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Field dependent deep learning enables high-throughput whole-cell 3D super-resolution imaging

Shuang Fu, Wei Shi, Tingdan Luo, Yingchuan He, Lulu Zhou, Jie Yang, Zhichao Yang, Jiadong Liu, Xiaotian Liu, Zhiyong Guo, Chengyu Yang, Chao Liu, Zhen-li Huang, Jonas Ries, Mingjie Zhang, Peng Xi, Dayong Jin, Yiming Li
doi: https://doi.org/10.1101/2022.10.14.512179
Shuang Fu
1Guangdong Provincial Key Laboratory of Advanced Biomaterials, Department of Biomedical Engineering, Southern University of Science and Technology, Shenzhen 518055, China
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Wei Shi
1Guangdong Provincial Key Laboratory of Advanced Biomaterials, Department of Biomedical Engineering, Southern University of Science and Technology, Shenzhen 518055, China
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Tingdan Luo
1Guangdong Provincial Key Laboratory of Advanced Biomaterials, Department of Biomedical Engineering, Southern University of Science and Technology, Shenzhen 518055, China
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Yingchuan He
1Guangdong Provincial Key Laboratory of Advanced Biomaterials, Department of Biomedical Engineering, Southern University of Science and Technology, Shenzhen 518055, China
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Lulu Zhou
1Guangdong Provincial Key Laboratory of Advanced Biomaterials, Department of Biomedical Engineering, Southern University of Science and Technology, Shenzhen 518055, China
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Jie Yang
1Guangdong Provincial Key Laboratory of Advanced Biomaterials, Department of Biomedical Engineering, Southern University of Science and Technology, Shenzhen 518055, China
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Zhichao Yang
1Guangdong Provincial Key Laboratory of Advanced Biomaterials, Department of Biomedical Engineering, Southern University of Science and Technology, Shenzhen 518055, China
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Jiadong Liu
2School of Life Sciences, Southern University of Science and Technology, Shenzhen 518055, China
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Xiaotian Liu
2School of Life Sciences, Southern University of Science and Technology, Shenzhen 518055, China
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Zhiyong Guo
1Guangdong Provincial Key Laboratory of Advanced Biomaterials, Department of Biomedical Engineering, Southern University of Science and Technology, Shenzhen 518055, China
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Chengyu Yang
1Guangdong Provincial Key Laboratory of Advanced Biomaterials, Department of Biomedical Engineering, Southern University of Science and Technology, Shenzhen 518055, China
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Chao Liu
1Guangdong Provincial Key Laboratory of Advanced Biomaterials, Department of Biomedical Engineering, Southern University of Science and Technology, Shenzhen 518055, China
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Zhen-li Huang
3Key Laboratory of Biomedical Engineering of Hainan Province, School of Biomedical Engineering, Hainan University, Haikou 570228, China
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Jonas Ries
4European Molecular Biology Laboratory, Cell Biology and Biophysics, Heidelberg 69117, Germany
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Mingjie Zhang
2School of Life Sciences, Southern University of Science and Technology, Shenzhen 518055, China
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Peng Xi
1Guangdong Provincial Key Laboratory of Advanced Biomaterials, Department of Biomedical Engineering, Southern University of Science and Technology, Shenzhen 518055, China
5Department of Biomedical Engineering, College of Future Technology, Peking University, Beijing 100871, China
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Dayong Jin
1Guangdong Provincial Key Laboratory of Advanced Biomaterials, Department of Biomedical Engineering, Southern University of Science and Technology, Shenzhen 518055, China
6Institute for Biomedical Materials and Devices (IBMD), Faculty of Science, University of Technology Sydney, NSW 2007, Australia
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Yiming Li
1Guangdong Provincial Key Laboratory of Advanced Biomaterials, Department of Biomedical Engineering, Southern University of Science and Technology, Shenzhen 518055, China
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  • For correspondence: liym2019@sustech.edu.cn
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Abstract

Single-molecule localization microscopy (SMLM) in a typical wide-field setup has been widely used for investigating sub-cellular structures with super resolution. However, field-dependent aberrations restrict the field of view (FOV) to only few tens of micrometers. Here, we present a deep learning method for precise localization of spatially variant point emitters (FD-DeepLoc) over a large FOV covering the full chip of a modern sCMOS camera. Using a graphic processing unit (GPU) based vectorial PSF fitter, we can fast and accurately model the spatially variant point spread function (PSF) of a high numerical aperture (NA) objective in the entire FOV. Combined with deformable mirror based optimal PSF engineering, we demonstrate high-accuracy 3D SMLM over a volume of ~180 × 180 × 5 μm3, allowing us to image mitochondria and nuclear pore complex in the entire cells in a single imaging cycle without hardware scanning - a 100-fold increase in throughput compared to the state-of-the-art.

Competing Interest Statement

The authors have declared no competing interest.

Footnotes

  • revise some typos and wrong descriptions, update the code demos, add a new supplementary movie

Copyright 
The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC-ND 4.0 International license.
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Posted November 15, 2022.
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Field dependent deep learning enables high-throughput whole-cell 3D super-resolution imaging
Shuang Fu, Wei Shi, Tingdan Luo, Yingchuan He, Lulu Zhou, Jie Yang, Zhichao Yang, Jiadong Liu, Xiaotian Liu, Zhiyong Guo, Chengyu Yang, Chao Liu, Zhen-li Huang, Jonas Ries, Mingjie Zhang, Peng Xi, Dayong Jin, Yiming Li
bioRxiv 2022.10.14.512179; doi: https://doi.org/10.1101/2022.10.14.512179
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Field dependent deep learning enables high-throughput whole-cell 3D super-resolution imaging
Shuang Fu, Wei Shi, Tingdan Luo, Yingchuan He, Lulu Zhou, Jie Yang, Zhichao Yang, Jiadong Liu, Xiaotian Liu, Zhiyong Guo, Chengyu Yang, Chao Liu, Zhen-li Huang, Jonas Ries, Mingjie Zhang, Peng Xi, Dayong Jin, Yiming Li
bioRxiv 2022.10.14.512179; doi: https://doi.org/10.1101/2022.10.14.512179

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