We present deep-learning-enabled super-resolution across different fluorescence microscopy modalities. This data-driven approach does not require numerical modeling of the imaging process or the estimation of a point-spread-function, and is based on training a generative adversarial network (GAN) to transform diffraction-limited input images into super-resolved ones. Using this framework, we improve the resolution of wide-field images acquired with low-numerical-aperture objectives, matching the resolution that is acquired using high-numerical-aperture objectives. We also demonstrate cross-modality super-resolution, transforming confocal microscopy images to match the resolution acquired with a stimulated emission depletion (STED) microscope. We further demonstrate that total internal reflection fluorescence (TIRF) microscopy images of subcellular structures within cells and tissues can be transformed to match the results obtained with a TIRF-based structured illumination microscope. The deep network rapidly outputs these super-resolved images, without any iterations or parameter search, and could serve to democratize super-resolution imaging.
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We declare that all the data supporting the findings of this work are available within the manuscript and Supplementary Information files. Raw images can be requested from the corresponding author. Deep learning models reported in this work used standard libraries and scripts that are publicly available in TensorFlow. The instruction manual for our Fiji/ImageJ plugin and trained models (available online as Supplementary Software 1–7) is provided as a Supplementary Protocol.
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The Ozcan Research Group at UCLA acknowledges the support of NSF Engineering Research Center (ERC, PATHS-UP), the Army Research Office (ARO; W911NF-13-1-0419 and W911NF-13-1-0197), the ARO Life Sciences Division, the National Science Foundation (NSF) CBET Division Biophotonics Program, the NSF Emerging Frontiers in Research and Innovation (EFRI) Award, the NSF INSPIRE Award, NSF Partnerships for Innovation: Building Innovation Capacity (PFI:BIC) Program, the National Institutes of Health (NIH, R21EB023115), the Howard Hughes Medical Institute (HHMI), Vodafone Americas Foundation, the Mary Kay Foundation, and Steven & Alexandra Cohen Foundation. Yair Rivenson is partially supported by the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie grant agreement No H2020-MSCA-IF-2014-659595 (MCMQCT). Confocal and STED laser scanning microscopy was performed at the California NanoSystems Institute (CNSI) Advanced Light Microscopy/Spectroscopy Shared Resource Facility at UCLA. We also thank the Advanced Imaging Center (AIC) at Janelia Research Campus for access to their TIRF-SIM microscope. The AIC is jointly supported by the Howard Hughes Medical Institute and the Gordon and Betty Moore Foundation. Finally, we thank H. Chang (Purdue University, West Lafayette, IN, USA) for sharing the CLC-mEmerald fly strain.
A.O., Y.R., and H.W. have a pending patent application on the contents of the presented results.
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Supplementary Notes 1–10, Supplementary Figures 1–14 and Supplementary Table 1
SISR-Fluorescent Fiji/ImageJ plugin: User Manual
Deep-learning enabled cross-modality image transformation from TIRF to TIRF-SIM. A video of deep-learning-enabled cross-modality image transformation from TIRF to TIRF-SIM, corresponding to a gene-edited SUM159 cell expressing AP2-eGFP, revealing the temporal dynamics of endocytic protein structures within the cell. The highlighted frames in this video correspond to subpanels of Fig. 6 (main text). Experiments were repeated with >1,000 images/frames, achieving similar results.
SISR-Fluorescent Fiji/ImageJ plugin
Pre-trained model: wide-field DAPI
Pre-trained model: wide-field FITC
Pre-trained model: wide-field TxRed
Pre-trained model: confocal STED (nanobeads)
Pre-trained model: confocal STED (nuclei)
Pre-trained model: TIRF-SIM
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Wang, H., Rivenson, Y., Jin, Y. et al. Deep learning enables cross-modality super-resolution in fluorescence microscopy. Nat Methods 16, 103–110 (2019). https://doi.org/10.1038/s41592-018-0239-0
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