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Kramer SN, Antarasen J, Reinholt CR, Kisley L. A practical guide to light-sheet microscopy for nanoscale imaging: Looking beyond the cell. JOURNAL OF APPLIED PHYSICS 2024; 136:091101. [PMID: 39247785 PMCID: PMC11380115 DOI: 10.1063/5.0218262] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/09/2024] [Accepted: 08/12/2024] [Indexed: 09/10/2024]
Abstract
We present a comprehensive guide to light-sheet microscopy (LSM) to assist scientists in navigating the practical implementation of this microscopy technique. Emphasizing the applicability of LSM to image both static microscale and nanoscale features, as well as diffusion dynamics, we present the fundamental concepts of microscopy, progressing through beam profile considerations, to image reconstruction. We outline key practical decisions in constructing a home-built system and provide insight into the alignment and calibration processes. We briefly discuss the conditions necessary for constructing a continuous 3D image and introduce our home-built code for data analysis. By providing this guide, we aim to alleviate the challenges associated with designing and constructing LSM systems and offer scientists new to LSM a valuable resource in navigating this complex field.
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Affiliation(s)
- Stephanie N Kramer
- Department of Physics, Case Western Reserve University, Rockefeller Building, 2076 Adelbert Road, Cleveland, Ohio 44106, USA
| | - Jeanpun Antarasen
- Department of Physics, Case Western Reserve University, Rockefeller Building, 2076 Adelbert Road, Cleveland, Ohio 44106, USA
| | - Cole R Reinholt
- Department of Physics, Case Western Reserve University, Rockefeller Building, 2076 Adelbert Road, Cleveland, Ohio 44106, USA
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2
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Bishop KW, Erion Barner LA, Baraznenok E, Lan L, Poudel C, Brenes D, Serafin RB, True LD, Vaughan JC, Glaser AK, Liu JTC. Axially swept open-top light-sheet microscopy for densely labeled clinical specimens. OPTICS LETTERS 2024; 49:3794-3797. [PMID: 38950270 DOI: 10.1364/ol.521591] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/15/2024] [Accepted: 05/17/2024] [Indexed: 07/03/2024]
Abstract
Open-top light-sheet (OTLS) microscopy offers rapid 3D imaging of large optically cleared specimens. This enables nondestructive 3D pathology, which provides key advantages over conventional slide-based histology including comprehensive sampling without tissue sectioning/destruction and visualization of diagnostically important 3D structures. With 3D pathology, clinical specimens are often labeled with small-molecule stains that broadly target nucleic acids and proteins, mimicking conventional hematoxylin and eosin (H&E) dyes. Tight optical sectioning helps to minimize out-of-focus fluorescence for high-contrast imaging in these densely labeled tissues but has been challenging to achieve in OTLS systems due to trade-offs between optical sectioning and field of view. Here we present an OTLS microscope with voice-coil-based axial sweeping to circumvent this trade-off, achieving 2 µm axial resolution over a 750 × 375 µm field of view. We implement our design in a non-orthogonal dual-objective (NODO) architecture, which enables a 10-mm working distance with minimal sensitivity to refractive index mismatches, for high-contrast 3D imaging of clinical specimens.
