1
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Ding P, Wahn H, Chen FD, Li J, Mu X, Stalmashonak A, Luo X, Lo GQ, Poon JKS, Sacher WD. Photonic neural probe enabled microendoscopes for light-sheet light-field computational fluorescence brain imaging. NEUROPHOTONICS 2024; 11:S11503. [PMID: 38322247 PMCID: PMC10846542 DOI: 10.1117/1.nph.11.s1.s11503] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/08/2023] [Revised: 12/14/2023] [Accepted: 12/20/2023] [Indexed: 02/08/2024]
Abstract
Significance Light-sheet fluorescence microscopy is widely used for high-speed, high-contrast, volumetric imaging. Application of this technique to in vivo brain imaging in non-transparent organisms has been limited by the geometric constraints of conventional light-sheet microscopes, which require orthogonal fluorescence excitation and collection objectives. We have recently demonstrated implantable photonic neural probes that emit addressable light sheets at depth in brain tissue, miniaturizing the excitation optics. Here, we propose a microendoscope consisting of a light-sheet neural probe packaged together with miniaturized fluorescence collection optics based on an image fiber bundle for lensless, light-field, computational fluorescence imaging. Aim Foundry-fabricated, silicon-based, light-sheet neural probes can be packaged together with commercially available image fiber bundles to form microendoscopes for light-sheet light-field fluorescence imaging at depth in brain tissue. Approach Prototype microendoscopes were developed using light-sheet neural probes with five addressable sheets and image fiber bundles. Fluorescence imaging with the microendoscopes was tested with fluorescent beads suspended in agarose and fixed mouse brain tissue. Results Volumetric light-sheet light-field fluorescence imaging was demonstrated using the microendoscopes. Increased imaging depth and enhanced reconstruction accuracy were observed relative to epi-illumination light-field imaging using only a fiber bundle. Conclusions Our work offers a solution toward volumetric fluorescence imaging of brain tissue with a compact size and high contrast. The proof-of-concept demonstrations herein illustrate the operating principles and methods of the imaging approach, providing a foundation for future investigations of photonic neural probe enabled microendoscopes for deep-brain fluorescence imaging in vivo.
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Affiliation(s)
- Peisheng Ding
- Max Planck Institute of Microstructure Physics, Halle, Germany
- University of Toronto, Department of Electrical and Computer Engineering, Toronto, Ontario, Canada
| | - Hannes Wahn
- Max Planck Institute of Microstructure Physics, Halle, Germany
| | - Fu-Der Chen
- Max Planck Institute of Microstructure Physics, Halle, Germany
- University of Toronto, Department of Electrical and Computer Engineering, Toronto, Ontario, Canada
- Max Planck-University of Toronto Centre for Neural Science and Technology, Toronto, Ontario, Canada
| | - Jianfeng Li
- Max Planck Institute of Microstructure Physics, Halle, Germany
- Max Planck-University of Toronto Centre for Neural Science and Technology, Toronto, Ontario, Canada
| | - Xin Mu
- Max Planck Institute of Microstructure Physics, Halle, Germany
- University of Toronto, Department of Electrical and Computer Engineering, Toronto, Ontario, Canada
- Max Planck-University of Toronto Centre for Neural Science and Technology, Toronto, Ontario, Canada
| | | | | | | | - Joyce K. S. Poon
- Max Planck Institute of Microstructure Physics, Halle, Germany
- University of Toronto, Department of Electrical and Computer Engineering, Toronto, Ontario, Canada
- Max Planck-University of Toronto Centre for Neural Science and Technology, Toronto, Ontario, Canada
| | - Wesley D. Sacher
- Max Planck Institute of Microstructure Physics, Halle, Germany
- Max Planck-University of Toronto Centre for Neural Science and Technology, Toronto, Ontario, Canada
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2
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Otomo K, Omura T, Nozawa Y, Edwards SJ, Sato Y, Saito Y, Yagishita S, Uchida H, Watakabe Y, Naitou K, Yanai R, Sahara N, Takagi S, Katayama R, Iwata Y, Shiokawa T, Hayakawa Y, Otsuka K, Watanabe-Takano H, Haneda Y, Fukuhara S, Fujiwara M, Nii T, Meno C, Takeshita N, Yashiro K, Rosales Rocabado JM, Kaku M, Yamada T, Oishi Y, Koike H, Cheng Y, Sekine K, Koga JI, Sugiyama K, Kimura K, Karube F, Kim H, Manabe I, Nemoto T, Tainaka K, Hamada A, Brismar H, Susaki EA. descSPIM: an affordable and easy-to-build light-sheet microscope optimized for tissue clearing techniques. Nat Commun 2024; 15:4941. [PMID: 38866781 PMCID: PMC11169475 DOI: 10.1038/s41467-024-49131-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2023] [Accepted: 05/24/2024] [Indexed: 06/14/2024] Open
Abstract
Despite widespread adoption of tissue clearing techniques in recent years, poor access to suitable light-sheet fluorescence microscopes remains a major obstacle for biomedical end-users. Here, we present descSPIM (desktop-equipped SPIM for cleared specimens), a low-cost ($20,000-50,000), low-expertise (one-day installation by a non-expert), yet practical do-it-yourself light-sheet microscope as a solution for this bottleneck. Even the most fundamental configuration of descSPIM enables multi-color imaging of whole mouse brains and a cancer cell line-derived xenograft tumor mass for the visualization of neurocircuitry, assessment of drug distribution, and pathological examination by false-colored hematoxylin and eosin staining in a three-dimensional manner. Academically open-sourced ( https://github.com/dbsb-juntendo/descSPIM ), descSPIM allows routine three-dimensional imaging of cleared samples in minutes. Thus, the dissemination of descSPIM will accelerate biomedical discoveries driven by tissue clearing technologies.
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Affiliation(s)
- Kohei Otomo
- Department of Biochemistry and Systems Biomedicine, Juntendo University Graduate School of Medicine, Tokyo, Japan
- Biochemistry II, Juntendo University School of Medicine, Tokyo, Japan
- Nakatani Biomedical Spatialomics Hub, Juntendo University Graduate School of Medicine, Tokyo, Japan
- Division of Biophotonics, National Institute for Physiological Sciences, National Institutes of Natural Sciences, Okazaki, Japan
- Biophotonics Research Group, Exploratory Research Center on Life and Living Systems, National Institutes of Natural Sciences, Okazaki, Japan
| | - Takaki Omura
- Department of Biochemistry and Systems Biomedicine, Juntendo University Graduate School of Medicine, Tokyo, Japan
- Nakatani Biomedical Spatialomics Hub, Juntendo University Graduate School of Medicine, Tokyo, Japan
- Department of Neurosurgery, University of Tokyo, Tokyo, Japan
- Department of Neurosurgery and Neuro-Oncology, National Cancer Center Hospital, Tokyo, Japan
| | - Yuki Nozawa
- Biochemistry II, Juntendo University School of Medicine, Tokyo, Japan
| | - Steven J Edwards
- Science for Life Laboratory, Department of Applied Physics, KTH Royal Institute of Technology, Stockholm, Sweden
| | - Yukihiko Sato
- Department of Biochemistry and Systems Biomedicine, Juntendo University Graduate School of Medicine, Tokyo, Japan
- Nakatani Biomedical Spatialomics Hub, Juntendo University Graduate School of Medicine, Tokyo, Japan
| | - Yuri Saito
- Department of Biochemistry and Systems Biomedicine, Juntendo University Graduate School of Medicine, Tokyo, Japan
- Nakatani Biomedical Spatialomics Hub, Juntendo University Graduate School of Medicine, Tokyo, Japan
| | - Shigehiro Yagishita
- Department of Pharmacology and Therapeutics, Fundamental Innovative Oncology Core, National Cancer Center Research Institute, Tokyo, Japan
- Division of Molecular Pharmacology, National Cancer Center Research Institute, Tokyo, Japan
| | - Hitoshi Uchida
- Department of System Pathology for Neurological Disorders, Brain Research Institute, Niigata University, Niigata, Japan
| | - Yuki Watakabe
- Division of Biophotonics, National Institute for Physiological Sciences, National Institutes of Natural Sciences, Okazaki, Japan
- Biophotonics Research Group, Exploratory Research Center on Life and Living Systems, National Institutes of Natural Sciences, Okazaki, Japan
| | - Kiyotada Naitou
- Department of Basic Veterinary Science, Joint Faculty of Veterinary Medicine, Kagoshima University, Kagoshima, Japan
| | - Rin Yanai
- Advanced Neuroimaging Center, Institute for Quantum Medical Sciences, National Institutes for Quantum Science and Technology, Chiba, Japan
| | - Naruhiko Sahara
- Advanced Neuroimaging Center, Institute for Quantum Medical Sciences, National Institutes for Quantum Science and Technology, Chiba, Japan
| | - Satoshi Takagi
- Division of Experimental Chemotherapy, Cancer Chemotherapy Center, Japanese Foundation for Cancer Research, Tokyo, Japan
| | - Ryohei Katayama
- Division of Experimental Chemotherapy, Cancer Chemotherapy Center, Japanese Foundation for Cancer Research, Tokyo, Japan
| | - Yusuke Iwata
- Department of Gastroenterology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Toshiro Shiokawa
- Department of Gastroenterology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Yoku Hayakawa
- Department of Gastroenterology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Kensuke Otsuka
- Biology and Environmental Chemistry Division, Sustainable System Research Laboratory, Central Research Institute of Electric Power Industry, Chiba, Japan
| | - Haruko Watanabe-Takano
- Department of Molecular Pathophysiology, Institute for Advanced Medical Sciences, Nippon Medical School, Tokyo, Japan
| | - Yuka Haneda
- Department of Molecular Pathophysiology, Institute for Advanced Medical Sciences, Nippon Medical School, Tokyo, Japan
| | - Shigetomo Fukuhara
- Department of Molecular Pathophysiology, Institute for Advanced Medical Sciences, Nippon Medical School, Tokyo, Japan
| | - Miku Fujiwara
- Department of Developmental Biology, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Takenobu Nii
- Department of Developmental Biology, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Chikara Meno
- Department of Developmental Biology, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Naoki Takeshita
- Anatomy and Developmental Biology, Kyoto Prefectural University of Medicine, Kyoto, Japan
- Department of Pediatrics, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Kenta Yashiro
- Anatomy and Developmental Biology, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Juan Marcelo Rosales Rocabado
- Division of Bio-prosthodontics, Faculty of Dentistry & Graduate School of Medical and Dental Sciences, Niigata University, Niigata, Japan
| | - Masaru Kaku
- Division of Bio-prosthodontics, Faculty of Dentistry & Graduate School of Medical and Dental Sciences, Niigata University, Niigata, Japan
| | - Tatsuya Yamada
- Department of Biochemistry, University of Nebraska-Lincoln, Lincoln, USA
| | - Yumiko Oishi
- Department of Meidical Biochemistry, Tokyo Medical and Dental University, Tokyo, Japan
| | - Hiroyuki Koike
- Department of Meidical Biochemistry, Tokyo Medical and Dental University, Tokyo, Japan
| | - Yinglan Cheng
- Department of Meidical Biochemistry, Tokyo Medical and Dental University, Tokyo, Japan
| | - Keisuke Sekine
- Laboratory of Cancer Cell Systems, National Cancer Center Research Institute, Tokyo, Japan
| | - Jun-Ichiro Koga
- The Second Department of Internal Medicine, University of Occupational and Environmental Health, Kitakyushu, Japan
| | - Kaori Sugiyama
- Institute for Advanced Research of Biosystem Dynamics, Research Institute for Science and Engineering, Waseda University, Tokyo, Japan
| | - Kenichi Kimura
- Life Science Center for Survival Dynamics, Tsukuba Advanced Research Alliance (TARA), University of Tsukuba, Tsukuba, Japan
| | - Fuyuki Karube
- Lab of Histology and Cytology, Graduate School of Medicine, Hokkaido University, Sapporo, Japan
| | - Hyeree Kim
- Department of Systems Medicine, Graduate School of Medicine, Chiba University, Chiba, Japan
| | - Ichiro Manabe
- Department of Systems Medicine, Graduate School of Medicine, Chiba University, Chiba, Japan
| | - Tomomi Nemoto
- Division of Biophotonics, National Institute for Physiological Sciences, National Institutes of Natural Sciences, Okazaki, Japan
- Biophotonics Research Group, Exploratory Research Center on Life and Living Systems, National Institutes of Natural Sciences, Okazaki, Japan
| | - Kazuki Tainaka
- Department of System Pathology for Neurological Disorders, Brain Research Institute, Niigata University, Niigata, Japan
| | - Akinobu Hamada
- Department of Pharmacology and Therapeutics, Fundamental Innovative Oncology Core, National Cancer Center Research Institute, Tokyo, Japan
- Division of Molecular Pharmacology, National Cancer Center Research Institute, Tokyo, Japan
| | - Hjalmar Brismar
- Science for Life Laboratory, Department of Applied Physics, KTH Royal Institute of Technology, Stockholm, Sweden
| | - Etsuo A Susaki
- Department of Biochemistry and Systems Biomedicine, Juntendo University Graduate School of Medicine, Tokyo, Japan.
- Biochemistry II, Juntendo University School of Medicine, Tokyo, Japan.
- Nakatani Biomedical Spatialomics Hub, Juntendo University Graduate School of Medicine, Tokyo, Japan.
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3
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Dibaji H, Kazemi Nasaban Shotorban A, Grattan RM, Lucero S, Schodt DJ, Lidke KA, Petruccelli J, Lidke DS, Liu S, Chakraborty T. Axial de-scanning using remote focusing in the detection arm of light-sheet microscopy. Nat Commun 2024; 15:5019. [PMID: 38866746 PMCID: PMC11169345 DOI: 10.1038/s41467-024-49291-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2023] [Accepted: 05/31/2024] [Indexed: 06/14/2024] Open
Abstract
Rapid, high-resolution volumetric imaging without moving heavy objectives or disturbing delicate samples remains challenging. Pupil-matched remote focusing offers a promising solution for high NA systems, but the fluorescence signal's incoherent and unpolarized nature complicates its application. Thus, remote focusing is mainly used in the illumination arm with polarized laser light to improve optical coupling. Here, we introduce a novel optical design that can de-scan the axial focus movement in the detection arm of a microscope. Our method splits the fluorescence signal into S and P-polarized light, lets them pass through the remote focusing module separately, and combines them with the camera. This allows us to use only one focusing element to perform aberration-free, multi-color, volumetric imaging without (a) compromising the fluorescent signal and (b) needing to perform sample/detection-objective translation. We demonstrate the capabilities of this scheme by acquiring fast dual-color 4D (3D space + time) image stacks with an axial range of 70 μm and camera-limited acquisition speed. Owing to its general nature, we believe this technique will find its application in many other microscopy techniques that currently use an adjustable Z-stage to carry out volumetric imaging, such as confocal, 2-photon, and light sheet variants.
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Affiliation(s)
- Hassan Dibaji
- Department of Physics and Astronomy, University of New Mexico, Albuquerque, NM, USA
| | | | - Rachel M Grattan
- Comprehensive Cancer Center, University of New Mexico Health Sciences Center, Albuquerque, NM, USA
- Department of Pathology, University of New Mexico Health Science Center, Albuquerque, NM, USA
| | - Shayna Lucero
- Comprehensive Cancer Center, University of New Mexico Health Sciences Center, Albuquerque, NM, USA
- Department of Pathology, University of New Mexico Health Science Center, Albuquerque, NM, USA
| | - David J Schodt
- Department of Physics and Astronomy, University of New Mexico, Albuquerque, NM, USA
| | - Keith A Lidke
- Department of Physics and Astronomy, University of New Mexico, Albuquerque, NM, USA
- Comprehensive Cancer Center, University of New Mexico Health Sciences Center, Albuquerque, NM, USA
| | - Jonathan Petruccelli
- Department of Physics, University at Albany-State University of NewYork, Albany, NY, USA
| | - Diane S Lidke
- Comprehensive Cancer Center, University of New Mexico Health Sciences Center, Albuquerque, NM, USA
- Department of Pathology, University of New Mexico Health Science Center, Albuquerque, NM, USA
| | - Sheng Liu
- Department of Physics and Astronomy, University of New Mexico, Albuquerque, NM, USA
| | - Tonmoy Chakraborty
- Department of Physics and Astronomy, University of New Mexico, Albuquerque, NM, USA.
- Comprehensive Cancer Center, University of New Mexico Health Sciences Center, Albuquerque, NM, USA.
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4
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Katoh TA, Fukai YT, Ishibashi T. Optical microscopic imaging, manipulation, and analysis methods for morphogenesis research. Microscopy (Oxf) 2024; 73:226-242. [PMID: 38102756 PMCID: PMC11154147 DOI: 10.1093/jmicro/dfad059] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Revised: 11/20/2023] [Accepted: 03/22/2024] [Indexed: 12/17/2023] Open
Abstract
Morphogenesis is a developmental process of organisms being shaped through complex and cooperative cellular movements. To understand the interplay between genetic programs and the resulting multicellular morphogenesis, it is essential to characterize the morphologies and dynamics at the single-cell level and to understand how physical forces serve as both signaling components and driving forces of tissue deformations. In recent years, advances in microscopy techniques have led to improvements in imaging speed, resolution and depth. Concurrently, the development of various software packages has supported large-scale, analyses of challenging images at the single-cell resolution. While these tools have enhanced our ability to examine dynamics of cells and mechanical processes during morphogenesis, their effective integration requires specialized expertise. With this background, this review provides a practical overview of those techniques. First, we introduce microscopic techniques for multicellular imaging and image analysis software tools with a focus on cell segmentation and tracking. Second, we provide an overview of cutting-edge techniques for mechanical manipulation of cells and tissues. Finally, we introduce recent findings on morphogenetic mechanisms and mechanosensations that have been achieved by effectively combining microscopy, image analysis tools and mechanical manipulation techniques.
