151
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Harder A, Nagarajan B, Odermatt B, Kubitscheck U. Automatic detector synchronization for long-term imaging using confocal light-sheet microscopy. Microsc Res Tech 2023; 86:125-136. [PMID: 36054690 DOI: 10.1002/jemt.24223] [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: 02/09/2022] [Revised: 06/08/2022] [Accepted: 07/28/2022] [Indexed: 01/21/2023]
Abstract
Light sheet fluorescence microscopy (LSFM) is an important tool in developmental biology. In this microscopy technique confocal line detection is often used to improve image contrast. To this end, the image of the illuminating scanned focused laser beam must be mapped onto a line detector. This is not trivial for long-term observations, since the spatial position of the laser beam and therefore its image on the detector may drift. The problem is aggravated in two-photon excitation LSFM, since pulsed laser light sources exhibit a lower laser beam pointing stability than continuous wave lasers. Here, we present a procedure for automatic synchronization between the excitation laser and detector, which does not require any additional hardware components and can therefore easily be integrated into existing systems. Since the recorded images are affected by noise, a specific, noise-tolerant focus metric was developed for calculating the relative displacement, which also allows for autofocusing in the detection direction. Furthermore, we developed an image analysis approach to determine a possible tilt of the excitation laser, which is executed in parallel to the autofocusing and enables the measurement of three solid angles. This allows to automatically correct for the tilting during a measurement. We demonstrated our approach by the observation of the migration of oligodendrocyte precursor cells in two-day-old fluorescent Tg(olig2:eGFP) reporter zebrafish larvae over a time span of more than 20 hours.
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Affiliation(s)
- Alexander Harder
- Clausius Institute of Physical and Theoretical Chemistry, University of Bonn, Bonn, Germany
| | | | - Benjamin Odermatt
- Institute of Anatomy, University Clinics, University of Bonn, Bonn, Germany
| | - Ulrich Kubitscheck
- Clausius Institute of Physical and Theoretical Chemistry, University of Bonn, Bonn, Germany
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152
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Lamb JR, Ward EN, Kaminski CF. Open-source software package for on-the-fly deskewing and live viewing of volumetric lightsheet microscopy data. BIOMEDICAL OPTICS EXPRESS 2023; 14:834-845. [PMID: 36874505 PMCID: PMC9979666 DOI: 10.1364/boe.479977] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/04/2022] [Revised: 01/06/2023] [Accepted: 01/12/2023] [Indexed: 06/18/2023]
Abstract
Oblique plane microscopy, OPM, is a form of lightsheet microscopy that permits volumetric imaging of biological samples at high temporal and spatial resolution. However, the imaging geometry of OPM, and related variants of light sheet microscopy, distorts the coordinate frame of the presented image sections with respect to the real space coordinate frame in which the sample is moved. This makes live viewing and practical operation of such microscopes difficult. We present an open-source software package that utilises GPU acceleration and multiprocessing to transform the display of OPM imaging data in real time to produce a live extended depth of field projection. Image stacks can be acquired, processed and plotted at rates of several Hz, making live operation of OPMs, and similar microscopes, more user friendly and intuitive.
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Affiliation(s)
- Jacob R. Lamb
- Department of Chemical Engineering and Biotechnology, University of Cambridge, Cambridge, UK
| | - Edward N. Ward
- Department of Chemical Engineering and Biotechnology, University of Cambridge, Cambridge, UK
| | - Clemens F. Kaminski
- Department of Chemical Engineering and Biotechnology, University of Cambridge, Cambridge, UK
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153
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Du X, Chen Z, Li Q, Yang S, Jiang L, Yang Y, Li Y, Gu Z. Organoids revealed: morphological analysis of the profound next generation in-vitro model with artificial intelligence. Biodes Manuf 2023; 6:319-339. [PMID: 36713614 PMCID: PMC9867835 DOI: 10.1007/s42242-022-00226-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2022] [Accepted: 12/06/2022] [Indexed: 01/21/2023]
Abstract
In modern terminology, "organoids" refer to cells that grow in a specific three-dimensional (3D) environment in vitro, sharing similar structures with their source organs or tissues. Observing the morphology or growth characteristics of organoids through a microscope is a commonly used method of organoid analysis. However, it is difficult, time-consuming, and inaccurate to screen and analyze organoids only manually, a problem which cannot be easily solved with traditional technology. Artificial intelligence (AI) technology has proven to be effective in many biological and medical research fields, especially in the analysis of single-cell or hematoxylin/eosin stained tissue slices. When used to analyze organoids, AI should also provide more efficient, quantitative, accurate, and fast solutions. In this review, we will first briefly outline the application areas of organoids and then discuss the shortcomings of traditional organoid measurement and analysis methods. Secondly, we will summarize the development from machine learning to deep learning and the advantages of the latter, and then describe how to utilize a convolutional neural network to solve the challenges in organoid observation and analysis. Finally, we will discuss the limitations of current AI used in organoid research, as well as opportunities and future research directions. Graphic abstract
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Affiliation(s)
- Xuan Du
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing, 210096 China
| | - Zaozao Chen
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing, 210096 China
| | - Qiwei Li
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing, 210096 China
| | - Sheng Yang
- Key Laboratory of Environmental Medicine Engineering, Ministry of Education, School of Public Health, Southeast University, Nanjing, 210009 China
| | - Lincao Jiang
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing, 210096 China
| | - Yi Yang
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing, 210096 China
| | - Yanhui Li
- State Key Laboratory for Novel Software Technology, Nanjing University, Nanjing, 210008 China
| | - Zhongze Gu
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing, 210096 China
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154
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Scott S, Weiss M, Selhuber-Unkel C, Barooji YF, Sabri A, Erler JT, Metzler R, Oddershede LB. Extracting, quantifying, and comparing dynamical and biomechanical properties of living matter through single particle tracking. Phys Chem Chem Phys 2023; 25:1513-1537. [PMID: 36546878 DOI: 10.1039/d2cp01384c] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
A panoply of new tools for tracking single particles and molecules has led to an explosion of experimental data, leading to novel insights into physical properties of living matter governing cellular development and function, health and disease. In this Perspective, we present tools to investigate the dynamics and mechanics of living systems from the molecular to cellular scale via single-particle techniques. In particular, we focus on methods to measure, interpret, and analyse complex data sets that are associated with forces, materials properties, transport, and emergent organisation phenomena within biological and soft-matter systems. Current approaches, challenges, and existing solutions in the associated fields are outlined in order to support the growing community of researchers at the interface of physics and the life sciences. Each section focuses not only on the general physical principles and the potential for understanding living matter, but also on details of practical data extraction and analysis, discussing limitations, interpretation, and comparison across different experimental realisations and theoretical frameworks. Particularly relevant results are introduced as examples. While this Perspective describes living matter from a physical perspective, highlighting experimental and theoretical physics techniques relevant for such systems, it is also meant to serve as a solid starting point for researchers in the life sciences interested in the implementation of biophysical methods.
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Affiliation(s)
- Shane Scott
- Institute of Physiology, Kiel University, Hermann-Rodewald-Straße 5, 24118 Kiel, Germany
| | - Matthias Weiss
- Experimental Physics I, University of Bayreuth, Universitätsstr. 30, D-95447 Bayreuth, Germany
| | - Christine Selhuber-Unkel
- Institute for Molecular Systems Engineering, Heidelberg University, D-69120 Heidelberg, Germany.,Max Planck School Matter to Life, Jahnstraße 29, D-69120 Heidelberg, Germany
| | - Younes F Barooji
- Niels Bohr Institute, Blegdamsvej 17, DK-2100 Copenhagen, Denmark.
| | - Adal Sabri
- Experimental Physics I, University of Bayreuth, Universitätsstr. 30, D-95447 Bayreuth, Germany
| | - Janine T Erler
- BRIC, University of Copenhagen, Ole Maaløes Vej 5, DK-2200 Copenhagen, Denmark.
| | - Ralf Metzler
- Institute of Physics and Astronomy, University of Potsdam, Karl-Liebknecht Str. 24/25, D-14476 Potsdam, Germany.,Asia Pacific Center for Theoretical Physics, Pohang 37673, Republic of Korea
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155
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Zhan YJ, Zhang SW, Zhu S, Jiang N. Tissue Clearing and Its Application in the Musculoskeletal System. ACS OMEGA 2023; 8:1739-1758. [PMID: 36687066 PMCID: PMC9850472 DOI: 10.1021/acsomega.2c05180] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/12/2022] [Accepted: 12/07/2022] [Indexed: 06/17/2023]
Abstract
The musculoskeletal system is an integral part of the human body. Currently, most skeletal muscle research is conducted through conventional histological sections due to technological limitations and the structure of skeletal muscles. For studying and observing bones and muscles, there is an urgent need for three-dimensional, objective imaging technologies. Optical tissue-clearing technologies seem to offer a novel and accessible approach to research of the musculoskeletal system. Using this approach, the components which cause refraction or prevent light from penetrating into the tissue are physically and chemically eliminated; then the liquid in the tissue is replaced with high-refractive-index chemicals. This innovative method, which allows three-dimensional reconstruction at the cellular and subcellular scale, significantly improves imaging depth and resolution. Nonetheless, this technology was not originally developed to image bones or muscles. When compared with brain and nerve organs which have attracted considerable attention in this field, the musculoskeletal system contains fewer lipids and has high levels of hemoglobin, collagen fibers, and inorganic hydroxyapatite crystals. Currently, three-dimensional imaging methods are widely used in the diagnosis and treatment of skeletal and muscular illnesses. In this regard, it is vitally important to review and evaluate the optical tissue-clearing technologies currently employed in the musculoskeletal system, so that researchers may make an informed decision. In the meantime, this study offers guidelines and recommendations for expanding the use of this technology in the musculoskeletal system.
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Affiliation(s)
- Yan-Jing Zhan
- State
Key Laboratory of Oral Diseases & National Clinical Research Center
for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu 610041, China
| | - Shi-Wen Zhang
- State
Key Laboratory of Oral Diseases & National Clinical Research Center
for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu 610041, China
- West
China Hospital of Stomatology, Sichuan University, Chengdu 610041, China
| | - SongSong Zhu
- State
Key Laboratory of Oral Diseases & National Clinical Research Center
for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu 610041, China
- West
China Hospital of Stomatology, Sichuan University, Chengdu 610041, China
| | - Nan Jiang
- State
Key Laboratory of Oral Diseases & National Clinical Research Center
for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu 610041, China
- West
China Hospital of Stomatology, Sichuan University, Chengdu 610041, China
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156
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Singh R, Subramanian K, Power RM, Paix A, Gil A, Ikmi A, Prevedel R. Oblique plane microscope for mesoscopic imaging of freely moving organisms with cellular resolution. OPTICS EXPRESS 2023; 31:2292-2301. [PMID: 36785246 DOI: 10.1364/oe.471845] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/27/2022] [Accepted: 11/25/2022] [Indexed: 05/25/2023]
Abstract
Several important questions in biology require non-invasive and three-dimensional imaging techniques with an appropriate spatiotemporal resolution that permits live organisms to move in an unconstrained fashion over an extended field-of-view. While selective-plane illumination microscopy (SPIM) has emerged as a powerful method to observe live biological specimens at high spatio-temporal resolution, typical implementations often necessitate constraining sample mounting or lack the required volumetric speed. Here, we report on an open-top, dual-objective oblique plane microscope (OPM) capable of observing millimeter-sized, freely moving animals at cellular resolution. We demonstrate the capabilities of our mesoscopic OPM (MesOPM) by imaging the behavioral dynamics of the sea anemone Nematostella vectensis over 1.56 × 1.56 × 0.25 mm at 1.5 × 2.8 × 5.3 µm resolution and 0.5 Hz volume rate.
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157
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Cheng X, Wang J, Li Q, Duan Y, Chen Y, Teng J, Chu S, Yang H, Wang S, Gong Q. Enhancing Weak-Signal Extraction for Single-Molecule Localization Microscopy. J Phys Chem A 2023; 127:329-338. [PMID: 36541035 DOI: 10.1021/acs.jpca.2c05164] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Single-molecule localization microscopy (SMLM) has been widely used in biological imaging due to its ultrahigh spatial resolution. However, due to the strategy of reducing photodamage to living cells, the fluorescence signals of emitters are usually weak and the detector noises become non-negligible, which leads to localization misalignments and signal losses, thus deteriorating the imaging capability of SMLM. Here, we propose an active modulation method to control the fluorescence of the probe emitters. It actually marks the emitters with artificial blinking character, which directly distinguishes weak signals from multiple detector noises. We demonstrated from simulations and experiments that this method improves the signal-to-noise ratio by about 10 dB over the non-modulated method and boosts the sensitivity of single-molecule localization down to -4 dB, which significantly reduces localization misalignments and signal losses in SMLM. This signal-noise decoupling strategy is generally applicable to the super-resolution system with versatile labeled probes to improve their imaging capability. We also showed its application to the densely labeled sample, showing its flexibility in super-resolution nanoscopy.
