51
|
Akemann W, Wolf S, Villette V, Mathieu B, Tangara A, Fodor J, Ventalon C, Léger JF, Dieudonné S, Bourdieu L. Fast optical recording of neuronal activity by three-dimensional custom-access serial holography. Nat Methods 2022; 19:100-110. [PMID: 34949810 DOI: 10.1038/s41592-021-01329-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2019] [Accepted: 10/25/2021] [Indexed: 11/08/2022]
Abstract
Optical recording of neuronal activity in three-dimensional (3D) brain circuits at cellular and millisecond resolution in vivo is essential for probing information flow in the brain. While random-access multiphoton microscopy permits fast optical access to neuronal targets in three dimensions, the method is challenged by motion artifacts when recording from behaving animals. Therefore, we developed three-dimensional custom-access serial holography (3D-CASH). Built on a fast acousto-optic light modulator, 3D-CASH performs serial sampling at 40 kHz from neurons at freely selectable 3D locations. Motion artifacts are eliminated by targeting each neuron with a size-optimized pattern of excitation light covering the cell body and its anticipated displacement field. Spike rates inferred from GCaMP6f recordings in visual cortex of awake mice tracked the phase of a moving bar stimulus with higher spike correlation between intra compared to interlaminar neuron pairs. 3D-CASH offers access to the millisecond correlation structure of in vivo neuronal activity in 3D microcircuits.
Collapse
Affiliation(s)
- Walther Akemann
- Institut de Biologie de l'ENS (IBENS), École Normale Supérieure, CNRS, INSERM, Université PSL, Paris, France
| | - Sébastien Wolf
- Institut de Biologie de l'ENS (IBENS), École Normale Supérieure, CNRS, INSERM, Université PSL, Paris, France
- Laboratoire de Physique de l'ENS (LPENS), École Normale Supérieure, CNRS, Université PSL, Paris, France
| | - Vincent Villette
- Institut de Biologie de l'ENS (IBENS), École Normale Supérieure, CNRS, INSERM, Université PSL, Paris, France
| | - Benjamin Mathieu
- Institut de Biologie de l'ENS (IBENS), École Normale Supérieure, CNRS, INSERM, Université PSL, Paris, France
| | - Astou Tangara
- Institut de Biologie de l'ENS (IBENS), École Normale Supérieure, CNRS, INSERM, Université PSL, Paris, France
| | - Jozsua Fodor
- Institut de Biologie de l'ENS (IBENS), École Normale Supérieure, CNRS, INSERM, Université PSL, Paris, France
| | - Cathie Ventalon
- Institut de Biologie de l'ENS (IBENS), École Normale Supérieure, CNRS, INSERM, Université PSL, Paris, France
| | - Jean-François Léger
- Institut de Biologie de l'ENS (IBENS), École Normale Supérieure, CNRS, INSERM, Université PSL, Paris, France
| | - Stéphane Dieudonné
- Institut de Biologie de l'ENS (IBENS), École Normale Supérieure, CNRS, INSERM, Université PSL, Paris, France.
| | - Laurent Bourdieu
- Institut de Biologie de l'ENS (IBENS), École Normale Supérieure, CNRS, INSERM, Université PSL, Paris, France.