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Affiliation(s)
- Takanobu A Katoh
- Department of Cell Biology, Graduate School of Medicine, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Yohsuke T Fukai
- Nonequilibrium Physics of Living Matter RIKEN Hakubi Research Team, RIKEN Center for Biosystems Dynamics Research, 2-2-3 Minatojima-minamimachi, Chuo-ku, Kobe, Hyogo 650-0047, Japan
| | - Tomoki Ishibashi
- Laboratory for Physical Biology, RIKEN Center for Biosystems Dynamics Research, 2-2-3 Minatojima-minamimachi, Chuo-ku, Kobe, Hyogo 650-0047, Japan
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5
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Boto T, Tomchik SM. Functional Imaging of Learning-Induced Plasticity in the Central Nervous System with Genetically Encoded Reporters in Drosophila. Cold Spring Harb Protoc 2024; 2024:pdb.top107799. [PMID: 37197830 DOI: 10.1101/pdb.top107799] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/19/2023]
Abstract
Learning and memory allow animals to adjust their behavior based on the predictive value of their past experiences. Memories often exist in complex representations, spread across numerous cells and synapses in the brain. Studying relatively simple forms of memory provides insights into the fundamental processes that underlie multiple forms of memory. Associative learning occurs when an animal learns the relationship between two previously unrelated sensory stimuli, such as when a hungry animal learns that a particular odor is followed by a tasty reward. Drosophila is a particularly powerful model to study how this type of memory works. The fundamental principles are widely shared among animals, and there is a wide range of genetic tools available to study circuit function in flies. In addition, the olfactory structures that mediate associative learning in flies, such as the mushroom body and its associated neurons, are anatomically organized, relatively well-characterized, and readily accessible to imaging. Here, we review the olfactory anatomy and physiology of the olfactory system, describe how plasticity in the olfactory pathway mediates learning and memory, and explain the general principles underlying calcium imaging approaches.
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Affiliation(s)
- Tamara Boto
- Department of Physiology, Trinity College Dublin, Dublin 2, Ireland
- Trinity College Institute of Neuroscience, Trinity College Dublin, Dublin 2, Ireland
| | - Seth M Tomchik
- Neuroscience and Pharmacology, University of Iowa Carver College of Medicine, Iowa City, Iowa 52242, USA
- Stead Family Department of Pediatrics, University of Iowa Carver College of Medicine, Iowa City, Iowa 52242, USA
- Iowa Neuroscience Institute, University of Iowa Carver College of Medicine, Iowa City, Iowa 52242, USA
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6
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Sarafraz H, Nöbauer T, Kim H, Soldevila F, Gigan S, Vaziri A. Speckle-enabled in vivo demixing of neural activity in the mouse brain. BIOMEDICAL OPTICS EXPRESS 2024; 15:3586-3608. [PMID: 38867774 PMCID: PMC11166431 DOI: 10.1364/boe.524521] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/22/2024] [Revised: 04/11/2024] [Accepted: 04/14/2024] [Indexed: 06/14/2024]
Abstract
Functional imaging of neuronal activity in awake animals, using a combination of fluorescent reporters of neuronal activity and various types of microscopy modalities, has become an indispensable tool in neuroscience. While various imaging modalities based on one-photon (1P) excitation and parallel (camera-based) acquisition have been successfully used for imaging more transparent samples, when imaging mammalian brain tissue, due to their scattering properties, two-photon (2P) microscopy systems are necessary. In 2P microscopy, the longer excitation wavelengths reduce the amount of scattering while the diffraction-limited 3D localization of excitation largely eliminates out-of-focus fluorescence. However, this comes at the cost of time-consuming serial scanning of the excitation spot and more complex and expensive instrumentation. Thus, functional 1P imaging modalities that can be used beyond the most transparent specimen are highly desirable. Here, we transform light scattering from an obstacle into a tool. We use speckles with their unique patterns and contrast, formed when fluorescence from individual neurons propagates through rodent cortical tissue, to encode neuronal activity. Spatiotemporal demixing of these patterns then enables functional recording of neuronal activity from a group of discriminable sources. For the first time, we provide an experimental, in vivo characterization of speckle generation, speckle imaging and speckle-assisted demixing of neuronal activity signals in the scattering mammalian brain tissue. We found that despite an initial fast speckle decorrelation, substantial correlation was maintained over minute-long timescales that contributed to our ability to demix temporal activity traces in the mouse brain in vivo. Informed by in vivo quantifications of speckle patterns from single and multiple neurons excited using 2P scanning excitation, we recorded and demixed activity from several sources excited using 1P oblique illumination. In our proof-of-principle experiments, we demonstrate in vivo speckle-assisted demixing of functional signals from groups of sources in a depth range of 220-320 µm in mouse cortex, limited by available speckle contrast. Our results serve as a basis for designing an in vivo functional speckle imaging modality and for maximizing the key resource in any such modality, the speckle contrast. We anticipate that our results will provide critical quantitative guidance to the community for designing techniques that overcome light scattering as a fundamental limitation in bioimaging.
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Affiliation(s)
- Hossein Sarafraz
- Laboratory of Neurotechnology and Biophysics, The Rockefeller University, New York, NY, USA
| | - Tobias Nöbauer
- Laboratory of Neurotechnology and Biophysics, The Rockefeller University, New York, NY, USA
- The Kavli Neural Systems Institute, The Rockefeller University, New York, NY, USA
| | - Hyewon Kim
- Laboratory of Neurotechnology and Biophysics, The Rockefeller University, New York, NY, USA
| | - Fernando Soldevila
- Laboratoire Kastler Brossel, ENS–Université PSL, CNRS, Sorbonne Université, College de France, 24 Rue Lhomond, F-75005 Paris, France
| | - Sylvain Gigan
- Laboratoire Kastler Brossel, ENS–Université PSL, CNRS, Sorbonne Université, College de France, 24 Rue Lhomond, F-75005 Paris, France
| | - Alipasha Vaziri
- Laboratory of Neurotechnology and Biophysics, The Rockefeller University, New York, NY, USA
- The Kavli Neural Systems Institute, The Rockefeller University, New York, NY, USA
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7
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Mandracchia B, Zheng C, Rajendran S, Liu W, Forghani P, Xu C, Jia S. High-speed optical imaging with sCMOS pixel reassignment. Nat Commun 2024; 15:4598. [PMID: 38816394 PMCID: PMC11139943 DOI: 10.1038/s41467-024-48987-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2023] [Accepted: 05/13/2024] [Indexed: 06/01/2024] Open
Abstract
Fluorescence microscopy has undergone rapid advancements, offering unprecedented visualization of biological events and shedding light on the intricate mechanisms governing living organisms. However, the exploration of rapid biological dynamics still poses a significant challenge due to the limitations of current digital camera architectures and the inherent compromise between imaging speed and other capabilities. Here, we introduce sHAPR, a high-speed acquisition technique that leverages the operating principles of sCMOS cameras to capture fast cellular and subcellular processes. sHAPR harnesses custom fiber optics to convert microscopy images into one-dimensional recordings, enabling acquisition at the maximum camera readout rate, typically between 25 and 250 kHz. We have demonstrated the utility of sHAPR with a variety of phantom and dynamic systems, including high-throughput flow cytometry, cardiomyocyte contraction, and neuronal calcium waves, using a standard epi-fluorescence microscope. sHAPR is highly adaptable and can be integrated into existing microscopy systems without requiring extensive platform modifications. This method pushes the boundaries of current fluorescence imaging capabilities, opening up new avenues for investigating high-speed biological phenomena.
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Affiliation(s)
- Biagio Mandracchia
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, GA, USA
- E.T.S.I. Telecomunicación, Universidad de Valladolid, Valladolid, Spain
| | - Corey Zheng
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, GA, USA
| | - Suraj Rajendran
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, GA, USA
| | - Wenhao Liu
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, GA, USA
| | - Parvin Forghani
- Department of Pediatrics, School of Medicine, Emory University, Atlanta, GA, USA
| | - Chunhui Xu
- Department of Pediatrics, School of Medicine, Emory University, Atlanta, GA, USA
- Parker H. Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, GA, USA
| | - Shu Jia
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, GA, USA.
- Parker H. Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, GA, USA.
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8
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McNulty P, Wu R, Yamaguchi A, Heckscher ES, Haas A, Nwankpa A, Skanata MM, Gershow M. CRASH2p: Closed-loop Two Photon Imaging in Freely Moving Animals. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.22.595209. [PMID: 38826435 PMCID: PMC11142166 DOI: 10.1101/2024.05.22.595209] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2024]
Abstract
Direct measurement of neural activity in freely moving animals is essential for understanding how the brain controls and represents behaviors. Genetically encoded calcium indicators report neural activity as changes in fluorescence intensity, but brain motion confounds quantitative measurement of fluorescence. Translation, rotation, and deformation of the brain and the movements of intervening scattering or auto-fluorescent tissue all alter the amount of fluorescent light captured by a microscope. Compared to single-photon approaches, two photon microscopy is less sensitive to scattering and off-target fluorescence, but more sensitive to motion, and two photon imaging has always required anchoring the microscope to the brain. We developed a closed-loop resonant axial-scanning high-speed two photon (CRASH2p) microscope for real-time 3D motion correction in unrestrained animals, without implantation of reference markers. We complemented CRASH2p with a novel scanning strategy and a multistage registration pipeline. We performed volumetric ratiometrically corrected functional imaging in the CNS of freely moving Drosophila larvae and discovered previously unknown neural correlates of behavior.
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Affiliation(s)
- Paul McNulty
- Department of Physics,New York University, New York, USA
| | - Rui Wu
- Department of Physics,New York University, New York, USA
| | | | - Ellie S. Heckscher
- Department of Molecular Genetics and Cell Biology, University of Chicago, Chicago, IL
| | - Andrew Haas
- Department of Physics,New York University, New York, USA
| | | | | | - Marc Gershow
- Department of Physics,New York University, New York, USA
- Center for Neural Science,New York University, New York, USA
- Neuroscience Institute, New York University, New York, USA
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9
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Rich PD, Thiberge SY, Scott BB, Guo C, Tervo DGR, Brody CD, Karpova AY, Daw ND, Tank DW. Magnetic voluntary head-fixation in transgenic rats enables lifespan imaging of hippocampal neurons. Nat Commun 2024; 15:4154. [PMID: 38755205 PMCID: PMC11099169 DOI: 10.1038/s41467-024-48505-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2023] [Accepted: 05/01/2024] [Indexed: 05/18/2024] Open
Abstract
The precise neural mechanisms within the brain that contribute to the remarkable lifetime persistence of memory are not fully understood. Two-photon calcium imaging allows the activity of individual cells to be followed across long periods, but conventional approaches require head-fixation, which limits the type of behavior that can be studied. We present a magnetic voluntary head-fixation system that provides stable optical access to the brain during complex behavior. Compared to previous systems that used mechanical restraint, there are no moving parts and animals can engage and disengage entirely at will. This system is failsafe, easy for animals to use and reliable enough to allow long-term experiments to be routinely performed. Animals completed hundreds of trials per session of an odor discrimination task that required 2-4 s fixations. Together with a reflectance fluorescence collection scheme that increases two-photon signal and a transgenic Thy1-GCaMP6f rat line, we are able to reliably image the cellular activity in the hippocampus during behavior over long periods (median 6 months), allowing us track the same neurons over a large fraction of animals' lives (up to 19 months).
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Affiliation(s)
- P Dylan Rich
- Princeton Neuroscience Institute, Princeton University, Princeton, NJ, USA.
| | | | - Benjamin B Scott
- Department of Psychological and Brain Sciences, Boston University, Boston, MA, USA
- Center for Systems Neuroscience, Boston University, Boston, MA, USA
- Neurophotonics Center, Boston University, Boston, MA, USA
| | - Caiying Guo
- Janelia Research Campus, Ashburn, VA, USA
- Howard Hughes Medical Institute, Ashburn, VA, USA
| | - D Gowanlock R Tervo
- Janelia Research Campus, Ashburn, VA, USA
- Howard Hughes Medical Institute, Ashburn, VA, USA
| | - Carlos D Brody
- Princeton Neuroscience Institute, Princeton University, Princeton, NJ, USA
- Howard Hughes Medical Institute, Princeton University, Princeton, NJ, USA
| | - Alla Y Karpova
- Janelia Research Campus, Ashburn, VA, USA
- Howard Hughes Medical Institute, Ashburn, VA, USA
| | - Nathaniel D Daw
- Princeton Neuroscience Institute, Princeton University, Princeton, NJ, USA
- Department of Psychology, Princeton University, Princeton, NJ, USA
| | - David W Tank
- Princeton Neuroscience Institute, Princeton University, Princeton, NJ, USA.
- Bezos Center for Neural Circuit Dynamics, Princeton University, Princeton, NJ, USA.
- Department of Molecular Biology, Princeton University, Princeton, NJ, USA.
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10
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Maharjan S, Ma C, Singh B, Kang H, Orive G, Yao J, Shrike Zhang Y. Advanced 3D imaging and organoid bioprinting for biomedical research and therapeutic applications. Adv Drug Deliv Rev 2024; 208:115237. [PMID: 38447931 PMCID: PMC11031334 DOI: 10.1016/j.addr.2024.115237] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2023] [Revised: 01/15/2024] [Accepted: 02/27/2024] [Indexed: 03/08/2024]
Abstract
Organoid cultures offer a valuable platform for studying organ-level biology, allowing for a closer mimicry of human physiology compared to traditional two-dimensional cell culture systems or non-primate animal models. While many organoid cultures use cell aggregates or decellularized extracellular matrices as scaffolds, they often lack precise biochemical and biophysical microenvironments. In contrast, three-dimensional (3D) bioprinting allows precise placement of organoids or spheroids, providing enhanced spatial control and facilitating the direct fusion for the formation of large-scale functional tissues in vitro. In addition, 3D bioprinting enables fine tuning of biochemical and biophysical cues to support organoid development and maturation. With advances in the organoid technology and its potential applications across diverse research fields such as cell biology, developmental biology, disease pathology, precision medicine, drug toxicology, and tissue engineering, organoid imaging has become a crucial aspect of physiological and pathological studies. This review highlights the recent advancements in imaging technologies that have significantly contributed to organoid research. Additionally, we discuss various bioprinting techniques, emphasizing their applications in organoid bioprinting. Integrating 3D imaging tools into a bioprinting platform allows real-time visualization while facilitating quality control, optimization, and comprehensive bioprinting assessment. Similarly, combining imaging technologies with organoid bioprinting can provide valuable insights into tissue formation, maturation, functions, and therapeutic responses. This approach not only improves the reproducibility of physiologically relevant tissues but also enhances understanding of complex biological processes. Thus, careful selection of bioprinting modalities, coupled with appropriate imaging techniques, holds the potential to create a versatile platform capable of addressing existing challenges and harnessing opportunities in these rapidly evolving fields.
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Affiliation(s)
- Sushila Maharjan
- Division of Engineering in Medicine, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Cambridge, MA 02139, USA
| | - Chenshuo Ma
- Department of Biomedical Engineering, Duke University, Durham, NC 27708, USA
| | - Bibhor Singh
- Winthrop L. Chenery Upper Elementary School, Belmont, MA 02478, USA
| | - Heemin Kang
- Department of Materials Science and Engineering, Korea University, Seoul 02841, Republic of Korea; College of Medicine, Korea University, Seoul 02841, Republic of Korea
| | - Gorka Orive
- NanoBioCel Research Group, School of Pharmacy, University of the Basque Country (UPV/EHU), Vitoria-Gasteiz, Spain; Bioaraba, NanoBioCel Research Group, Vitoria-Gasteiz, Spain; Biomedical Research Networking Centre in Bioengineering, Biomaterials and Nanomedicine (CIBER-BBN). Vitoria-Gasteiz, Spain; University Institute for Regenerative Medicine and Oral Implantology - UIRMI (UPV/EHU-Fundación Eduardo Anitua), Vitoria, 01007, Spain; Singapore Eye Research Institute, The Academia, 20 College Road, Discovery Tower, Singapore 169856, Singapore
| | - Junjie Yao
- Department of Biomedical Engineering, Duke University, Durham, NC 27708, USA.
| | - Yu Shrike Zhang
- Division of Engineering in Medicine, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Cambridge, MA 02139, USA.
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11
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Moos F, Suppinger S, de Medeiros G, Oost KC, Boni A, Rémy C, Weevers SL, Tsiairis C, Strnad P, Liberali P. Open-top multisample dual-view light-sheet microscope for live imaging of large multicellular systems. Nat Methods 2024; 21:798-803. [PMID: 38509326 PMCID: PMC11093739 DOI: 10.1038/s41592-024-02213-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2023] [Accepted: 02/15/2024] [Indexed: 03/22/2024]
Abstract
Multicellular systems grow over the course of weeks from single cells to tissues or even full organisms, making live imaging challenging. To bridge spatiotemporal scales, we present an open-top dual-view and dual-illumination light-sheet microscope dedicated to live imaging of large specimens at single-cell resolution. The configuration of objectives together with a customizable multiwell mounting system combines dual view with high-throughput multiposition imaging. We use this microscope to image a wide variety of samples and highlight its capabilities to gain quantitative single-cell information in large specimens such as mature intestinal organoids and gastruloids.