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Affiliation(s)
- Xue Cheng
- State Key Laboratory for Artificial Microstructure and Mesoscopic Physics, Department of Physics, Peking University, Beijing100871, China
| | - Ju Wang
- State Key Laboratory for Artificial Microstructure and Mesoscopic Physics, Department of Physics, Peking University, Beijing100871, China
| | - Qi Li
- Key Laboratory of Cell Proliferation and Differentiation of the Ministry of Education and State Key Laboratory of Membrane Biology, College of Life Sciences, Peking University, Beijing100871, China
| | - Yiqun Duan
- State Key Laboratory for Artificial Microstructure and Mesoscopic Physics, Department of Physics, Peking University, Beijing100871, China
| | - Yan Chen
- State Key Laboratory for Artificial Microstructure and Mesoscopic Physics, Department of Physics, Peking University, Beijing100871, China
| | - Junlin Teng
- Key Laboratory of Cell Proliferation and Differentiation of the Ministry of Education and State Key Laboratory of Membrane Biology, College of Life Sciences, Peking University, Beijing100871, China
| | - Saisai Chu
- State Key Laboratory for Artificial Microstructure and Mesoscopic Physics, Department of Physics, Peking University, Beijing100871, China.,Collaborative Innovation Center of Extreme Optics, Shanxi University, Taiyuan, Shanxi030006, China.,Frontiers Science Center for Nano-optoelectronics, Peking University, Beijing100871, China.,Peking University Yangtze Delta Institute of Optoelectronics, Nantong, Jiangsu226010, China
| | - Hong Yang
- State Key Laboratory for Artificial Microstructure and Mesoscopic Physics, Department of Physics, Peking University, Beijing100871, China.,Collaborative Innovation Center of Extreme Optics, Shanxi University, Taiyuan, Shanxi030006, China.,Frontiers Science Center for Nano-optoelectronics, Peking University, Beijing100871, China.,Peking University Yangtze Delta Institute of Optoelectronics, Nantong, Jiangsu226010, China
| | - Shufeng Wang
- State Key Laboratory for Artificial Microstructure and Mesoscopic Physics, Department of Physics, Peking University, Beijing100871, China.,Collaborative Innovation Center of Extreme Optics, Shanxi University, Taiyuan, Shanxi030006, China.,Frontiers Science Center for Nano-optoelectronics, Peking University, Beijing100871, China.,Peking University Yangtze Delta Institute of Optoelectronics, Nantong, Jiangsu226010, China
| | - Qihuang Gong
- State Key Laboratory for Artificial Microstructure and Mesoscopic Physics, Department of Physics, Peking University, Beijing100871, China.,Collaborative Innovation Center of Extreme Optics, Shanxi University, Taiyuan, Shanxi030006, China.,Frontiers Science Center for Nano-optoelectronics, Peking University, Beijing100871, China.,Peking University Yangtze Delta Institute of Optoelectronics, Nantong, Jiangsu226010, China
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158
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Hedde PN, Le BT, Gomez EL, Duong L, Steele RE, Ahrar S. SPIM-Flow: An Integrated Light Sheet and Microfluidics Platform for Hydrodynamic Studies of Hydra. BIOLOGY 2023; 12:biology12010116. [PMID: 36671808 PMCID: PMC9856110 DOI: 10.3390/biology12010116] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/06/2022] [Revised: 01/08/2023] [Accepted: 01/09/2023] [Indexed: 01/13/2023]
Abstract
Selective plane illumination microscopy (SPIM), or light sheet microscopy, is a powerful imaging approach. However, access to and interfacing microscopes with microfluidics have remained challenging. Complex interfacing with microfluidics has limited the SPIM's utility for studying the hydrodynamics of freely moving multicellular organisms. We developed SPIM-Flow, an inexpensive light sheet platform that enables easy integration with microfluidics. We used SPIM-Flow to investigate the hydrodynamics of a freely moving Hydra polyp via particle tracking in millimeter-sized chambers. Initial experiments across multiple animals, feeding on a chip (Artemia franciscana nauplii used as food), and baseline behaviors (tentacle swaying, elongation, and bending) indicated the organisms' health inside the system. Fluidics were used to investigate Hydra's response to flow. The results suggested that the animals responded to an established flow by bending and swaying their tentacles in the flow direction. Finally, using SPIM-Flow in a proof-of-concept experiment, the shear stress required to detach an animal from a surface was demonstrated. Our results demonstrated SPIM-Flow's utility for investigating the hydrodynamics of freely moving animals.
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Affiliation(s)
- Per Niklas Hedde
- Beckman Laser Institute and Medical Clinic, University of California Irvine, Irvine, CA 92612, USA
- Correspondence: (P.N.H.); (S.A.)
| | - Brian T. Le
- Department of Biomedical Engineering, CSU Long Beach, Long Beach, CA 90840, USA
| | - Erika L. Gomez
- Department of Biomedical Engineering, CSU Long Beach, Long Beach, CA 90840, USA
| | - Leora Duong
- Department of Molecular Biology and Biochemistry, University of California Irvine, Irvine, CA 92697, USA
| | - Robert E. Steele
- Department of Biological Chemistry, University of California Irvine, Irvine, CA 92697, USA
| | - Siavash Ahrar
- Department of Biomedical Engineering, CSU Long Beach, Long Beach, CA 90840, USA
- Department of Physics and Astronomy, University of California Irvine, Irvine, CA 92697, USA
- Correspondence: (P.N.H.); (S.A.)
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159
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Li X, Li M. The application of zebrafish patient-derived xenograft tumor models in the development of antitumor agents. Med Res Rev 2023; 43:212-236. [PMID: 36029178 DOI: 10.1002/med.21924] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2021] [Revised: 03/09/2022] [Accepted: 07/28/2022] [Indexed: 02/04/2023]
Abstract
The cost of antitumor drug development is enormous, yet the clinical outcomes are less than satisfactory. Therefore, it is of great importance to develop effective drug screening methods that enable accurate, rapid, and high-throughput discovery of lead compounds in the process of preclinical antitumor drug research. An effective solution is to use the patient-derived xenograft (PDX) tumor animal models, which are applicable for the elucidation of tumor pathogenesis and the preclinical testing of novel antitumor compounds. As a promising screening model organism, zebrafish has been widely applied in the construction of the PDX tumor model and the discovery of antineoplastic agents. Herein, we systematically survey the recent cutting-edge advances in zebrafish PDX models (zPDX) for studies of pathogenesis mechanisms and drug screening. In addition, the techniques used in the construction of zPDX are summarized. The advantages and limitations of the zPDX are also discussed in detail. Finally, the prospects of zPDX in drug discovery, translational medicine, and clinical precision medicine treatment are well presented.
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Affiliation(s)
- Xiang Li
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, China
| | - Minyong Li
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, China
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160
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Cao Y, Lee S, Kim K, Kang SH. Minimizing the Optical Illusion of Nanoparticles in Single Cells Using Four-Dimensional Cuboid Multiangle Illumination-Based Light-Sheet Super-Resolution Imaging. Anal Chem 2022; 94:17877-17884. [PMID: 36509731 DOI: 10.1021/acs.analchem.2c03729] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Although light-sheet-based super-resolution microscopy is an excellent detection technique for biological samples because of minimal photodamage, uneven light paths due to solid-angle illumination limits it, resulting in an optical illusion. Furthermore, the optical illusion limits the observations of individual molecules in diffraction. In this study, a four-dimensional cuboid multiangle illumination-based light-sheet super-resolution (4D CMLS) imaging system was developed to minimize optical illusions in cells. The lab-built 4D CMLS imaging system was integrated with total internal reflection fluorescence and a differential interference contrast microscope. A specially designed rotatable cuboid prism simply overcame the optical illusion by rotating a specimen on the prism to change the direction of light coming from an illumination lens. 4D CMLS reconstructed images of nanoparticles of different sizes were acquired in multi-illumination angles of 0°, 90°, 180°, and 270°. Additionally, a 4D multiangle illumination-based algorithm was created to select the optimal illumination angle by combining three-dimensional super-resolution imaging with multiangle observation, even in the presence of obstacles. The 4D CMLS imaging method demonstrates the in-depth 4D observation of samples at an optimum angle that can be used in various applications, such as single-molecule and subcellular organelle observations in single cells at subdiffraction limit resolutions that describe the scenario of nature.
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Affiliation(s)
- Yingying Cao
- Department of Chemistry, Graduate School, Kyung Hee University, Yongin-si, Gyeonggi-do17104, Republic of Korea
| | - Seungah Lee
- Department of Applied Chemistry and Institute of Natural Sciences, Kyung Hee University, Yongin-si, Gyeonggi-do17104, Republic of Korea
| | - Kyungsoo Kim
- Department of Applied Mathematics, Kyung Hee University, Yongin-si, Gyeonggi-do17104, Republic of Korea
| | - Seong Ho Kang
- Department of Chemistry, Graduate School, Kyung Hee University, Yongin-si, Gyeonggi-do17104, Republic of Korea.,Department of Applied Chemistry and Institute of Natural Sciences, Kyung Hee University, Yongin-si, Gyeonggi-do17104, Republic of Korea
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161
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Shao W, Chang M, Emmerich K, Kanold PO, Mumm JS, Yi J. Mesoscopic oblique plane microscopy with a diffractive light-sheet for large-scale 4D cellular resolution imaging. OPTICA 2022; 9:1374-1385. [PMID: 38384442 PMCID: PMC10881189 DOI: 10.1364/optica.471101] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/21/2022] [Accepted: 10/31/2022] [Indexed: 02/23/2024]
Abstract
Fundamental understanding of large-scale dynamic connectivity within a living organism requires volumetric imaging over a large field of view (FOV) at biologically relevant speed and resolution. However, most microscopy methods make trade-offs between FOV and axial resolution, making it challenging to observe highly dynamic processes at cellular resolution in 3D across mesoscopic scales (e.g., whole zebrafish larva). To overcome this limitation, we have developed mesoscopic oblique plane microscopy (Meso-OPM) with a diffractive light sheet. By augmenting the illumination angle of the light sheet with a transmission grating, we improved the axial resolution approximately sixfold over existing methods and approximately twofold beyond the diffraction limitation of the primary objective lens. We demonstrated a FOV up to 5.4 mm × 3.3 mm with resolution of 2.5 μm × 3 μm × 6 μm, allowing volumetric imaging of 3D cellular structures with a single scan. Applying Meso-OPM for in vivo imaging of zebrafish larvae, we report here in toto whole-body volumetric recordings of neuronal activity at 2 Hz volume rate and whole-body volumetric recordings of blood flow dynamics at 5 Hz with 3D cellular resolution.
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Affiliation(s)
- Wenjun Shao
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, Maryland 21231, USA
- Department of Ophthalmology, Johns Hopkins University, Baltimore, Maryland 21231, USA
| | - Minzi Chang
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, Maryland 21231, USA
| | - Kevin Emmerich
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, Maryland 21231, USA
| | - Patrick O. Kanold
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, Maryland 21231, USA
| | - Jeff S. Mumm
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, Maryland 21231, USA
| | - Ji Yi
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, Maryland 21231, USA
- Department of Ophthalmology, Johns Hopkins University, Baltimore, Maryland 21231, USA
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162
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Abstract
The rodent pancreas is the prevalent model system for preclinical diabetes research. However, due to the compound endocrine-exocrine organization of the gland, with the endocrine islets of Langerhans scattered by the thousands throughout the much greater exocrine parenchyma, stereological assessments of endocrine cell mass, commonly insulin-producing ß-cells, are exceedingly challenging. In recent years, optical mesoscopic imaging techniques such as optical projection tomography (OPT) and light sheet fluorescence microscopy (LSFM) have seen dramatic developments, enabling 3D visualization of fluorescently labeled cells in mm- to cm-sized tissues with μm resolution. Here we present a protocol for 3D visualization and "absolute" quantitative assessments of, for example, islet mass throughout the volume of rodent pancreata with maintained spatial context.
