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

Weigert, Martin; Schmidt, Uwe; Boothe, Tobias; Müller, Andreas; Dibrov, Alexandr; Jain, Akanksha; Wilhelm, Benjamin; Schmidt, Deborah; Broaddus, Coleman; Culley, Sian; Rocha-Martins, Mauricio; Segovia-Miranda, Fabián; Norden, Caren; Henriques, Ricardo; Zerial, Marino; Solimena, Michele; Rink, Jochen; Tomancak, Pavel; Royer, Loic; Jug, Florian; Myers, Eugene W

doi:10.1038/s41592-018-0216-7

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

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Weigert, Martin
Max Planck Institute for Molecular Cell Biology and Genetics, Max Planck Society;

/persons/resource/persons221539

Schmidt, Uwe
Max Planck Institute for Molecular Cell Biology and Genetics, Max Planck Society;

/persons/resource/persons220042

Boothe, Tobias
Max Planck Institute for Molecular Cell Biology and Genetics, Max Planck Society;

/persons/resource/persons219109

Dibrov, Alexandr
Max Planck Institute for Molecular Cell Biology and Genetics, Max Planck Society;

/persons/resource/persons219264

Jain, Akanksha
Max Planck Institute for Molecular Cell Biology and Genetics, Max Planck Society;

/persons/resource/persons219037

Broaddus, Coleman
Max Planck Institute for Molecular Cell Biology and Genetics, Max Planck Society;

/persons/resource/persons222005

Rocha-Martins, Mauricio
Max Planck Institute for Molecular Cell Biology and Genetics, Max Planck Society;

/persons/resource/persons222343

Segovia-Miranda, Fabián
Max Planck Institute for Molecular Cell Biology and Genetics, Max Planck Society;

/persons/resource/persons219494

Norden, Caren
Max Planck Institute for Molecular Cell Biology and Genetics, Max Planck Society;

/persons/resource/persons219807

Zerial, Marino
Max Planck Institute for Molecular Cell Biology and Genetics, Max Planck Society;

/persons/resource/persons219677

Solimena, Michele
Max Planck Institute for Molecular Cell Biology and Genetics, Max Planck Society;

/persons/resource/persons219585

Rink, Jochen
Max Planck Institute for Molecular Cell Biology and Genetics, Max Planck Society;

/persons/resource/persons219742

Tomancak, Pavel
Max Planck Institute for Molecular Cell Biology and Genetics, Max Planck Society;

/persons/resource/persons219593

Royer, Loic
Max Planck Institute for Molecular Cell Biology and Genetics, Max Planck Society;

/persons/resource/persons219280

Jug, Florian
Max Planck Institute for Molecular Cell Biology and Genetics, Max Planck Society;

/persons/resource/persons219475

Myers, Eugene W
Max Planck Institute for Molecular Cell Biology and Genetics, Max Planck Society;

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Citation

Weigert, M., Schmidt, U., Boothe, T., Müller, A., Dibrov, A., Jain, A., et al. (2018). Content-aware image restoration: pushing the limits of fluorescence microscopy. Nature methods, 15(12), 1090-1097. doi:10.1038/s41592-018-0216-7.

Cite as: https://hdl.handle.net/21.11116/0000-0003-F6BD-3

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.