Isotropic Reconstruction of 3D Fluorescence Microscopy Images Using Convolutional Neural Networks

  • Martin WeigertEmail author
  • Loic Royer
  • Florian Jug
  • Gene Myers
Conference paper
Part of the Lecture Notes in Computer Science book series (LNCS, volume 10434)


Fluorescence microscopy images usually show severe anisotropy in axial versus lateral resolution. This hampers downstream processing, i.e. the automatic extraction of quantitative biological data. While deconvolution methods and other techniques to address this problem exist, they are either time consuming to apply or limited in their ability to remove anisotropy. We propose a method to recover isotropic resolution from readily acquired anisotropic data. We achieve this using a convolutional neural network that is trained end-to-end from the same anisotropic body of data we later apply the network to. The network effectively learns to restore the full isotropic resolution by restoring the image under a trained, sample specific image prior. We apply our method to 3 synthetic and 3 real datasets and show that our results improve on results from deconvolution and state-of-the-art super-resolution techniques. Finally, we demonstrate that a standard 3D segmentation pipeline performs on the output of our network with comparable accuracy as on the full isotropic data.



We thank V. Stamataki, C. Schmied (Tomancak lab), S. Merret and S. Janosch (Sarov Group), H.A. Morales-Navarrete (Zerial lab) for providing the datasets, and U. Schmidt (all MPI-CBG) for helpful feedback. Datasets were recorded by the Light Microscopy Facility (LMF) of MPI-CBG.


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Copyright information

© Springer International Publishing AG 2017

Authors and Affiliations

  • Martin Weigert
    • 1
    • 2
    Email author
  • Loic Royer
    • 1
    • 2
  • Florian Jug
    • 1
    • 2
  • Gene Myers
    • 1
    • 2
  1. 1.Max Planck Institute of Molecular Cell Biology and GeneticsDresdenGermany
  2. 2.Center for Systems Biology DresdenDresdenGermany

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