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163
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Liu Z, Zhu Y, Zhang L, Jiang W, Liu Y, Tang Q, Cai X, Li J, Wang L, Tao C, Yin X, Li X, Hou S, Jiang D, Liu K, Zhou X, Zhang H, Liu M, Fan C, Tian Y. Structural and functional imaging of brains. Sci China Chem 2022; 66:324-366. [PMID: 36536633 PMCID: PMC9753096 DOI: 10.1007/s11426-022-1408-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2022] [Accepted: 09/28/2022] [Indexed: 12/23/2022]
Abstract
Analyzing the complex structures and functions of brain is the key issue to understanding the physiological and pathological processes. Although neuronal morphology and local distribution of neurons/blood vessels in the brain have been known, the subcellular structures of cells remain challenging, especially in the live brain. In addition, the complicated brain functions involve numerous functional molecules, but the concentrations, distributions and interactions of these molecules in the brain are still poorly understood. In this review, frontier techniques available for multiscale structure imaging from organelles to the whole brain are first overviewed, including magnetic resonance imaging (MRI), computed tomography (CT), positron emission tomography (PET), serial-section electron microscopy (ssEM), light microscopy (LM) and synchrotron-based X-ray microscopy (XRM). Specially, XRM for three-dimensional (3D) imaging of large-scale brain tissue with high resolution and fast imaging speed is highlighted. Additionally, the development of elegant methods for acquisition of brain functions from electrical/chemical signals in the brain is outlined. In particular, the new electrophysiology technologies for neural recordings at the single-neuron level and in the brain are also summarized. We also focus on the construction of electrochemical probes based on dual-recognition strategy and surface/interface chemistry for determination of chemical species in the brain with high selectivity and long-term stability, as well as electrochemophysiological microarray for simultaneously recording of electrochemical and electrophysiological signals in the brain. Moreover, the recent development of brain MRI probes with high contrast-to-noise ratio (CNR) and sensitivity based on hyperpolarized techniques and multi-nuclear chemistry is introduced. Furthermore, multiple optical probes and instruments, especially the optophysiological Raman probes and fiber Raman photometry, for imaging and biosensing in live brain are emphasized. Finally, a brief perspective on existing challenges and further research development is provided.
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Affiliation(s)
- Zhichao Liu
- Shanghai Key Laboratory of Green Chemistry and Chemical Processes, School of Chemistry and Molecular Engineering, East China Normal University, Shanghai, 200241 China
| | - Ying Zhu
- Interdisciplinary Research Center, Shanghai Synchrotron Radiation Facility, Zhangjiang Laboratory, Shanghai Advanced Research Institute, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai, 201210 China
| | - Liming Zhang
- Shanghai Key Laboratory of Green Chemistry and Chemical Processes, School of Chemistry and Molecular Engineering, East China Normal University, Shanghai, 200241 China
| | - Weiping Jiang
- State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, Chinese Academy of Sciences, Wuhan National Laboratory for Optoelectronics, Wuhan, 430071 China
| | - Yawei Liu
- State Key Laboratory of Rare Earth Resource Utilization, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, 130022 China
| | - Qiaowei Tang
- Interdisciplinary Research Center, Shanghai Synchrotron Radiation Facility, Zhangjiang Laboratory, Shanghai Advanced Research Institute, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai, 201210 China
| | - Xiaoqing Cai
- Interdisciplinary Research Center, Shanghai Synchrotron Radiation Facility, Zhangjiang Laboratory, Shanghai Advanced Research Institute, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai, 201210 China
| | - Jiang Li
- Interdisciplinary Research Center, Shanghai Synchrotron Radiation Facility, Zhangjiang Laboratory, Shanghai Advanced Research Institute, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai, 201210 China
| | - Lihua Wang
- Interdisciplinary Research Center, Shanghai Synchrotron Radiation Facility, Zhangjiang Laboratory, Shanghai Advanced Research Institute, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai, 201210 China
| | - Changlu Tao
- Interdisciplinary Center for Brain Information, Brain Cognition and Brain Disease Institute, Shenzhen-Hong Kong Institute of Brain Science-Shenzhen Fundamental Research Institutions, Faculty of Life and Health Sciences, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055 China
| | | | - Xiaowei Li
- School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, 200240 China
| | - Shangguo Hou
- Institute of Systems and Physical Biology, Shenzhen Bay Laboratory, Shenzhen, 518055 China
| | - Dawei Jiang
- Department of Nuclear Medicine, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022 China
| | - Kai Liu
- Department of Chemistry, Tsinghua University, Beijing, 100084 China
| | - Xin Zhou
- State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, Chinese Academy of Sciences, Wuhan National Laboratory for Optoelectronics, Wuhan, 430071 China
| | - Hongjie Zhang
- State Key Laboratory of Rare Earth Resource Utilization, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, 130022 China
- Department of Chemistry, Tsinghua University, Beijing, 100084 China
| | - Maili Liu
- State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, Chinese Academy of Sciences, Wuhan National Laboratory for Optoelectronics, Wuhan, 430071 China
| | - Chunhai Fan
- School of Chemistry and Chemical Engineering, Frontiers Science Center for Transformative Molecules, Institute of Translational Medicine, Shanghai Jiao Tong University, Shanghai, 200240 China
| | - Yang Tian
- Shanghai Key Laboratory of Green Chemistry and Chemical Processes, School of Chemistry and Molecular Engineering, East China Normal University, Shanghai, 200241 China
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164
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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: 3.3] [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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165
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Ye H, Xu X, Wang J, Wang J, He Y, Mu Y, Shi G. Polarization effects on the fluorescence emission of zebrafish neurons using light-sheet microscopy. BIOMEDICAL OPTICS EXPRESS 2022; 13:6733-6744. [PMID: 36589590 PMCID: PMC9774877 DOI: 10.1364/boe.474588] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Revised: 11/21/2022] [Accepted: 11/22/2022] [Indexed: 06/17/2023]
Abstract
Light-sheet fluorescence microscopy (LSFM) makes use of a thin plane of light to optically section and image transparent tissues or organisms in vivo, which has the advantages of fast imaging speed and low phototoxicity. In this paper, we have employed light-sheet microscopy to investigate the polarization effects on fluorescence emission of zebrafish neurons via modifying the electric oscillation orientation of the excitation light. The intensity of the fluorescence emission from the excited zebrafish larvae follows a cosine square function with respect to the polarization state of the excitation light and reveals a 40% higher fluorescence emission when the polarization orientation is orthogonal to the illumination and detection axes. Through registration and subtraction of fluorescence images under different polarization states, we have demonstrated that most of the enhanced fluorescence signals are from the neuronal cells rather than the extracellular substance. This provides us a way to distinguish the cell boundaries and observe the organism structures with improved contrast and resolution.
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Affiliation(s)
- Hong Ye
- Jiangsu Key Laboratory of Medical Optics,
Suzhou Institute of Biomedical Engineering and Technology,
Chinese Academy of Sciences, Suzhou,
China
| | - Xin Xu
- Jiangsu Key Laboratory of Medical Optics,
Suzhou Institute of Biomedical Engineering and Technology,
Chinese Academy of Sciences, Suzhou,
China
- School of Biomedical Engineering (Suzhou),
Division of Life Sciences and Medicine, University of
Science and Technology of China, Hefei, China
| | - Jixiang Wang
- Jiangsu Key Laboratory of Medical Optics,
Suzhou Institute of Biomedical Engineering and Technology,
Chinese Academy of Sciences, Suzhou,
China
- School of Biomedical Engineering (Suzhou),
Division of Life Sciences and Medicine, University of
Science and Technology of China, Hefei, China
| | - Jing Wang
- Jiangsu Key Laboratory of Medical Optics,
Suzhou Institute of Biomedical Engineering and Technology,
Chinese Academy of Sciences, Suzhou,
China
- School of Biomedical Engineering (Suzhou),
Division of Life Sciences and Medicine, University of
Science and Technology of China, Hefei, China
| | - Yi He
- Jiangsu Key Laboratory of Medical Optics,
Suzhou Institute of Biomedical Engineering and Technology,
Chinese Academy of Sciences, Suzhou,
China
| | - Yu Mu
- Institute of Neuroscience, State Key
Laboratory of Neuroscience, Center for Excellence in Brain Science and
Intelligence Technology, Chinese Academy of
Sciences, Shanghai, China
| | - Guohua Shi
- Jiangsu Key Laboratory of Medical Optics,
Suzhou Institute of Biomedical Engineering and Technology,
Chinese Academy of Sciences, Suzhou,
China
- School of Biomedical Engineering (Suzhou),
Division of Life Sciences and Medicine, University of
Science and Technology of China, Hefei, China
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166
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Abstract
PURPOSE OF REVIEW Heart failure results in the high incidence and mortality all over the world. Mechanical properties of myocardium are critical determinants of cardiac function, with regional variations in myocardial contractility demonstrated within infarcted ventricles. Quantitative assessment of cardiac contractile function is therefore critical to identify myocardial infarction for the early diagnosis and therapeutic intervention. RECENT FINDINGS Current advancement of cardiac functional assessments is in pace with the development of imaging techniques. The methods tailored to advanced imaging have been widely used in cardiac magnetic resonance, echocardiography, and optical microscopy. In this review, we introduce fundamental concepts and applications of representative methods for each imaging modality used in both fundamental research and clinical investigations. All these methods have been designed or developed to quantify time-dependent 2-dimensional (2D) or 3D cardiac mechanics, holding great potential to unravel global or regional myocardial deformation and contractile function from end-systole to end-diastole. Computational methods to assess cardiac contractile function provide a quantitative insight into the analysis of myocardial mechanics during cardiac development, injury, and remodeling.
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167
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Su C, Gao Y, Zhou Y, Sun Y, Yan C, Yin H, Xiong B. AutoDeconJ: a GPU-accelerated ImageJ plugin for 3D light-field deconvolution with optimal iteration numbers predicting. Bioinformatics 2022; 39:6849514. [PMID: 36440906 PMCID: PMC9805591 DOI: 10.1093/bioinformatics/btac760] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2022] [Revised: 10/25/2022] [Accepted: 11/24/2022] [Indexed: 11/30/2022] Open
Abstract
MOTIVATION Light-field microscopy (LFM) is a compact solution to high-speed 3D fluorescence imaging. Usually, we need to do 3D deconvolution to the captured raw data. Although there are deep neural network methods that can accelerate the reconstruction process, the model is not universally applicable for all system parameters. Here, we develop AutoDeconJ, a GPU-accelerated ImageJ plugin for 4.4× faster and more accurate deconvolution of LFM data. We further propose an image quality metric for the deconvolution process, aiding in automatically determining the optimal number of iterations with higher reconstruction accuracy and fewer artifacts. RESULTS Our proposed method outperforms state-of-the-art light-field deconvolution methods in reconstruction time and optimal iteration numbers prediction capability. It shows better universality of different light-field point spread function (PSF) parameters than the deep learning method. The fast, accurate and general reconstruction performance for different PSF parameters suggests its potential for mass 3D reconstruction of LFM data. AVAILABILITY AND IMPLEMENTATION The codes, the documentation and example data are available on an open source at: https://github.com/Onetism/AutoDeconJ.git. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Changqing Su
- School of Mechanical, Electrical & Information Engineering, Shandong University, Weihai 264209, China,National Engineering Laboratory for Video Technology (NELVT), Peking University, Beijing 100871, China
| | - Yuhan Gao
- Lishui Institute of Hangzhou Dianzi University, Hangzhou 323000, China
| | - You Zhou
- School of Electronic Science and Engineering, Nanjing University, Nanjing 210023, China
| | - Yaoqi Sun
- Lishui Institute of Hangzhou Dianzi University, Hangzhou 323000, China
| | - Chenggang Yan
- School of Mechanical, Electrical & Information Engineering, Shandong University, Weihai 264209, China,Lishui Institute of Hangzhou Dianzi University, Hangzhou 323000, China
| | - Haibing Yin
- Lishui Institute of Hangzhou Dianzi University, Hangzhou 323000, China
| | - Bo Xiong
- To whom correspondence should be addressed.
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168
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Kim JJH, Parajuli S, Sinha A, Mahamdeh M, van den Boomen M, Coll-Font J, Chen LS, Fan Y, Eder RA, Phipps K, Yuan S, Nguyen C. Pocket CLARITY enables distortion-mitigated cardiac microstructural tissue characterization of large-scale specimens. Front Cardiovasc Med 2022; 9:1037500. [PMID: 36451924 PMCID: PMC9701703 DOI: 10.3389/fcvm.2022.1037500] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2022] [Accepted: 10/27/2022] [Indexed: 11/15/2022] Open
Abstract
Molecular phenotyping by imaging of intact tissues has been used to reveal 3D molecular and structural coherence in tissue samples using tissue clearing techniques. However, clearing and imaging of cardiac tissue remains challenging for large-scale (>100 mm3) specimens due to sample distortion. Thus, directly assessing tissue microstructural geometric properties confounded by distortion such as cardiac helicity has been limited. To combat sample distortion, we developed a passive CLARITY technique (Pocket CLARITY) that utilizes a permeable cotton mesh pocket to encapsulate the sample to clear large-scale cardiac swine samples with minimal tissue deformation and protein loss. Combined with light sheet auto-fluorescent and scattering microscopy, Pocket CLARITY enabled the characterization of myocardial microstructural helicity of cardiac tissue from control, heart failure, and myocardial infarction in swine. Pocket CLARITY revealed with high fidelity that transmural microstructural helicity of the heart is significantly depressed in cardiovascular disease (CVD), thereby revealing new insights at the tissue level associated with impaired cardiac function.