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Affiliation(s)
- Franziska Moos
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
- University of Basel, Basel, Switzerland
| | - Simon Suppinger
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
- University of Basel, Basel, Switzerland
| | - Gustavo de Medeiros
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
- Viventis Microscopy Sàrl, Lausanne, Switzerland
| | | | - Andrea Boni
- Viventis Microscopy Sàrl, Lausanne, Switzerland
| | | | - Sera Lotte Weevers
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
- University of Basel, Basel, Switzerland
| | - Charisios Tsiairis
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
- University of Basel, Basel, Switzerland
| | - Petr Strnad
- Viventis Microscopy Sàrl, Lausanne, Switzerland.
| | - Prisca Liberali
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland.
- University of Basel, Basel, Switzerland.
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12
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Bodén A, Ollech D, York AG, Millett-Sikking A, Testa I. Super-sectioning with multi-sheet reversible saturable optical fluorescence transitions (RESOLFT) microscopy. Nat Methods 2024; 21:882-888. [PMID: 38395993 PMCID: PMC11093742 DOI: 10.1038/s41592-024-02196-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2023] [Accepted: 01/24/2024] [Indexed: 02/25/2024]
Abstract
Light-sheet fluorescence microscopy is an invaluable tool for four-dimensional biological imaging of multicellular systems due to the rapid volumetric imaging and minimal illumination dosage. However, it is challenging to retrieve fine subcellular information, especially in living cells, due to the width of the sheet of light (>1 μm). Here, using reversibly switchable fluorescent proteins (RSFPs) and a periodic light pattern for photoswitching, we demonstrate a super-resolution imaging method for rapid volumetric imaging of subcellular structures called multi-sheet RESOLFT. Multiple emission-sheets with a width that is far below the diffraction limit are created in parallel increasing recording speed (1-2 Hz) to provide super-sectioning ability (<100 nm). Our technology is compatible with various RSFPs due to its minimal requirement in the number of switching cycles and can be used to study a plethora of cellular structures. We track cellular processes such as cell division, actin motion and the dynamics of virus-like particles in three dimensions.
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Affiliation(s)
- Andreas Bodén
- Department of Applied Physics and Science for Life Laboratory, KTH Royal Institute of Technology, Stockholm, Sweden
| | - Dirk Ollech
- Department of Applied Physics and Science for Life Laboratory, KTH Royal Institute of Technology, Stockholm, Sweden
| | - Andrew G York
- Calico Life Sciences LLC, South San Francisco, CA, USA
| | | | - Ilaria Testa
- Department of Applied Physics and Science for Life Laboratory, KTH Royal Institute of Technology, Stockholm, Sweden.
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13
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Dibaji H, Nasaban Shotorban AK, Grattan RM, Lucero S, Schodt DJ, Lidke KA, Petruccelli J, Lidke DS, Liu S, Chakraborty T. Axial de-scanning using remote focusing in the detection arm of light-sheet microscopy. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.09.07.556729. [PMID: 38659774 PMCID: PMC11042218 DOI: 10.1101/2023.09.07.556729] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/26/2024]
Abstract
The ability to image at high speeds is necessary for biological imaging to capture fast-moving or transient events or to efficiently image large samples. However, due to the lack of rigidity of biological specimens, carrying out fast, high-resolution volumetric imaging without moving and agitating the sample has been a challenging problem. Pupil-matched remote focusing has been promising for high NA imaging systems with their low aberrations and wavelength independence, making it suitable for multicolor imaging. However, owing to the incoherent and unpolarized nature of the fluorescence signal, manipulating this emission light through remote focusing is challenging. Therefore, remote focusing has been primarily limited to the illumination arm, using polarized laser light to facilitate coupling in and out of the remote focusing optics. Here, we introduce a novel optical design that can de-scan the axial focus movement in the detection arm of a microscope. Our method splits the fluorescence signal into S and P-polarized light, lets them pass through the remote focusing module separately, and combines them with the camera. This allows us to use only one focusing element to perform aberration-free, multi-color, volumetric imaging without (a) compromising the fluorescent signal and (b) needing to perform sample/detection-objective translation. We demonstrate the capabilities of this scheme by acquiring fast dual-color 4D (3D space + time) image stacks with an axial range of 70 μm and camera-limited acquisition speed. Owing to its general nature, we believe this technique will find its application in many other microscopy techniques that currently use an adjustable Z-stage to carry out volumetric imaging, such as confocal, 2-photon, and light sheet variants.
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14
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Bishop KW, Erion Barner LA, Han Q, Baraznenok E, Lan L, Poudel C, Gao G, Serafin RB, Chow SSL, Glaser AK, Janowczyk A, Brenes D, Huang H, Miyasato D, True LD, Kang S, Vaughan JC, Liu JTC. An end-to-end workflow for nondestructive 3D pathology. Nat Protoc 2024; 19:1122-1148. [PMID: 38263522 DOI: 10.1038/s41596-023-00934-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2023] [Accepted: 10/23/2023] [Indexed: 01/25/2024]
Abstract
Recent advances in 3D pathology offer the ability to image orders of magnitude more tissue than conventional pathology methods while also providing a volumetric context that is not achievable with 2D tissue sections, and all without requiring destructive tissue sectioning. Generating high-quality 3D pathology datasets on a consistent basis, however, is not trivial and requires careful attention to a series of details during tissue preparation, imaging and initial data processing, as well as iterative optimization of the entire process. Here, we provide an end-to-end procedure covering all aspects of a 3D pathology workflow (using light-sheet microscopy as an illustrative imaging platform) with sufficient detail to perform well-controlled preclinical and clinical studies. Although 3D pathology is compatible with diverse staining protocols and computationally generated color palettes for visual analysis, this protocol focuses on the use of a fluorescent analog of hematoxylin and eosin, which remains the most common stain used for gold-standard pathological reports. We present our guidelines for a broad range of end users (e.g., biologists, clinical researchers and engineers) in a simple format. The end-to-end workflow requires 3-6 d to complete, bearing in mind that data analysis may take longer.
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Affiliation(s)
- Kevin W Bishop
- Department of Mechanical Engineering, University of Washington, Seattle, WA, USA
- Department of Bioengineering, University of Washington, Seattle, WA, USA
| | | | - Qinghua Han
- Department of Mechanical Engineering, University of Washington, Seattle, WA, USA
- Department of Bioengineering, University of Washington, Seattle, WA, USA
| | - Elena Baraznenok
- Department of Mechanical Engineering, University of Washington, Seattle, WA, USA
- Department of Bioengineering, University of Washington, Seattle, WA, USA
| | - Lydia Lan
- Department of Mechanical Engineering, University of Washington, Seattle, WA, USA
- Department of Biology, University of Washington, Seattle, WA, USA
| | - Chetan Poudel
- Department of Chemistry, University of Washington, Seattle, WA, USA
| | - Gan Gao
- Department of Mechanical Engineering, University of Washington, Seattle, WA, USA
| | - Robert B Serafin
- Department of Mechanical Engineering, University of Washington, Seattle, WA, USA
| | - Sarah S L Chow
- Department of Mechanical Engineering, University of Washington, Seattle, WA, USA
| | - Adam K Glaser
- Allen Institute for Neural Dynamics, Seattle, WA, USA
| | - Andrew Janowczyk
- Department of Biomedical Engineering, Emory University, Atlanta, GA, USA
- Department of Oncology, Division of Precision Oncology, University Hospital of Geneva, Geneva, Switzerland
- Department of Diagnostics, Division of Clinical Pathology, University Hospital of Geneva, Geneva, Switzerland
| | - David Brenes
- Department of Mechanical Engineering, University of Washington, Seattle, WA, USA
| | - Hongyi Huang
- Department of Mechanical Engineering, University of Washington, Seattle, WA, USA
| | - Dominie Miyasato
- Department of Mechanical Engineering, University of Washington, Seattle, WA, USA
| | - Lawrence D True
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, USA
| | - Soyoung Kang
- Department of Mechanical Engineering, University of Washington, Seattle, WA, USA
| | - Joshua C Vaughan
- Department of Chemistry, University of Washington, Seattle, WA, USA
- Department of Physiology and Biophysics, University of Washington, Seattle, WA, USA
| | - Jonathan T C Liu
- Department of Mechanical Engineering, University of Washington, Seattle, WA, USA.
- Department of Bioengineering, University of Washington, Seattle, WA, USA.
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, USA.
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15
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Harken AD, Deoli NT, Perez Campos C, Ponnaiya B, Garty G, Lee GS, Casper MJ, Dhingra S, Li W, Johnson GW, Amundson SA, Grabham PW, Hillman EMC, Brenner DJ. Combined ion beam irradiation platform and 3D fluorescence microscope for cellular cancer research. BIOMEDICAL OPTICS EXPRESS 2024; 15:2561-2577. [PMID: 38633084 PMCID: PMC11019671 DOI: 10.1364/boe.522969] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/06/2024] [Accepted: 03/06/2024] [Indexed: 04/19/2024]
Abstract
To improve particle radiotherapy, we need a better understanding of the biology of radiation effects, particularly in heavy ion radiation therapy, where global responses are observed despite energy deposition in only a subset of cells. Here, we integrated a high-speed swept confocally-aligned planar excitation (SCAPE) microscope into a focused ion beam irradiation platform to allow real-time 3D structural and functional imaging of living biological samples during and after irradiation. We demonstrate dynamic imaging of the acute effects of irradiation on 3D cultures of U87 human glioblastoma cells, revealing characteristic changes in cellular movement and intracellular calcium signaling following ionizing irradiation.
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Affiliation(s)
- Andrew D Harken
- Radiological Research Accelerator Facility, Columbia University Irving Medical Center, 136 S. Broadway, P.O. Box 21, Irvington, New York 10533, USA
- Center for Radiological Research, Columbia University Irving Medical Center, 630 W. 168th Street, New York, NY 10032, USA
| | - Naresh T Deoli
- Radiological Research Accelerator Facility, Columbia University Irving Medical Center, 136 S. Broadway, P.O. Box 21, Irvington, New York 10533, USA
- Center for Radiological Research, Columbia University Irving Medical Center, 630 W. 168th Street, New York, NY 10032, USA
| | - Citlali Perez Campos
- Laboratory for Functional Optical Imaging, Departments of Biomedical Engineering and Radiology, Zuckerman Mind Brain Behavior Institute and Kavli Institute for Brain Sciences, Columbia University, New York, NY, 10027, USA
| | - Brian Ponnaiya
- Radiological Research Accelerator Facility, Columbia University Irving Medical Center, 136 S. Broadway, P.O. Box 21, Irvington, New York 10533, USA
- Center for Radiological Research, Columbia University Irving Medical Center, 630 W. 168th Street, New York, NY 10032, USA
| | - Guy Garty
- Radiological Research Accelerator Facility, Columbia University Irving Medical Center, 136 S. Broadway, P.O. Box 21, Irvington, New York 10533, USA
- Center for Radiological Research, Columbia University Irving Medical Center, 630 W. 168th Street, New York, NY 10032, USA
| | - Grace S Lee
- Laboratory for Functional Optical Imaging, Departments of Biomedical Engineering and Radiology, Zuckerman Mind Brain Behavior Institute and Kavli Institute for Brain Sciences, Columbia University, New York, NY, 10027, USA
| | - Malte J Casper
- Laboratory for Functional Optical Imaging, Departments of Biomedical Engineering and Radiology, Zuckerman Mind Brain Behavior Institute and Kavli Institute for Brain Sciences, Columbia University, New York, NY, 10027, USA
| | - Shikhar Dhingra
- Laboratory for Functional Optical Imaging, Departments of Biomedical Engineering and Radiology, Zuckerman Mind Brain Behavior Institute and Kavli Institute for Brain Sciences, Columbia University, New York, NY, 10027, USA
| | - Wenze Li
- Laboratory for Functional Optical Imaging, Departments of Biomedical Engineering and Radiology, Zuckerman Mind Brain Behavior Institute and Kavli Institute for Brain Sciences, Columbia University, New York, NY, 10027, USA
| | - Gary W Johnson
- Center for Radiological Research, Columbia University Irving Medical Center, 630 W. 168th Street, New York, NY 10032, USA
| | - Sally A Amundson
- Center for Radiological Research, Columbia University Irving Medical Center, 630 W. 168th Street, New York, NY 10032, USA
| | - Peter W Grabham
- Center for Radiological Research, Columbia University Irving Medical Center, 630 W. 168th Street, New York, NY 10032, USA
| | - Elizabeth M C Hillman
- Laboratory for Functional Optical Imaging, Departments of Biomedical Engineering and Radiology, Zuckerman Mind Brain Behavior Institute and Kavli Institute for Brain Sciences, Columbia University, New York, NY, 10027, USA
| | - David J Brenner
- Radiological Research Accelerator Facility, Columbia University Irving Medical Center, 136 S. Broadway, P.O. Box 21, Irvington, New York 10533, USA
- Center for Radiological Research, Columbia University Irving Medical Center, 630 W. 168th Street, New York, NY 10032, USA
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16
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Kume D, Kozawa Y, Kawakami R, Ishii H, Watakabe Y, Uesugi Y, Imamura T, Nemoto T, Sato S. Graded arc beam in light needle microscopy for axially resolved, rapid volumetric imaging without nonlinear processes. OPTICS EXPRESS 2024; 32:7289-7306. [PMID: 38439413 DOI: 10.1364/oe.516437] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/21/2023] [Accepted: 02/06/2024] [Indexed: 03/06/2024]
Abstract
High-speed three-dimensional (3D) imaging is essential for revealing the structure and functions of biological specimens. Confocal laser scanning microscopy has been widely employed for this purpose. However, it requires a time-consuming image-stacking procedure. As a solution, we previously developed light needle microscopy using a Bessel beam with a wavefront-engineered approach [Biomed. Opt. Express13, 1702 (2022)10.1364/BOE.449329]. However, this method applies only to multiphoton excitation microscopy because of the requirement to reduce the sidelobes of the Bessel beam. Here, we introduce a beam that produces a needle spot while eluding the intractable artifacts due to the sidelobes. This beam can be adopted even in one-photon excitation fluorescence 3D imaging. The proposed method can achieve real-time, rapid 3D observation of 200-nm particles in water at a rate of over 50 volumes per second. In addition, fine structures, such as the spines of neurons in fixed mouse brain tissue, can be visualized in 3D from a single raster scan of the needle spot. The proposed method can be applied to various modalities in biological imaging, enabling rapid 3D image acquisition.
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17
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Thibodeaux DN, Shaik MA, Kim SH, Voleti V, Zhao HT, Benezra SE, Nwokeabia CJ, Hillman EMC. Audiovisualization of real-time neuroimaging data. PLoS One 2024; 19:e0297435. [PMID: 38381733 PMCID: PMC10881001 DOI: 10.1371/journal.pone.0297435] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2023] [Accepted: 01/04/2024] [Indexed: 02/23/2024] Open
Abstract
Advancements in brain imaging techniques have significantly expanded the size and complexity of real-time neuroimaging and behavioral data. However, identifying patterns, trends and synchronies within these datasets presents a significant computational challenge. Here, we demonstrate an approach that can translate time-varying neuroimaging data into unique audiovisualizations consisting of audible representations of dynamic data merged with simplified, color-coded movies of spatial components and behavioral recordings. Multiple variables can be encoded as different musical instruments, letting the observer differentiate and track multiple dynamic parameters in parallel. This representation enables intuitive assimilation of these datasets for behavioral correlates and spatiotemporal features such as patterns, rhythms and motifs that could be difficult to detect through conventional data interrogation methods. These audiovisual representations provide a novel perception of the organization and patterns of real-time activity in the brain, and offer an intuitive and compelling method for complex data visualization for a wider range of applications.