| |
Collapse
|
52
|
Abdelfattah AS, Ahuja S, Akkin T, Allu SR, Brake J, Boas DA, Buckley EM, Campbell RE, Chen AI, Cheng X, Čižmár T, Costantini I, De Vittorio M, Devor A, Doran PR, El Khatib M, Emiliani V, Fomin-Thunemann N, Fainman Y, Fernandez-Alfonso T, Ferri CGL, Gilad A, Han X, Harris A, Hillman EMC, Hochgeschwender U, Holt MG, Ji N, Kılıç K, Lake EMR, Li L, Li T, Mächler P, Miller EW, Mesquita RC, Nadella KMNS, Nägerl UV, Nasu Y, Nimmerjahn A, Ondráčková P, Pavone FS, Perez Campos C, Peterka DS, Pisano F, Pisanello F, Puppo F, Sabatini BL, Sadegh S, Sakadzic S, Shoham S, Shroff SN, Silver RA, Sims RR, Smith SL, Srinivasan VJ, Thunemann M, Tian L, Tian L, Troxler T, Valera A, Vaziri A, Vinogradov SA, Vitale F, Wang LV, Uhlířová H, Xu C, Yang C, Yang MH, Yellen G, Yizhar O, Zhao Y. Neurophotonic tools for microscopic measurements and manipulation: status report. NEUROPHOTONICS 2022; 9:013001. [PMID: 35493335 PMCID: PMC9047450 DOI: 10.1117/1.nph.9.s1.013001] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
Neurophotonics was launched in 2014 coinciding with the launch of the BRAIN Initiative focused on development of technologies for advancement of neuroscience. For the last seven years, Neurophotonics' agenda has been well aligned with this focus on neurotechnologies featuring new optical methods and tools applicable to brain studies. While the BRAIN Initiative 2.0 is pivoting towards applications of these novel tools in the quest to understand the brain, this status report reviews an extensive and diverse toolkit of novel methods to explore brain function that have emerged from the BRAIN Initiative and related large-scale efforts for measurement and manipulation of brain structure and function. Here, we focus on neurophotonic tools mostly applicable to animal studies. A companion report, scheduled to appear later this year, will cover diffuse optical imaging methods applicable to noninvasive human studies. For each domain, we outline the current state-of-the-art of the respective technologies, identify the areas where innovation is needed, and provide an outlook for the future directions.
Collapse
Affiliation(s)
- Ahmed S. Abdelfattah
- Brown University, Department of Neuroscience, Providence, Rhode Island, United States
| | - Sapna Ahuja
- University of Pennsylvania, Perelman School of Medicine, Department of Biochemistry and Biophysics, Philadelphia, Pennsylvania, United States
- University of Pennsylvania, School of Arts and Sciences, Department of Chemistry, Philadelphia, Pennsylvania, United States
| | - Taner Akkin
- University of Minnesota, Department of Biomedical Engineering, Minneapolis, Minnesota, United States
| | - Srinivasa Rao Allu
- University of Pennsylvania, Perelman School of Medicine, Department of Biochemistry and Biophysics, Philadelphia, Pennsylvania, United States
- University of Pennsylvania, School of Arts and Sciences, Department of Chemistry, Philadelphia, Pennsylvania, United States
| | - Joshua Brake
- Harvey Mudd College, Department of Engineering, Claremont, California, United States
| | - David A. Boas
- Boston University, Department of Biomedical Engineering, Boston, Massachusetts, United States
| | - Erin M. Buckley
- Georgia Institute of Technology and Emory University, Wallace H. Coulter Department of Biomedical Engineering, Atlanta, Georgia, United States
- Emory University, Department of Pediatrics, Atlanta, Georgia, United States
| | - Robert E. Campbell
- University of Tokyo, Department of Chemistry, Tokyo, Japan
- University of Alberta, Department of Chemistry, Edmonton, Alberta, Canada
| | - Anderson I. Chen
- Boston University, Department of Biomedical Engineering, Boston, Massachusetts, United States
| | - Xiaojun Cheng
- Boston University, Department of Biomedical Engineering, Boston, Massachusetts, United States
| | - Tomáš Čižmár
- Institute of Scientific Instruments of the Czech Academy of Sciences, Brno, Czech Republic
| | - Irene Costantini
- University of Florence, European Laboratory for Non-Linear Spectroscopy, Department of Biology, Florence, Italy
- National Institute of Optics, National Research Council, Rome, Italy
| | - Massimo De Vittorio
- Istituto Italiano di Tecnologia, Center for Biomolecular Nanotechnologies, Arnesano, Italy
| | - Anna Devor
- Boston University, Department of Biomedical Engineering, Boston, Massachusetts, United States
- Massachusetts General Hospital, Harvard Medical School, Athinoula A. Martinos Center for Biomedical Imaging, Charlestown, Massachusetts, United States
| | - Patrick R. Doran
- Boston University, Department of Biomedical Engineering, Boston, Massachusetts, United States
| | - Mirna El Khatib