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3
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Wang J, Xu X, Ye H, Zhang X, Shi G. Interferometric modulation for generating extended light sheet: improving field of view. JOURNAL OF BIOMEDICAL OPTICS 2024; 29:046501. [PMID: 38629030 PMCID: PMC11020319 DOI: 10.1117/1.jbo.29.4.046501] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/23/2024] [Revised: 03/20/2024] [Accepted: 03/27/2024] [Indexed: 04/19/2024]
Abstract
Significance Light-sheet fluorescence microscopy (LSFM) has emerged as a powerful and versatile imaging technique renowned for its remarkable features, including high-speed 3D tomography, minimal photobleaching, and low phototoxicity. The interference light-sheet fluorescence microscope, with its larger field of view (FOV) and more uniform axial resolution, possesses significant potential for a wide range of applications in biology and medicine. Aim The aim of this study is to investigate the interference behavior among multiple light sheets (LSs) in LSFM and optimize the FOV and resolution of the light-sheet fluorescence microscope. Approach We conducted a detailed investigation of the interference effects among LSs through theoretical derivation and numerical simulations, aiming to find optimal parameters. Subsequently, we constructed a customized system of multi-LSFM that incorporates both interference light sheets (ILS) and noninterference light-sheet configurations. We performed beam imaging and microsphere imaging tests to evaluate the FOV and axial resolution of these systems. Results Using our custom-designed light-sheet fluorescence microscope, we captured the intensity distribution profiles of both interference and noninterference light sheets (NILS). Additionally, we conducted imaging tests on microspheres to assess their imaging outcomes. The ILS not only exhibits a larger FOV compared to the NILS but also demonstrates a more uniform axial resolution. Conclusions By effectively modulating the interference among multiple LSs, it is possible to optimize the intensity distribution of the LSs, expand the FOV, and achieve a more uniform axial resolution.
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Affiliation(s)
- Jixiang Wang
- University of Science and Technology of China, School of Biomedical Engineering (Suzhou), Division of Life Sciences and Medicine, Hefei, China
- Chinese Academy of Science, Suzhou Institute of Biomedical Engineering and Technology, Jiangsu Key Laboratory of Medical Optics, Suzhou, China
| | - Xin Xu
- University of Science and Technology of China, School of Biomedical Engineering (Suzhou), Division of Life Sciences and Medicine, Hefei, China
- Chinese Academy of Science, Suzhou Institute of Biomedical Engineering and Technology, Jiangsu Key Laboratory of Medical Optics, Suzhou, China
| | - Hong Ye
- Chinese Academy of Science, Suzhou Institute of Biomedical Engineering and Technology, Jiangsu Key Laboratory of Medical Optics, Suzhou, China
| | - Xin Zhang
- Chinese Academy of Science, Suzhou Institute of Biomedical Engineering and Technology, Jiangsu Key Laboratory of Medical Optics, Suzhou, China
| | - Guohua Shi
- University of Science and Technology of China, School of Biomedical Engineering (Suzhou), Division of Life Sciences and Medicine, Hefei, China
- Chinese Academy of Science, Suzhou Institute of Biomedical Engineering and Technology, Jiangsu Key Laboratory of Medical Optics, Suzhou, China
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4
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Park S, Na M, Chang S, Kim KH. High-resolution open-top axially swept light sheet microscopy. BMC Biol 2023; 21:248. [PMID: 37940973 PMCID: PMC10634022 DOI: 10.1186/s12915-023-01747-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2023] [Accepted: 10/24/2023] [Indexed: 11/10/2023] Open
Abstract
BACKGROUND Open-top light-sheet microscopy (OT-LSM) is a specialized microscopic technique for the high-throughput cellular imaging of optically cleared, large-sized specimens, such as the brain. Despite the development of various OT-LSM techniques, achieving submicron resolution in all dimensions remains. RESULTS We developed a high-resolution open-top axially swept LSM (HR-OTAS-LSM) for high-throughput and high-resolution imaging in all dimensions. High axial and lateral resolutions were achieved by using an aberration-corrected axially swept excitation light sheet in the illumination arm and a high numerical aperture (NA) immersion objective lens in the imaging arm, respectively. The high-resolution, high-throughput visualization of neuronal networks in mouse brain and retina specimens validated the performance of HR-OTAS-LSM. CONCLUSIONS The proposed HR-OTAS-LSM method represents a significant advancement in the high-resolution mapping of cellular networks in biological systems such as the brain and retina.