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Affiliation(s)
- David N. Thibodeaux
- Laboratory for Functional Optical Imaging, Departments of Biomedical Engineering and Radiology, Mortimer B. Zuckerman Mind Brain Behavior Institute, Columbia University, New York, NY, United States of America
| | - Mohammed A. Shaik
- Laboratory for Functional Optical Imaging, Departments of Biomedical Engineering and Radiology, Mortimer B. Zuckerman Mind Brain Behavior Institute, Columbia University, New York, NY, United States of America
| | - Sharon H. Kim
- Laboratory for Functional Optical Imaging, Departments of Biomedical Engineering and Radiology, Mortimer B. Zuckerman Mind Brain Behavior Institute, Columbia University, New York, NY, United States of America
| | - Venkatakaushik Voleti
- Laboratory for Functional Optical Imaging, Departments of Biomedical Engineering and Radiology, Mortimer B. Zuckerman Mind Brain Behavior Institute, Columbia University, New York, NY, United States of America
| | - Hanzhi T. Zhao
- Laboratory for Functional Optical Imaging, Departments of Biomedical Engineering and Radiology, Mortimer B. Zuckerman Mind Brain Behavior Institute, Columbia University, New York, NY, United States of America
| | - Sam E. Benezra
- Laboratory for Functional Optical Imaging, Departments of Biomedical Engineering and Radiology, Mortimer B. Zuckerman Mind Brain Behavior Institute, Columbia University, New York, NY, United States of America
| | - Chinwendu J. Nwokeabia
- Laboratory for Functional Optical Imaging, Departments of Biomedical Engineering and Radiology, Mortimer B. Zuckerman Mind Brain Behavior Institute, Columbia University, New York, NY, United States of America
| | - Elizabeth M. C. Hillman
- Laboratory for Functional Optical Imaging, Departments of Biomedical Engineering and Radiology, Mortimer B. Zuckerman Mind Brain Behavior Institute, Columbia University, New York, NY, United States of America
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18
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Sommernes JR, Millett-Sikking A, Ströhl F. S-polarized light-sheets improve resolution and light-efficiency in oblique plane microscopy. Sci Rep 2024; 14:3540. [PMID: 38347049 PMCID: PMC10861444 DOI: 10.1038/s41598-024-53900-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2023] [Accepted: 02/06/2024] [Indexed: 02/15/2024] Open
Abstract
Oblique plane microscopy (OPM) offers 3D optically sectioned imaging with high spatial- and temporal-resolution while enabling conventional sample mounting. The technique uses a concatenation of three microscopes, two for remote focusing and a tilted tertiary microscope, often including an immersion objective, to image an oblique sample plane. This design induces Fresnel reflections and a reduced effective aperture, thus impacting the resolution and light efficiency of the system. Using vectorial diffraction simulations, the system performance was characterized based on illumination angle and polarization, signal to noise ratio, and refractive index of the tertiary objective immersion. We show that for samples with high fluorescent anisotropy, s-polarized light-sheets yield higher average resolution for all system configurations, as well as higher light-efficiency. We also provide a tool for performance characterization of arbitrary light-sheet imaging systems.
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Affiliation(s)
- Jon-Richard Sommernes
- Department of Physics and Technology, UiT The Arctic University of Norway, Tromsø, Norway
| | | | - Florian Ströhl
- Department of Physics and Technology, UiT The Arctic University of Norway, Tromsø, Norway.
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19
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Longden TA, Lederer WJ. Electro-metabolic signaling. J Gen Physiol 2024; 156:e202313451. [PMID: 38197953 PMCID: PMC10783436 DOI: 10.1085/jgp.202313451] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2023] [Revised: 10/27/2023] [Accepted: 12/14/2023] [Indexed: 01/11/2024] Open
Abstract
Precise matching of energy substrate delivery to local metabolic needs is essential for the health and function of all tissues. Here, we outline a mechanistic framework for understanding this critical process, which we refer to as electro-metabolic signaling (EMS). All tissues exhibit changes in metabolism over varying spatiotemporal scales and have widely varying energetic needs and reserves. We propose that across tissues, common signatures of elevated metabolism or increases in energy substrate usage that exceed key local thresholds rapidly engage mechanisms that generate hyperpolarizing electrical signals in capillaries that then relax contractile elements throughout the vasculature to quickly adjust blood flow to meet changing needs. The attendant increase in energy substrate delivery serves to meet local metabolic requirements and thus avoids a mismatch in supply and demand and prevents metabolic stress. We discuss in detail key examples of EMS that our laboratories have discovered in the brain and the heart, and we outline potential further EMS mechanisms operating in tissues such as skeletal muscle, pancreas, and kidney. We suggest that the energy imbalance evoked by EMS uncoupling may be central to cellular dysfunction from which the hallmarks of aging and metabolic diseases emerge and may lead to generalized organ failure states-such as diverse flavors of heart failure and dementia. Understanding and manipulating EMS may be key to preventing or reversing these dysfunctions.
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Affiliation(s)
- Thomas A. Longden
- Department of Physiology, University of Maryland School of Medicine, Baltimore, MD, USA
- Laboratory of Neurovascular Interactions, Center for Biomedical Engineering and Technology, University of Maryland School of Medicine, Baltimore, MD, USA
| | - W. Jonathan Lederer
- Department of Physiology, University of Maryland School of Medicine, Baltimore, MD, USA
- Laboratory of Molecular Cardiology, Center for Biomedical Engineering and Technology, University of Maryland School of Medicine, Baltimore, MD, USA
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20
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Park CF, Barzegar-Keshteli M, Korchagina K, Delrocq A, Susoy V, Jones CL, Samuel ADT, Rahi SJ. Automated neuron tracking inside moving and deforming C. elegans using deep learning and targeted augmentation. Nat Methods 2024; 21:142-149. [PMID: 38052988 DOI: 10.1038/s41592-023-02096-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2022] [Accepted: 10/20/2023] [Indexed: 12/07/2023]
Abstract
Reading out neuronal activity from three-dimensional (3D) functional imaging requires segmenting and tracking individual neurons. This is challenging in behaving animals if the brain moves and deforms. The traditional approach is to train a convolutional neural network with ground-truth (GT) annotations of images representing different brain postures. For 3D images, this is very labor intensive. We introduce 'targeted augmentation', a method to automatically synthesize artificial annotations from a few manual annotations. Our method ('Targettrack') learns the internal deformations of the brain to synthesize annotations for new postures by deforming GT annotations. This reduces the need for manual annotation and proofreading. A graphical user interface allows the application of the method end-to-end. We demonstrate Targettrack on recordings where neurons are labeled as key points or 3D volumes. Analyzing freely moving animals exposed to odor pulses, we uncover rich patterns in interneuron dynamics, including switching neuronal entrainment on and off.
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Affiliation(s)
- Core Francisco Park
- Department of Physics and Center for Brain Science, Harvard University, Cambridge, MA, USA
| | - Mahsa Barzegar-Keshteli
- Laboratory of the Physics of Biological Systems, Institute of Physics, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Kseniia Korchagina
- Laboratory of the Physics of Biological Systems, Institute of Physics, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Ariane Delrocq
- Laboratory of the Physics of Biological Systems, Institute of Physics, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Vladislav Susoy
- Department of Physics and Center for Brain Science, Harvard University, Cambridge, MA, USA
| | - Corinne L Jones
- Swiss Data Science Center, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Aravinthan D T Samuel
- Department of Physics and Center for Brain Science, Harvard University, Cambridge, MA, USA
| | - Sahand Jamal Rahi
- Laboratory of the Physics of Biological Systems, Institute of Physics, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland.
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21
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Cooney PC, Huang Y, Li W, Perera DM, Hormigo R, Tabachnik T, Godage IS, Hillman EMC, Grueber WB, Zarin AA. Neuromuscular basis of Drosophila larval rolling escape behavior. Proc Natl Acad Sci U S A 2023; 120:e2303641120. [PMID: 38096410 PMCID: PMC10743538 DOI: 10.1073/pnas.2303641120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2023] [Accepted: 10/06/2023] [Indexed: 12/18/2023] Open
Abstract
When threatened by dangerous or harmful stimuli, animals engage in diverse forms of rapid escape behaviors. In Drosophila larvae, one type of escape response involves C-shaped bending and lateral rolling followed by rapid forward crawling. The sensory circuitry that promotes larval escape has been extensively characterized; however, the motor programs underlying rolling are unknown. Here, we characterize the neuromuscular basis of rolling escape behavior. We used high-speed, volumetric, Swept Confocally Aligned Planar Excitation (SCAPE) microscopy to image muscle activity during larval rolling. Unlike sequential peristaltic muscle contractions that progress from segment to segment during forward and backward crawling, muscle activity progresses circumferentially during bending and rolling escape behavior. We propose that progression of muscular contraction around the larva's circumference results in a transient misalignment between weight and the ground support forces, which generates a torque that induces stabilizing body rotation. Therefore, successive cycles of slight misalignment followed by reactive aligning rotation lead to continuous rolling motion. Supporting our biomechanical model, we found that disrupting the activity of muscle groups undergoing circumferential contraction progression leads to rolling defects. We use EM connectome data to identify premotor to motor connectivity patterns that could drive rolling behavior and perform neural silencing approaches to demonstrate the crucial role of a group of glutamatergic premotor neurons in rolling. Our data reveal body-wide muscle activity patterns and putative premotor circuit organization for execution of the rolling escape response.
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Affiliation(s)
- Patricia C. Cooney
- Grueber Laboratory, Mortimer B. Zuckerman Mind Brain Behavior Institute, Columbia University, New York, NY10027
- Department of Neuroscience, Columbia University, New York, NY10027
| | - Yuhan Huang
- Department of Biology, Texas A&M University, College Station, TX77843
- Zarin Laboratory, Texas A&M Institute for Neuroscience, Texas A&M University, College Station, TX77843
| | - Wenze Li
- Laboratory for Functional Optical Imaging, Mortimer B. Zuckerman Mind Brain Behavior Institute, Columbia University, New York, NY10027
- Department of Electrical Engineering, Columbia University, New York, NY10027
| | - Dulanjana M. Perera
- Department of Multidisciplinary Engineering, Texas A&M University, College Station, TX77843
| | - Richard Hormigo
- Grueber Laboratory, Mortimer B. Zuckerman Mind Brain Behavior Institute, Columbia University, New York, NY10027
| | - Tanya Tabachnik
- Grueber Laboratory, Mortimer B. Zuckerman Mind Brain Behavior Institute, Columbia University, New York, NY10027
| | - Isuru S. Godage
- Department of Multidisciplinary Engineering, Texas A&M University, College Station, TX77843
- Department of Engineering Technology and Industrial Distribution, Texas A&M University, College Station, TX77843
- J. Mike Walker ‘66 Department of Mechanical Engineering, Texas A&M University, College Station, TX77843
| | - Elizabeth M. C. Hillman
- Laboratory for Functional Optical Imaging, Mortimer B. Zuckerman Mind Brain Behavior Institute, Columbia University, New York, NY10027
- Department of Biomedical Engineering, Columbia University, New York, NY10027
- Laboratory for Functional Optical Imaging, Kavli Institute for Brain Science, Columbia University, New York, NY10032
| | - Wesley B. Grueber
- Grueber Laboratory, Mortimer B. Zuckerman Mind Brain Behavior Institute, Columbia University, New York, NY10027
- Department of Neuroscience, Columbia University, New York, NY10027
- Department of Physiology and Cellular Biophysics, Jerome L. Greene Science Center, New York, NY10027
| | - Aref A. Zarin
- Department of Biology, Texas A&M University, College Station, TX77843
- Zarin Laboratory, Texas A&M Institute for Neuroscience, Texas A&M University, College Station, TX77843
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22
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Wang Z, Zhang J, Symvoulidis P, Guo W, Zhang L, Wilson MA, Boyden ES. Imaging the voltage of neurons distributed across entire brains of larval zebrafish. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.12.15.571964. [PMID: 38168290 PMCID: PMC10760087 DOI: 10.1101/2023.12.15.571964] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/05/2024]
Abstract
Neurons interact in networks distributed throughout the brain. Although much effort has focused on whole-brain calcium imaging, recent advances in genetically encoded voltage indicators (GEVIs) raise the possibility of imaging voltage of neurons distributed across brains. To achieve this, a microscope must image at high volumetric rate and signal-to-noise ratio. We present a remote scanning light-sheet microscope capable of imaging GEVI-expressing neurons distributed throughout entire brains of larval zebrafish at a volumetric rate of 200.8 Hz. We measured voltage of ∼1/3 of the neurons of the brain, distributed throughout. We observed that neurons firing at different times during a sequence were located at different brain locations, for sequences elicited by a visual stimulus, which mapped onto locations throughout the optic tectum, as well as during stimulus-independent bursts, which mapped onto locations in the cerebellum and medulla. Whole-brain voltage imaging may open up frontiers in the fundamental operation of neural systems.
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23
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Hoffmann M, Henninger J, Veith J, Richter L, Judkewitz B. Blazed oblique plane microscopy reveals scale-invariant inference of brain-wide population activity. Nat Commun 2023; 14:8019. [PMID: 38049412 PMCID: PMC10695970 DOI: 10.1038/s41467-023-43741-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2023] [Accepted: 11/17/2023] [Indexed: 12/06/2023] Open
Abstract
Due to the size and opacity of vertebrate brains, it has until now been impossible to simultaneously record neuronal activity at cellular resolution across the entire adult brain. As a result, scientists are forced to choose between cellular-resolution microscopy over limited fields-of-view or whole-brain imaging at coarse-grained resolution. Bridging the gap between these spatial scales of understanding remains a major challenge in neuroscience. Here, we introduce blazed oblique plane microscopy to perform brain-wide recording of neuronal activity at cellular resolution in an adult vertebrate. Contrary to common belief, we find that inferences of neuronal population activity are near-independent of spatial scale: a set of randomly sampled neurons has a comparable predictive power as the same number of coarse-grained macrovoxels. Our work thus links cellular resolution with brain-wide scope, challenges the prevailing view that macroscale methods are generally inferior to microscale techniques and underscores the value of multiscale approaches to studying brain-wide activity.
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Affiliation(s)
- Maximilian Hoffmann
- Einstein Center for Neurosciences, NeuroCure Cluster of Excellence, Charité - Universitätsmedizin Berlin, Berlin, Germany
- Rockefeller University, New York, USA
| | - Jörg Henninger
- Einstein Center for Neurosciences, NeuroCure Cluster of Excellence, Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - Johannes Veith
- Einstein Center for Neurosciences, NeuroCure Cluster of Excellence, Charité - Universitätsmedizin Berlin, Berlin, Germany
- Department of Biology, Humboldt University Berlin, Berlin, Germany
| | - Lars Richter
- Department of Chemistry and Center for NanoScience, Ludwig Maximilians University, Munich, Germany
| | - Benjamin Judkewitz
- Einstein Center for Neurosciences, NeuroCure Cluster of Excellence, Charité - Universitätsmedizin Berlin, Berlin, Germany.
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24
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Park S, Na M, Chang S, Kim KH. High-resolution open-top axially swept light sheet microscopy. BMC Biol 2023; 21:248. [PMID: 37940973 PMCID: PMC10634022 DOI: 10.1186/s12915-023-01747-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2023] [Accepted: 10/24/2023] [Indexed: 11/10/2023] Open
Abstract
BACKGROUND Open-top light-sheet microscopy (OT-LSM) is a specialized microscopic technique for the high-throughput cellular imaging of optically cleared, large-sized specimens, such as the brain. Despite the development of various OT-LSM techniques, achieving submicron resolution in all dimensions remains. RESULTS We developed a high-resolution open-top axially swept LSM (HR-OTAS-LSM) for high-throughput and high-resolution imaging in all dimensions. High axial and lateral resolutions were achieved by using an aberration-corrected axially swept excitation light sheet in the illumination arm and a high numerical aperture (NA) immersion objective lens in the imaging arm, respectively. The high-resolution, high-throughput visualization of neuronal networks in mouse brain and retina specimens validated the performance of HR-OTAS-LSM. CONCLUSIONS The proposed HR-OTAS-LSM method represents a significant advancement in the high-resolution mapping of cellular networks in biological systems such as the brain and retina.
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Affiliation(s)
- Soohyun Park
- Department of Mechanical Engineering, Pohang University of Science and Technology, 77 Cheongam-Ro, Nam-gu, Pohang, Gyeongbuk, 37673, Republic of Korea
| | - Myeongsu Na
- Department of Research and Development Center, Crayon Technologies, 19 Sanmaru-ro, Guri, Gyeonggi-do, 11901, Republic of Korea
| | - Sunghoe Chang
- Department of Physiology and Biomedical Sciences, Seoul National University College of Medicine, 103 Daehak-ro, Jongno-gu, Seoul, 03080, Republic of Korea
- Neuroscience Research Institute, Seoul National University College of Medicine, 103 Daehak-ro, Jongno-gu, Seoul, 03080, Republic of Korea
| | - Ki Hean Kim
- Department of Mechanical Engineering, Pohang University of Science and Technology, 77 Cheongam-Ro, Nam-gu, Pohang, Gyeongbuk, 37673, Republic of Korea.
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25
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Balasubramanian H, Hobson CM, Chew TL, Aaron JS. Imagining the future of optical microscopy: everything, everywhere, all at once. Commun Biol 2023; 6:1096. [PMID: 37898673 PMCID: PMC10613274 DOI: 10.1038/s42003-023-05468-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2023] [Accepted: 10/16/2023] [Indexed: 10/30/2023] Open
Abstract
The optical microscope has revolutionized biology since at least the 17th Century. Since then, it has progressed from a largely observational tool to a powerful bioanalytical platform. However, realizing its full potential to study live specimens is hindered by a daunting array of technical challenges. Here, we delve into the current state of live imaging to explore the barriers that must be overcome and the possibilities that lie ahead. We venture to envision a future where we can visualize and study everything, everywhere, all at once - from the intricate inner workings of a single cell to the dynamic interplay across entire organisms, and a world where scientists could access the necessary microscopy technologies anywhere.
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Affiliation(s)
| | - Chad M Hobson
- Advanced Imaging Center; Howard Hughes Medical Institute Janelia Research Campus, Ashburn, VA, 20147, USA
| | - Teng-Leong Chew
- Advanced Imaging Center; Howard Hughes Medical Institute Janelia Research Campus, Ashburn, VA, 20147, USA
| | - Jesse S Aaron
- Advanced Imaging Center; Howard Hughes Medical Institute Janelia Research Campus, Ashburn, VA, 20147, USA.