- University of Pennsylvania, Perelman School of Medicine, Department of Biochemistry and Biophysics, Philadelphia, Pennsylvania, United States
- University of Pennsylvania, School of Arts and Sciences, Department of Chemistry, Philadelphia, Pennsylvania, United States
| | | | - Natalie Fomin-Thunemann
- Boston University, Department of Biomedical Engineering, Boston, Massachusetts, United States
| | - Yeshaiahu Fainman
- University of California San Diego, Department of Electrical and Computer Engineering, La Jolla, California, United States
| | - Tomas Fernandez-Alfonso
- University College London, Department of Neuroscience, Physiology and Pharmacology, London, United Kingdom
| | - Christopher G. L. Ferri
- University of California San Diego, Departments of Neurosciences, La Jolla, California, United States
| | - Ariel Gilad
- The Hebrew University of Jerusalem, Institute for Medical Research Israel–Canada, Department of Medical Neurobiology, Faculty of Medicine, Jerusalem, Israel
| | - Xue Han
- Boston University, Department of Biomedical Engineering, Boston, Massachusetts, United States
| | - Andrew Harris
- Weizmann Institute of Science, Department of Brain Sciences, Rehovot, Israel
| | | | - Ute Hochgeschwender
- Central Michigan University, Department of Neuroscience, Mount Pleasant, Michigan, United States
| | - Matthew G. Holt
- University of Porto, Instituto de Investigação e Inovação em Saúde (i3S), Porto, Portugal
| | - Na Ji
- University of California Berkeley, Department of Physics, Berkeley, California, United States
| | - Kıvılcım Kılıç
- Boston University, Department of Biomedical Engineering, Boston, Massachusetts, United States
| | - Evelyn M. R. Lake
- Yale School of Medicine, Department of Radiology and Biomedical Imaging, New Haven, Connecticut, United States
| | - Lei Li
- California Institute of Technology, Andrew and Peggy Cherng Department of Medical Engineering, Department of Electrical Engineering, Pasadena, California, United States
| | - Tianqi Li
- University of Minnesota, Department of Biomedical Engineering, Minneapolis, Minnesota, United States
| | - Philipp Mächler
- Boston University, Department of Biomedical Engineering, Boston, Massachusetts, United States
| | - Evan W. Miller
- University of California Berkeley, Departments of Chemistry and Molecular & Cell Biology and Helen Wills Neuroscience Institute, Berkeley, California, United States
| | | | | | - U. Valentin Nägerl
- Interdisciplinary Institute for Neuroscience University of Bordeaux & CNRS, Bordeaux, France
| | - Yusuke Nasu
- University of Tokyo, Department of Chemistry, Tokyo, Japan
| | - Axel Nimmerjahn
- Salk Institute for Biological Studies, Waitt Advanced Biophotonics Center, La Jolla, California, United States
| | - Petra Ondráčková
- Institute of Scientific Instruments of the Czech Academy of Sciences, Brno, Czech Republic
| | - Francesco S. Pavone
- National Institute of Optics, National Research Council, Rome, Italy
- University of Florence, European Laboratory for Non-Linear Spectroscopy, Department of Physics, Florence, Italy
| | - Citlali Perez Campos
- Columbia University, Zuckerman Mind Brain Behavior Institute, New York, United States
| | - Darcy S. Peterka
- Columbia University, Zuckerman Mind Brain Behavior Institute, New York, United States
| | - Filippo Pisano
- Istituto Italiano di Tecnologia, Center for Biomolecular Nanotechnologies, Arnesano, Italy
| | - Ferruccio Pisanello
- Istituto Italiano di Tecnologia, Center for Biomolecular Nanotechnologies, Arnesano, Italy
| | - Francesca Puppo
- University of California San Diego, Departments of Neurosciences, La Jolla, California, United States
| | - Bernardo L. Sabatini
- Harvard Medical School, Howard Hughes Medical Institute, Department of Neurobiology, Boston, Massachusetts, United States
| | - Sanaz Sadegh
- University of California San Diego, Departments of Neurosciences, La Jolla, California, United States
| | - Sava Sakadzic
- Massachusetts General Hospital, Harvard Medical School, Athinoula A. Martinos Center for Biomedical Imaging, Charlestown, Massachusetts, United States
| | - Shy Shoham
- New York University Grossman School of Medicine, Tech4Health and Neuroscience Institutes, New York, New York, United States
| | - Sanaya N. Shroff
- Boston University, Department of Biomedical Engineering, Boston, Massachusetts, United States
| | - R. Angus Silver
- University College London, Department of Neuroscience, Physiology and Pharmacology, London, United Kingdom
| | - Ruth R. Sims
- Sorbonne University, INSERM, CNRS, Institut de la Vision, Paris, France
| | - Spencer L. Smith