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Affiliation(s)
- Joan J. H. Kim
- Cardiovascular Research Center, Massachusetts General Hospital, Charlestown, MA, United States
| | - Shestruma Parajuli
- Cardiovascular Research Center, Massachusetts General Hospital, Charlestown, MA, United States
| | - Aman Sinha
- Cardiovascular Research Center, Massachusetts General Hospital, Charlestown, MA, United States
| | - Mohammed Mahamdeh
- Cardiovascular Research Center, Massachusetts General Hospital, Charlestown, MA, United States,A.A. Martinos Center for Biomedical Imaging, Massachusetts General Hospital, Boston, MA, United States
| | - Maaike van den Boomen
- Cardiovascular Research Center, Massachusetts General Hospital, Charlestown, MA, United States,A.A. Martinos Center for Biomedical Imaging, Massachusetts General Hospital, Boston, MA, United States,Department of Radiology, University Medical Center Groningen, University of Groningen, Groningen, Netherlands,Department of Medicine, Harvard Medical School, Boston, MA, United States
| | - Jaume Coll-Font
- Cardiovascular Research Center, Massachusetts General Hospital, Charlestown, MA, United States,A.A. Martinos Center for Biomedical Imaging, Massachusetts General Hospital, Boston, MA, United States,Department of Medicine, Harvard Medical School, Boston, MA, United States
| | - Lily Shi Chen
- Cardiovascular Research Center, Massachusetts General Hospital, Charlestown, MA, United States
| | - Yiling Fan
- Cardiovascular Research Center, Massachusetts General Hospital, Charlestown, MA, United States,A.A. Martinos Center for Biomedical Imaging, Massachusetts General Hospital, Boston, MA, United States,Department of Mechanical Engineering, Massachusetts Institute of Technology, Cambridge, MA, United States
| | - Robert A. Eder
- Cardiovascular Research Center, Massachusetts General Hospital, Charlestown, MA, United States
| | - Kellie Phipps
- Cardiovascular Research Center, Massachusetts General Hospital, Charlestown, MA, United States
| | - Shiaulou Yuan
- Cardiovascular Research Center, Massachusetts General Hospital, Charlestown, MA, United States,A.A. Martinos Center for Biomedical Imaging, Massachusetts General Hospital, Boston, MA, United States,Department of Medicine, Harvard Medical School, Boston, MA, United States
| | - Christopher Nguyen
- Cardiovascular Research Center, Massachusetts General Hospital, Charlestown, MA, United States,A.A. Martinos Center for Biomedical Imaging, Massachusetts General Hospital, Boston, MA, United States,Department of Medicine, Harvard Medical School, Boston, MA, United States,Division of Health Science Technology, Harvard-Massachusetts Institute of Technology, Cambridge, MA, United States,Cardiovascular Innovation Research Center, Heart, Vascular, and Thoracic Institute, Cleveland Clinic, Cleveland, OH, United States,*Correspondence: Christopher Nguyen,
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169
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Xia Q, Yin J, Guo Z, Cheng JX. Mid-Infrared Photothermal Microscopy: Principle, Instrumentation, and Applications. J Phys Chem B 2022; 126:8597-8613. [PMID: 36285985 DOI: 10.1021/acs.jpcb.2c05827] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
Midinfrared photothermal (MIP) microscopy, also called optical photothermal infrared (O-PTIR) microscopy, is an emerging tool for bond-selective chemical imaging of living biological and material samples. In MIP microscopy, a visible probe beam detects the photothermal-based contrast induced by a vibrational absorption. With submicron spatial resolution, high spectral fidelity, and reduced water absorption background, MIP microscopy has overcome the limitations in infrared chemical imaging methods. In this review, we summarize the basic principle of MIP microscopy, the different origins of MIP contrasts, and recent technology development that pushed the resolution, speed, and sensitivity of MIP imaging to a new stage. We further emphasize its broad applications in life science and material characterization, and provide a perspective of future technical advances.
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Affiliation(s)
- Qing Xia
- Department of Electrical and Computer Engineering, Boston University, Boston, Massachusetts 02215, United States.,Photonics Center, Boston University, Boston, Massachusetts 02215, United States
| | - Jiaze Yin
- Department of Electrical and Computer Engineering, Boston University, Boston, Massachusetts 02215, United States.,Photonics Center, Boston University, Boston, Massachusetts 02215, United States
| | - Zhongyue Guo
- Photonics Center, Boston University, Boston, Massachusetts 02215, United States.,Department of Biomedical Engineering, Boston University, Boston, Massachusetts 02215, United States
| | - Ji-Xin Cheng
- Department of Electrical and Computer Engineering, Boston University, Boston, Massachusetts 02215, United States.,Photonics Center, Boston University, Boston, Massachusetts 02215, United States.,Department of Biomedical Engineering, Boston University, Boston, Massachusetts 02215, United States
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170
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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: 0.3] [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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171
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Keomanee-Dizon K, Jones M, Luu P, Fraser SE, Truong TV. Extended depth-of-field light-sheet microscopy improves imaging of large volumes at high numerical aperture. APPLIED PHYSICS LETTERS 2022; 121:163701. [PMID: 36276589 PMCID: PMC9586705 DOI: 10.1063/5.0101426] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Accepted: 09/23/2022] [Indexed: 06/16/2023]
Abstract
Light-sheet microscopes must compromise among field of view, optical sectioning, resolution, and detection efficiency. High-numerical-aperture (NA) detection objective lenses provide higher resolution, but their narrow depth of field inefficiently captures the fluorescence signal generated throughout the thickness of the illumination light sheet when imaging large volumes. Here, we present ExD-SPIM (extended depth-of-field selective-plane illumination microscopy), an improved light-sheet microscopy strategy that solves this limitation by extending the depth of field (DOF) of high-NA detection objectives to match the thickness of the illumination light sheet. This extension of the DOF uses a phase mask to axially stretch the point-spread function of the objective lens while largely preserving lateral resolution. This matching of the detection DOF to the illumination-sheet thickness increases the total fluorescence collection, reduces the background, and improves the overall signal-to-noise ratio (SNR), as shown by numerical simulations, imaging of bead phantoms, and imaging living animals. In comparison to conventional light sheet imaging with low-NA detection that yields equivalent DOF, the results show that ExD-SPIM increases the SNR by more than threefold and dramatically reduces the rate of photobleaching. Compared to conventional high-NA detection, ExD-SPIM improves the signal sensitivity and volumetric coverage of whole-brain activity imaging, increasing the number of detected neurons by over a third.
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Affiliation(s)
- Kevin Keomanee-Dizon
- Translational Imaging Center, University of Southern California, Los Angeles, California 90089, USA
| | - Matt Jones
- Translational Imaging Center, University of Southern California, Los Angeles, California 90089, USA
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172
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Rodriguez-Gatica JE, Iefremova V, Sokhranyaeva L, Yeung SWCA, Breitkreuz Y, Brüstle O, Schwarz MK, Kubitscheck U. Imaging three-dimensional brain organoid architecture from meso- to nanoscale across development. Development 2022; 149:276135. [DOI: 10.1242/dev.200439] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2021] [Accepted: 06/28/2022] [Indexed: 11/20/2022]
Abstract
ABSTRACT
Organoids are stem cell-derived three-dimensional cultures offering a new avenue to model human development and disease. Brain organoids allow the study of various aspects of human brain development in the finest details in vitro in a tissue-like context. However, spatial relationships of subcellular structures, such as synaptic contacts between distant neurons, are hardly accessible by conventional light microscopy. This limitation can be overcome by systems that quickly image the entire organoid in three dimensions and in super-resolution. To that end we have developed a system combining tissue expansion and light-sheet fluorescence microscopy for imaging and quantifying diverse spatial parameters during organoid development. This technique enables zooming from a mesoscopic perspective into super-resolution within a single imaging session, thus revealing cellular and subcellular structural details in three spatial dimensions, including unequivocal delineation of mitotic cleavage planes as well as the alignment of pre- and postsynaptic proteins. We expect light-sheet fluorescence expansion microscopy to facilitate qualitative and quantitative assessment of organoids in developmental and disease-related studies.
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Affiliation(s)
| | - Vira Iefremova
- Institute of Reconstructive Neurobiology, University of Bonn Medical Faculty and University Hospital Bonn 2 , Venusberg-Campus 1, 53127 Bonn , Germany
| | - Liubov Sokhranyaeva
- Institute of Experimental Epileptology and Cognition Research (IEECR), University of Bonn Medical School 3 , Sigmund-Freud-Str. 25, 53127 Bonn , Germany
| | - Si Wah Christina Au Yeung
- Institute of Reconstructive Neurobiology, University of Bonn Medical Faculty and University Hospital Bonn 2 , Venusberg-Campus 1, 53127 Bonn , Germany
| | - Yannik Breitkreuz
- LIFE & BRAIN GmbH 4 , Cellomics Unit, Venusberg-Campus 1, D-53127 Bonn , Germany
| | - Oliver Brüstle
- Institute of Reconstructive Neurobiology, University of Bonn Medical Faculty and University Hospital Bonn 2 , Venusberg-Campus 1, 53127 Bonn , Germany
- LIFE & BRAIN GmbH 4 , Cellomics Unit, Venusberg-Campus 1, D-53127 Bonn , Germany
| | - Martin Karl Schwarz
- Institute of Experimental Epileptology and Cognition Research (IEECR), University of Bonn Medical School 3 , Sigmund-Freud-Str. 25, 53127 Bonn , Germany
- LIFE & BRAIN GmbH 4 , Cellomics Unit, Venusberg-Campus 1, D-53127 Bonn , Germany
| | - Ulrich Kubitscheck
- Institute of Physical and Theoretical Chemistry, University of Bonn 1 , Wegelerstr. 12, 53115 Bonn , Germany
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173
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Light-field microscopy with correlated beams for high-resolution volumetric imaging. Sci Rep 2022; 12:16823. [PMID: 36207387 PMCID: PMC9547068 DOI: 10.1038/s41598-022-21240-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2022] [Accepted: 09/26/2022] [Indexed: 11/16/2022] Open
Abstract
Light-field microscopy represents a promising solution for microscopic volumetric imaging, thanks to its capability to encode information on multiple planes in a single acquisition. This is achieved through its peculiar simultaneous capture of information on light spatial distribution and propagation direction. However, state-of-the-art light-field microscopes suffer from a detrimental loss of spatial resolution compared to standard microscopes. In this article, we experimentally demonstrate the working principle of a new scheme, called Correlation Light-field Microscopy (CLM), where the correlation between two light beams is exploited to achieve volumetric imaging with a resolution that is only limited by diffraction. In CLM, a correlation image is obtained by measuring intensity correlations between a large number of pairs of ultra-short frames; each pair of frames is illuminated by the two correlated beams, and is exposed for a time comparable with the source coherence time. We experimentally show the capability of CLM to recover the information contained in out-of-focus planes within three-dimensional test targets and biomedical phantoms. In particular, we demonstrate the improvement of the depth of field enabled by CLM with respect to a conventional microscope characterized by the same resolution. Moreover, the multiple perspectives contained in a single correlation image enable reconstructing over 50 distinguishable transverse planes within a 1 mm3 sample.
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174
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Bissardon C, Mermet X, Quintard C, Sanjuan F, Fouillet Y, Bottausci F, Carriere M, Rivera F, Blandin P. Selective plane illumination microscope dedicated to volumetric imaging in microfluidic chambers. BIOMEDICAL OPTICS EXPRESS 2022; 13:5261-5274. [PMID: 36425641 PMCID: PMC9664896 DOI: 10.1364/boe.455377] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Revised: 04/11/2022] [Accepted: 04/11/2022] [Indexed: 05/31/2023]
Abstract
In this article, we are presenting an original selective plane illumination fluorescence microscope dedicated to image "Organ-on-chip"-like biostructures in microfluidic chips. In order to be able to morphologically analyze volumetric samples in development at the cellular scale inside microfluidic chambers, the setup presents a compromise between relatively large field of view (∼ 200 µm) and moderate resolution (∼ 5 µm). The microscope is based on a simple design, built around the chip and its microfluidic environment to allow 3D imaging inside the chip. In particular, the sample remains horizontally avoiding to disturb the fluidics phenomena. The experimental setup, its optical characterization and the first volumetric images are reported.