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26
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Lu X, Wang Y, Liu Z, Gou Y, Jaeger D, St-Pierre F. Widefield imaging of rapid pan-cortical voltage dynamics with an indicator evolved for one-photon microscopy. Nat Commun 2023; 14:6423. [PMID: 37828037 PMCID: PMC10570354 DOI: 10.1038/s41467-023-41975-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2022] [Accepted: 09/20/2023] [Indexed: 10/14/2023] Open
Abstract
Widefield imaging with genetically encoded voltage indicators (GEVIs) is a promising approach for understanding the role of large cortical networks in the neural coding of behavior. However, the limited performance of current GEVIs restricts their deployment for single-trial imaging of rapid neuronal voltage dynamics. Here, we developed a high-throughput platform to screen for GEVIs that combine fast kinetics with high brightness, sensitivity, and photostability under widefield one-photon illumination. Rounds of directed evolution produced JEDI-1P, a green-emitting fluorescent indicator with enhanced performance across all metrics. Next, we optimized a neonatal intracerebroventricular delivery method to achieve cost-effective and wide-spread JEDI-1P expression in mice. We also developed an approach to correct optical measurements from hemodynamic and motion artifacts effectively. Finally, we achieved stable brain-wide voltage imaging and successfully tracked gamma-frequency whisker and visual stimulations in awake mice in single trials, opening the door to investigating the role of high-frequency signals in brain computations.
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Affiliation(s)
- Xiaoyu Lu
- Systems, Synthetic, and Physical Biology Program, Rice University, Houston, TX, 77005, USA
- Department of Neuroscience, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Yunmiao Wang
- Neuroscience Graduate Program, Emory University, Atlanta, GA, 30322, USA
- Biology Department, Emory University, Atlanta, GA, 30322, USA
| | - Zhuohe Liu
- Department of Electrical and Computer Engineering, Rice University, Houston, TX, 77005, USA
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Yueyang Gou
- Department of Neuroscience, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Dieter Jaeger
- Biology Department, Emory University, Atlanta, GA, 30322, USA.
| | - François St-Pierre
- Systems, Synthetic, and Physical Biology Program, Rice University, Houston, TX, 77005, USA.
- Department of Electrical and Computer Engineering, Rice University, Houston, TX, 77005, USA.
- Department of Neuroscience, Baylor College of Medicine, Houston, TX, 77030, USA.
- Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX, 77030, USA.
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27
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DIBAJI HASSAN, SHOTORBAN ALIKAZEMINASABAN, HABIBI MAHSA, GRATTAN RACHELM, LUCERO SHAYNA, SCHODT DAVIDJ, LIDKE KEITHA, PETRUCCELLI JONATHAN, LIDKE DIANES, LIU SHENG, CHAKRABORTY TONMOY. Axial de-scanning using remote focusing in the detection arm of light-sheet microscopy. RESEARCH SQUARE 2023:rs.3.rs-3338831. [PMID: 37886461 PMCID: PMC10602066 DOI: 10.21203/rs.3.rs-3338831/v1] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/28/2023]
Abstract
The ability to image at high speeds is necessary in biological imaging to capture fast-moving or transient events or to efficiently image large samples. However, due to the lack of rigidity of biological specimens, carrying out fast, high-resolution volumetric imaging without moving and agitating the sample has been a challenging problem. Pupil-matched remote focusing has been promising for high NA imaging systems with their low aberrations and wavelength independence, making it suitable for multicolor imaging. However, owing to the incoherent and unpolarized nature of the fluorescence signal, manipulating this emission light through remote focusing is challenging. Therefore, remote focusing has been primarily limited to the illumination arm, using polarized laser light for facilitating coupling in and out of the remote focusing optics. Here we introduce a novel optical design that can de-scan the axial focus movement in the detection arm of a microscope. Our method splits the fluorescence signal into S and P-polarized light and lets them pass through the remote focusing module separately and combines them with the camera. This allows us to use only one focusing element to perform aberration-free, multi-color, volumetric imaging without (a) compromising the fluorescent signal and (b) needing to perform sample/detection-objective translation. We demonstrate the capabilities of this scheme by acquiring fast dual-color 4D (3D space + time) image stacks, with an axial range of 70 μm and camera limited acquisition speed. Owing to its general nature, we believe this technique will find its application to many other microscopy techniques that currently use an adjustable Z-stage to carry out volumetric imaging such as confocal, 2-photon, and light sheet variants.
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Affiliation(s)
- HASSAN DIBAJI
- Department of Physics and Astronomy, University of New Mexico, Albuquerque, New Mexico 87131, USA
| | | | - MAHSA HABIBI
- Department of Physics and Astronomy, University of New Mexico, Albuquerque, New Mexico 87131, USA
| | - RACHEL M GRATTAN
- Comprehensive Cancer Center, University of New Mexico Health Sciences Center, Albuquerque, New Mexico, 87131, USA
- Department of Pathology, University of New Mexico Health Science Center, Albuquerque, NM, USA
| | - SHAYNA LUCERO
- Comprehensive Cancer Center, University of New Mexico Health Sciences Center, Albuquerque, New Mexico, 87131, USA
- Department of Pathology, University of New Mexico Health Science Center, Albuquerque, NM, USA
| | - DAVID J. SCHODT
- Department of Physics and Astronomy, University of New Mexico, Albuquerque, New Mexico 87131, USA
| | - KEITH A. LIDKE
- Department of Physics and Astronomy, University of New Mexico, Albuquerque, New Mexico 87131, USA
- Comprehensive Cancer Center, University of New Mexico Health Sciences Center, Albuquerque, New Mexico, 87131, USA
| | - JONATHAN PETRUCCELLI
- Department of Physics, University at Albany–State University of NewYork,1400 Washington Avenue, Albany, NY 12222, USA
| | - DIANE S. LIDKE
- Comprehensive Cancer Center, University of New Mexico Health Sciences Center, Albuquerque, New Mexico, 87131, USA
- Department of Pathology, University of New Mexico Health Science Center, Albuquerque, NM, USA
| | - SHENG LIU
- Department of Physics and Astronomy, University of New Mexico, Albuquerque, New Mexico 87131, USA
| | - TONMOY CHAKRABORTY
- Department of Physics and Astronomy, University of New Mexico, Albuquerque, New Mexico 87131, USA
- Comprehensive Cancer Center, University of New Mexico Health Sciences Center, Albuquerque, New Mexico, 87131, USA
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28
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Hennig G, Saxena P, Broemer E, Herrera GM, Roccabianca S, Tykocki NR. Quantifying whole bladder biomechanics using the novel pentaplanar reflected image macroscopy system. Biomech Model Mechanobiol 2023; 22:1685-1695. [PMID: 37249760 PMCID: PMC10511590 DOI: 10.1007/s10237-023-01727-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2022] [Accepted: 05/10/2023] [Indexed: 05/31/2023]
Abstract
Optimal bladder compliance is essential to urinary bladder storage and voiding functions. Calculated as the change in filling volume per change in pressure, bladder compliance is used clinically to characterize changes in bladder wall biomechanical properties that associate with lower urinary tract dysfunction. But because this method calculates compliance without regard to wall structure or wall volume, it gives little insight into the mechanical properties of the bladder wall during filling. Thus, we developed Pentaplanar Reflected Image Macroscopy (PRIM): a novel ex vivo imaging method to accurately calculate bladder wall stress and stretch in real time during bladder filling. The PRIM system simultaneously records intravesical pressure, infused volume, and an image of the bladder in five distinct visual planes. Wall thickness and volume were then measured and used to calculate stress and stretch during filling. As predicted, wall stress was nonlinear; only when intravesical pressure exceeded ~ 15 mmHg did bladder wall stress rapidly increase with respect to stretch. This method of calculating compliance as stress vs stretch also showed that the mechanical properties of the bladder wall remain similar in bladders of varying capacity. This study demonstrates how wall tension, stress and stretch can be measured, quantified, and used to accurately define bladder wall biomechanics in terms of actual material properties and not pressure/volume changes. This method is especially useful for determining how changes in bladder biomechanics are altered in pathologies where profound bladder wall remodeling occurs, such as diabetes and spinal cord injury.
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Affiliation(s)
- Grant Hennig
- Department of Pharmacology, University of Vermont Larner College of Medicine, Burlington, VT, 05405, USA
| | - Pragya Saxena
- Department of Pharmacology and Toxicology, Michigan State University College of Osteopathic Medicine, East Lansing, MI, 48824, USA
| | - Eli Broemer
- Department of Mechanical Engineering, Michigan State University College of Engineering, East Lansing, MI, 48824, USA
| | - Gerald M Herrera
- Department of Pharmacology, University of Vermont Larner College of Medicine, Burlington, VT, 05405, USA
| | - Sara Roccabianca
- Department of Mechanical Engineering, Michigan State University College of Engineering, East Lansing, MI, 48824, USA
| | - Nathan R Tykocki
- Department of Pharmacology and Toxicology, Michigan State University College of Osteopathic Medicine, East Lansing, MI, 48824, USA.
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29
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Carbo-Tano M, Lapoix M, Jia X, Thouvenin O, Pascucci M, Auclair F, Quan FB, Albadri S, Aguda V, Farouj Y, Hillman EMC, Portugues R, Del Bene F, Thiele TR, Dubuc R, Wyart C. The mesencephalic locomotor region recruits V2a reticulospinal neurons to drive forward locomotion in larval zebrafish. Nat Neurosci 2023; 26:1775-1790. [PMID: 37667039 PMCID: PMC10545542 DOI: 10.1038/s41593-023-01418-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2022] [Accepted: 07/24/2023] [Indexed: 09/06/2023]
Abstract
The mesencephalic locomotor region (MLR) is a brain stem area whose stimulation triggers graded forward locomotion. How MLR neurons recruit downstream vsx2+ (V2a) reticulospinal neurons (RSNs) is poorly understood. Here, to overcome this challenge, we uncovered the locus of MLR in transparent larval zebrafish and show that the MLR locus is distinct from the nucleus of the medial longitudinal fasciculus. MLR stimulations reliably elicit forward locomotion of controlled duration and frequency. MLR neurons recruit V2a RSNs via projections onto somata in pontine and retropontine areas, and onto dendrites in the medulla. High-speed volumetric imaging of neuronal activity reveals that strongly MLR-coupled RSNs are active for steering or forward swimming, whereas weakly MLR-coupled medullary RSNs encode the duration and frequency of the forward component. Our study demonstrates how MLR neurons recruit specific V2a RSNs to control the kinematics of forward locomotion and suggests conservation of the motor functions of V2a RSNs across vertebrates.
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Affiliation(s)
- Martin Carbo-Tano
- Sorbonne Université, Paris Brain Institute (Institut du Cerveau, ICM), Institut National de la Santé et de la Recherche Médicale U1127, Centre National de la Recherche Scientifique Unité Mixte de Recherche 7225, Assistance Publique-Hôpitaux de Paris, Campus Hospitalier Pitié-Salpêtrière, Paris, France
| | - Mathilde Lapoix
- Sorbonne Université, Paris Brain Institute (Institut du Cerveau, ICM), Institut National de la Santé et de la Recherche Médicale U1127, Centre National de la Recherche Scientifique Unité Mixte de Recherche 7225, Assistance Publique-Hôpitaux de Paris, Campus Hospitalier Pitié-Salpêtrière, Paris, France
| | - Xinyu Jia
- Sorbonne Université, Paris Brain Institute (Institut du Cerveau, ICM), Institut National de la Santé et de la Recherche Médicale U1127, Centre National de la Recherche Scientifique Unité Mixte de Recherche 7225, Assistance Publique-Hôpitaux de Paris, Campus Hospitalier Pitié-Salpêtrière, Paris, France
| | - Olivier Thouvenin
- Institut Langevin, École Supérieure de Physique et de Chimie Industrielles de la Ville de Paris, Paris Sciences et Lettres, Centre National de la Recherche Scientifique, Paris, France
| | - Marco Pascucci
- Sorbonne Université, Paris Brain Institute (Institut du Cerveau, ICM), Institut National de la Santé et de la Recherche Médicale U1127, Centre National de la Recherche Scientifique Unité Mixte de Recherche 7225, Assistance Publique-Hôpitaux de Paris, Campus Hospitalier Pitié-Salpêtrière, Paris, France
- Université Paris-Saclay, Commissariat à l'Énergie Atomique et aux Énergies Alternatives, Centre National de la Recherche Scientifique, NeuroSpin, Baobab, Centre d'études de Saclay, Gif-sur-Yvette, France
- The American University of Paris, Paris, France
| | - François Auclair
- Département de Neurosciences, Faculté de Médecine, Université de Montréal, Montréal, Quebec, Canada
| | - Feng B Quan
- Sorbonne Université, Paris Brain Institute (Institut du Cerveau, ICM), Institut National de la Santé et de la Recherche Médicale U1127, Centre National de la Recherche Scientifique Unité Mixte de Recherche 7225, Assistance Publique-Hôpitaux de Paris, Campus Hospitalier Pitié-Salpêtrière, Paris, France
| | - Shahad Albadri
- Sorbonne Université, Institut National de la Santé et de la Recherche Médicale, Centre National de la Recherche Scientifique, Institut de la Vision, Paris, France
| | - Vernie Aguda
- Department of Biological Sciences, University of Toronto Scarborough, Toronto, Ontario, Canada
| | - Younes Farouj
- Institute of Neuroscience, Technical University of Munich, Munich, Germany
| | - Elizabeth M C Hillman
- Laboratory for Functional Optical Imaging, Mortimer B. Zuckerman Mind Brain Behavior Institute, Columbia University, New York, NY, USA
- Department of Biomedical Engineering, Columbia University, New York, NY, USA
- Kavli Institute for Brain Science, Columbia University, New York, NY, USA
| | - Ruben Portugues
- Institute of Neuroscience, Technical University of Munich, Munich, Germany
- Munich Cluster of Systems Neurology (SyNergy), Munich, Germany
| | - Filippo Del Bene
- Sorbonne Université, Institut National de la Santé et de la Recherche Médicale, Centre National de la Recherche Scientifique, Institut de la Vision, Paris, France
| | - Tod R Thiele
- Department of Biological Sciences, University of Toronto Scarborough, Toronto, Ontario, Canada
| | - Réjean Dubuc
- Département de Neurosciences, Faculté de Médecine, Université de Montréal, Montréal, Quebec, Canada.
- Groupe de Recherche en Activité Physique Adaptée, Department of Exercise Science, Université du Québec à Montréal, Montréal, Quebec, Canada.
| | - Claire Wyart
- Sorbonne Université, Paris Brain Institute (Institut du Cerveau, ICM), Institut National de la Santé et de la Recherche Médicale U1127, Centre National de la Recherche Scientifique Unité Mixte de Recherche 7225, Assistance Publique-Hôpitaux de Paris, Campus Hospitalier Pitié-Salpêtrière, Paris, France.
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30
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Schaffer ES, Mishra N, Whiteway MR, Li W, Vancura MB, Freedman J, Patel KB, Voleti V, Paninski L, Hillman EMC, Abbott LF, Axel R. The spatial and temporal structure of neural activity across the fly brain. Nat Commun 2023; 14:5572. [PMID: 37696814 PMCID: PMC10495430 DOI: 10.1038/s41467-023-41261-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2022] [Accepted: 08/29/2023] [Indexed: 09/13/2023] Open
Abstract
What are the spatial and temporal scales of brainwide neuronal activity? We used swept, confocally-aligned planar excitation (SCAPE) microscopy to image all cells in a large volume of the brain of adult Drosophila with high spatiotemporal resolution while flies engaged in a variety of spontaneous behaviors. This revealed neural representations of behavior on multiple spatial and temporal scales. The activity of most neurons correlated (or anticorrelated) with running and flailing over timescales that ranged from seconds to a minute. Grooming elicited a weaker global response. Significant residual activity not directly correlated with behavior was high dimensional and reflected the activity of small clusters of spatially organized neurons that may correspond to genetically defined cell types. These clusters participate in the global dynamics, indicating that neural activity reflects a combination of local and broadly distributed components. This suggests that microcircuits with highly specified functions are provided with knowledge of the larger context in which they operate.