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Affiliation(s)
- Soohyun Park
- Department of Mechanical Engineering, Pohang University of Science and Technology, 77 Cheongam-Ro, Nam-gu, Pohang, Gyeongbuk, 37673, Republic of Korea
| | - Myeongsu Na
- Department of Research and Development Center, Crayon Technologies, 19 Sanmaru-ro, Guri, Gyeonggi-do, 11901, Republic of Korea
| | - Sunghoe Chang
- Department of Physiology and Biomedical Sciences, Seoul National University College of Medicine, 103 Daehak-ro, Jongno-gu, Seoul, 03080, Republic of Korea
- Neuroscience Research Institute, Seoul National University College of Medicine, 103 Daehak-ro, Jongno-gu, Seoul, 03080, Republic of Korea
| | - Ki Hean Kim
- Department of Mechanical Engineering, Pohang University of Science and Technology, 77 Cheongam-Ro, Nam-gu, Pohang, Gyeongbuk, 37673, Republic of Korea.
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5
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Prince MNH, Garcia B, Henn C, Yi Y, Susaki EA, Watakabe Y, Nemoto T, Lidke KA, Zhao H, Remiro IS, Liu S, Chakraborty T. Signal Improved ultra-Fast Light-sheet Microscope (SIFT) for large tissue imaging. RESEARCH SQUARE 2023:rs.3.rs-2990328. [PMID: 37461705 PMCID: PMC10350224 DOI: 10.21203/rs.3.rs-2990328/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/23/2023]
Abstract
Light-sheet fluorescence microscopy (LSFM) in conjunction with tissue clearing techniques enables morphological investigation of large tissues faster and with excellent optical sectioning. Recently, cleared tissue axially swept light-sheet microscope (ctASLM) demonstrated three-dimensional isotropic resolution in millimeter-scaled tissues. But ASLM based microscopes suffer from low detection signal and slow imaging speed. Here we report a simple and efficient imaging platform that employs precise control of two fixed distant light-sheet foci to carry out ASLM. This allowed us to carry out full field of view (FOV) imaging at 40 frames per second (fps) which is a four-fold improvement compared to the current state-of-the-art. In addition, in a particular frame rate, our method doubles the signal compared to the current ASLM technique. To augment the overall imaging performance, we also developed a deep learning based tissue information classifier that enables faster determination of tissue boundary. We demonstrated the performance of our imaging platform on various cleared tissue samples and demonstrated its robustness over a wide range of clearing protocols.
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Affiliation(s)
- Md Nasful Huda Prince
- Department of Physics and Astronomy, University of New Mexico, Albuquerque, NM 87131, USA
| | - Benjamin Garcia
- Department of Biology, University of New Mexico, Albuquerque, NM 87131, USA
| | - Cory Henn
- Department of Biology, University of New Mexico, Albuquerque, NM 87131, USA
| | - Yating Yi
- Chinese Institute for Brain Research, Beijing 102206, China
| | - Etsuo A. Susaki
- Department of Biochemistry and Systems Biomedicine, Graduate School of Medicine, Juntendo University, Tokyo, Japan
| | - Yuki Watakabe
- Division of Biophotonics, National Institute for Physiological Sciences, National Institutes of Natural Sciences, 5-1 Higashiyama, Okazaki, Aichi, 444-8787, Japan
- Biophotonics Research Group, Exploratory Research Center for Life and Living Systems, National Institutes of Natural Sciences, 5-1 Higashiyama, Okazaki, Aichi, 444-8787, Japan
| | - Tomomi Nemoto
- Division of Biophotonics, National Institute for Physiological Sciences, National Institutes of Natural Sciences, 5-1 Higashiyama, Okazaki, Aichi, 444-8787, Japan
- Biophotonics Research Group, Exploratory Research Center for Life and Living Systems, National Institutes of Natural Sciences, 5-1 Higashiyama, Okazaki, Aichi, 444-8787, Japan
| | - Keith A Lidke
- Department of Physics and Astronomy, University of New Mexico, Albuquerque, NM 87131, USA
| | - Hu Zhao
- Chinese Institute for Brain Research, Beijing 102206, China
| | | | - Sheng Liu
- Department of Physics and Astronomy, University of New Mexico, Albuquerque, NM 87131, USA
| | - Tonmoy Chakraborty
- Department of Physics and Astronomy, University of New Mexico, Albuquerque, NM 87131, USA
- Comprehensive Cancer Center, University of New Mexico, Albuquerque, NM 87102, USA
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6
