Alternative deep learning method for fast spatial-frequency shift imaging microscopy
Spatial-frequency shift (SFS) imaging microscopy can break the diffraction limit of fluorescently labeled and label-free samples by transferring the high spatial-frequency information into the passband of microscope. However, the resolution improvement is at the cost of decreasing temporal resolutio...
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| Published in | Optics express Vol. 31; no. 3; p. 3719 |
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| Main Authors | , , , , , , , |
| Format | Journal Article |
| Language | English |
| Published |
United States
30.01.2023
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| Online Access | Get full text |
| ISSN | 1094-4087 1094-4087 |
| DOI | 10.1364/OE.482062 |
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| Abstract | Spatial-frequency shift (SFS) imaging microscopy can break the diffraction limit of fluorescently labeled and label-free samples by transferring the high spatial-frequency information into the passband of microscope. However, the resolution improvement is at the cost of decreasing temporal resolution since dozens of raw SFS images are needed to expand the frequency spectrum. Although some deep learning methods have been proposed to solve this problem, no neural network that is compatible to both labeled and label-free SFS imaging has been proposed. Here, we propose the joint spatial-Fourier channel attention network (JSFCAN), which learns the general connection between the spatial domain and Fourier frequency domain from complex samples. We demonstrate that JSFCAN can achieve a resolution similar to the traditional algorithm using nearly 1/4 raw images and increase the reconstruction speed by two orders of magnitude. Subsequently, we prove that JSFCAN can be applied to both fluorescently labeled and label-free samples without architecture changes. We also demonstrate that compared with the typical spatial domain optimization network U-net, JSFCAN is more robust to deal with deep-SFS images and noisy images. The proposed JSFCAN provides an alternative route for fast SFS imaging reconstruction, enabling future applications for real-time living cell research. |
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| AbstractList | Spatial-frequency shift (SFS) imaging microscopy can break the diffraction limit of fluorescently labeled and label-free samples by transferring the high spatial-frequency information into the passband of microscope. However, the resolution improvement is at the cost of decreasing temporal resolution since dozens of raw SFS images are needed to expand the frequency spectrum. Although some deep learning methods have been proposed to solve this problem, no neural network that is compatible to both labeled and label-free SFS imaging has been proposed. Here, we propose the joint spatial-Fourier channel attention network (JSFCAN), which learns the general connection between the spatial domain and Fourier frequency domain from complex samples. We demonstrate that JSFCAN can achieve a resolution similar to the traditional algorithm using nearly 1/4 raw images and increase the reconstruction speed by two orders of magnitude. Subsequently, we prove that JSFCAN can be applied to both fluorescently labeled and label-free samples without architecture changes. We also demonstrate that compared with the typical spatial domain optimization network U-net, JSFCAN is more robust to deal with deep-SFS images and noisy images. The proposed JSFCAN provides an alternative route for fast SFS imaging reconstruction, enabling future applications for real-time living cell research. Spatial-frequency shift (SFS) imaging microscopy can break the diffraction limit of fluorescently labeled and label-free samples by transferring the high spatial-frequency information into the passband of microscope. However, the resolution improvement is at the cost of decreasing temporal resolution since dozens of raw SFS images are needed to expand the frequency spectrum. Although some deep learning methods have been proposed to solve this problem, no neural network that is compatible to both labeled and label-free SFS imaging has been proposed. Here, we propose the joint spatial-Fourier channel attention network (JSFCAN), which learns the general connection between the spatial domain and Fourier frequency domain from complex samples. We demonstrate that JSFCAN can achieve a resolution similar to the traditional algorithm using nearly 1/4 raw images and increase the reconstruction speed by two orders of magnitude. Subsequently, we prove that JSFCAN can be applied to both fluorescently labeled and label-free samples without architecture changes. We also demonstrate that compared with the typical spatial domain optimization network U-net, JSFCAN is more robust to deal with deep-SFS images and noisy images. The proposed JSFCAN provides an alternative route for fast SFS imaging reconstruction, enabling future applications for real-time living cell research.Spatial-frequency shift (SFS) imaging microscopy can break the diffraction limit