- University of California Santa Barbara, Department of Electrical and Computer Engineering, Santa Barbara, California, United States
| | - Vivek J. Srinivasan
- New York University Langone Health, Departments of Ophthalmology and Radiology, New York, New York, United States
| | - Martin Thunemann
- Boston University, Department of Biomedical Engineering, Boston, Massachusetts, United States
| | - Lei Tian
- Boston University, Departments of Electrical Engineering and Biomedical Engineering, Boston, Massachusetts, United States
| | - Lin Tian
- University of California Davis, Department of Biochemistry and Molecular Medicine, Davis, California, United States
| | - Thomas Troxler
- University of Pennsylvania, Perelman School of Medicine, Department of Biochemistry and Biophysics, Philadelphia, Pennsylvania, United States
- University of Pennsylvania, School of Arts and Sciences, Department of Chemistry, Philadelphia, Pennsylvania, United States
| | - Antoine Valera
- University College London, Department of Neuroscience, Physiology and Pharmacology, London, United Kingdom
| | - Alipasha Vaziri
- Rockefeller University, Laboratory of Neurotechnology and Biophysics, New York, New York, United States
- The Rockefeller University, The Kavli Neural Systems Institute, New York, New York, United States
| | - Sergei A. Vinogradov
- University of Pennsylvania, Perelman School of Medicine, Department of Biochemistry and Biophysics, Philadelphia, Pennsylvania, United States
- University of Pennsylvania, School of Arts and Sciences, Department of Chemistry, Philadelphia, Pennsylvania, United States
| | - Flavia Vitale
- Center for Neuroengineering and Therapeutics, Departments of Neurology, Bioengineering, Physical Medicine and Rehabilitation, Philadelphia, Pennsylvania, United States
| | - Lihong V. Wang
- California Institute of Technology, Andrew and Peggy Cherng Department of Medical Engineering, Department of Electrical Engineering, Pasadena, California, United States
| | - Hana Uhlířová
- Institute of Scientific Instruments of the Czech Academy of Sciences, Brno, Czech Republic
| | - Chris Xu
- Cornell University, School of Applied and Engineering Physics, Ithaca, New York, United States
| | - Changhuei Yang
- California Institute of Technology, Departments of Electrical Engineering, Bioengineering and Medical Engineering, Pasadena, California, United States
| | - Mu-Han Yang
- University of California San Diego, Department of Electrical and Computer Engineering, La Jolla, California, United States
| | - Gary Yellen
- Harvard Medical School, Department of Neurobiology, Boston, Massachusetts, United States
| | - Ofer Yizhar
- Weizmann Institute of Science, Department of Brain Sciences, Rehovot, Israel
| | - Yongxin Zhao
- Carnegie Mellon University, Department of Biological Sciences, Pittsburgh, Pennsylvania, United States
| |
Collapse
|
53
|
Akondi V, Kowalski B, Dubra A. Dynamic wavefront distortion in resonant scanners. APPLIED OPTICS 2021; 60:11189-11195. [PMID: 35201107 PMCID: PMC8887785 DOI: 10.1364/ao.443972] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/22/2021] [Accepted: 11/13/2021] [Indexed: 06/14/2023]
Abstract
Dynamic mirror deformation can substantially degrade the performance of optical instruments using resonant scanners. Here, we evaluate two scanners with resonant frequencies >12kHz with low dynamic distortion. First, we tested an existing galvanometric motor with a novel, to the best of our knowledge, mirror substrate material, silicon carbide, which resonates at 13.8 kHz. This material is stiffer than conventional optical glasses and has lower manufacturing toxicity than beryllium, the stiffest material currently used for this application. Then, we tested a biaxial microelectromechanical (MEMS) scanner with the resonant axis operating at 29.4 kHz. Dynamic deformation measurements show that wavefront aberrations in the galvanometric scanner are dominated by linear oblique astigmatism (90%), while wavefront aberrations in the MEMS scanner are dominated by horizontal coma (30%) and oblique trefoil (27%). In both scanners, distortion amplitude increases linearly with deflection angle, yielding diffraction-limited performance over half of the maximum possible deflection for wavelengths longer than 450 nm and over the full deflection range for wavelengths above 850 nm. Diffraction-limited performance for shorter wavelengths or over larger fractions of the deflection range can be achieved by reducing the beam diameter at the mirror surface. The small dynamic distortion of the MEMS scanner offers a promising alternative to galvanometric resonant scanners with desirable but currently unattainably high resonant frequencies.