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Son J, Mandracchia B, Silva Trenkle AD, Kwong GA, Jia S. Portable light-sheet optofluidic microscopy for 3D fluorescence imaging flow cytometry. LAB ON A CHIP 2023; 23:624-630. [PMID: 36633262 PMCID: PMC9931680 DOI: 10.1039/d2lc01024k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/17/2023]
Abstract
Imaging flow cytometry (IFC) combines conventional flow cytometry with optical microscopy, allowing for high-throughput, multi-parameter screening of single-cell specimens with morphological and spatial information. However, current 3D IFC systems are limited by instrumental complexity and incompatibility with available microfluidic devices or operations. Here, we report portable light-sheet optofluidic microscopy (PLSOM) for 3D fluorescence cytometric imaging. PLSOM exploits a compact, open-top light-sheet configuration compatible with commonly adopted microfluidic chips. The system offers a subcellular resolution (2-4 μm) in all three dimensions, high throughput (∼1000 cells per s), and portability (30 cm (l) × 10 cm (w) × 26 cm (h)). We demonstrated PLSOM for 3D IFC using various phantom and cell systems. The low-cost and custom-built architecture of PLSOM permits easy adaptability and dissemination for broad 3D flow cytometric investigations.
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Affiliation(s)
- Jeonghwan Son
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, GA 30332, USA.
| | - Biagio Mandracchia
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, GA 30332, USA.
| | - Aaron D Silva Trenkle
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, GA 30332, USA.
| | - Gabriel A Kwong
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, GA 30332, USA.
- Parker H. Petit Institute of Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - Shu Jia
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, GA 30332, USA.
- Parker H. Petit Institute of Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, GA 30332, USA
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7
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Practical considerations for quantitative light sheet fluorescence microscopy. Nat Methods 2022; 19:1538-1549. [PMID: 36266466 DOI: 10.1038/s41592-022-01632-x] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2022] [Accepted: 08/31/2022] [Indexed: 12/25/2022]
Abstract
Fluorescence microscopy has evolved from a purely observational tool to a platform for quantitative, hypothesis-driven research. As such, the demand for faster and less phototoxic imaging modalities has spurred a rapid growth in light sheet fluorescence microscopy (LSFM). By restricting the excitation to a thin plane, LSFM reduces the overall light dose to a specimen while simultaneously improving image contrast. However, the defining characteristics of light sheet microscopes subsequently warrant unique considerations in their use for quantitative experiments. In this Perspective, we outline many of the pitfalls in LSFM that can compromise analysis and confound interpretation. Moreover, we offer guidance in addressing these caveats when possible. In doing so, we hope to provide a useful resource for life scientists seeking to adopt LSFM to quantitatively address complex biological hypotheses.
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8
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Wang Z, Qiao W, Jiang T, Chen S, Lu B, Ning K, Jin R, Gong H, Yuan J. Axial resolution and imaging contrast enhancement in inverted light-sheet microscopy by natural illumination modulation. Front Neurosci 2022; 16:1032195. [PMID: 36330343 PMCID: PMC9623180 DOI: 10.3389/fnins.2022.1032195] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2022] [Accepted: 10/03/2022] [Indexed: 02/07/2024] Open
Abstract
Inverted light-sheet microscopy (ILSM) is widely employed for fast large-volume imaging of biological tissue. However, the scattering especially in an uncleared sample, and the divergent propagation of the illumination beam lead to a trade-off between axial resolution and imaging depth. Herein, we propose naturally modulated ILSM (NM-ILSM) as a technique to improve axial resolution while simultaneously maintaining the wide field-of-view (FOV), and enhancing imaging contrast via background suppression. Theoretical derivations, simulations, and experimental imaging demonstrate 15% axial resolution increases, and fivefold greater image contrast compared with conventional ILSM. Therefore, NM-ILSM allows convenient imaging quality improvement for uncleared tissue and could extend the biological application scope of ILSM.