of fluorescently labeled and label-free samples by transferring the high spatial-frequency information into the passband of microscope. However, the resolution improvement is at the cost of decreasing temporal resolution since dozens of raw SFS images are needed to expand the frequency spectrum. Although some deep learning methods have been proposed to solve this problem, no neural network that is compatible to both labeled and label-free SFS imaging has been proposed. Here, we propose the joint spatial-Fourier channel attention network (JSFCAN), which learns the general connection between the spatial domain and Fourier frequency domain from complex samples. We demonstrate that JSFCAN can achieve a resolution similar to the traditional algorithm using nearly 1/4 raw images and increase the reconstruction speed by two orders of magnitude. Subsequently, we prove that JSFCAN can be applied to both fluorescently labeled and label-free samples without architecture changes. We also demonstrate that compared with the typical spatial domain optimization network U-net, JSFCAN is more robust to deal with deep-SFS images and noisy images. The proposed JSFCAN provides an alternative route for fast SFS imaging reconstruction, enabling future applications for real-time living cell research. |
| Author | Lin, Muchun Han, Yubing Liu, Xu Liang, Chenhui Zhang, Qianwei Yang, Xiaoyu Yang, Qing Tang, Mingwei |
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| BackLink | https://www.ncbi.nlm.nih.gov/pubmed/36785358$$D View this record in MEDLINE/PubMed |
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| References | Shah (oe-31-3-3719-R8) 2021; 9 Cao (oe-31-3-3719-R26) 2018; 9 Gustafsson (oe-31-3-3719-R1) 2000; 198 Tang (oe-31-3-3719-R5) 2022; 9 Qiao (oe-31-3-3719-R22) 2021; 18 Christensen (oe-31-3-3719-R17) 2021; 12 oe-31-3-3719-R15 Gerchberg (oe-31-3-3719-R25) 1972; 35 Zheng (oe-31-3-3719-R3) 2013; 7 Ling (oe-31-3-3719-R11) 2020; 8 Tian (oe-31-3-3719-R4) 2014; 5 Liu (oe-31-3-3719-R7) 2021; 64 Nehme (oe-31-3-3719-R16) 2018; 5 Ouyang (oe-31-3-3719-R12) 2018; 36 Rego (oe-31-3-3719-R2) 2012; 109 Nguyen (oe-31-3-3719-R14) 2018; 26 Lim (oe-31-3-3719-R18) 2020; 2 Tang (oe-31-3-3719-R6) 2020 Yang (oe-31-3-3719-R24) 2018; 37 Cheng (oe-31-3-3719-R13) 2019; 27 Jin (oe-31-3-3719-R10) 2020; 11 Wang (oe-31-3-3719-R19) 2019; 16 Zhang (oe-31-3-3719-R20) 2021; 7 |
| References_xml | – year: 2020 ident: oe-31-3-3719-R6 – volume: 8 start-page: 1350 year: 2020 ident: oe-31-3-3719-R11 publication-title: Photonics Res. doi: 10.1364/PRJ.396122 – volume: 26 start-page: 26470 year: 2018 ident: oe-31-3-3719-R14 publication-title: Opt. Express doi: 10.1364/OE.26.026470 – volume: 27 start-page: 644 year: 2019 ident: oe-31-3-3719-R13 publication-title: Opt. Express doi: 10.1364/OE.27.000644 – volume: 5 start-page: 2376 year: 2014 ident: oe-31-3-3719-R4 publication-title: Biomed. Opt. Express doi: 10.1364/BOE.5.002376 – volume: 11 start-page: 1934 year: 2020 ident: oe-31-3-3719-R10 publication-title: Nat. Commun. doi: 10.1038/s41467-020-15784-x – volume: 64 start-page: 294211 year: 2021 ident: oe-31-3-3719-R7 publication-title: Sci. China-Phys. Mech. Astron. doi: 10.1007/s11433-020-1682-1 – volume: 12 start-page: 2720 year: 2021 ident: oe-31-3-3719-R17 publication-title: Biomed. Opt. Express doi: 10.1364/BOE.414680 – volume: 7 start-page: 739 year: 2013 ident: oe-31-3-3719-R3 publication-title: Nat. Photonics doi: 10.1038/nphoton.2013.187 – volume: 37 start-page: 1310 year: 2018 ident: oe-31-3-3719-R24 publication-title: IEEE Trans. Med. Imaging doi: 10.1109/TMI.2017.2785879 – volume: 7 start-page: 1 year: 2021 ident: oe-31-3-3719-R20 publication-title: IEEE Trans. Comput. Imaging doi: 10.1109/TCI.2020.3046472 – volume: 36 start-page: 460 year: 2018 ident: oe-31-3-3719-R12 publication-title: Nat. Biotechnol. doi: 10.1038/nbt.4106 – volume: 2 start-page: 1 year: 2020 ident: oe-31-3-3719-R18 publication-title: Adv. Photonics doi: 10.1117/1.AP.2.2.026001 – ident: oe-31-3-3719-R15 – volume: 18 start-page: 194 year: 2021 ident: oe-31-3-3719-R22 publication-title: Nat. Methods doi: 10.1038/s41592-020-01048-5 – volume: 35 start-page: 237 year: 1972 ident: oe-31-3-3719-R25 publication-title: Optik – volume: 198 start-page: 82 year: 2000 ident: oe-31-3-3719-R1 publication-title: J. Microsc. doi: 10.1046/j.1365-2818.2000.00710.x – volume: 9 start-page: 2103835 year: 2022 ident: oe-31-3-3719-R5 publication-title: Adv. Sci. doi: 10.1002/advs.202103835 – volume: 9 start-page: 5037 year: 2018 ident: oe-31-3-3719-R26 publication-title: Biomed. Opt. Express doi: 10.1364/BOE.9.005037 – volume: 9 start-page: B168 year: 2021 ident: oe-31-3-3719-R8 publication-title: Photonics Res. doi: 10.1364/PRJ.416437 – volume: 5 start-page: 458 year: 2018 ident: oe-31-3-3719-R16 publication-title: Optica doi: 10.1364/OPTICA.5.000458 – volume: 109 start-page: E135 year: 2012 ident: oe-31-3-3719-R2 publication-title: Proc. Natl. Acad. Sci. U. S. A. doi: 10.1073/pnas.1107547108 – volume: 16 start-page: 103 year: 2019 ident: oe-31-3-3719-R19 publication-title: Nat. Methods doi: 10.1038/s41592-018-0239-0 |
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