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Affiliation(s)
- Evan S Schaffer
- Mortimer B. Zuckerman Mind Brain Behavior Institute and Department of Neuroscience, Columbia University, New York, NY, 10027, USA.
| | - Neeli Mishra
- Mortimer B. Zuckerman Mind Brain Behavior Institute and Department of Neuroscience, Columbia University, New York, NY, 10027, USA
| | - Matthew R Whiteway
- Mortimer B. Zuckerman Mind Brain Behavior Institute and Department of Neuroscience, Columbia University, New York, NY, 10027, USA
- Department of Statistics and the Grossman Center for the Statistics of Mind, Columbia University, New York, NY, 10027, USA
| | - Wenze Li
- Mortimer B. Zuckerman Mind Brain Behavior Institute and Department of Neuroscience, Columbia University, New York, NY, 10027, USA
- Department of Biomedical Engineering, Columbia University, New York, NY, 10027, USA
| | - Michelle B Vancura
- Mortimer B. Zuckerman Mind Brain Behavior Institute and Department of Neuroscience, Columbia University, New York, NY, 10027, USA
| | - Jason Freedman
- Mortimer B. Zuckerman Mind Brain Behavior Institute and Department of Neuroscience, Columbia University, New York, NY, 10027, USA
| | - Kripa B Patel
- Mortimer B. Zuckerman Mind Brain Behavior Institute and Department of Neuroscience, Columbia University, New York, NY, 10027, USA
- Department of Biomedical Engineering, Columbia University, New York, NY, 10027, USA
| | - Venkatakaushik Voleti
- Mortimer B. Zuckerman Mind Brain Behavior Institute and Department of Neuroscience, Columbia University, New York, NY, 10027, USA
- Department of Biomedical Engineering, Columbia University, New York, NY, 10027, USA
| | - Liam Paninski
- Mortimer B. Zuckerman Mind Brain Behavior Institute and Department of Neuroscience, Columbia University, New York, NY, 10027, USA
- Department of Statistics and the Grossman Center for the Statistics of Mind, Columbia University, New York, NY, 10027, USA
| | - Elizabeth M C Hillman
- Mortimer B. Zuckerman Mind Brain Behavior Institute and Department of Neuroscience, Columbia University, New York, NY, 10027, USA
- Department of Biomedical Engineering, Columbia University, New York, NY, 10027, USA
- Department of Radiology, Columbia University, New York, NY, 10027, USA
| | - L F Abbott
- Mortimer B. Zuckerman Mind Brain Behavior Institute and Department of Neuroscience, Columbia University, New York, NY, 10027, USA
- Department of Physiology and Cellular Biophysics, Columbia University, New York, NY, 10032, USA
| | - Richard Axel
- Mortimer B. Zuckerman Mind Brain Behavior Institute and Department of Neuroscience, Columbia University, New York, NY, 10027, USA
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, 10032, USA
- Howard Hughes Medical Institute, Columbia University, New York, NY, 10027, USA
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31
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Karthik S, Joseph J, Jayakumar J, Manoj R, Shetty M, Bota M, Verma R, Mitra P, Sivaprakasam M. Wide field block face imaging using deep ultraviolet induced autofluorescence of the human brain. J Neurosci Methods 2023; 397:109921. [PMID: 37459898 DOI: 10.1016/j.jneumeth.2023.109921] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2023] [Revised: 06/26/2023] [Accepted: 07/13/2023] [Indexed: 08/22/2023]
Abstract
BACKGROUND Imaging large volume human brains at cellular resolution involve histological methods that cause structural changes. A reference point prior to sectioning is needed to quantify these changes and is achieved by serial block face imaging (BFI) methods that have been applied to small volume tissue (∼1 cm3). NEW METHOD We have developed a BFI uniquely designed for large volume tissues (∼1300 cm3) with a very large field of view (20 × 20 cm) at a resolution of 70 µm/pixel under deep ultraviolet (UV-C) illumination which highlights key features. RESULTS The UV-C imaging ensures high contrast imaging of the brain tissue and highlights salient features of the brain. The system is designed to provide uniform and stable illumination across the entire surface area of the tissue and to work at low temperatures, which are required during cryosectioning. Most importantly, it has been designed to maintain its optical focus over the large depth of tissue and over long periods of time, without readjustments. The BFI was installed within a cryomacrotome, and was used to image a large cryoblock of an adult human cerebellum and brainstem (∼6 cm depth resulting in 2995 serial images) with precise optical focus and no loss during continuous serial acquisition. COMPARISON WITH EXISTING METHOD(S) The deep UV-C induced BFI highlights several large fibre tracts within the brain including the cerebellar peduncles, and the corticospinal tract providing important advantage over white light BFI. CONCLUSIONS The 3D reconstructed serial BFI images can assist in the registration and alignment of the microscopic high-resolution histological tissue sections.
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Affiliation(s)
- Srinivasa Karthik
- Healthcare Technology Innovation Centre, No. 1, 5th Floor, 'C' Block, Phase-II, IIT Madras Research Park, Kanagam Road, Taramani, Chennai 600113, India; Department of Electrical Engineering, Indian Institute of Technology Madras, IIT P.O., Chennai 600036, India.
| | - Jayaraj Joseph
- Department of Electrical Engineering, Indian Institute of Technology Madras, IIT P.O., Chennai 600036, India
| | - Jaikishan Jayakumar
- Sudha Gopalakrishnan Brain Centre (SGBC), Indian Institute of Technology Madras, NAC Building 1, Stilt Floor, IIT P.O., Chennai 600036, India; Center for Computational Brain Research, Indian Institute of Technology Madras, IIT P.O., Chennai 600036, India
| | - Rahul Manoj
- Healthcare Technology Innovation Centre, No. 1, 5th Floor, 'C' Block, Phase-II, IIT Madras Research Park, Kanagam Road, Taramani, Chennai 600113, India; Department of Electrical Engineering, Indian Institute of Technology Madras, IIT P.O., Chennai 600036, India
| | - Mahesh Shetty
- Sudha Gopalakrishnan Brain Centre (SGBC), Indian Institute of Technology Madras, NAC Building 1, Stilt Floor, IIT P.O., Chennai 600036, India
| | - Mihail Bota
- Sudha Gopalakrishnan Brain Centre (SGBC), Indian Institute of Technology Madras, NAC Building 1, Stilt Floor, IIT P.O., Chennai 600036, India
| | - Richa Verma
- Sudha Gopalakrishnan Brain Centre (SGBC), Indian Institute of Technology Madras, NAC Building 1, Stilt Floor, IIT P.O., Chennai 600036, India
| | - Partha Mitra
- Center for Computational Brain Research, Indian Institute of Technology Madras, IIT P.O., Chennai 600036, India; Cold Spring Harbor Laboratory, 1, Bungtown Road, Cold Spring Harbor, New York 11724, United States
| | - Mohanasankar Sivaprakasam
- Healthcare Technology Innovation Centre, No. 1, 5th Floor, 'C' Block, Phase-II, IIT Madras Research Park, Kanagam Road, Taramani, Chennai 600113, India; Department of Electrical Engineering, Indian Institute of Technology Madras, IIT P.O., Chennai 600036, India; Sudha Gopalakrishnan Brain Centre (SGBC), Indian Institute of Technology Madras, NAC Building 1, Stilt Floor, IIT P.O., Chennai 600036, India
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32
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Cooney PC, Huang Y, Li W, Perera DM, Hormigo R, Tabachnik T, Godage I, Hillman EMC, Grueber WB, Zarin AA. Neuromuscular Basis of Drosophila larval rolling escape behavior. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.02.01.526733. [PMID: 36778508 PMCID: PMC9915593 DOI: 10.1101/2023.02.01.526733] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
When threatened by dangerous or harmful stimuli, animals engage in diverse forms of rapid escape behaviors. In Drosophila larvae, one type of escape response involves C-shaped bending and lateral rolling followed by rapid forward crawling. The sensory circuitry that promotes larval escape has been extensively characterized; however, the motor programs underlying rolling are unknown. Here, we characterize the neuromuscular basis of rolling escape behavior. We used high-speed, volumetric, Swept Confocally-Aligned Planar Excitation (SCAPE) microscopy to image muscle activity during larval rolling. Unlike sequential peristaltic muscle contractions that progress from segment to segment during forward and backward crawling, the muscle activity progresses circumferentially during bending and rolling escape behavior. We propose that progression of muscular contraction around the larval circumference results in a transient misalignment between weight and the ground support forces, which generates a torque that induces stabilizing body rotation. Therefore, successive cycles of slight misalignment followed by reactive aligning rotation lead to continuous rolling motion. Supporting our biomechanical model, we found that disrupting the activity of muscle groups undergoing circumferential contraction progression lead to rolling defects. We use EM connectome data to identify premotor to motor connectivity patterns that could drive rolling behavior, and perform neural silencing approaches to demonstrate the crucial role of a group of glutamatergic premotor neurons in rolling. Our data reveal body-wide muscle activity patterns and putative premotor circuit organization for execution of the rolling escape response.
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33
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Bishop KW, Barner LAE, Han Q, Baraznenok E, Lan L, Poudel C, Gao G, Serafin RB, Chow SS, Glaser AK, Janowczyk A, Brenes D, Huang H, Miyasato D, True LD, Kang S, Vaughan JC, Liu JT. An end-to-end workflow for non-destructive 3D pathology. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.08.03.551845. [PMID: 37577615 PMCID: PMC10418226 DOI: 10.1101/2023.08.03.551845] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/15/2023]
Abstract
Recent advances in 3D pathology offer the ability to image orders-of-magnitude more tissue than conventional pathology while providing a volumetric context that is lacking with 2D tissue sections, all without requiring destructive tissue sectioning. Generating high-quality 3D pathology datasets on a consistent basis is non-trivial, requiring careful attention to many details regarding tissue preparation, imaging, and data/image processing in an iterative process. Here we provide an end-to-end protocol covering all aspects of a 3D pathology workflow (using light-sheet microscopy as an illustrative imaging platform) with sufficient detail to perform well-controlled preclinical and clinical studies. While 3D pathology is compatible with diverse staining protocols and computationally generated color palettes for visual analysis, this protocol will focus on a fluorescent analog of hematoxylin and eosin (H&E), which remains the most common stain for gold-standard diagnostic determinations. We present our guidelines for a broad range of end-users (e.g., biologists, clinical researchers, and engineers) in a simple tutorial format.
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Affiliation(s)
- Kevin W. Bishop
- Department of Mechanical Engineering, University of Washington, Seattle, Washington, USA
- Department of Bioengineering, University of Washington, Seattle, Washington, USA
| | | | - Qinghua Han
- Department of Mechanical Engineering, University of Washington, Seattle, Washington, USA
- Department of Bioengineering, University of Washington, Seattle, Washington, USA
| | - Elena Baraznenok
- Department of Mechanical Engineering, University of Washington, Seattle, Washington, USA
- Department of Bioengineering, University of Washington, Seattle, Washington, USA
| | - Lydia Lan
- Department of Mechanical Engineering, University of Washington, Seattle, Washington, USA
- Department of Biology, University of Washington, Seattle, Washington, USA
| | - Chetan Poudel
- Department of Chemistry, University of Washington, Seattle, Washington, USA
| | - Gan Gao
- Department of Mechanical Engineering, University of Washington, Seattle, Washington, USA
| | - Robert B. Serafin
- Department of Mechanical Engineering, University of Washington, Seattle, Washington, USA
| | - Sarah S.L. Chow
- Department of Mechanical Engineering, University of Washington, Seattle, Washington, USA
| | - Adam K. Glaser
- Department of Mechanical Engineering, University of Washington, Seattle, Washington, USA
| | - Andrew Janowczyk
- Department of Biomedical Engineering, Emory University and Georgia Institute of Technology, Atlanta, GA, USA
- Department of Oncology, Division of Precision Oncology, University Hospital of Geneva, Geneva, Switzerland
- Department of Clinical Pathology, Division of Clinical Pathology, University Hospital of Geneva, Geneva, Switzerland
| | - David Brenes
- Department of Mechanical Engineering, University of Washington, Seattle, Washington, USA
| | - Hongyi Huang
- Department of Mechanical Engineering, University of Washington, Seattle, Washington, USA
| | - Dominie Miyasato
- Department of Mechanical Engineering, University of Washington, Seattle, Washington, USA
| | - Lawrence D. True
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, Washington, USA
| | - Soyoung Kang
- Department of Mechanical Engineering, University of Washington, Seattle, Washington, USA
| | - Joshua C. Vaughan
- Department of Chemistry, University of Washington, Seattle, Washington, USA
- Department of Physiology and Biophysics, University of Washington, Seattle, Washington, USA
| | - Jonathan T.C. Liu
- Department of Mechanical Engineering, University of Washington, Seattle, Washington, USA
- Department of Bioengineering, University of Washington, Seattle, Washington, USA
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, Washington, USA
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34
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Wu J, Boominathan V, Veeraraghavan A, Robinson JT. Real-time, deep-learning aided lensless microscope. BIOMEDICAL OPTICS EXPRESS 2023; 14:4037-4051. [PMID: 37799697 PMCID: PMC10549754 DOI: 10.1364/boe.490199] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/17/2023] [Revised: 06/28/2023] [Accepted: 06/29/2023] [Indexed: 10/07/2023]
Abstract
Traditional miniaturized fluorescence microscopes are critical tools for modern biology. Invariably, they struggle to simultaneously image with a high spatial resolution and a large field of view (FOV). Lensless microscopes offer a solution to this limitation. However, real-time visualization of samples is not possible with lensless imaging, as image reconstruction can take minutes to complete. This poses a challenge for usability, as real-time visualization is a crucial feature that assists users in identifying and locating the imaging target. The issue is particularly pronounced in lensless microscopes that operate at close imaging distances. Imaging at close distances requires shift-varying deconvolution to account for the variation of the point spread function (PSF) across the FOV. Here, we present a lensless microscope that achieves real-time image reconstruction by eliminating the use of an iterative reconstruction algorithm. The neural network-based reconstruction method we show here, achieves more than 10000 times increase in reconstruction speed compared to iterative reconstruction. The increased reconstruction speed allows us to visualize the results of our lensless microscope at more than 25 frames per second (fps), while achieving better than 7 µm resolution over a FOV of 10 mm2. This ability to reconstruct and visualize samples in real-time empowers a more user-friendly interaction with lensless microscopes. The users are able to use these microscopes much like they currently do with conventional microscopes.
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Affiliation(s)
- Jimin Wu
- Department of Bioengineering,
Rice University, Houston, Texas 77005, USA
| | - Vivek Boominathan
- Department of Electrical and Computer Engineering,
Rice University, Houston, Texas 77005, USA
| | - Ashok Veeraraghavan
- Department of Electrical and Computer Engineering,
Rice University, Houston, Texas 77005, USA
- Department of Computer Science, Rice University, Houston, Texas 77005, USA
| | - Jacob T. Robinson
- Department of Bioengineering,
Rice University, Houston, Texas 77005, USA
- Department of Electrical and Computer Engineering,
Rice University, Houston, Texas 77005, USA
- Department of Neuroscience, Baylor College of Medicine, One Baylor Plaza, Houston, Texas 77030, USA
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35
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Gardini L, Vignolini T, Curcio V, Pavone FS, Capitanio M. Optimization of highly inclined illumination for diffraction-limited and super-resolution microscopy. OPTICS EXPRESS 2023; 31:26208-26225. [PMID: 37710487 DOI: 10.1364/oe.492152] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/03/2023] [Accepted: 06/12/2023] [Indexed: 09/16/2023]
Abstract
In HILO microscopy, a highly inclined and laminated light sheet is used to illuminate the sample, thus drastically reducing background fluorescence in wide-field microscopy, but maintaining the simplicity of the use of a single objective for both illumination and detection. Although the technique has become widely popular, particularly in single molecule and super-resolution microscopy, a limited understanding of how to finely shape the illumination beam and of how this impacts on the image quality complicates the setting of HILO to fit the experimental needs. In this work, we build up a simple and comprehensive guide to optimize the beam shape and alignment in HILO and to predict its performance in conventional fluorescence and super-resolution microscopy. We model the beam propagation through Gaussian optics and validate the model through far- and near-field experiments, thus characterizing the main geometrical features of the beam. Further, we fully quantify the effects of a progressive reduction of the inclined beam thickness on the image quality of both diffraction-limited and super-resolution images and we show that the most relevant impact is obtained by reducing the beam thickness to sub-cellular dimensions (< 3 µm). Based on this, we present a simple optical solution that exploits a rectangular slit to reduce the inclined beam thickness down to 2.6 µm while keeping a field-of-view dimension suited for cell imaging and allowing an increase in the number of localizations in super-resolution imaging of up to 2.6 folds.
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36
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Kalva SK, Deán-Ben XL, Reiss M, Razansky D. Spiral volumetric optoacoustic tomography for imaging whole-body biodynamics in small animals. Nat Protoc 2023; 18:2124-2142. [PMID: 37208409 DOI: 10.1038/s41596-023-00834-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2022] [Accepted: 03/20/2023] [Indexed: 05/21/2023]
Abstract
Fast tracking of biological dynamics across multiple murine organs using the currently commercially available whole-body preclinical imaging systems is hindered by their limited contrast, sensitivity and spatial or temporal resolution. Spiral volumetric optoacoustic tomography (SVOT) provides optical contrast, with an unprecedented level of spatial and temporal resolution, by rapidly scanning a mouse using spherical arrays, thus overcoming the current limitations in whole-body imaging. The method enables the visualization of deep-seated structures in living mammalian tissues in the near-infrared spectral window, while further providing unrivalled image quality and rich spectroscopic optical contrast. Here, we describe the detailed procedures for SVOT imaging of mice and provide specific details on how to implement a SVOT system, including component selection, system arrangement and alignment, as well as the image processing methods. The step-by-step guide for the rapid panoramic (360°) head-to-tail whole-body imaging of a mouse includes the rapid visualization of contrast agent perfusion and biodistribution. The isotropic spatial resolution possible with SVOT can reach 90 µm in 3D, while alternative steps enable whole-body scans in less than 2 s, unattainable with other preclinical imaging modalities. The method further allows the real-time (100 frames per second) imaging of biodynamics at the whole-organ level. The multiscale imaging capacity provided by SVOT can be used for visualizing rapid biodynamics, monitoring responses to treatments and stimuli, tracking perfusion, and quantifying total body accumulation and clearance dynamics of molecular agents and drugs. Depending on the imaging procedure, the protocol requires 1-2 h to complete by users trained in animal handling and biomedical imaging.