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Affiliation(s)
- Zhi Wang
- Wuhan National Laboratory for Optoelectronics, Britton Chance Center for Biomedical Photonics, Huazhong University of Science and Technology, Wuhan, China
- MoE Key Laboratory for Biomedical Photonics, School of Engineering Sciences, Huazhong University of Science and Technology, Wuhan, China
| | - Wei Qiao
- Wuhan National Laboratory for Optoelectronics, Britton Chance Center for Biomedical Photonics, Huazhong University of Science and Technology, Wuhan, China
- MoE Key Laboratory for Biomedical Photonics, School of Engineering Sciences, Huazhong University of Science and Technology, Wuhan, China
| | - Tao Jiang
- HUST-Suzhou Institute for Brainsmatics, Jiangsu Industrial Technology Research Institute (JITRI) Institute for Brainsmatics, Jiangsu, China
| | - Siqi Chen
- Wuhan National Laboratory for Optoelectronics, Britton Chance Center for Biomedical Photonics, Huazhong University of Science and Technology, Wuhan, China
- MoE Key Laboratory for Biomedical Photonics, School of Engineering Sciences, Huazhong University of Science and Technology, Wuhan, China
| | - Bolin Lu
- Wuhan National Laboratory for Optoelectronics, Britton Chance Center for Biomedical Photonics, Huazhong University of Science and Technology, Wuhan, China
- MoE Key Laboratory for Biomedical Photonics, School of Engineering Sciences, Huazhong University of Science and Technology, Wuhan, China
| | - Kefu Ning
- Wuhan National Laboratory for Optoelectronics, Britton Chance Center for Biomedical Photonics, Huazhong University of Science and Technology, Wuhan, China
- MoE Key Laboratory for Biomedical Photonics, School of Engineering Sciences, Huazhong University of Science and Technology, Wuhan, China
| | - Rui Jin
- Wuhan National Laboratory for Optoelectronics, Britton Chance Center for Biomedical Photonics, Huazhong University of Science and Technology, Wuhan, China
- MoE Key Laboratory for Biomedical Photonics, School of Engineering Sciences, Huazhong University of Science and Technology, Wuhan, China
| | - Hui Gong
- Wuhan National Laboratory for Optoelectronics, Britton Chance Center for Biomedical Photonics, Huazhong University of Science and Technology, Wuhan, China
- MoE Key Laboratory for Biomedical Photonics, School of Engineering Sciences, Huazhong University of Science and Technology, Wuhan, China
- HUST-Suzhou Institute for Brainsmatics, Jiangsu Industrial Technology Research Institute (JITRI) Institute for Brainsmatics, Jiangsu, China
| | - Jing Yuan
- Wuhan National Laboratory for Optoelectronics, Britton Chance Center for Biomedical Photonics, Huazhong University of Science and Technology, Wuhan, China
- MoE Key Laboratory for Biomedical Photonics, School of Engineering Sciences, Huazhong University of Science and Technology, Wuhan, China
- HUST-Suzhou Institute for Brainsmatics, Jiangsu Industrial Technology Research Institute (JITRI) Institute for Brainsmatics, Jiangsu, China
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9
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Park WY, Kim B, Chun JH, Hong SM, Oh BH, Kim KH. High-contrast visualization of human skin cancers with combined reflectance confocal and moxifloxacin-based two-photon microscopy: An ex vivo study. Lasers Surg Med 2022; 54:1226-1237. [PMID: 36087014 DOI: 10.1002/lsm.23600] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2022] [Revised: 08/18/2022] [Accepted: 08/28/2022] [Indexed: 11/10/2022]
Abstract