Collapse
|
54
|
Zhang Y, Lu Z, Wu J, Lin X, Jiang D, Cai Y, Xie J, Wang Y, Zhu T, Ji X, Dai Q. Computational optical sectioning with an incoherent multiscale scattering model for light-field microscopy. Nat Commun 2021; 12:6391. [PMID: 34737278 PMCID: PMC8568979 DOI: 10.1038/s41467-021-26730-w] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2020] [Accepted: 10/14/2021] [Indexed: 11/09/2022] Open
Abstract
Quantitative volumetric fluorescence imaging at high speed across a long term is vital to understand various cellular and subcellular behaviors in living organisms. Light-field microscopy provides a compact computational solution by imaging the entire volume in a tomographic way, while facing severe degradation in scattering tissue or densely-labelled samples. To address this problem, we propose an incoherent multiscale scattering model in a complete space for quantitative 3D reconstruction in complicated environments, which is called computational optical sectioning. Without the requirement of any hardware modifications, our method can be generally applied to different light-field schemes with reduction in background fluorescence, reconstruction artifacts, and computational costs, facilitating more practical applications of LFM in a broad community. We validate the superior performance by imaging various biological dynamics in Drosophila embryos, zebrafish larvae, and mice.
Collapse
Affiliation(s)
- Yi Zhang
- Department of Automation, Tsinghua University, 100084, Beijing, China
- Institute for Brain and Cognitive Sciences, Tsinghua University, 100084, Beijing, China
| | - Zhi Lu
- Department of Automation, Tsinghua University, 100084, Beijing, China
- Institute for Brain and Cognitive Sciences, Tsinghua University, 100084, Beijing, China
| | - Jiamin Wu
- Department of Automation, Tsinghua University, 100084, Beijing, China.
- Institute for Brain and Cognitive Sciences, Tsinghua University, 100084, Beijing, China.
| | - Xing Lin
- Department of Automation, Tsinghua University, 100084, Beijing, China
- Institute for Brain and Cognitive Sciences, Tsinghua University, 100084, Beijing, China
- Beijing National Research Center for Information Science and Technology, Tsinghua University, 100084, Beijing, China
| | - Dong Jiang
- State Key Laboratory of Membrane Biology, Tsinghua University-Peking University Joint Centre for Life Sciences, Beijing Frontier Research Centre for Biological Structure, School of Life Sciences, Tsinghua University, 100084, Beijing, China
| | - Yeyi Cai
- Department of Automation, Tsinghua University, 100084, Beijing, China
| | - Jiachen Xie
- Department of Automation, Tsinghua University, 100084, Beijing, China
- Institute for Brain and Cognitive Sciences, Tsinghua University, 100084, Beijing, China
| | - Yuling Wang
- Department of Automation, Tsinghua University, 100084, Beijing, China
| | - Tianyi Zhu
- Department of Automation, Tsinghua University, 100084, Beijing, China
- Institute for Brain and Cognitive Sciences, Tsinghua University, 100084, Beijing, China
| | - Xiangyang Ji
- Department of Automation, Tsinghua University, 100084, Beijing, China.