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Affiliation(s)
| | - Xavier Mermet
- Univ. Grenoble Alpes, CEA, LETI, DTBS, F-38000 Grenoble, France
| | | | - Federico Sanjuan
- Univ. de Pau et des Pays de l'Adour, E2S UPPA, CNRS, Total, LFCR, Pau, France
| | - Yves Fouillet
- Univ. Grenoble Alpes, CEA, LETI, DTBS, F-38000 Grenoble, France
| | | | - Marie Carriere
- Univ. Grenoble-Alpes, CEA, CNRS, IRIG, SyMMES, F-38000 Grenoble, France
| | - Florence Rivera
- Univ. Grenoble Alpes, CEA, LETI, DTBS, F-38000 Grenoble, France
| | - Pierre Blandin
- Univ. Grenoble Alpes, CEA, LETI, DTBS, F-38000 Grenoble, France
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175
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Yang G, Wang L, Qin X, Chen X, Liang Y, Jin X, Chen C, Zhang W, Pan W, Li H. Heterogeneities of zebrafish vasculature development studied by a high throughput light-sheet flow imaging system. BIOMEDICAL OPTICS EXPRESS 2022; 13:5344-5357. [PMID: 36425637 PMCID: PMC9664872 DOI: 10.1364/boe.470058] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/11/2022] [Revised: 08/17/2022] [Accepted: 08/30/2022] [Indexed: 06/16/2023]
Abstract
Zebrafish is one of the ideal model animals to study the structural and functional heterogeneities in development. However, the lack of high throughput 3D imaging techniques has limited studies to only a few samples, despite zebrafish spawning tens of embryos at once. Here, we report a light-sheet flow imaging system (LS-FIS) based on light-sheet illumination and a continuous flow imager. LS-FIS enables whole-larva 3D imaging of tens of samples within half an hour. The high throughput 3D imaging capability of LS-FIS was demonstrated with the developmental study of the zebrafish vasculature from 3 to 9 days post-fertilization. Statistical analysis shows significant variances in trunk vessel development but less in hyaloid vessel development.
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Affiliation(s)
- Guang Yang
- School of Biomedical Engineering (Suzhou), Division of Life Sciences and Medicine, University of Science and Technology of China, Suzhou 215163, China
- Jiangsu Key Laboratory of Medical Optics,
Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Sciences, Suzhou 215163, China
| | - Linbo Wang
- School of Biomedical Engineering (Suzhou), Division of Life Sciences and Medicine, University of Science and Technology of China, Suzhou 215163, China
- Jiangsu Key Laboratory of Medical Optics,
Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Sciences, Suzhou 215163, China
| | - Xiaofei Qin
- Jiangsu Key Laboratory of Medical Optics,
Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Sciences, Suzhou 215163, China
| | - Xiaohu Chen
- Jiangsu Key Laboratory of Medical Optics,
Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Sciences, Suzhou 215163, China
| | - Yong Liang
- School of Biomedical Engineering (Suzhou), Division of Life Sciences and Medicine, University of Science and Technology of China, Suzhou 215163, China
- Jiangsu Key Laboratory of Medical Optics,
Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Sciences, Suzhou 215163, China
| | - Xin Jin
- Jiangsu Key Laboratory of Medical Optics,
Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Sciences, Suzhou 215163, China
| | - Chong Chen
- School of Biomedical Engineering (Suzhou), Division of Life Sciences and Medicine, University of Science and Technology of China, Suzhou 215163, China
- Jiangsu Key Laboratory of Medical Optics,
Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Sciences, Suzhou 215163, China
| | - Wenjuan Zhang
- Shanghai Institute of Nutrition and Health, Chinese Academy of Sciences, Shanghai 200031, China
| | - Weijun Pan
- Shanghai Institute of Nutrition and Health, Chinese Academy of Sciences, Shanghai 200031, China
| | - Hui Li
- Jiangsu Key Laboratory of Medical Optics,
Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Sciences, Suzhou 215163, China
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176
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Abstract
When the microscope was first introduced to scientists in the 17th century, it started a revolution. Suddenly, a whole new world, invisible to the naked eye, was opened to curious explorers. In response to this realization, Nehemiah Grew, an English plant anatomist and physiologist and one of the early microscopists, noted in 1682 "that Nothing hereof remains further to be known, is a Thought not well Calculated". Since Grew made his observations, the microscope has undergone numerous variations, developing from early compound microscopes-hollow metal tubes with a lens on each end-to the modern, sophisticated, out-of-the-box super-resolution microscopes available to researchers today. In this Overview article, I describe these developments and discuss how each new and improved variant of the microscope led to major breakthroughs in the life sciences, with a focus on the plant field. These advances start with Grew's simple and-at the time-surprising realization that plant cells are as complex as animals cells, and that the different parts of the plant body indeed qualify to be called "organs", then move on to the development of the groundbreaking "cell theory" in the mid-19th century and the description of eu- and heterochromatin in the early 20th century, and finish with the precise localization of individual proteins in intact, living cells that we can perform today. Indeed, Grew was right; with ever-increasing resolution, there really does not seem to be an end to what can be explored with a microscope. © 2022 The Authors. Current Protocols published by Wiley Periodicals LLC.
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Affiliation(s)
- Marc Somssich
- School of BioSciencesUniversity of MelbourneParkvilleVictoriaAustralia
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177
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Intravital microscopy for real-time monitoring of drug delivery and nanobiological processes. Adv Drug Deliv Rev 2022; 189:114528. [PMID: 36067968 DOI: 10.1016/j.addr.2022.114528] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2022] [Revised: 08/10/2022] [Accepted: 08/30/2022] [Indexed: 01/24/2023]
Abstract
Intravital microscopy (IVM) expands our understanding of cellular and molecular processes, with applications ranging from fundamental biology to (patho)physiology and immunology, as well as from drug delivery to drug processing and drug efficacy testing. In this review, we highlight modalities, methods and model organisms that make up today's IVM landscape, and we present how IVM - via its high spatiotemporal resolution - enables analysis of metabolites, small molecules, nanoparticles, immune cells, and the (tumor) tissue microenvironment. We furthermore present examples of how IVM facilitates the elucidation of nanomedicine kinetics and targeting mechanisms, as well as of biological processes such as immune cell death, host-pathogen interactions, metabolic states, and disease progression. We conclude by discussing the prospects of IVM clinical translation and examining the integration of machine learning in future IVM practice.
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178
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Ahmad A, Sala F, Paiè P, Candeo A, D'Annunzio S, Zippo A, Frindel C, Osellame R, Bragheri F, Bassi A, Rousseau D. On the robustness of machine learning algorithms toward microfluidic distortions for cell classification via on-chip fluorescence microscopy. LAB ON A CHIP 2022; 22:3453-3463. [PMID: 35946995 DOI: 10.1039/d2lc00482h] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Single-cell imaging and sorting are critical technologies in biology and clinical applications. The power of these technologies is increased when combined with microfluidics, fluorescence markers, and machine learning. However, this quest faces several challenges. One of these is the effect of the sample flow velocity on the classification performances. Indeed, cell flow speed affects the quality of image acquisition by increasing motion blur and decreasing the number of acquired frames per sample. We investigate how these visual distortions impact the final classification task in a real-world use-case of cancer cell screening, using a microfluidic platform in combination with light sheet fluorescence microscopy. We demonstrate, by analyzing both simulated and experimental data, that it is possible to achieve high flow speed and high accuracy in single-cell classification. We prove that it is possible to overcome the 3D slice variability of the acquired 3D volumes, by relying on their 2D sum z-projection transformation, to reach an efficient real time classification with an accuracy of 99.4% using a convolutional neural network with transfer learning from simulated data. Beyond this specific use-case, we provide a web platform to generate a synthetic dataset and to investigate the effect of flow speed on cell classification for any biological samples and a large variety of fluorescence microscopes (https://www.creatis.insa-lyon.fr/site7/en/MicroVIP).
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Affiliation(s)
- Ali Ahmad
- Laboratoire Angevin de Recherche en Ingénierie des Systèmes (LARIS), UMR INRAE IRHS, Université d'Angers, 62 Avenue Notre Dame du Lac, 49000 Angers, France.
- Centre de Recherche en Acquisition et Traitement de l'Image pour la Santé (CREATIS), CNRS UMR 5220 - INSERM U1206, Université Lyon 1, Insa de Lyon, Lyon, France
| | - Federico Sala
- Department of Physics, Politecnico di Milano, Piazza Leonardo da Vinci 32, 20133 Milano, Italy
- Istituto di Fotonica e Nanotecnologie, CNR, Piazza Leonardo da Vinci 32, 20133 Milano, Italy
| | - Petra Paiè
- Istituto di Fotonica e Nanotecnologie, CNR, Piazza Leonardo da Vinci 32, 20133 Milano, Italy
| | - Alessia Candeo
- Department of Physics, Politecnico di Milano, Piazza Leonardo da Vinci 32, 20133 Milano, Italy
| | | | | | - Carole Frindel
- Centre de Recherche en Acquisition et Traitement de l'Image pour la Santé (CREATIS), CNRS UMR 5220 - INSERM U1206, Université Lyon 1, Insa de Lyon, Lyon, France
| | - Roberto Osellame
- Department of Physics, Politecnico di Milano, Piazza Leonardo da Vinci 32, 20133 Milano, Italy
- Istituto di Fotonica e Nanotecnologie, CNR, Piazza Leonardo da Vinci 32, 20133 Milano, Italy
| | - Francesca Bragheri
- Istituto di Fotonica e Nanotecnologie, CNR, Piazza Leonardo da Vinci 32, 20133 Milano, Italy
| | - Andrea Bassi
- Department of Physics, Politecnico di Milano, Piazza Leonardo da Vinci 32, 20133 Milano, Italy
- Istituto di Fotonica e Nanotecnologie, CNR, Piazza Leonardo da Vinci 32, 20133 Milano, Italy
| | - David Rousseau
- Laboratoire Angevin de Recherche en Ingénierie des Systèmes (LARIS), UMR INRAE IRHS, Université d'Angers, 62 Avenue Notre Dame du Lac, 49000 Angers, France.
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179
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Olesker D, Harvey AR, Taylor JM. Snapshot volumetric imaging with engineered point-spread functions. OPTICS EXPRESS 2022; 30:33490-33501. [PMID: 36242384 DOI: 10.1364/oe.465113] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/25/2022] [Accepted: 08/11/2022] [Indexed: 06/16/2023]
Abstract
The biological world involves intracellular and intercellular interactions that occur at high speed, at multiple scales and in three dimensions. Acquiring 3D images, however, typically requires a compromise in either spatial or temporal resolution compared to 2D imaging. Conventional 2D fluorescence imaging provides high spatial resolution but requires plane-by-plane imaging of volumes. Conversely, snapshot methods such as light-field microscopy allow video-rate imaging, but at the cost of spatial resolution. Here we introduce 3D engineered point-spread function microscopy (3D-EPM), enabling snapshot imaging of real-world 3D extended biological structures while retaining the native resolution of the microscope in space and time. Our new computational recovery strategy is the key to volumetrically reconstructing arbitrary 3D structures from the information encapsulated in 2D raw EPM images. We validate our technique on both point-like and extended samples, and demonstrate its power by imaging the intracellular motion of chloroplasts undergoing cyclosis in a sample of Egeria densa. Our technique represents a generalised computational methodology for 3D image recovery which is readily adapted to a diverse range of existing microscopy platforms and engineered point-spread functions. We therefore expect it to find broad applicability in the study of rapid biological dynamics in 3D.
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180
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Isotropic imaging across spatial scales with axially swept light-sheet microscopy. Nat Protoc 2022; 17:2025-2053. [PMID: 35831614 PMCID: PMC10111370 DOI: 10.1038/s41596-022-00706-6] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2021] [Accepted: 03/30/2022] [Indexed: 11/09/2022]
Abstract
Light-sheet fluorescence microscopy is a rapidly growing technique that has gained tremendous popularity in the life sciences owing to its high-spatiotemporal resolution and gentle, non-phototoxic illumination. In this protocol, we provide detailed directions for the assembly and operation of a versatile light-sheet fluorescence microscopy variant, referred to as axially swept light-sheet microscopy (ASLM), that delivers an unparalleled combination of field of view, optical resolution and optical sectioning. To democratize ASLM, we provide an overview of its working principle and applications to biological imaging, as well as pragmatic tips for the assembly, alignment and control of its optical systems. Furthermore, we provide detailed part lists and schematics for several variants of ASLM that together can resolve molecular detail in chemically expanded samples, subcellular organization in living cells or the anatomical composition of chemically cleared intact organisms. We also provide software for instrument control and discuss how users can tune imaging parameters to accommodate diverse sample types. Thus, this protocol will serve not only as a guide for both introductory and advanced users adopting ASLM, but as a useful resource for any individual interested in deploying custom imaging technology. We expect that building an ASLM will take ~1-2 months, depending on the experience of the instrument builder and the version of the instrument.