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Affiliation(s)
- Sandeep Kumar Kalva
- Institute of Pharmacology and Toxicology and Institute for Biomedical Engineering, Faculty of Medicine, University of Zurich, Zurich, Switzerland
- Institute for Biomedical Engineering, Department of Information Technology and Electrical Engineering, ETH Zurich, Zurich, Switzerland
| | - Xosé Luís Deán-Ben
- Institute of Pharmacology and Toxicology and Institute for Biomedical Engineering, Faculty of Medicine, University of Zurich, Zurich, Switzerland
- Institute for Biomedical Engineering, Department of Information Technology and Electrical Engineering, ETH Zurich, Zurich, Switzerland
| | - Michael Reiss
- Institute of Pharmacology and Toxicology and Institute for Biomedical Engineering, Faculty of Medicine, University of Zurich, Zurich, Switzerland
- Institute for Biomedical Engineering, Department of Information Technology and Electrical Engineering, ETH Zurich, Zurich, Switzerland
| | - Daniel Razansky
- Institute of Pharmacology and Toxicology and Institute for Biomedical Engineering, Faculty of Medicine, University of Zurich, Zurich, Switzerland.
- Institute for Biomedical Engineering, Department of Information Technology and Electrical Engineering, ETH Zurich, Zurich, Switzerland.
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37
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Jia D, Zhang Y, Yang Q, Xue Y, Tan Y, Guo Z, Zhang M, Tian L, Cheng JX. 3D Chemical Imaging by Fluorescence-detected Mid-Infrared Photothermal Fourier Light Field Microscopy. CHEMICAL & BIOMEDICAL IMAGING 2023; 1:260-267. [PMID: 37388959 PMCID: PMC10302888 DOI: 10.1021/cbmi.3c00022] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/05/2023] [Revised: 03/04/2023] [Accepted: 03/08/2023] [Indexed: 07/01/2023]
Abstract
Three-dimensional molecular imaging of living organisms and cells plays a significant role in modern biology. Yet, current volumetric imaging modalities are largely fluorescence-based and thus lack chemical content information. Mid-infrared photothermal microscopy as a chemical imaging technology provides infrared spectroscopic information at submicrometer spatial resolution. Here, by harnessing thermosensitive fluorescent dyes to sense the mid-infrared photothermal effect, we demonstrate 3D fluorescence-detected mid-infrared photothermal Fourier light field (FMIP-FLF) microscopy at the speed of 8 volumes per second and submicron spatial resolution. Protein contents in bacteria and lipid droplets in living pancreatic cancer cells are visualized. Altered lipid metabolism in drug-resistant pancreatic cancer cells is observed with the FMIP-FLF microscope.
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Affiliation(s)
- Danchen Jia
- Department
of Electrical and Computer Engineering, Boston University, Boston, Massachusetts 02215, United States
| | - Yi Zhang
- Department
of Physics, Boston University, Boston, Massachusetts 02215, United States
| | - Qianwan Yang
- Department
of Electrical and Computer Engineering, Boston University, Boston, Massachusetts 02215, United States
| | - Yujia Xue
- Department
of Electrical and Computer Engineering, Boston University, Boston, Massachusetts 02215, United States
| | - Yuying Tan
- Department
of Biomedical Engineering, Boston University, Boston, Massachusetts 02215, United States
| | - Zhongyue Guo
- Department
of Biomedical Engineering, Boston University, Boston, Massachusetts 02215, United States
| | - Meng Zhang
- Department
of Biomedical Engineering, Boston University, Boston, Massachusetts 02215, United States
| | - Lei Tian
- Department
of Electrical and Computer Engineering, 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
- Department
of Biomedical Engineering, Boston University, Boston, Massachusetts 02215, United States
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38
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Olivieri L, Peters L, Cecconi V, Cutrona A, Rowley M, Totero Gongora JS, Pasquazi A, Peccianti M. Terahertz Nonlinear Ghost Imaging via Plane Decomposition: Toward Near-Field Micro-Volumetry. ACS PHOTONICS 2023; 10:1726-1734. [PMID: 37363629 PMCID: PMC10288534 DOI: 10.1021/acsphotonics.2c01727] [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: 12/12/2022] [Indexed: 06/28/2023]
Abstract
Terahertz time-domain imaging targets the reconstruction of the full electromagnetic morphology of an object. In this spectral range, the near-field propagation strongly affects the information in the space-time domain in items with microscopic features. While this often represents a challenge, as the information needs to be disentangled to obtain high image fidelity, here, we show that such a phenomenon can enable three-dimensional microscopy. Specifically, we investigate the capability of the time-resolved nonlinear ghost imaging methodology to implement field-sensitive micro-volumetry by plane decomposition. We leverage the temporally resolved, field-sensitive detection to "refocus" an image plane at an arbitrary distance from the source, which defines the near-field condition, and within a microscopic sample. Since space-time coupling rapidly evolves and diffuses within subwavelength length scales, our technique can separate and discriminate the information originating from different planes at different depths. Our approach is particularly suitable for objects with sparse micrometric details. Building upon this principle, we demonstrate complex, time-domain volumetry resolving internal object planes with subwavelength resolution, discussing the range of applicability of our technique.
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Affiliation(s)
- Luana Olivieri
- Emergent
Photonics Research Centre, Department of Physics, Loughborough University, Loughborough LE11 3TU, UK
- Emergent
Photonics Lab (Epic), Department of Physics and Astronomy, University of Sussex, Brighton BN1 9QH, UK
| | - Luke Peters
- Emergent
Photonics Research Centre, Department of Physics, Loughborough University, Loughborough LE11 3TU, UK
- Emergent
Photonics Lab (Epic), Department of Physics and Astronomy, University of Sussex, Brighton BN1 9QH, UK
| | - Vittorio Cecconi
- Emergent
Photonics Research Centre, Department of Physics, Loughborough University, Loughborough LE11 3TU, UK
- Emergent
Photonics Lab (Epic), Department of Physics and Astronomy, University of Sussex, Brighton BN1 9QH, UK
| | - Antonio Cutrona
- Emergent
Photonics Research Centre, Department of Physics, Loughborough University, Loughborough LE11 3TU, UK
- Emergent
Photonics Lab (Epic), Department of Physics and Astronomy, University of Sussex, Brighton BN1 9QH, UK
| | - Maxwell Rowley
- Emergent
Photonics Lab (Epic), Department of Physics and Astronomy, University of Sussex, Brighton BN1 9QH, UK
| | - Juan Sebastian Totero Gongora
- Emergent
Photonics Research Centre, Department of Physics, Loughborough University, Loughborough LE11 3TU, UK
- Emergent
Photonics Lab (Epic), Department of Physics and Astronomy, University of Sussex, Brighton BN1 9QH, UK
| | - Alessia Pasquazi
- Emergent
Photonics Research Centre, Department of Physics, Loughborough University, Loughborough LE11 3TU, UK
- Emergent
Photonics Lab (Epic), Department of Physics and Astronomy, University of Sussex, Brighton BN1 9QH, UK
| | - Marco Peccianti
- Emergent
Photonics Research Centre, Department of Physics, Loughborough University, Loughborough LE11 3TU, UK
- Emergent
Photonics Lab (Epic), Department of Physics and Astronomy, University of Sussex, Brighton BN1 9QH, UK
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39
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Yamaguchi A, Wu R, McNulty P, Karagyozov D, Mihovilovic Skanata M, Gershow M. Multi-neuronal recording in unrestrained animals with all acousto-optic random-access line-scanning two-photon microscopy. Front Neurosci 2023; 17:1135457. [PMID: 37389365 PMCID: PMC10303936 DOI: 10.3389/fnins.2023.1135457] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2022] [Accepted: 05/18/2023] [Indexed: 07/01/2023] Open
Abstract
To understand how neural activity encodes and coordinates behavior, it is desirable to record multi-neuronal activity in freely behaving animals. Imaging in unrestrained animals is challenging, especially for those, like larval Drosophila melanogaster, whose brains are deformed by body motion. A previously demonstrated two-photon tracking microscope recorded from individual neurons in freely crawling Drosophila larvae but faced limits in multi-neuronal recording. Here we demonstrate a new tracking microscope using acousto-optic deflectors (AODs) and an acoustic GRIN lens (TAG lens) to achieve axially resonant 2D random access scanning, sampling along arbitrarily located axial lines at a line rate of 70 kHz. With a tracking latency of 0.1 ms, this microscope recorded activities of various neurons in moving larval Drosophila CNS and VNC including premotor neurons, bilateral visual interneurons, and descending command neurons. This technique can be applied to the existing two-photon microscope to allow for fast 3D tracking and scanning.
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Affiliation(s)
- Akihiro Yamaguchi
- Department of Physics, New York University, New York, NY, United States
| | - Rui Wu
- Department of Physics, New York University, New York, NY, United States
| | - Paul McNulty
- Department of Physics, New York University, New York, NY, United States
| | - Doycho Karagyozov
- Department of Physics, New York University, New York, NY, United States
| | | | - Marc Gershow
- Department of Physics, New York University, New York, NY, United States
- Center for Neural Science, New York University, New York, NY, United States
- Neuroscience Institute, New York University, New York, NY, United States
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40
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Liu JTC, Glaser AK, Poudel C, Vaughan JC. Nondestructive 3D Pathology with Light-Sheet Fluorescence Microscopy for Translational Research and Clinical Assays. ANNUAL REVIEW OF ANALYTICAL CHEMISTRY (PALO ALTO, CALIF.) 2023; 16:231-252. [PMID: 36854208 DOI: 10.1146/annurev-anchem-091222-092734] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
In recent years, there has been a revived appreciation for the importance of spatial context and morphological phenotypes for both understanding disease progression and guiding treatment decisions. Compared with conventional 2D histopathology, which is the current gold standard of medical diagnostics, nondestructive 3D pathology offers researchers and clinicians the ability to visualize orders of magnitude more tissue within their natural volumetric context. This has been enabled by rapid advances in tissue-preparation methods, high-throughput 3D microscopy instrumentation, and computational tools for processing these massive feature-rich data sets. Here, we provide a brief overview of many of these technical advances along with remaining challenges to be overcome. We also speculate on the future of 3D pathology as applied in translational investigations, preclinical drug development, and clinical decision-support assays.
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Affiliation(s)
- Jonathan T C Liu
- Department of Mechanical Engineering, University of Washington, Seattle, Washington, USA;
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, Washington, USA
- Department of Bioengineering, University of Washington, Seattle, Washington, USA
| | - Adam K Glaser
- Department of Mechanical Engineering, University of Washington, Seattle, Washington, USA;
- Allen Institute for Neural Dynamics, Seattle, Washington, USA
| | - Chetan Poudel
- Department of Chemistry, University of Washington, Seattle, Washington, USA
| | - Joshua C Vaughan
- Department of Chemistry, University of Washington, Seattle, Washington, USA
- Department of Physiology and Biophysics, University of Washington, Seattle, Washington, USA
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41
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Djutanta F, Brown PT, Nainggolan B, Coullomb A, Radhakrishnan S, Sentosa J, Yurke B, Hariadi RF, Shepherd DP. Decoding the hydrodynamic properties of microscale helical propellers from Brownian fluctuations. Proc Natl Acad Sci U S A 2023; 120:e2220033120. [PMID: 37235635 PMCID: PMC10235983 DOI: 10.1073/pnas.2220033120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2022] [Accepted: 04/12/2023] [Indexed: 05/28/2023] Open
Abstract
The complex motility of bacteria, ranging from single-swimmer behaviors such as chemotaxis to collective dynamics, including biofilm formation and active matter phenomena, is driven by their microscale propellers. Despite extensive study of swimming flagellated bacteria, the hydrodynamic properties of their helical-shaped propellers have never been directly measured. The primary challenges to directly studying microscale propellers are 1) their small size and fast, correlated motion, 2) the necessity of controlling fluid flow at the microscale, and 3) isolating the influence of a single propeller from a propeller bundle. To solve the outstanding problem of characterizing the hydrodynamic properties of these propellers, we adopt a dual statistical viewpoint that connects to the hydrodynamics through the fluctuation-dissipation theorem (FDT). We regard the propellers as colloidal particles and characterize their Brownian fluctuations, described by 21 diffusion coefficients for translation, rotation, and correlated translation-rotation in a static fluid. To perform this measurement, we applied recent advances in high-resolution oblique plane microscopy to generate high-speed volumetric movies of fluorophore-labeled, freely diffusing Escherichia coli flagella. Analyzing these movies with a bespoke helical single-particle tracking algorithm, we extracted trajectories, calculated the full set of diffusion coefficients, and inferred the average propulsion matrix using a generalized Einstein relation. Our results provide a direct measurement of a microhelix's propulsion matrix and validate proposals that the flagella are highly inefficient propellers, with a maximum propulsion efficiency of less than 3%. Our approach opens broad avenues for studying the motility of particles in complex environments where direct hydrodynamic approaches are not feasible.
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Affiliation(s)
- Franky Djutanta
- Biodesign Center for Molecular Design and Biomimetics at the Biodesign Institute, Arizona State University, Tempe, AZ85287
- School for Engineering of Matter, Transport and Energy, Arizona State University, Tempe, AZ85287
| | - Peter T. Brown
- Center for Biological Physics and Department of Physics, Arizona State University, Tempe, AZ85287
| | - Bonfilio Nainggolan
- Center for Biological Physics and Department of Physics, Arizona State University, Tempe, AZ85287
| | - Alexis Coullomb
- Center for Biological Physics and Department of Physics, Arizona State University, Tempe, AZ85287
| | - Sritharini Radhakrishnan
- Biodesign Center for Molecular Design and Biomimetics at the Biodesign Institute, Arizona State University, Tempe, AZ85287
- School of Electrical, Computer and Energy Engineering, Arizona State University, Tempe, AZ85287
| | - Jason Sentosa
- Biodesign Center for Molecular Design and Biomimetics at the Biodesign Institute, Arizona State University, Tempe, AZ85287
| | - Bernard Yurke
- Micron School of Materials Science and Electrical and Computer Engineering Department, Boise State University, Boise, ID83725
| | - Rizal F. Hariadi
- Biodesign Center for Molecular Design and Biomimetics at the Biodesign Institute, Arizona State University, Tempe, AZ85287
- Center for Biological Physics and Department of Physics, Arizona State University, Tempe, AZ85287
| | - Douglas P. Shepherd
- Center for Biological Physics and Department of Physics, Arizona State University, Tempe, AZ85287
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42
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Daetwyler S, Fiolka RP. Light-sheets and smart microscopy, an exciting future is dawning. Commun Biol 2023; 6:502. [PMID: 37161000 PMCID: PMC10169780 DOI: 10.1038/s42003-023-04857-4] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2023] [Accepted: 04/20/2023] [Indexed: 05/11/2023] Open
Abstract
Light-sheet fluorescence microscopy has transformed our ability to visualize and quantitatively measure biological processes rapidly and over long time periods. In this review, we discuss current and future developments in light-sheet fluorescence microscopy that we expect to further expand its capabilities. This includes smart and adaptive imaging schemes to overcome traditional imaging trade-offs, i.e., spatiotemporal resolution, field of view and sample health. In smart microscopy, a microscope will autonomously decide where, when, what and how to image. We further assess how image restoration techniques provide avenues to overcome these tradeoffs and how "open top" light-sheet microscopes may enable multi-modal imaging with high throughput. As such, we predict that light-sheet microscopy will fulfill an important role in biomedical and clinical imaging in the future.
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Affiliation(s)
- Stephan Daetwyler
- Lyda Hill Department of Bioinformatics, University of Texas Southwestern Medical Center, Dallas, TX, USA
- Department of Cell Biology, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Reto Paul Fiolka
- Lyda Hill Department of Bioinformatics, University of Texas Southwestern Medical Center, Dallas, TX, USA.
- Department of Cell Biology, University of Texas Southwestern Medical Center, Dallas, TX, USA.
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43
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Lu Z, Liu Y, Jin M, Luo X, Yue H, Wang Z, Zuo S, Zeng Y, Fan J, Pang Y, Wu J, Yang J, Dai Q. Virtual-scanning light-field microscopy for robust snapshot high-resolution volumetric imaging. Nat Methods 2023; 20:735-746. [PMID: 37024654 PMCID: PMC10172145 DOI: 10.1038/s41592-023-01839-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2022] [Accepted: 03/07/2023] [Indexed: 04/08/2023]
Abstract
High-speed three-dimensional (3D) intravital imaging in animals is useful for studying transient subcellular interactions and functions in health and disease. Light-field microscopy (LFM) provides a computational solution for snapshot 3D imaging with low phototoxicity but is restricted by low resolution and reconstruction artifacts induced by optical aberrations, motion and noise. Here, we propose virtual-scanning LFM (VsLFM), a physics-based deep learning framework to increase the resolution of LFM up to the diffraction limit within a snapshot. By constructing a 40 GB high-resolution scanning LFM dataset across different species, we exploit physical priors between phase-correlated angular views to address the frequency aliasing problem. This enables us to bypass hardware scanning and associated motion artifacts. Here, we show that VsLFM achieves ultrafast 3D imaging of diverse processes such as the beating heart in embryonic zebrafish, voltage activity in Drosophila brains and neutrophil migration in the mouse liver at up to 500 volumes per second.