- Institute for Brain and Cognitive Sciences, Tsinghua University, 100084, Beijing, China.
- Beijing National Research Center for Information Science and Technology, Tsinghua University, 100084, Beijing, China.
| | - Qionghai Dai
- Department of Automation, Tsinghua University, 100084, Beijing, China.
- Institute for Brain and Cognitive Sciences, Tsinghua University, 100084, Beijing, China.
- Beijing National Research Center for Information Science and Technology, Tsinghua University, 100084, Beijing, China.
| |
Collapse
|
55
|
Streich L, Boffi JC, Wang L, Alhalaseh K, Barbieri M, Rehm R, Deivasigamani S, Gross CT, Agarwal A, Prevedel R. High-resolution structural and functional deep brain imaging using adaptive optics three-photon microscopy. Nat Methods 2021; 18:1253-1258. [PMID: 34594033 PMCID: PMC8490155 DOI: 10.1038/s41592-021-01257-6] [Citation(s) in RCA: 55] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2021] [Accepted: 07/30/2021] [Indexed: 02/08/2023]
Abstract
Multiphoton microscopy has become a powerful tool with which to visualize the morphology and function of neural cells and circuits in the intact mammalian brain. However, tissue scattering, optical aberrations and motion artifacts degrade the imaging performance at depth. Here we describe a minimally invasive intravital imaging methodology based on three-photon excitation, indirect adaptive optics (AO) and active electrocardiogram gating to advance deep-tissue imaging. Our modal-based, sensorless AO approach is robust to low signal-to-noise ratios as commonly encountered in deep scattering tissues such as the mouse brain, and permits AO correction over large axial fields of view. We demonstrate near-diffraction-limited imaging of deep cortical spines and (sub)cortical dendrites up to a depth of 1.4 mm (the edge of the mouse CA1 hippocampus). In addition, we show applications to deep-layer calcium imaging of astrocytes, including fibrous astrocytes that reside in the highly scattering corpus callosum.
Collapse
Affiliation(s)
- Lina Streich
- Cell Biology and Biophysics Unit, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
- Collaboration for joint PhD degree between EMBL and Heidelberg University, Faculty of Biosciences, Heidelberg University, Heidelberg, Germany
| | - Juan Carlos Boffi
- Cell Biology and Biophysics Unit, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
| | - Ling Wang
- Cell Biology and Biophysics Unit, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
| | - Khaleel Alhalaseh
- The Chica and Heinz Schaller Research Group, Institute for Anatomy and Cell Biology, Heidelberg University, Heidelberg, Germany
| | - Matteo Barbieri
- Cell Biology and Biophysics Unit, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
| | - Ronja Rehm
- Cell Biology and Biophysics Unit, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
| | | | - Cornelius T Gross
- Epigenetics and Neurobiology Unit, European Molecular Biology Laboratory, Monterotondo, Italy
| | - Amit Agarwal
- The Chica and Heinz Schaller Research Group, Institute for Anatomy and Cell Biology, Heidelberg University, Heidelberg, Germany
- Interdisciplinary Center for Neurosciences, Heidelberg University, Heidelberg, Germany
| | - Robert Prevedel
- Cell Biology and Biophysics Unit, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany.
- Epigenetics and Neurobiology Unit, European Molecular Biology Laboratory, Monterotondo, Italy.
- Interdisciplinary Center for Neurosciences, Heidelberg University, Heidelberg, Germany.
- Developmental Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany.