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181
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Dalmasso G, Musy M, Niksic M, Robert-Moreno A, Badía-Careaga C, Sanz-Ezquerro JJ, Sharpe J. 4D reconstruction of murine developmental trajectories using spherical harmonics. Dev Cell 2022; 57:2140-2150.e5. [PMID: 36055247 PMCID: PMC9481268 DOI: 10.1016/j.devcel.2022.08.005] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2021] [Revised: 05/02/2022] [Accepted: 08/11/2022] [Indexed: 11/30/2022]
Abstract
Normal organogenesis cannot be recapitulated in vitro for mammalian organs, unlike in species including Drosophila and zebrafish. Available 3D data in the form of ex vivo images only provide discrete snapshots of the development of an organ morphology. Here, we propose a computer-based approach to recreate its continuous evolution in time and space from a set of 3D volumetric images. Our method is based on the remapping of shape data into the space of the coefficients of a spherical harmonics expansion where a smooth interpolation over time is simpler. We tested our approach on mouse limb buds and embryonic hearts. A key advantage of this method is that the resulting 4D trajectory can take advantage of all the available data while also being able to interpolate well through time intervals for which there are little or no data. This allows for a quantitative, data-driven 4D description of mouse limb morphogenesis. Computer-based method recreating a 3D plus time evolution of a set of volumetric images Technique based on the interpolation of the coefficients of spherical harmonics Data-driven quantitative 4D description of limb and heart morphogenesis Quantitatively reliable baseline description of organ development
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Affiliation(s)
- Giovanni Dalmasso
- European Molecular Biology Laboratory (EMBL-Barcelona), 08003 Barcelona, Spain.
| | - Marco Musy
- European Molecular Biology Laboratory (EMBL-Barcelona), 08003 Barcelona, Spain
| | - Martina Niksic
- Centre for Genomic Regulation (CRG), 08003 Barcelona, Spain
| | | | | | - Juan Jose Sanz-Ezquerro
- Centro Nacional de Investigaciones Cardiovasculares (CNIC), 28029 Madrid, Spain; Centro Nacional de Biotecnologia (CSIC Madrid), 28049 Madrid, Spain
| | - James Sharpe
- European Molecular Biology Laboratory (EMBL-Barcelona), 08003 Barcelona, Spain; Institució Catalana de Recerca i Estudis Avançats (ICREA), 08010 Barcelona, Spain.
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182
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Guan G, Zhao Z, Tang C. Delineating the mechanisms and design principles of Caenorhabditis elegans embryogenesis using in toto high-resolution imaging data and computational modeling. Comput Struct Biotechnol J 2022; 20:5500-5515. [PMID: 36284714 PMCID: PMC9562942 DOI: 10.1016/j.csbj.2022.08.024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2022] [Revised: 08/10/2022] [Accepted: 08/11/2022] [Indexed: 11/19/2022] Open
Abstract
The nematode (roundworm) Caenorhabditis elegans is one of the most popular animal models for the study of developmental biology, as its invariant development and transparent body enable in toto cellular-resolution fluorescence microscopy imaging of developmental processes at 1-min intervals. This has led to the development of various computational tools for the systematic and automated analysis of imaging data to delineate the molecular and cellular processes throughout the embryogenesis of C. elegans, such as those associated with cell lineage, cell migration, cell morphology, and gene activity. In this review, we first introduce C. elegans embryogenesis and the development of techniques for tracking cell lineage and reconstructing cell morphology during this process. We then contrast the developmental modes of C. elegans and the customized technologies used for studying them with the ones of other animal models, highlighting its advantage for studying embryogenesis with exceptional spatial and temporal resolution. This is followed by an examination of the physical models that have been devised-based on accurate determinations of developmental processes afforded by analyses of imaging data-to interpret the early embryonic development of C. elegans from subcellular to intercellular levels of multiple cells, which focus on two key processes: cell polarization and morphogenesis. We subsequently discuss how quantitative data-based theoretical modeling has improved our understanding of the mechanisms of C. elegans embryogenesis. We conclude by summarizing the challenges associated with the acquisition of C. elegans embryogenesis data, the construction of algorithms to analyze them, and the theoretical interpretation.
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Affiliation(s)
- Guoye Guan
- Center for Quantitative Biology, Peking University, Beijing 100871, China
| | - Zhongying Zhao
- Department of Biology, Hong Kong Baptist University, Hong Kong 999077, China
- State Key Laboratory of Environmental and Biological Analysis, Hong Kong Baptist University, Hong Kong 999077, China
| | - Chao Tang
- Center for Quantitative Biology, Peking University, Beijing 100871, China
- Peking–Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China
- School of Physics, Peking University, Beijing 100871, China
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183
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Bon P, Cognet L. On Some Current Challenges in High-Resolution Optical Bioimaging. ACS PHOTONICS 2022; 9:2538-2546. [PMID: 35996373 PMCID: PMC9389608 DOI: 10.1021/acsphotonics.2c00606] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
In this Perspective we propose our current point of view and a suggestive roadmap on the field of high-resolution optical microscopy dedicated to bioimaging. Motivated by biological applications, researchers have indeed devised an impressive amount of strategies to address the diverse constraints of imaging and studying biological matter down to the molecular scale, making this interdisciplinary research field a vibrant forum for creativity. Throughout the discussion, we highlight several striking recent successes in this quest. We also identify some next challenges still ahead to apprehend biological questions in increasingly complex living organisms for integrative studies in a minimally invasive manner.
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Affiliation(s)
- Pierre Bon
- Laboratoire
Photonique Numérique et Nanosciences, University of Bordeaux, F-33400 Talence, France
- LP2N
UMR 5298, Institut d’Optique Graduate
School, CNRS, F-33400 Talence, France
| | - Laurent Cognet
- Laboratoire
Photonique Numérique et Nanosciences, University of Bordeaux, F-33400 Talence, France
- LP2N
UMR 5298, Institut d’Optique Graduate
School, CNRS, F-33400 Talence, France
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184
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Ye H, Shi G. High-Resolution Multiscale Imaging Enabled by Hybrid Open-Top Light-Sheet Microscopy. BME FRONTIERS 2022; 2022:9761314. [PMID: 37850184 PMCID: PMC10521721 DOI: 10.34133/2022/9761314] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2022] [Accepted: 07/14/2022] [Indexed: 10/19/2023] Open
Affiliation(s)
- Hong Ye
- Jiangsu Key Laboratory of Medical Optics, Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Science, Suzhou, China
| | - Guohua Shi
- Jiangsu Key Laboratory of Medical Optics, Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Science, Suzhou, China
- School of Biomedical Engineering (Suzhou), Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China
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185
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Hu Y, Liang D, Wang J, Xuan Y, Zhao F, Liu J, Li R. Background-free wide-field fluorescence imaging using edge detection combined with HiLo. JOURNAL OF BIOPHOTONICS 2022; 15:e202200031. [PMID: 35488180 DOI: 10.1002/jbio.202200031] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/08/2022] [Revised: 04/01/2022] [Accepted: 04/28/2022] [Indexed: 06/14/2023]
Abstract
Fluorescence microscopy has been widely used in the field of biological imaging, but the disturbance of background noise has always been an unavoidable phenomenon. To obtain a background free image, a virtual HiLo based on edge detection (V-HiLo-ED) method for background removing is proposed, which is different from the existing popular software algorithms that obtain the background-free image by subtracting the estimated background, but the background-free image is directly reconstructed by estimating the foreground. Compared with two other popular software-based methods, the wavelet-based background and noise subtraction algorithm (WBNS) and the rolling ball algorithm (RBA), the V-HiLo-ED owns a better quality on achieving background-free imaging. Compared with hardware-based method such as HiLo method, V-HiLo-ED exhibits almost the same performance but faster speed. In combination with light sheet microscopy, the V-HiLo-ED further improves the signal-to-noise ratio of images with thick light-sheet. These experiment results indicate that the V-HiLo-ED owns the potentiality in many other image applications such as endoscopy.
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Affiliation(s)
- Yuyao Hu
- State Key Laboratory of High Field Laser Physics and CAS Center for Excellence in Ultra-intense Laser Science, Shanghai Institute of Optics and Fine Mechanics, Chinese Academy of Sciences, Shanghai, China
- University Center of Materials Science and Optoelectronics Engineering, University of Chinese Academy of Sciences, Beijing, China
| | - Dong Liang
- State Key Laboratory of High Field Laser Physics and CAS Center for Excellence in Ultra-intense Laser Science, Shanghai Institute of Optics and Fine Mechanics, Chinese Academy of Sciences, Shanghai, China
- School of Physics Science and Engineering, Tongji University, Shanghai, China
| | - Jing Wang
- Institute of Photonic Chips, University of Shanghai for Science and Technology, Shanghai, China
- Centre for Artificial-Intelligence Nanophotonics, School of Optical-Electrical and Computer Engineering, University of Shanghai for Science and Technology, Shanghai, China
| | - Yaping Xuan
- State Key Laboratory of High Field Laser Physics and CAS Center for Excellence in Ultra-intense Laser Science, Shanghai Institute of Optics and Fine Mechanics, Chinese Academy of Sciences, Shanghai, China
- University Center of Materials Science and Optoelectronics Engineering, University of Chinese Academy of Sciences, Beijing, China
| | - Fu Zhao
- State Key Laboratory of High Field Laser Physics and CAS Center for Excellence in Ultra-intense Laser Science, Shanghai Institute of Optics and Fine Mechanics, Chinese Academy of Sciences, Shanghai, China
- University Center of Materials Science and Optoelectronics Engineering, University of Chinese Academy of Sciences, Beijing, China
| | - Jun Liu
- State Key Laboratory of High Field Laser Physics and CAS Center for Excellence in Ultra-intense Laser Science, Shanghai Institute of Optics and Fine Mechanics, Chinese Academy of Sciences, Shanghai, China
- University Center of Materials Science and Optoelectronics Engineering, University of Chinese Academy of Sciences, Beijing, China
| | - Ruxin Li
- State Key Laboratory of High Field Laser Physics and CAS Center for Excellence in Ultra-intense Laser Science, Shanghai Institute of Optics and Fine Mechanics, Chinese Academy of Sciences, Shanghai, China
- University Center of Materials Science and Optoelectronics Engineering, University of Chinese Academy of Sciences, Beijing, China
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186
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Cai Y, Chen Y, Xia Y, Zheng S, Liu Z, Shi K. Single-Lens Light-Sheet Fluorescence Microscopy Based on Micro-Mirror Array. LASER & PHOTONICS REVIEWS 2022; 16:2100026. [PMID: 36389089 PMCID: PMC9648671 DOI: 10.1002/lpor.202100026] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
Conventional light sheet fluorescence microscopy (LSFM) utilizes two perpendicularly arranged objective lenses for optical excitation and detection, respectively. Such a configuration often limits the use of high-numerical-aperture (NA) objectives or requires specially designed long-working-distance objectives. Here, a LSFM based on a micro-mirror array (MMA) to enable light sheet imaging with a single objective lens is reported. The planar fluorescent emission excited by the light sheet illumination is collected by the same objective, relayed onto an MMA and detected by a side-view camera. The proposed scheme makes LSFM compatible to single objective imaging system and shows promising candidacy for high spatiotemporal imaging.
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Affiliation(s)
- Yanhui Cai
- State Key Laboratory for Mesoscopic Physics, Department of Physics, Peking University, Beijing 100871, P. R. China; Collaborative Innovation Center of Extreme Optics, Shanxi University, Taiyuan, Shanxi 030006, P. R. China; Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai 519000, P. R. China
| | - Yizhu Chen
- Department of Electrical Engineering, The Pennsylvania State University, University Park, PA 16802, USA
| | - Yiqiu Xia
- Department of Biomedical Engineering, Penn State Material Research Institute, The Pennsylvania State University, University Park, PA 16802, USA
| | - Siyang Zheng
- Biomedical Engineering and Electrical & Computer Engineering, Carnegie Mellon University, Pittsburgh, PA 15213, USA
| | - Zhiwen Liu
- Department of Electrical Engineering, The Pennsylvania State University, University Park, PA 16802, USA
| | - Kebin Shi
- State Key Laboratory for Mesoscopic Physics, Department of Physics, Peking University, Beijing 100871, P. R. China; Collaborative Innovation Center of Extreme Optics, Shanxi University, Taiyuan, Shanxi 030006, P. R. China; Peking University Yangtze Delta Institute of Optoelectronics, Nantong, Jiangsu 226010, P. R. China
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187
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Gan Y, Ma Y, Gong W, Liu W, Wang Z, Hao X, Han Y, Kuang C, Liu X. Enhanced axial resolution of lattice light sheet microscopy by fluorescence differential detection. OPTICS EXPRESS 2022; 30:27381-27394. [PMID: 36236910 DOI: 10.1364/oe.462516] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/27/2022] [Accepted: 07/01/2022] [Indexed: 06/16/2023]
Abstract
Lattice light-sheet microscopy (LLSM) is promising in long-term biological volumetric imaging due to its high spatiotemporal resolution and low phototoxicity. However, three-dimensional (3D) isotropic spatial resolution remains an unmet goal in LLSM because of its poorer axial resolution. Combing LLSM with fluorescence differential detection, namely LLSDM, has been proposed to improve the axial resolution of LLSM in simulation. It demonstrates the possibility of further enhancing the axial resolution in 3D volumetric imaging with LLSM by specifically discarding the off-focus photons captured using a complementary optical lattice (OL) profile generated with additional 0-π phase modulation at the objective pupil plane. The direct generation of the complementary lattice profile using the binary phase modulator conjugated to the sample plane for amplitude modulation, as used in LLSM, is also permittable. Nevertheless, the previously proposed configuration fails to provide a symmetric complementary lattice pattern along the axial axis, thus leading to the imbalanced off-focus photon suppression in the reconstructed images after subtraction [Opt. Lett.45, 2854 (2020)10.1364/OL.393378]. Here, we modified the LLSDM theory which can produce an ideal complementary lattice pattern with central zero intensity and symmetrically distributed sidelobes. We also analyzed the impact of numerical aperture matching between the original and complementary lattice patterns and presented the consistency between the simulated and experimental results. As demonstrated by imaging the distribution of fluorescent beads and microtubules in fixed U2OS cells, as well as the dynamics of filopodia in live U2OS cells, LLSDM provides about 1.5 times improvement in axial resolution, and higher imaging contrast compared with traditional LLSM.
