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Regular version of the site

3D Neuroimaging

This project encompasses all stages of reconstruction and analysis of 3D mouse brain images:

  • registration of 2D and 3D images
  • segmentation of images
  • preprocessing of images
  • gene expression estimation
  • statistical analysis of gene expression

We work with various sources of data:

  • Nissl stained sections
  • Anatomical atlas data
  • In situ hybridization
  • Cryogenic block-face imaging
  • Synchrotron heavy X-ray tomography

The project is carried out in joint collaboration with NBIC centre of Kurchatov Institute.

  • A. Osokin, D. Vetrov, A. Lebedev, V. Galatenko, D. Kropotov, and K. Anokhin. An Interactive Method of Anatomical Segmentation and Gene Expression Estimation for an Experimental Mouse Brain Slice. Lecture Notes in Computer Science (LNCS), vol. 6685, pp. 86–97, 2011. link
  • A. Tikhonov, P. Voronin. Towards a better removal of subsurface fluoresence artifacts in block-face imaging // Proceedings of GraphiCon-2011, Moscow, 2011. pdf
  • A. Osokin, D. Vetrov, and D. Kropotov. 3D Reconstruction of Mouse Brain from a Sequence of 2D Brain Slices in Application to Allen Brain Atlas. Lecture Notes in Computer Science (LNCS), vol. 6160, pp. 291-303, 2010. link
  • P. Voronin and D. Vetrov. Intermodal Registration Algorithm for Segmentation of Mouse Brain Images. Proceedings of International Conference on Pattern Recognition and Image Analysis (PRIA), vol. 2, pp. 377-381, 2010. pdf


Reconstruction of a mouse brain from histological and anatomical images of Allen Mouse Brain Atlas:

Reconstruction of a mouse brain hemisphere from cryogenic block-face imaging data:

Reconstruction of a mouse embrion from synchrotron heavy x-ray tomography images:


Registration of experimental data (brown slice with gene expression information) into atlas image of different modality (grey slice) with simultaneuos detection of anatomic zones (right part) through keypoint matching:

Intermodal registration via mutual information optimization:

Gene expression

Estimating gene expression:

Analyzing gene expression using 


Suppressing subsurface fluoresence in cryogenic block-face imaging data:


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