BACKGROUND AND OBJECTIVES Precise determination of cancer margin during skin cancer surgery is crucial for complete resection and further clinical prognosis. Although reflection confocal microscopy (RCM) has been used for perioperative guiding, its reflection contrast has limitations in detecting cancer cells in the dermis. We previously developed combined reflection confocal (RC) and moxifloxacin-based two-photon (MB-TP) microscopy for sensitive cancer detection by using multiple contrast mechanisms. In this study, the performance of combined microscopy was characterized in various skin cancer specimens and compared with standard methods. MATERIALS AND METHODS Seven human skin specimens in total including two normal ones, three basal cell carcinomas (BCCs), and two squamous cell carcinomas (SCCs) were collected and imaged in fresh condition. Moxifloxacin ophthalmic solution was topically instilled for cell labeling for 3-5 minutes, then mosaic imaging with the combined microscopy was conducted. The imaged specimens were imaged again after exogenous nuclear labeling for comparison and then processed for standard hematoxylin and eosin histology. RESULTS Combined RC and MB-TP microscopy visualized both cell and extracellular matrix structures of the skin specimens with multiple contrasts of reflection, moxifloxacin fluorescence, autofluorescence, and second harmonic generation. It distinguished normal cell structures in the skin dermis such as hair follicles, sebaceous and eccrine glands from BCC nests, and SCCs based on cell organization. Normal cell structures had organized cell arrangements for their functions, while cancer cell structures had dense and disorganized cell arrangements. Cellular features found by combined microscopy images were confirmed by both TP microscopy with nuclear labeling and histological examination. CONCLUSIONS The imaging results showed the potential of combined microscopy for sensitive cancer detection and in vivo guiding of skin cancer surgery.
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Affiliation(s)
- Won Yeong Park
- Department of Mechanical Engineering, Pohang University of Science and Technology, Pohang, Gyeongbuk, Republic of Korea
| | - Bumju Kim
- Division of Integrative Biosciences and Biotechnology, Pohang University of Science and Technology, Pohang, Gyeongbuk, Republic of Korea
| | - Ji Hyun Chun
- Department of Pathology, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Republic of Korea
| | - Seung-Mo Hong
- Department of Pathology, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Republic of Korea
| | - Byung Ho Oh
- Department of Dermatology, College of Medicine, Yonsei University, Seoul, Republic of Korea
| | - Ki Hean Kim
- Department of Mechanical Engineering, Pohang University of Science and Technology, Pohang, Gyeongbuk, Republic of Korea.,Division of Integrative Biosciences and Biotechnology, Pohang University of Science and Technology, Pohang, Gyeongbuk, Republic of Korea
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10
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Park H, Na M, Kim B, Park S, Kim KH, Chang S, Ye JC. Deep learning enables reference-free isotropic super-resolution for volumetric fluorescence microscopy. Nat Commun 2022; 13:3297. [PMID: 35676288 PMCID: PMC9178036 DOI: 10.1038/s41467-022-30949-6] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2021] [Accepted: 05/10/2022] [Indexed: 11/09/2022] Open
Abstract
Volumetric imaging by fluorescence microscopy is often limited by anisotropic spatial resolution, in which the axial resolution is inferior to the lateral resolution. To address this problem, we present a deep-learning-enabled unsupervised super-resolution technique that enhances anisotropic images in volumetric fluorescence microscopy. In contrast to the existing deep learning approaches that require matched high-resolution target images, our method greatly reduces the effort to be put into practice as the training of a network requires only a single 3D image stack, without a priori knowledge of the image formation process, registration of training data, or separate acquisition of target data. This is achieved based on the optimal transport-driven cycle-consistent generative adversarial network that learns from an unpaired matching between high-resolution 2D images in the lateral image plane and low-resolution 2D images in other planes. Using fluorescence confocal microscopy and light-sheet microscopy, we demonstrate that the trained network not only enhances axial resolution but also restores suppressed visual details between the imaging planes and removes imaging artifacts.
