Journals Articles Conferences News About CLP
Submit a paper Email Alert
Search
Search
Articles
Journals
News
Advanced Search
Top Searches
2D MaterialsTransformation opticsQuantum PhotonicsSmall lasersSemiconductor UV PhotonicsSupersymmetric microring laser arrays

Photonics Research, Volume. 11, Issue 1, 1(2023)

Self-supervised deep-learning two-photon microscopy

Yuezhi He1,2, Jing Yao1,2, Lina Liu1,2, Yufeng Gao1,2, Jia Yu1,2, Shiwei Ye1,2, Hui Li1,2, and Wei Zheng1,2、*
Author Affiliations
  • 1Research Center for Biomedical Optics and Molecular Imaging, Shenzhen Key Laboratory for Molecular Imaging, Guangdong Provincial Key Laboratory of Biomedical Optical Imaging Technology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
  • 2CAS Key Laboratory of Health Informatics, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
    • show less
    Full TextGet PDF
    Figures&Tables (10)
    Equations (8)
    Suppl.&Mat.
    References (30)
    Cited By (12)
    Tools
    Paper Information
    Topics
    References(30)

    [1] W. Denk, J. H. Strickler, W. W. Webb. Two-photon laser scanning fluorescence microscopy. Science, 248, 73-76(1990).

    [2] J. Wu, N. Ji, K. K. Tsia. Speed scaling in multiphoton fluorescence microscopy. Nat. Photonics, 15, 800-812(2021).

    [3] M. Weigert, U. Schmidt, T. Boothe, A. Müller, A. Dibrov, A. Jain, B. Wilhelm, D. Schmidt, C. Broaddus, S. Culley, M. Rocha-Martins, F. Segovia-Miranda, C. Norden, R. Henriques, M. Zerial, M. Solimena, J. Rink, P. Tomancak, L. Royer, F. Jug, E. W. Myers. Content-aware image restoration: pushing the limits of fluorescence microscopy. Nat. Methods, 15, 1090-1097(2018).

    [4] T. Zhang, O. Hernandez, R. Chrapkiewicz, A. Shai, M. J. Wagner, Y. Zhang, C. H. Wu, J. Z. Li, M. Inoue, Y. Gong, B. Ahanonu, H. Zeng, H. Bito, M. J. Schnitzer. Kilohertz two-photon brain imaging in awake mice. Nat. Methods, 16, 1119-1122(2019).

    [5] E. Papagiakoumou, E. Ronzitti, V. Emiliani. Scanless two-photon excitation with temporal focusing. Nat. Methods, 17, 571-581(2020).

    [6] D. R. Beaulieu, I. G. Davison, K. Kılıç, T. G. Bifano, J. Mertz. Simultaneous multiplane imaging with reverberation two-photon microscopy. Nat. Methods, 17, 283-286(2020).

    [7] Y. Lecun, Y. Bengio, G. Hinton. Deep learning. Nature, 521, 436-444(2015).

    [8] H. Wang, Y. Rivenson, Y. Jin, Z. Wei, R. Gao, H. Günaydın, L. A. Bentolila, C. Kural, A. Ozcan. Deep learning enables cross-modality super-resolution in fluorescence microscopy. Nat. Methods, 16, 103-110(2019).

    [9] J. Chen, H. Sasaki, H. Lai, Y. Su, J. Liu, Y. Wu, A. Zhovmer, C. A. Combs, I. Rey-Suarez, H. Y. Chang, C. C. Huang, X. Li, M. Guo, S. Nizambad, A. Upadhyaya, S. J. J. Lee, L. A. G. Lucas, H. Shroff. Three-dimensional residual channel attention networks denoise and sharpen fluorescence microscopy image volumes. Nat. Methods, 18, 678-687(2021).

    [10] S. McAleer, A. Fast, Y. Xue, M. J. Seiler, W. C. Tang, M. Balu, P. Baldi, A. W. Browne. Deep learning-assisted multiphoton microscopy to reduce light exposure and expedite imaging in tissues with high and low light sensitivity. Transl. Vis. Sci. Technol., 10, 30(2021).

    [11] W. Ouyang, A. Aristov, M. Lelek, X. Hao, C. Zimmer. Deep learning massively accelerates super-resolution localization microscopy. Nat. Biotechnol., 36, 460-468(2018).

    [12] S. Kumar Gaire, Y. Zhang, H. Li, R. Yu, H. F. Zhang, L. Ying. Accelerating multicolor spectroscopic single-molecule localization microscopy using deep learning. Biomed. Opt. Express, 11, 2705-2721(2020).

    [13] Y. Wu, Y. Rivenson, H. Wang, Y. Luo, E. Ben-David, L. A. Bentolila, C. Pritz, A. Ozcan. Three-dimensional virtual refocusing of fluorescence microscopy images using deep learning. Nat. Methods, 16, 1323-1331(2019).

    [14] J. T. Smith, R. Yao, N. Sinsuebphon, A. Rudkouskaya, N. Un, J. Mazurkiewicz, M. Barroso, P. Yan, X. Intes. Fast fit-free analysis of fluorescence lifetime imaging via deep learning. Proc. Natl. Acad. Sci. USA, 116, 24019-24030(2019).

