Deep learning-based aberration compensation improves contrast and resolution in fluorescence microscopy.

Journal: Nature communications
PMID: 39747824

Abstract

Optical aberrations hinder fluorescence microscopy of thick samples, reducing image signal, contrast, and resolution. Here we introduce a deep learning-based strategy for aberration compensation, improving image quality without slowing image acquisition, applying additional dose, or introducing more optics. Our method (i) introduces synthetic aberrations to images acquired on the shallow side of image stacks, making them resemble those acquired deeper into the volume and (ii) trains neural networks to reverse the effect of these aberrations. We use simulations and experiments to show that applying the trained 'de-aberration' networks outperforms alternative methods, providing restoration on par with adaptive optics techniques; and subsequently apply the networks to diverse datasets captured with confocal, light-sheet, multi-photon, and super-resolution microscopy. In all cases, the improved quality of the restored data facilitates qualitative image inspection and improves downstream image quantitation, including orientational analysis of blood vessels in mouse tissue and improved membrane and nuclear segmentation in C. elegans embryos.

Authors

  • Min Guo
    Key Laboratory of Biology and Sustainable Management of Plant Diseases and Pests of Anhui Higher Education Institutes, Hefei, People's Republic of China.
  • Yicong Wu
    Laboratory of High Resolution Optical Imaging, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, MD, USA. yicong.wu@nih.gov.
  • Chad M Hobson
    Janelia Research Campus, Howard Hughes Medical Institute (HHMI), Ashburn, VA, USA.
  • Yijun Su
    Laboratory of High Resolution Optical Imaging, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, MD, USA.
  • Shuhao Qian
    State Key Laboratory of Extreme Photonics and Instrumentation, College of Optical Science and Engineering, Zhejiang University, Hangzhou, China.
  • Eric Krueger
    Laboratory of High Resolution Optical Imaging, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, Maryland, USA.
  • Ryan Christensen
    Laboratory of High Resolution Optical Imaging, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, MD, USA.
  • Grant Kroeschell
    Laboratory of High Resolution Optical Imaging, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, Maryland, USA.
  • Johnny Bui
    Laboratory of High Resolution Optical Imaging, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, Maryland, USA.
  • Matthew Chaw
    Laboratory of High Resolution Optical Imaging, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, Maryland, USA.
  • Lixia Zhang
    Research Center for Agricultural and Sideline Products Processing, Henan Academy of Agricultural Sciences, 116 Park Road, Zhengzhou 450002, PR China.
  • Jiamin Liu
  • Xuekai Hou
    State Key Laboratory of Extreme Photonics and Instrumentation, College of Optical Science and Engineering, Zhejiang University, Hangzhou, China.
  • Xiaofei Han
    Laboratory of High Resolution Optical Imaging, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, MD, USA.
  • Zhiye Lu
    Laboratory of Molecular Cardiology, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, USA.
  • Xuefei Ma
    Laboratory of Molecular Cardiology, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, USA.
  • Alexander Zhovmer
    Center for Biologics Evaluation and Research, U.S. Food and Drug Administration, Silver Spring, MD, USA.
  • Christian Combs
    NHLBI Light Microscopy Facility, National Institutes of Health, Bethesda, MD, USA.
  • Mark Moyle
    Department of Biology, Brigham Young University-Idaho, Rexburg, ID, USA.
  • Eviatar Yemini
    Department of Neurobiology, UMass Chan Medical School, Worcester, MA, USA.
  • Huafeng Liu
    State Key Laboratory of Modern Optical Instrumentation, Department of Optical Engineering, Zhejiang University, Hangzhou, China.
  • Zhiyi Liu
    Department of Biomedical Engineering, Tufts University, Medford, MA, 02155, USA.
  • Alexandre Benedetto
    Faculty of Health and Medicine, Division of Biomedical and Life Sciences, Lancaster University, Lancaster, UK.
  • Patrick La Riviere
    Department of Radiology, University of Chicago, Chicago, IL, USA.
  • Daniel Colón-Ramos
    Department of Neuroscience and Department of Cell Biology, Yale University School of Medicine, New Haven, CT, USA.
  • Hari Shroff
    Laboratory of High Resolution Optical Imaging, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, MD, USA.

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