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Affiliation(s)
- Hyoungjun Park
- Department of Bio and Brain Engineering, Korea Advanced Institute of Science and Technology, Daejeon, South Korea
| | - Myeongsu Na
- Department of Physiology and Biomedical Sciences, Seoul National University College of Medicine, Seoul, South Korea
| | - Bumju Kim
- Division of Integrative Biosciences and Biotechnology, Pohang University of Science and Technology, Pohang, South Korea
| | - Soohyun Park
- Department of Mechanical Engineering, Pohang University of Science and Technology, Pohang, South Korea
| | - Ki Hean Kim
- Division of Integrative Biosciences and Biotechnology, Pohang University of Science and Technology, Pohang, South Korea
- Department of Mechanical Engineering, Pohang University of Science and Technology, Pohang, South Korea
| | - Sunghoe Chang
- Department of Physiology and Biomedical Sciences, Seoul National University College of Medicine, Seoul, South Korea
- Neuroscience Research Institute, Seoul National University College of Medicine, Seoul, South Korea
| | - Jong Chul Ye
- Department of Bio and Brain Engineering, Korea Advanced Institute of Science and Technology, Daejeon, South Korea.
- Kim Jaechul Graduate School of AI, Korea Advanced Institute of Science and Technology, Daejeon, South Korea.
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11
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Yang B, Lange M, Millett-Sikking A, Zhao X, Bragantini J, VijayKumar S, Kamb M, Gómez-Sjöberg R, Solak AC, Wang W, Kobayashi H, McCarroll MN, Whitehead LW, Fiolka RP, Kornberg TB, York AG, Royer LA. DaXi-high-resolution, large imaging volume and multi-view single-objective light-sheet microscopy. Nat Methods 2022; 19:461-469. [PMID: 35314838 PMCID: PMC9007742 DOI: 10.1038/s41592-022-01417-2] [Citation(s) in RCA: 55] [Impact Index Per Article: 27.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2021] [Accepted: 02/08/2022] [Indexed: 11/19/2022]
Abstract
The promise of single-objective light-sheet microscopy is to combine the convenience of standard single-objective microscopes with the speed, coverage, resolution and gentleness of light-sheet microscopes. We present DaXi, a single-objective light-sheet microscope design based on oblique plane illumination that achieves: (1) a wider field of view and high-resolution imaging via a custom remote focusing objective; (2) fast volumetric imaging over larger volumes without compromising image quality or necessitating tiled acquisition; (3) fuller image coverage for large samples via multi-view imaging and (4) higher throughput multi-well imaging via remote coverslip placement. Our instrument achieves a resolution of 450 nm laterally and 2 μm axially over an imaging volume of 3,000 × 800 × 300 μm. We demonstrate the speed, field of view, resolution and versatility of our instrument by imaging various systems, including Drosophila egg chamber development, zebrafish whole-brain activity and zebrafish embryonic development – up to nine embryos at a time. The DaXi single-objective light-sheet microscope achieves fast, high-quality imaging of large volumes. DaXi’s design allows increased scanning range without sacrificing imaging speed or quality, multiview imaging and versatile sample mounting.
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Affiliation(s)
- Bin Yang
- Chan Zuckerberg Biohub, San Francisco, CA, USA.
| | | | | | - Xiang Zhao
- Chan Zuckerberg Biohub, San Francisco, CA, USA
| | | | | | - Mason Kamb
- Chan Zuckerberg Biohub, San Francisco, CA, USA
| | | | | | - Wanpeng Wang
- Cardiovascular Research Institute, University of California, San Francisco (UCSF), San Francisco, CA, USA
| | | | - Matthew N McCarroll
- Department of Pharmaceutical Chemistry, University of California, San Francisco (UCSF), San Francisco, CA, USA
| | - Lachlan W Whitehead
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia.,Department of Medical Biology, The University of Melbourne, Parkville, Victoria, Australia
| | - Reto P Fiolka
- Department of Cell Biology, University of Texas Southwestern Medical Center, Dallas, TX, USA.,Lyda Hill Department of Bioinformatics, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Thomas B Kornberg
- Cardiovascular Research Institute, University of California, San Francisco (UCSF), San Francisco, CA, USA
| | - Andrew G York
- Calico Life Sciences LLC, South San Francisco, CA, USA
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