    [15] R. Yao, M. Ochoa, P. Yan, X. Intes. Net-FLICS: fast quantitative wide-field fluorescence lifetime imaging with compressed sensing: a deep learning approach. Light Sci. Appl., 8, 26(2019).

    [16] Y. Rivenson, H. Wang, Z. Wei, K. de Haan, Y. Zhang, Y. Wu, H. Günaydın, J. E. Zuckerman, T. Chong, A. E. Sisk, L. M. Westbrook, W. D. Wallace, A. Ozcan. Virtual histological staining of unlabelled tissue-autofluorescence images via deep learning. Nat. Biomed. Eng., 3, 466-477(2019).

    [17] X. Li, G. Zhang, H. Qiao, F. Bao, Y. Deng, J. Wu, Y. He, J. Yun, X. Lin, H. Xie, H. Wang, Q. Dai. Unsupervised content-preserving transformation for optical microscopy. Light Sci. Appl., 10, 44(2021).

    [18] L. Huang, H. Chen, Y. Luo, Y. Rivenson, A. Ozcan. Recurrent neural network-based volumetric fluorescence microscopy. Light Sci. Appl., 10, 62(2021).

    [19] L. Jin, Y. Tang, Y. Wu, J. B. Coole, M. T. Tan, X. Zhao, H. Badaoui, J. T. Robinson, M. D. Williams, A. M. Gillenwater, R. R. Richards-Kortum, A. Veeraraghavan. Deep learning extended depth-of-field microscope for fast and slide-free histology. Proc. Natl. Acad. Sci. USA, 117, 33051-33060(2020).

    [20] Y. Rivenson, Z. Göröcs, H. Günaydin, Y. Zhang, H. Wang, A. Ozcan. Deep learning microscopy. Optica, 4, 1437-1443(2017).

    [21] C. Dong, C. C. Loy, X. Tang. Accelerating the super-resolution convolutional neural network. European Conference on Computer Vision, 391-407(2016).

    [22] L. Jin, B. Liu, F. Zhao, S. Hahn, B. Dong, R. Song, T. C. Elston, Y. Xu, K. M. Hahn. Deep learning enables structured illumination microscopy with low light levels and enhanced speed. Nat. Commun., 11, 1934(2020).

    [23] H. Zhang, Y. Zhao, C. Fang, G. Li, M. Zhang, Y.-H. Zhang, P. Fei. Exceeding the limits of 3D fluorescence microscopy using a dual-stage-processing network. Optica, 7, 1627-1640(2020).

    [24] L. Fang, F. Monroe, S. W. Novak, L. Kirk, C. R. Schiavon, S. B. Yu, T. Zhang, M. Wu, K. Kastner, A. A. Latif, Z. Lin, A. Shaw, Y. Kubota, J. Mendenhall, Z. Zhang, G. Pekkurnaz, K. Harris, J. Howard, U. Manor. Deep learning-based point-scanning super-resolution imaging. Nat. Methods, 18, 406-416(2021).

    [25] M. Zontak, M. Irani. Internal statistics of a single natural image. Proceedings of the IEEE Computer Society Conference on Computer Vision and Pattern Recognition, 977-984(2011).

    [26] A. Shocher, N. Cohen, M. Irani. Zero-shot super-resolution using deep internal learning. Proceedings of the IEEE Computer Society Conference on Computer Vision and Pattern Recognition, 3118-3126(2018).

    [27] X. Li, G. Zhang, J. Wu, Y. Zhang, Z. Zhao, X. Lin, H. Qiao, H. Xie, H. Wang, L. Fang, Q. Dai. Reinforcing neuron extraction and spike inference in calcium imaging using deep self-supervised denoising. Nat. Methods, 18, 1395-1400(2021).

    [28] Y. He, J. Yao, L. Liu, Y. Gao, J. Yu, S. Ye, H. Li, W. Zheng. Self-supervised deep-learning two-photon microscopy: supplemental document.

    [29] C. Qiao, D. Li, Y. Guo, C. Liu, T. Jiang, Q. Dai, D. Li. Evaluation and development of deep neural networks for image super-resolution in optical microscopy. Nat. Methods, 18, 194-202(2021).

    [30] J. Yao, Y. Gao, Y. Yin, P. Lai, S. Ye, W. Zheng. Exploiting the potential of commercial objectives to extend the field of view of two-photon microscopy by adaptive optics. Opt. Lett., 47, 989-992(2022).

    Tools

    Get Citation

    Copy Citation Text

    Yuezhi He, Jing Yao, Lina Liu, Yufeng Gao, Jia Yu, Shiwei Ye, Hui Li, Wei Zheng, "Self-supervised deep-learning two-photon microscopy," Photonics Res. 11, 1 (2023)

    Download Citation

    EndNote(RIS)BibTexPlain Text
    Set citation alerts for article
    Save article for my favorites
    Paper Information

    Category: Imaging Systems, Microscopy, and Displays

    Received: Jun. 29, 2022

    Accepted: Oct. 20, 2022

    Published Online: Dec. 15, 2022

    The Author Email: Wei Zheng (zhengwei@siat.ac.cn)

    DOI:10.1364/PRJ.469231

    Topics

    laser devices and laser physics
    Lasers and Laser Optics
    Laser physics
    laser manufacturing
    Instrumentation, Measurement and Metrology