Signal, Image and Video Processing

, Volume 8, Supplement 1, pp 41–48 | Cite as

Graph-regularized 3D shape reconstruction from highly anisotropic and noisy images

  • Christian Widmer
  • Stephanie Heinrich
  • Philipp Drewe
  • Xinghua Lou
  • Shefali Umrania
  • Gunnar Rätsch
Original Paper


Analysis of microscopy images can provide insight into many biological processes. One particularly challenging problem is cellular nuclear segmentation in highly anisotropic and noisy 3D image data. Manually localizing and segmenting each and every cellular nucleus is very time-consuming, which remains a bottleneck in large-scale biological experiments. In this work, we present a tool for automated segmentation of cellular nuclei from 3D fluorescent microscopic data. Our tool is based on state-of-the-art image processing and machine learning techniques and provides a user-friendly graphical user interface. We show that our tool is as accurate as manual annotation and greatly reduces the time for the registration.


Cell nuclei detection Shape reconstruction 3D fluorescent microscopic data Nuclear segmentation 



We gratefully acknowledge core funding from the Sloan Kettering Institute (to G.R.), from the Ernst Schering foundation (to S.H.) and from the Max Planck Society (to G.R. and S.H.). Part of this work was done while C.W., S.H., P.D. and G.R. were at the Friedrich Miescher Laboratory of the Max Planck Society and while C.W. was at the Machine Learning Group at TU-Berlin.

Supplementary material

11760_2014_694_MOESM1_ESM.pdf (2.1 mb)
Supplementary material 1 (pdf 2152 KB)
11760_2014_694_MOESM2_ESM.pdf (137 kb)
Supplementary material 2 (pdf 137 KB)


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Copyright information

© Springer-Verlag London 2014

Authors and Affiliations

  • Christian Widmer
    • 1
  • Stephanie Heinrich
    • 2
  • Philipp Drewe
    • 1
  • Xinghua Lou
    • 1
  • Shefali Umrania
    • 1
  • Gunnar Rätsch
    • 1
  1. 1.Sloan Kettering InstituteNew YorkUSA
  2. 2.Institute for BiochemistryETH ZurichZurichSwitzerland

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