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188
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A 3D Analysis of Cleared Human Melanoma. Biomedicines 2022; 10:biomedicines10071580. [PMID: 35884885 PMCID: PMC9313268 DOI: 10.3390/biomedicines10071580] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2022] [Revised: 06/29/2022] [Accepted: 06/30/2022] [Indexed: 11/16/2022] Open
Abstract
Cutaneous melanoma is one of the most aggressive and deadliest cancers in human beings due to its invasiveness and other factors. Histopathological analysis is crucial for a proper diagnosis. Optical tissue clearing is a novel field that allows 3D image acquisition of large-scale biological tissues. Optical clearing and immunolabeling for 3D fluorescence imaging has yet to be extensively applied to melanoma. In the present manuscript, we establish, for the first time, an optical clearing and immunostaining procedure for human melanoma and human cell line-derived melanoma xenograft models using the CUBIC (clear, unobstructed brain imaging cocktails) technique. We have successfully cleared the samples and achieved 3D volumetric visualization of the tumor microenvironment, vasculature, and cell populations.
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189
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Dyer L, Parker A, Paphiti K, Sanderson J. Lightsheet Microscopy. Curr Protoc 2022; 2:e448. [PMID: 35838628 DOI: 10.1002/cpz1.448] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
In this paper, we review lightsheet (selective plane illumination) microscopy for mouse developmental biologists. There are different means of forming the illumination sheet, and we discuss these. We explain how we introduced the lightsheet microscope economically into our core facility and present our results on fixed and living samples. We also describe methods of clearing fixed samples for three-dimensional imaging and discuss the various means of preparing samples with particular reference to mouse cilia, adipose spheroids, and cochleae. © 2022 The Authors. Current Protocols published by Wiley Periodicals LLC.
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Affiliation(s)
- Laura Dyer
- MRC Harwell Institute, Mammalian Genetics Unit, Harwell Campus, Oxfordshire, UK
| | - Andrew Parker
- MRC Harwell Institute, Mammalian Genetics Unit, Harwell Campus, Oxfordshire, UK
| | - Keanu Paphiti
- MRC Harwell Institute, Mammalian Genetics Unit, Harwell Campus, Oxfordshire, UK
| | - Jeremy Sanderson
- MRC Harwell Institute, Mammalian Genetics Unit, Harwell Campus, Oxfordshire, UK
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190
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Jiang W, Chen L, Wang J, Shao X, Jiang M, Chen Z, Wang J, Huang Y, Fei P. Open-top light-sheet imaging of CLEAR emulsion for high-throughput loss-free analysis of massive fluorescent droplets. Biomed Phys Eng Express 2022; 8. [PMID: 35767965 DOI: 10.1088/2057-1976/ac7d0f] [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: 04/04/2022] [Accepted: 06/29/2022] [Indexed: 11/12/2022]
Abstract
Digital droplet PCR (ddPCR) is classified as the third-generation PCR technology that enables absolute quantitative detection of nucleic acid molecules and has become an increasingly powerful tool for clinic diagnosis. We previously established a CLEAR-dPCR technique based on the combination of CLEAR droplets generated by micro-centrifuge-based microtubule arrays (MiCA) andinsitu3D readout by light-sheet fluorescence imaging. This CLEAR-dPCR technique attains very high readout speed and dynamic range. Meanwhile, it is free from sample loss and contamination, showing its advantages over commercial d-PCR technologies. However, a conventional orthogonal light-sheet imaging setup in CLEAR d-PCR cannot image multiple centrifuge tubes, thereby limiting its widespread application to large-scale, high-speed dd-PCR assays. Herein, we propose an in-parallel 3D dd-PCR readout technique based on an open-top light-sheet microscopy setup. This approach can continuously scan multiple centrifuge tubes which contain CLEAR emulsions with highly diverse concentrations, and thus further boost the scale and throughput of our 3D dd-PCR technique.
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Affiliation(s)
- Wen Jiang
- School of Optical and Electronic Information , Huazhong University of Science and Technology, E417, Wuhan, Hubei, 430074, CHINA
| | - Longbiao Chen
- School of Optical and Electronic Information , Huazhong University of Science and Technology, E417, Wuhan, Hubei, 430074, CHINA
| | - Jie Wang
- Huazhong University of Science and Technology, E417, School of Optical and Electronic Information, Wuhan, Hubei, 430074, CHINA
| | - Xinyang Shao
- Peking-Tsinghua Center for Life Sciences, Peking University, Peking-Tsinghua Center for Life Sciences, Beijing, Beijing, 100871, CHINA
| | - Mengcheng Jiang
- Biomedical Pioneering Innovation Center (BIOPIC), Peking University, Biomedical Pioneering Innovation Center (BIOPIC), Beijing, Beijing, 100871, CHINA
| | - Zitian Chen
- Biomedical Pioneering Innovation Center (BIOPIC), Peking University, Biomedical Pioneering Innovation Center (BIOPIC), Beijing, Beijing, 100871, CHINA
| | - Jianbin Wang
- School of Life Sciences, Tsinghua University, School of Life Sciences, Beijing, Beijing, 100084, CHINA
| | - Yanyi Huang
- College of Engineering, and Biodynamic Optical Imaging Center (BIOPIC), Peking University, College of Engineering, and Biodynamic Optical Imaging Center (BIOPIC), Beijing, 100871, CHINA
| | - Peng Fei
- School of Optical and Electronic Information, Huazhong University of Science and Technology, E417, Wuhan, 430074, CHINA
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191
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Nienhaus K, Nienhaus GU. Genetically encodable fluorescent protein markers in advanced optical imaging. Methods Appl Fluoresc 2022; 10. [PMID: 35767981 DOI: 10.1088/2050-6120/ac7d3f] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Accepted: 06/29/2022] [Indexed: 11/12/2022]
Abstract
Optical fluorescence microscopy plays a pivotal role in the exploration of biological structure and dynamics, especially on live specimens. Progress in the field relies, on the one hand, on technical advances in imaging and data processing and, on the other hand, on progress in fluorescent marker technologies. Among these, genetically encodable fluorescent proteins (FPs) are invaluable tools, as they allow facile labeling of live cells, tissues or organisms, as these produce the FP markers all by themselves after introduction of a suitable gene. Here we cover FP markers from the GFP family of proteins as well as tetrapyrrole-binding proteins, which further complement the FP toolbox in important ways. A broad range of FP variants have been endowed, by using protein engineering, with photophysical properties that are essential for specific fluorescence microscopy techniques, notably those offering nanoscale image resolution. We briefly introduce various advanced imaging methods and show how they utilize the distinct properties of the FP markers in exciting imaging applications, with the aim to guide researchers toward the design of powerful imaging experiments that are optimally suited to address their biological questions.
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Affiliation(s)
- Karin Nienhaus
- Institute of Applied Physics, Karlsruhe Institute of Technology, Wolfgang Gaede Str. 1, Karlsruhe, 76131, GERMANY
| | - Gerd Ulrich Nienhaus
- Karlsruhe Institute of Technology, Wolfgang Gaede Str. 1, Karlsruhe, 76131, GERMANY
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192
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Matsui T, Fujiwara D. Optical sectioning robotic microscopy for everyone: the structured illumination microscope with the OpenFlexure stages. OPTICS EXPRESS 2022; 30:23208-23216. [PMID: 36225006 DOI: 10.1364/oe.461910] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/28/2022] [Accepted: 05/30/2022] [Indexed: 06/16/2023]
Abstract
We report on the 3D-printed structured illumination microscope (SIM) with optical sectioning capability. Optically sectioned images are obtained by projecting a single-spatial-frequency grid pattern onto the specimen and recording three images with the grid pattern at different spatial phases, and then post-processing with simple mathematics. For the precise actuation of the grid for the structured illumination and the positioning of the sample, stages of the open-sourced, 3D-printable OpenFlexure families, which are capable of highly precise positioning control of tens of nanometers based on the flexure mechanism of the flexible plastics, are utilized. Our system has optical sectioning strength of a few microns, which is equivalent to that achievable with the confocal microscopes. The operation of our system can be automated with the Raspberry Pi and can be remotely operated from a PC via a wireless local area network.
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193
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Lightsheet optical tweezer (LOT) for optical manipulation of microscopic particles and live cells. Sci Rep 2022; 12:10229. [PMID: 35715431 PMCID: PMC9205896 DOI: 10.1038/s41598-022-13095-3] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2022] [Accepted: 05/20/2022] [Indexed: 11/09/2022] Open
Abstract
Optical trapping and patterning cells or microscopic particles is fascinating. We developed a light sheet-based optical tweezer to trap dielectric particles and live HeLa cells. The technique requires the generation of a tightly focussed diffraction-limited light-sheet realized by a combination of cylindrical lens and high NA objective lens. The resultant field is a focussed line (along x-axis) perpendicular to the beam propagation direction (z-axis). This is unlike traditional optical tweezers that are fundamentally point-traps and can trap one particle at a time. Several spherical beads undergoing Brownian motion in the solution are trapped by the lightsheet gradient potential, and the time (to reach trap-centre) is estimated from the video captured at 230 frames/s. High-speed imaging of beads with increasing laser power shows a steady increase in trap stiffness with a maximum of 0.00118 pN/nm at 52.5 mW. This is order less than the traditional point-traps, and hence may be suitable for applications requiring delicate optical forces. On the brighter side, light sheet tweezer (LOT) can simultaneously trap multiple objects with the distinct ability to manipulate them in the transverse (xy) plane via translation and rotation. However, the trapped beads displayed free movement along the light-sheet axis (x-axis), exhibiting a single degree of freedom. Furthermore, the tweezer is used to trap and pattern live HeLa cells in various shapes and structures. Subsequently, the cells were cultured for a prolonged period of time (> 18 h), and cell viability was ascertained. We anticipate that LOT can be used to study constrained dynamics of microscopic particles and help understand the patterned cell growth that has implications in optical imaging, microscopy, and cell biology.
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194
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In toto light sheet fluorescence microscopy live imaging datasets of Ceratitis capitata embryonic development. Sci Data 2022; 9:340. [PMID: 35705572 PMCID: PMC9200851 DOI: 10.1038/s41597-022-01443-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Accepted: 06/01/2022] [Indexed: 11/09/2022] Open
Abstract
The Mediterranean fruit fly (medfly), Ceratitis capitata, is an important model organism in biology and agricultural research with high economic relevance. However, information about its embryonic development is still sparse. We share nine long-term live imaging datasets acquired with light sheet fluorescence microscopy (484.5 h total recording time, 373 995 images, 256 Gb) with the scientific community. Six datasets show the embryonic development in toto for about 60 hours at 30 minutes intervals along four directions in three spatial dimensions, covering approximately 97% of the entire embryonic development period. Three datasets focus on germ cell formation and head involution. All imaged embryos hatched morphologically intact. Based on these data, we suggest a two-level staging system that functions as a morphogenetic framework for upcoming studies on medfly. Our data supports research on wild-type or aberrant morphogenesis, quantitative analyses, comparative approaches to insect development as well as studies related to pest control. Further, they can be used to test advanced image processing approaches or to train machine learning algorithms and/or neuronal networks.
