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Content-Aware Image Restoration: Pushing the Limits of Fluorescence Microscopy

View ORCID ProfileMartin Weigert, View ORCID ProfileUwe Schmidt, View ORCID ProfileTobias Boothe, View ORCID ProfileAndreas Müller, View ORCID ProfileAlexandr Dibrov, View ORCID ProfileAkanksha Jain, View ORCID ProfileBenjamin Wilhelm, View ORCID ProfileDeborah Schmidt, View ORCID ProfileColeman Broaddus, View ORCID ProfileSiân Culley, View ORCID ProfileMaurício Rocha-Martins, View ORCID ProfileFabián Segovia-Miranda, View ORCID ProfileCaren Norden, View ORCID ProfileRicardo Henriques, View ORCID ProfileMarino Zerial, View ORCID ProfileMichele Solimena, View ORCID ProfileJochen Rink, View ORCID ProfilePavel Tomancak, View ORCID ProfileLoic Royer, View ORCID ProfileFlorian Jug, View ORCID ProfileEugene W. Myers
doi: https://doi.org/10.1101/236463
Martin Weigert
Center for Systems Biology Dresden (CSBD);
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Uwe Schmidt
Center for Systems Biology Dresden (CSBD);
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Tobias Boothe
Max-Planck Institute of Molecular Cell Biology and Genetics;
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Andreas Müller
University Hospital and Faculty of Medicine Carl Gustav Carus, TU Dresden;
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Alexandr Dibrov
Center for Systems Biology Dresden (CSBD);
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Akanksha Jain
Max-Planck Institute of Molecular Cell Biology and Genetics;
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Benjamin Wilhelm
Center for Systems Biology Dresden (CSBD);
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Deborah Schmidt
Center for Systems Biology Dresden (CSBD);
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Coleman Broaddus
Center for Systems Biology Dresden (CSBD);
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Siân Culley
University College London;
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Maurício Rocha-Martins
Center for Systems Biology Dresden (CSBD);
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Fabián Segovia-Miranda
Max-Planck Institute of Molecular Cell Biology and Genetics;
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Caren Norden
Max-Planck Institute of Molecular Cell Biology and Genetics;
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Ricardo Henriques
University College London;
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Marino Zerial
Max-Planck Institute of Molecular Cell Biology and Genetics;
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Michele Solimena
Faculty of Medicine, TU Dresden;
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Jochen Rink
Max-Planck Institute of Molecular Cell Biology and Genetics;
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Pavel Tomancak
Max-Planck Institute of Molecular Cell Biology and Genetics;
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Loic Royer
CZ Biohub
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Florian Jug
Center for Systems Biology Dresden (CSBD);
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  • For correspondence: jug@mpi-cbg.de
Eugene W. Myers
Center for Systems Biology Dresden (CSBD);
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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 image restoration based on deep learning extends the range of biological phenomena observable by microscopy. On seven concrete examples we demonstrate 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 10-fold 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.

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The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC-ND 4.0 International license.
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Posted July 03, 2018.
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Content-Aware Image Restoration: Pushing the Limits of Fluorescence Microscopy
Martin Weigert, Uwe Schmidt, Tobias Boothe, Andreas Müller, Alexandr Dibrov, Akanksha Jain, Benjamin Wilhelm, Deborah Schmidt, Coleman Broaddus, Siân Culley, Maurício Rocha-Martins, Fabián Segovia-Miranda, Caren Norden, Ricardo Henriques, Marino Zerial, Michele Solimena, Jochen Rink, Pavel Tomancak, Loic Royer, Florian Jug, Eugene W. Myers
bioRxiv 236463; doi: https://doi.org/10.1101/236463
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Content-Aware Image Restoration: Pushing the Limits of Fluorescence Microscopy
Martin Weigert, Uwe Schmidt, Tobias Boothe, Andreas Müller, Alexandr Dibrov, Akanksha Jain, Benjamin Wilhelm, Deborah Schmidt, Coleman Broaddus, Siân Culley, Maurício Rocha-Martins, Fabián Segovia-Miranda, Caren Norden, Ricardo Henriques, Marino Zerial, Michele Solimena, Jochen Rink, Pavel Tomancak, Loic Royer, Florian Jug, Eugene W. Myers
bioRxiv 236463; doi: https://doi.org/10.1101/236463

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