- Molecular Medicine Partnership Unit (MMPU), European Molecular Biology Laboratory, Heidelberg, Germany.
| |
Collapse
|
56
|
Borah BJ, Lee JC, Chi HH, Hsiao YT, Yen CT, Sun CK. Nyquist-exceeding high voxel rate acquisition in mesoscopic multiphoton microscopy for full-field submicron resolution resolvability. iScience 2021; 24:103041. [PMID: 34585109 PMCID: PMC8450254 DOI: 10.1016/j.isci.2021.103041] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2021] [Revised: 07/15/2021] [Accepted: 08/23/2021] [Indexed: 12/04/2022] Open
Abstract
The Nyquist-Shannon criterion has never been realized in a laser-scanning mesoscopic multiphoton microscope (MPM) with a large field-of-view (FOV)-resolution ratio, especially when employing a high-frequency resonant-raster-scanning. With a high optical resolution nature, a current mesoscopic-MPM either neglects the criterion and degrades the digital resolution to twice the pixel size, or reduces the FOV and/or the raster-scanning speed to avoid aliasing. We introduce a Nyquist figure-of-merit (NFOM) parameter to characterize a laser-scanning MPM in terms of its optical-resolution retrieving ability. Based on NFOM, we define the maximum aliasing-free FOV, and subsequently, a cross-over excitation wavelength, below which the FOV becomes NFOM-constrained irrespective of an optimized optical design. We validate our idea in a custom-built mesoscopic-MPM with millimeter-scale FOV yielding an ultra-high FOV-resolution ratio of >3,000, while securing up-to a 1.6 mm Nyquist-satisfied aliasing-free FOV, a ∼400 nm lateral resolution, and a 70 M/s effective voxel-sampling rate, all at the same time. Nyquist figure-of-merit is introduced to characterize laser-scanning MPM digitization Maximum aliasing-free FOV and cross-over excitation wavelength are formulated High repetition-rate laser can enable high-speed large-FOV high-resolution MPM imaging Up-to 1.6 mm-wide non-aliased FOV and ∼400 nm digital resolution at 8 kHz line-rate
Collapse
Affiliation(s)
- Bhaskar Jyoti Borah
- Department of Electrical Engineering and Graduate Institute of Photonics and Optoelectronics, National Taiwan University, Taipei 10617, Taiwan
| | - Jye-Chang Lee
- Department of Life Science, National Taiwan University, Taipei 10617, Taiwan
| | - Han-Hsiung Chi
- Department of Life Science, National Taiwan University, Taipei 10617, Taiwan
| | - Yang-Ting Hsiao
- Department of Electrical Engineering and Graduate Institute of Photonics and Optoelectronics, National Taiwan University, Taipei 10617, Taiwan
| | - Chen-Tung Yen
- Department of Life Science, National Taiwan University, Taipei 10617, Taiwan
| | - Chi-Kuang Sun
- Department of Electrical Engineering and Graduate Institute of Photonics and Optoelectronics, National Taiwan University, Taipei 10617, Taiwan.,Graduate Institute of Biomedical Electronics and Bioinformatics, National Taiwan University, Taipei 10617, Taiwan.,Molecular Imaging Center, National Taiwan University, Taipei 10617, Taiwan
| |
Collapse
|
57
|
High-speed, cortex-wide volumetric recording of neuroactivity at cellular resolution using light beads microscopy. Nat Methods 2021; 18:1103-1111. [PMID: 34462592 PMCID: PMC8958902 DOI: 10.1038/s41592-021-01239-8] [Citation(s) in RCA: 77] [Impact Index Per Article: 25.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2020] [Accepted: 07/09/2021] [Indexed: 02/07/2023]
Abstract
Two-photon microscopy has enabled high-resolution imaging of neuroactivity at depth within scattering brain tissue. However, its various realizations have not overcome the tradeoffs between speed and spatiotemporal sampling that would be necessary to enable mesoscale volumetric recording of neuroactivity at cellular resolution and speed compatible with resolving calcium transients. Here, we introduce light beads microscopy (LBM), a scalable and spatiotemporally optimal acquisition approach limited only by fluorescence lifetime, where a set of axially separated and temporally distinct foci record the entire axial imaging range near-simultaneously, enabling volumetric recording at 1.41 × 108 voxels per second. Using LBM, we demonstrate mesoscopic and volumetric imaging at multiple scales in the mouse cortex, including cellular-resolution recordings within ~3 × 5 × 0.5 mm volumes containing >200,000 neurons at ~5 Hz and recordings of populations of ~1 million neurons within ~5.4 × 6 × 0.5 mm volumes at ~2 Hz, as well as higher speed (9.6 Hz) subcellular-resolution volumetric recordings. LBM provides an opportunity for discovering the neurocomputations underlying cortex-wide encoding and processing of information in the mammalian brain.