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195
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Calisesi G, Ancora D, Tacconi C, Fantin A, Perin P, Pizzala R, Valentini G, Farina A, Bassi A. Enlarged Field of View in Spatially Modulated Selective Volume Illumination Microscopy. MICROSCOPY AND MICROANALYSIS : THE OFFICIAL JOURNAL OF MICROSCOPY SOCIETY OF AMERICA, MICROBEAM ANALYSIS SOCIETY, MICROSCOPICAL SOCIETY OF CANADA 2022; 28:1-10. [PMID: 35698867 DOI: 10.1017/s1431927622012077] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Three-dimensional fluorescence microscopy is a key technology for inspecting biological samples, ranging from single cells to entire organisms. We recently proposed a novel approach called spatially modulated Selective Volume Illumination Microscopy (smSVIM) to suppress illumination artifacts and to reduce the required number of measurements using an LED source. Here, we discuss a new strategy based on smSVIM for imaging large transparent specimens or voluminous chemically cleared tissues. The strategy permits steady mounting of the sample, achieving uniform resolution over a large field of view thanks to the synchronized motion of the illumination lens and the camera rolling shutter. Aided by a tailored deconvolution method for image reconstruction, we demonstrate significant improvement of the resolution at different magnification using samples of varying sizes and spatial features.
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Affiliation(s)
| | - Daniele Ancora
- Department of Physics, Politecnico di Milano, 20133Milano, Italy
| | - Carlotta Tacconi
- Department of Biosciences, University of Milano, 20133Milano, Italy
| | | | - Paola Perin
- Department of Brain and Behaviour Science, University of Pavia, 27100Pavia, Italy
| | - Roberto Pizzala
- Department of Molecular Medicine, University of Pavia, 27100Pavia, Italy
| | - Gianluca Valentini
- Department of Physics, Politecnico di Milano, 20133Milano, Italy
- Istituto di Fotonica e Nanotecnologie, Consiglio Nazionale delle ricerche, 20133Milano, Italy
| | - Andrea Farina
- Istituto di Fotonica e Nanotecnologie, Consiglio Nazionale delle ricerche, 20133Milano, Italy
| | - Andrea Bassi
- Department of Physics, Politecnico di Milano, 20133Milano, Italy
- Istituto di Fotonica e Nanotecnologie, Consiglio Nazionale delle ricerche, 20133Milano, Italy
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196
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Battistella E, Quintana JF, McConnell G. Application of Light-Sheet Mesoscopy to Image Host-Pathogen Interactions in Intact Organs. Front Cell Infect Microbiol 2022; 12:903957. [PMID: 35774409 PMCID: PMC9237429 DOI: 10.3389/fcimb.2022.903957] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2022] [Accepted: 05/17/2022] [Indexed: 11/17/2022] Open
Abstract
Human African Trypanosomiasis (HAT) is a disease caused by the extracellular parasite Trypanosoma brucei that affects the central nervous system (CNS) during the chronic stage of the infection, inducing neuroinflammation, coma, and death if left untreated. However, little is known about the structural change happening in the brain as result of the infection. So far, infection-induced neuroinflammation has been observed with conventional methods, such as immunohistochemistry, electron microscopy, and 2-photon microscopy only in small portions of the brain, which may not be representative of the disease. In this paper, we have used a newly-developed light-sheet illuminator to image the level of neuroinflammation in chronically infected mice and compared it to naïve controls. This system was developed for imaging in combination with the Mesolens objective lens, providing fast sub-cellular resolution for tens of mm3-large imaging volumes. The mouse brain specimens were cleared using CUBIC+, followed by antibody staining to locate Glial Fibrillary Acid Protein (GFAP) expressing cells, primarily astrocytes and ependymocytes, used here as a proxy for cell reactivity and gliosis. The large capture volume allowed us to detect GFAP+ cells and spatially resolve the response to T. brucei infection. Based on morphometric analyses and spatial distribution of GFAP+ cells, our data demonstrates a significant increase in cell dendrite branching around the lateral ventricle, as well as dorsal and ventral third ventricles, that are negatively correlated with the branch extension in distal sites from the circumventricular spaces. To our knowledge, this is the first report highlighting the potential of light-sheet mesoscopy to characterise the inflammatory responses of the mouse brain to parasitic infection at the cellular level in intact cleared organs, opening new avenues for the development of new mesoscale imaging techniques for the study of host-pathogen interactions.
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Affiliation(s)
- Eliana Battistella
- Department of Physics, SUPA, University of Strathclyde, Glasgow, United Kingdom
| | - Juan F. Quintana
- Wellcome Centre for Integrative Parasitology (WCIP) University of Glasgow, Glasgow, United Kingdom
- Institute of Biodiversity, Animal Health, and Comparative Medicine (IBAHCM). University of Glasgow, Glasgow, United Kingdom
| | - Gail McConnell
- Department of Physics, SUPA, University of Strathclyde, Glasgow, United Kingdom
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197
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Kohmura Y, Yang SM, Chen HH, Takano H, Chang CJ, Wang YS, Lee TT, Chiu CY, Yang KE, Chien YT, Hu HM, Su TL, Petibois C, Chen YY, Hsu CH, Chen P, Hueng DY, Chen SJ, Yang CL, Chin AL, Low CM, Tan FCK, Teo A, Tok ES, Cai XX, Lin HM, Boeckl J, Stampfl AP, Yamada J, Matsuyama S, Ishikawa T, Margaritondo G, Chiang AS, Hwu Y. The new X-ray/visible microscopy MAXWELL technique for fast three-dimensional nanoimaging with isotropic resolution. Sci Rep 2022; 12:9668. [PMID: 35690597 PMCID: PMC9188605 DOI: 10.1038/s41598-022-13377-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2021] [Accepted: 05/05/2022] [Indexed: 11/09/2022] Open
Abstract
Microscopy by Achromatic X-rays With Emission of Laminar Light (MAXWELL) is a new X-ray/visible technique with attractive characteristics including isotropic resolution in all directions, large-volume imaging and high throughput. An ultrathin, laminar X-ray beam produced by a Wolter type I mirror irradiates the sample stimulating the emission of visible light by scintillating nanoparticles, captured by an optical system. Three-dimensional (3D) images are obtained by scanning the specimen with respect to the laminar beam. We implemented and tested the technique with a high-brightness undulator at SPring-8, demonstrating its validity for a variety of specimens. This work was performed under the Synchrotrons for Neuroscience-an Asia-Pacific Strategic Enterprise (SYNAPSE) collaboration.
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Affiliation(s)
| | - Shun-Min Yang
- Institute of Physics, Academia Sinica, Nankang, Taipei, 11529, Taiwan
| | - Hsiang-Hsin Chen
- Institute of Physics, Academia Sinica, Nankang, Taipei, 11529, Taiwan
| | | | - Chia-Ju Chang
- Institute of Physics, Academia Sinica, Nankang, Taipei, 11529, Taiwan
| | - Ya-Sian Wang
- Institute of Physics, Academia Sinica, Nankang, Taipei, 11529, Taiwan
| | - Tsung-Tse Lee
- Institute of Physics, Academia Sinica, Nankang, Taipei, 11529, Taiwan
| | - Ching-Yu Chiu
- Institute of Physics, Academia Sinica, Nankang, Taipei, 11529, Taiwan
| | - Kai-En Yang
- Institute of Physics, Academia Sinica, Nankang, Taipei, 11529, Taiwan
| | - Yu-Ting Chien
- Institute of Physics, Academia Sinica, Nankang, Taipei, 11529, Taiwan
| | - Huan-Ming Hu
- Institute of Physics, Academia Sinica, Nankang, Taipei, 11529, Taiwan
| | - Tzu-Ling Su
- Institute of Physics, Academia Sinica, Nankang, Taipei, 11529, Taiwan
| | - Cyril Petibois
- Institute of Physics, Academia Sinica, Nankang, Taipei, 11529, Taiwan
| | - Yi-Yun Chen
- Institute of Physics, Academia Sinica, Nankang, Taipei, 11529, Taiwan
| | - Cheng-Huan Hsu
- Institute of Physics, Academia Sinica, Nankang, Taipei, 11529, Taiwan
| | - Peilin Chen
- Institute of Physics, Academia Sinica, Nankang, Taipei, 11529, Taiwan
- Research Center for Applied Sciences, Academia Sinica, Taipei, 11529, Taiwan
| | - Dueng-Yuan Hueng
- Department of Surgery, School of Medicine, National Defense Medical Center, Taipei, Taiwan
| | - Shean-Jen Chen
- College of Photonics, National Yang Ming Chiao Tung University, Tainan, Taiwan
| | - Chi Lin Yang
- Brain Research Center, National Tsing Hua University, Hsinchu, Taiwan
| | - An-Lun Chin
- Brain Research Center, National Tsing Hua University, Hsinchu, Taiwan
| | - Chian-Ming Low
- Department of Pharmacology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
- Department of Anaesthesia, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Francis Chee Kuan Tan
- Department of Anaesthesia, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Alvin Teo
- School of Chemical and Life Sciences, Nanyang Polytechnic, Singapore, Singapore
| | - Eng Soon Tok
- ƐMaGIC-Lab, Department of Physics, National University of Singapore, Singapore, Singapore
| | - Xu Xiang Cai
- Mechanical and Materials Department, Tatung University, Taipei, Taiwan
| | - Hong-Ming Lin
- Mechanical and Materials Department, Tatung University, Taipei, Taiwan
| | - John Boeckl
- US Air Force Research Laboratory, Materials and Manufacturing Directorate, WPAFB, Fairborn, OH, 43455, USA
| | - Anton P Stampfl
- Australian Nuclear Science and Technology Organisation, Sydney, NSW, 2234, Australia
| | | | - Satoshi Matsuyama
- Department of Materials Physics, Graduate School of Engineering, Nagoya University, Furo-cho, Chikusa, Nagoya, 464-8603, Japan
| | | | | | - Ann-Shyn Chiang
- Institute of Physics, Academia Sinica, Nankang, Taipei, 11529, Taiwan
- Brain Research Center, National Tsing Hua University, Hsinchu, Taiwan
| | - Yeukuang Hwu
- Institute of Physics, Academia Sinica, Nankang, Taipei, 11529, Taiwan.
- Brain Research Center, National Tsing Hua University, Hsinchu, Taiwan.
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198
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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: 20] [Impact Index Per Article: 6.7] [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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199
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Ugawa M, Ota S. High‐Throughput Parallel Optofluidic 3D‐Imaging Flow Cytometry. SMALL SCIENCE 2022. [DOI: 10.1002/smsc.202100126] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022] Open
Affiliation(s)
- Masashi Ugawa
- Research Center for Advanced Science and Technology The University of Tokyo 4-6-1 Komaba, Meguro-ku Tokyo 153-8904 Japan
| | - Sadao Ota
- Research Center for Advanced Science and Technology The University of Tokyo 4-6-1 Komaba, Meguro-ku Tokyo 153-8904 Japan
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200
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Hériché M, Arnould C, Wipf D, Courty PE. Imaging plant tissues: advances and promising clearing practices. TRENDS IN PLANT SCIENCE 2022; 27:601-615. [PMID: 35339361 DOI: 10.1016/j.tplants.2021.12.006] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/14/2021] [Revised: 12/03/2021] [Accepted: 12/09/2021] [Indexed: 06/14/2023]
Abstract
The study of the organ structure of plants and understanding their physiological complexity requires 3D imaging with subcellular resolution. Most plant organs are highly opaque to light, and their study under optical sectioning microscopes is therefore difficult. In animals, many protocols have been developed to make organs transparent to light using clearing protocols (CPs). By contrast, clearing plant tissues is challenging because of the presence of fibers and pigments. We describe progress in the development of plant CPs over the past 20 years through a modified taxonomy of CPs based on their physical and optical parameters that affect tissue properties. We also discuss successful approaches that combine CPs with new microscopy methods and their future applications in plant science research.
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Affiliation(s)
- Mathilde Hériché
- Agroécologie, AgroSup Dijon, Centre National de la Recherche Scientifique (CNRS), Université de Bourgogne, Institut National de Recherche pour l'Agriculture, l'Alimentation, et l'Environnement (INRAE), Université Bourgogne Franche-Comté, Dijon, France
| | - Christine Arnould
- Agroécologie, AgroSup Dijon, Centre National de la Recherche Scientifique (CNRS), Université de Bourgogne, Institut National de Recherche pour l'Agriculture, l'Alimentation, et l'Environnement (INRAE), Université Bourgogne Franche-Comté, Dijon, France
| | - Daniel Wipf
- Agroécologie, AgroSup Dijon, Centre National de la Recherche Scientifique (CNRS), Université de Bourgogne, Institut National de Recherche pour l'Agriculture, l'Alimentation, et l'Environnement (INRAE), Université Bourgogne Franche-Comté, Dijon, France
| | - Pierre-Emmanuel Courty
- Agroécologie, AgroSup Dijon, Centre National de la Recherche Scientifique (CNRS), Université de Bourgogne, Institut National de Recherche pour l'Agriculture, l'Alimentation, et l'Environnement (INRAE), Université Bourgogne Franche-Comté, Dijon, France.
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