Content-aware image restoration: pushing the limits of fluorescence microscopy

Research output: Contribution to journalResearch articleContributedpeer-review

Contributors

  • Martin Weigert - , Center for Systems Biology Dresden (CSBD), Max Planck Institute of Molecular Cell Biology and Genetics (Author)
  • Uwe Schmidt - , Center for Systems Biology Dresden (CSBD), Max Planck Institute of Molecular Cell Biology and Genetics (Author)
  • Tobias Boothe - , Center for Systems Biology Dresden (CSBD), Max Planck Institute of Molecular Cell Biology and Genetics (Author)
  • Andreas Müller - , Molecular Diabetology, Medical Faculty Carl Gustav Carus, German Center for Diabetes Research (DZD e.V.) (Author)
  • Alexandr Dibrov - , Center for Systems Biology Dresden (CSBD), Max Planck Institute of Molecular Cell Biology and Genetics (Author)
  • Akanksha Jain - , Max Planck Institute of Molecular Cell Biology and Genetics (Author)
  • Benjamin Wilhelm - , Center for Systems Biology Dresden (CSBD), University of Konstanz (Author)
  • Deborah Schmidt - , Center for Systems Biology Dresden (CSBD) (Author)
  • Coleman Broaddus - , Center for Systems Biology Dresden (CSBD), Max Planck Institute of Molecular Cell Biology and Genetics (Author)
  • Siân Culley - , University College London, The Francis Crick Institute (Author)
  • Mauricio Rocha-Martins - , Center for Systems Biology Dresden (CSBD), Max Planck Institute of Molecular Cell Biology and Genetics (Author)
  • Fabián Segovia-Miranda - , Max Planck Institute of Molecular Cell Biology and Genetics (Author)
  • Caren Norden - , Max Planck Institute of Molecular Cell Biology and Genetics (Author)
  • Ricardo Henriques - , University College London, The Francis Crick Institute (Author)
  • Marino Zerial - , Max Planck Institute of Molecular Cell Biology and Genetics (Author)
  • Michele Solimena - , Molecular Diabetology, Max Planck Institute of Molecular Cell Biology and Genetics, Medical Faculty Carl Gustav Carus, German Center for Diabetes Research (DZD e.V.) (Author)
  • Jochen Rink - , Max Planck Institute of Molecular Cell Biology and Genetics (Author)
  • Pavel Tomancak - , Max Planck Institute of Molecular Cell Biology and Genetics (Author)
  • Loic Royer - , Center for Systems Biology Dresden (CSBD), Max Planck Institute of Molecular Cell Biology and Genetics, CZ Biohub (Author)
  • Florian Jug - , Center for Systems Biology Dresden (CSBD), Max Planck Institute of Molecular Cell Biology and Genetics (Author)
  • Eugene W. Myers - , Center for Systems Biology Dresden (CSBD), Max Planck Institute of Molecular Cell Biology and Genetics, TUD Dresden University of Technology (Author)

Abstract

Fluorescence microscopy is a key driver of discoveries in the life sciences, with observable phenomena being limited by the optics of the microscope, the chemistry of the fluorophores, and the maximum photon exposure tolerated by the sample. These limits necessitate trade-offs between imaging speed, spatial resolution, light exposure, and imaging depth. In this work we show how content-aware image restoration based on deep learning extends the range of biological phenomena observable by microscopy. We demonstrate on eight concrete examples how microscopy images can be restored even if 60-fold fewer photons are used during acquisition, how near isotropic resolution can be achieved with up to tenfold under-sampling along the axial direction, and how tubular and granular structures smaller than the diffraction limit can be resolved at 20-times-higher frame rates compared to state-of-the-art methods. All developed image restoration methods are freely available as open source software in Python, FIJI, and KNIME.

Details

Original languageEnglish
Pages (from-to)1090-1097
Number of pages8
JournalNature methods
Volume15
Issue number12
Publication statusPublished - 1 Dec 2018
Peer-reviewedYes

External IDs

PubMed 30478326