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Affiliation(s)
- Zhi Lu
- Department of Automation, Tsinghua University, Beijing, China
- Institute for Brain and Cognitive Sciences, Tsinghua University, Beijing, China
| | - Yu Liu
- School of Electrical and Information Engineering, Tianjin University, Tianjin, China
| | - Manchang Jin
- School of Electrical and Information Engineering, Tianjin University, Tianjin, China
| | - Xin Luo
- School of Electrical and Information Engineering, Tianjin University, Tianjin, China
| | - Huanjing Yue
- School of Electrical and Information Engineering, Tianjin University, Tianjin, China
| | - Zian Wang
- Department of Automation, Tsinghua University, Beijing, China
| | - Siqing Zuo
- Department of Automation, Tsinghua University, Beijing, China
- Institute for Brain and Cognitive Sciences, Tsinghua University, Beijing, China
| | - Yunmin Zeng
- Department of Automation, Tsinghua University, Beijing, China
- Institute for Brain and Cognitive Sciences, Tsinghua University, Beijing, China
| | - Jiaqi Fan
- Institute for Brain and Cognitive Sciences, Tsinghua University, Beijing, China
| | - Yanwei Pang
- School of Electrical and Information Engineering, Tianjin University, Tianjin, China
| | - Jiamin Wu
- Department of Automation, Tsinghua University, Beijing, China.
- Institute for Brain and Cognitive Sciences, Tsinghua University, Beijing, China.
- IDG/McGovern Institute for Brain Research, Tsinghua University, Beijing, China.
| | - Jingyu Yang
- School of Electrical and Information Engineering, Tianjin University, Tianjin, China.
| | - Qionghai Dai
- Department of Automation, Tsinghua University, Beijing, China.
- Institute for Brain and Cognitive Sciences, Tsinghua University, Beijing, China.
- IDG/McGovern Institute for Brain Research, Tsinghua University, Beijing, China.
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44
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Kalva SK, Deán-Ben XL, Reiss M, Razansky D. Head-to-tail imaging of mice with spiral volumetric optoacoustic tomography. PHOTOACOUSTICS 2023; 30:100480. [PMID: 37025111 PMCID: PMC10070820 DOI: 10.1016/j.pacs.2023.100480] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/01/2022] [Revised: 11/13/2022] [Accepted: 03/23/2023] [Indexed: 06/19/2023]
Abstract
Optoacoustic tomography has been established as a powerful modality for preclinical imaging. However, efficient whole-body imaging coverage has not been achieved owing to the arduous requirement for continuous acoustic coupling around the animal. In this work, we introduce panoramic (3600) head-to-tail 3D imaging of mice with spiral volumetric optoacoustic tomography (SVOT). The system combines multi-beam illumination and a dedicated head holder enabling uninterrupted acoustic coupling for whole-body scans. Image fidelity is optimized with self-gated respiratory motion rejection and dual speed-of-sound reconstruction algorithms to attain spatial resolution down to 90 µm. The developed system is thus highly suitable for visualizing rapid biodynamics across scales, such as hemodynamic changes in individual organs, responses to treatments and stimuli, perfusion, total body accumulation, or clearance of molecular agents and drugs with unmatched contrast, spatial and temporal resolution.
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Affiliation(s)
- Sandeep Kumar Kalva
- Institute of Pharmacology and Toxicology and Institute for Biomedical Engineering, Faculty of Medicine, University of Zurich, Zurich CH-8057, Switzerland
- Institute for Biomedical Engineering, Department of Information Technology and Electrical Engineering, ETH Zurich, Zurich CH-8093, Switzerland
| | - Xosé Luís Deán-Ben
- Institute of Pharmacology and Toxicology and Institute for Biomedical Engineering, Faculty of Medicine, University of Zurich, Zurich CH-8057, Switzerland
- Institute for Biomedical Engineering, Department of Information Technology and Electrical Engineering, ETH Zurich, Zurich CH-8093, Switzerland
| | - Michael Reiss
- Institute of Pharmacology and Toxicology and Institute for Biomedical Engineering, Faculty of Medicine, University of Zurich, Zurich CH-8057, Switzerland
- Institute for Biomedical Engineering, Department of Information Technology and Electrical Engineering, ETH Zurich, Zurich CH-8093, Switzerland
| | - Daniel Razansky
- Institute of Pharmacology and Toxicology and Institute for Biomedical Engineering, Faculty of Medicine, University of Zurich, Zurich CH-8057, Switzerland
- Institute for Biomedical Engineering, Department of Information Technology and Electrical Engineering, ETH Zurich, Zurich CH-8093, Switzerland
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45
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Zhu T, Nie J, Yu T, Zhu D, Huang Y, Chen Z, Gu Z, Tang J, Li D, Fei P. Large-scale high-throughput 3D culture, imaging, and analysis of cell spheroids using microchip-enhanced light-sheet microscopy. BIOMEDICAL OPTICS EXPRESS 2023; 14:1659-1669. [PMID: 37078040 PMCID: PMC10110308 DOI: 10.1364/boe.485217] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/10/2023] [Revised: 02/24/2023] [Accepted: 03/06/2023] [Indexed: 05/03/2023]
Abstract
Light sheet microscopy combined with a microchip is an emerging tool in biomedical research that notably improves efficiency. However, microchip-enhanced light-sheet microscopy is limited by noticeable aberrations induced by the complex refractive indices in the chip. Herein, we report a droplet microchip that is specifically engineered to be capable of large-scale culture of 3D spheroids (over 600 samples per chip) and has a polymer index matched to water (difference <1%). When combined with a lab-built open-top light-sheet microscope, this microchip-enhanced microscopy technique allows 3D time-lapse imaging of the cultivated spheroids with ∼2.5-µm single-cell resolution and a high throughput of ∼120 spheroids per minute. This technique was validated by a comparative study on the proliferation and apoptosis rates of hundreds of spheroids with or without treatment with the apoptosis-inducing drug Staurosporine.
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Affiliation(s)
- Tingting Zhu
- School of Optical and Electronic Information - Wuhan National Laboratory for Optoelectronics - Advanced Biomedical Imaging Facility, Huazhong University of Science and Technology, Wuhan 430074, China
| | - Jun Nie
- Institute for Cell Analysis, Shenzhen Bay Laboratory, Shenzhen 518132, China
| | - Tingting Yu
- Britton Chance Center for Biomedical Photonics - MoE Key Laboratory for Biomedical Photonics, Wuhan National Laboratory for Optoelectronics - Advanced Biomedical Imaging Facility, Huazhong University of Science and Technology, Wuhan 430074, Hubei, China
| | - Dan Zhu
- Britton Chance Center for Biomedical Photonics - MoE Key Laboratory for Biomedical Photonics, Wuhan National Laboratory for Optoelectronics - Advanced Biomedical Imaging Facility, Huazhong University of Science and Technology, Wuhan 430074, Hubei, China
| | - Yanyi Huang
- Institute for Cell Analysis, Shenzhen Bay Laboratory, Shenzhen 518132, China
- College of Chemistry, Biomedical Pioneering Innovation Center (BIOPIC), Peking University, Beijing 100871, China
| | - Zaozao Chen
- State Key Laboratory of Bioelectronics School of Biological Science and Medical Engineering, Southeast University, Nanjing 210096, China
| | - Zhongze Gu
- State Key Laboratory of Bioelectronics School of Biological Science and Medical Engineering, Southeast University, Nanjing 210096, China
| | - Jiang Tang
- School of Optical and Electronic Information - Wuhan National Laboratory for Optoelectronics - Advanced Biomedical Imaging Facility, Huazhong University of Science and Technology, Wuhan 430074, China
| | - Dongyu Li
- School of Optical and Electronic Information - Wuhan National Laboratory for Optoelectronics - Advanced Biomedical Imaging Facility, Huazhong University of Science and Technology, Wuhan 430074, China
| | - Peng Fei
- School of Optical and Electronic Information - Wuhan National Laboratory for Optoelectronics - Advanced Biomedical Imaging Facility, Huazhong University of Science and Technology, Wuhan 430074, China
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46
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Al-Rekabi Z, Dondi C, Faruqui N, Siddiqui NS, Elowsson L, Rissler J, Kåredal M, Mudway I, Larsson-Callerfelt AK, Shaw M. Uncovering the cytotoxic effects of air pollution with multi-modal imaging of in vitro respiratory models. ROYAL SOCIETY OPEN SCIENCE 2023; 10:221426. [PMID: 37063998 PMCID: PMC10090883 DOI: 10.1098/rsos.221426] [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: 01/03/2023] [Accepted: 03/17/2023] [Indexed: 06/19/2023]
Abstract
Annually, an estimated seven million deaths are linked to exposure to airborne pollutants. Despite extensive epidemiological evidence supporting clear associations between poor air quality and a range of short- and long-term health effects, there are considerable gaps in our understanding of the specific mechanisms by which pollutant exposure induces adverse biological responses at the cellular and tissue levels. The development of more complex, predictive, in vitro respiratory models, including two- and three-dimensional cell cultures, spheroids, organoids and tissue cultures, along with more realistic aerosol exposure systems, offers new opportunities to investigate the cytotoxic effects of airborne particulates under controlled laboratory conditions. Parallel advances in high-resolution microscopy have resulted in a range of in vitro imaging tools capable of visualizing and analysing biological systems across unprecedented scales of length, time and complexity. This article considers state-of-the-art in vitro respiratory models and aerosol exposure systems and how they can be interrogated using high-resolution microscopy techniques to investigate cell-pollutant interactions, from the uptake and trafficking of particles to structural and functional modification of subcellular organelles and cells. These data can provide a mechanistic basis from which to advance our understanding of the health effects of airborne particulate pollution and develop improved mitigation measures.
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Affiliation(s)
- Zeinab Al-Rekabi
- Department of Chemical and Biological Sciences, National Physical Laboratory, Teddington, UK
| | - Camilla Dondi
- Department of Chemical and Biological Sciences, National Physical Laboratory, Teddington, UK
| | - Nilofar Faruqui
- Department of Chemical and Biological Sciences, National Physical Laboratory, Teddington, UK
| | - Nazia S. Siddiqui
- Faculty of Medical Sciences, University College London, London, UK
- Kingston Hospital NHS Foundation Trust, Kingston upon Thames, UK
| | - Linda Elowsson
- Lung Biology, Department of Experimental Medical Science, Lund University, Lund, Sweden
| | - Jenny Rissler
- Bioeconomy and Health, RISE Research Institutes of Sweden, Lund, Sweden
- Ergonomics and Aerosol Technology, Lund University, Lund, Sweden
| | - Monica Kåredal
- Occupational and Environmental Medicine, Lund University, Lund, Sweden
| | - Ian Mudway
- MRC Centre for Environment and Health, Imperial College London, London, UK
- National Institute of Health Protection Research Unit in Environmental Exposures and Health, London, UK
- Asthma UK Centre in Allergic Mechanisms of Asthma, London, UK
| | | | - Michael Shaw
- Department of Chemical and Biological Sciences, National Physical Laboratory, Teddington, UK
- Department of Computer Science, University College London, London, UK
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47
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Benavides OR, Gibbs HC, White BP, Kaunas R, Gregory CA, Walsh AJ, Maitland KC. Volumetric imaging of human mesenchymal stem cells (hMSCs) for non-destructive quantification of 3D cell culture growth. PLoS One 2023; 18:e0282298. [PMID: 36976801 PMCID: PMC10047548 DOI: 10.1371/journal.pone.0282298] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2022] [Accepted: 02/11/2023] [Indexed: 03/29/2023] Open
Abstract
The adoption of cell-based therapies into the clinic will require tremendous large-scale expansion to satisfy future demand, and bioreactor-microcarrier cultures are best suited to meet this challenge. The use of spherical microcarriers, however, precludes in-process visualization and monitoring of cell number, morphology, and culture health. The development of novel expansion methods also motivates the advancement of analytical methods used to characterize these microcarrier cultures. A robust optical imaging and image-analysis assay to non-destructively quantify cell number and cell volume was developed. This method preserves 3D cell morphology and does not require membrane lysing, cellular detachment, or exogenous labeling. Complex cellular networks formed in microcarrier aggregates were imaged and analyzed in toto. Direct cell enumeration of large aggregates was performed in toto for the first time. This assay was successfully applied to monitor cellular growth of mesenchymal stem cells attached to spherical hydrogel microcarriers over time. Elastic scattering and fluorescence lightsheet microscopy were used to quantify cell volume and cell number at varying spatial scales. The presented study motivates the development of on-line optical imaging and image analysis systems for robust, automated, and non-destructive monitoring of bioreactor-microcarrier cell cultures.
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Affiliation(s)
- Oscar R. Benavides
- Department of Biomedical Engineering, Texas A&M University, College Station, Texas, United States of America
- * E-mail:
| | - Holly C. Gibbs
- Department of Biomedical Engineering, Texas A&M University, College Station, Texas, United States of America
- Microscopy and Imaging Center, Texas A&M University, College Station, Texas, United States of America
| | - Berkley P. White
- Department of Biomedical Engineering, Texas A&M University, College Station, Texas, United States of America
| | - Roland Kaunas
- Department of Biomedical Engineering, Texas A&M University, College Station, Texas, United States of America
| | - Carl A. Gregory
- School of Medicine, Texas A&M Health Science Center, Bryan, Texas, United States of America
| | - Alex J. Walsh
- Department of Biomedical Engineering, Texas A&M University, College Station, Texas, United States of America
| | - Kristen C. Maitland
- Department of Biomedical Engineering, Texas A&M University, College Station, Texas, United States of America
- Microscopy and Imaging Center, Texas A&M University, College Station, Texas, United States of America
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48
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Zhai J, Jin C, Kong L. Compact, Hybrid Light-Sheet and Fourier Light-Field Microscopy with a Single Objective for High-Speed Volumetric Imaging In Vivo. J Phys Chem A 2023; 127:2873-2879. [PMID: 36926932 DOI: 10.1021/acs.jpca.3c00325] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/18/2023]
Abstract
Volumetric imaging of biodynamics at high spatiotemporal resolutions in vivo is vital in biomedical studies, in which Fourier light field microscopy (FLFM) is a promising technique. However, the commonly used wide-field illumination strategy in FLFM introduces intense out of depth-of-field background, which not only degrades the image quality, but also introduces reconstruction artifacts. Employing light sheet illumination is an effective way to alleviate the background and reduce photobleaching in light-field microscopy. Unfortunately, the introduction of light-sheet illumination often requires an extra objective and precise alignment, which increases the system complexity. Here, we propose the compact, hybrid light-sheet and FLFM (CLS-FLFM), which uses only a single objective to achieve both light-sheet illumination and Fourier light-field imaging simultaneously. With a micromirror under the objective, we focus the light sheet, which ensures selective-volume-illumination, on the imaging plane of the FLFM to perform volumetric imaging. We demonstrate the superior performance of CLS-FLFM in inhibiting background in both structural and dynamical imaging of larval zebrafish in vivo. We envision that CLS-FLFM finds wide applications in high-speed, background-inhibited volumetric imaging of biodynamics in vivo.
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Affiliation(s)
- Jiazhen Zhai
- State Key Laboratory of Precision Measurement Technology and Instruments, Department of Precision Instrument, Tsinghua University, Beijing 100084, China
| | - Cheng Jin
- State Key Laboratory of Precision Measurement Technology and Instruments, Department of Precision Instrument, Tsinghua University, Beijing 100084, China
| | - Lingjie Kong
- State Key Laboratory of Precision Measurement Technology and Instruments, Department of Precision Instrument, Tsinghua University, Beijing 100084, China.,IDG/McGovern Institute for Brain Research, Tsinghua University, Beijing 100084, China
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49
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Efficient 3D light-sheet imaging of very large-scale optically cleared human brain and prostate tissue samples. Commun Biol 2023; 6:170. [PMID: 36781939 PMCID: PMC9925784 DOI: 10.1038/s42003-023-04536-4] [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: 07/26/2022] [Accepted: 01/26/2023] [Indexed: 02/15/2023] Open
Abstract
The ability to image human tissue samples in 3D, with both cellular resolution and a large field of view (FOV), can improve fundamental and clinical investigations. Here, we demonstrate the feasibility of light-sheet imaging of ~5 cm3 sized formalin fixed human brain and up to ~7 cm3 sized formalin fixed paraffin embedded (FFPE) prostate cancer samples, processed with the FFPE-MASH protocol. We present a light-sheet microscopy prototype, the cleared-tissue dual view Selective Plane Illumination Microscope (ct-dSPIM), capable of fast 3D high-resolution acquisitions of cm3 scale cleared tissue. We used mosaic scans for fast 3D overviews of entire tissue samples or higher resolution overviews of large ROIs with various speeds: (a) Mosaic 16 (16.4 µm isotropic resolution, ~1.7 h/cm3), (b) Mosaic 4 (4.1 µm isotropic resolution, ~ 5 h/cm3) and (c) Mosaic 0.5 (0.5 µm near isotropic resolution, ~15.8 h/cm3). We could visualise cortical layers and neurons around the border of human brain areas V1&V2, and could demonstrate suitable imaging quality for Gleason score grading in thick prostate cancer samples. We show that ct-dSPIM imaging is an excellent technique to quantitatively assess entire MASH prepared large-scale human tissue samples in 3D, with considerable future clinical potential.
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50
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Xu L, Zou DJ, Firestein S. Odor mixtures: A chord with silent notes. Front Ecol Evol 2023. [DOI: 10.3389/fevo.2023.1135486] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/10/2023] Open
Abstract
The olfactory world is one of complex mixtures and blends containing up to hundreds of molecules. Many of those molecules can act as agonists, antagonists or enhancers at different receptors. This complicates the mechanism by which higher centers construct perceptions of complex mixtures. We propose that along with structural chemistry, psychophysics, the techniques of medicinal chemistry and machine learning can begin to shed light on this difficult neural problem.
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