 3
  1. 1.Moscow State UniversityMoscowRussia
  2. 2.Dorodnicyn Computing Centre of Russian Academy of SciencesMoscowRussia
  3. 3.P.K. Anokhin Institute of Normal PhysiologyMoscowRussia

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