Collapse
|
58
|
In Vivo Calcium Imaging of CA3 Pyramidal Neuron Populations in Adult Mouse Hippocampus. eNeuro 2021; 8:ENEURO.0023-21.2021. [PMID: 34330817 PMCID: PMC8387150 DOI: 10.1523/eneuro.0023-21.2021] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2021] [Revised: 06/09/2021] [Accepted: 06/15/2021] [Indexed: 11/21/2022] Open
Abstract
Neuronal population activity in the hippocampal CA3 subfield is implicated in cognitive brain functions such as memory processing and spatial navigation. However, because of its deep location in the brain, the CA3 area has been difficult to target with modern calcium imaging approaches. Here, we achieved chronic two-photon calcium imaging of CA3 pyramidal neurons with the red fluorescent calcium indicator R-CaMP1.07 in anesthetized and awake mice. We characterize CA3 neuronal activity at both the single-cell and population level and assess its stability across multiple imaging days. During both anesthesia and wakefulness, nearly all CA3 pyramidal neurons displayed calcium transients. Most of the calcium transients were consistent with a high incidence of bursts of action potentials (APs), based on calibration measurements using simultaneous juxtacellular recordings and calcium imaging. In awake mice, we found state-dependent differences with striking large and prolonged calcium transients during locomotion. We estimate that trains of >30 APs over 3 s underlie these salient events. Their abundance in particular subsets of neurons was relatively stable across days. At the population level, we found that co-activity within the CA3 network was above chance level and that co-active neuron pairs maintained their correlated activity over days. Our results corroborate the notion of state-dependent spatiotemporal activity patterns in the recurrent network of CA3 and demonstrate that at least some features of population activity, namely co-activity of cell pairs and likelihood to engage in prolonged high activity, are maintained over days.
Collapse
|
59
|
Reinforcing neuron extraction and spike inference in calcium imaging using deep self-supervised denoising. Nat Methods 2021; 18:1395-1400. [PMID: 34400836 DOI: 10.1038/s41592-021-01225-0] [Citation(s) in RCA: 50] [Impact Index Per Article: 16.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2020] [Accepted: 06/28/2021] [Indexed: 12/11/2022]
Abstract
Calcium imaging has transformed neuroscience research by providing a methodology for monitoring the activity of neural circuits with single-cell resolution. However, calcium imaging is inherently susceptible to detection noise, especially when imaging with high frame rate or under low excitation dosage. Here we developed DeepCAD, a self-supervised deep-learning method for spatiotemporal enhancement of calcium imaging data that does not require any high signal-to-noise ratio (SNR) observations. DeepCAD suppresses detection noise and improves the SNR more than tenfold, which reinforces the accuracy of neuron extraction and spike inference and facilitates the functional analysis of neural circuits.
Collapse
|
60
|
Universal autofocus for quantitative volumetric microscopy of whole mouse brains. Nat Methods 2021; 18:953-958. [PMID: 34312564 DOI: 10.1038/s41592-021-01208-1] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2020] [Accepted: 06/14/2021] [Indexed: 11/08/2022]
Abstract
Unbiased quantitative analysis of macroscopic biological samples demands fast imaging systems capable of maintaining high resolution across large volumes. Here we introduce RAPID (rapid autofocusing via pupil-split image phase detection), a real-time autofocus method applicable in every widefield-based microscope. RAPID-enabled light-sheet microscopy reliably reconstructs intact, cleared mouse brains with subcellular resolution, and allowed us to characterize the three-dimensional (3D) spatial clustering of somatostatin-positive neurons in the whole encephalon, including densely labeled areas. Furthermore, it enabled 3D morphological analysis of microglia across the entire brain. Beyond light-sheet microscopy, we demonstrate that RAPID maintains high image quality in various settings, from in vivo fluorescence imaging to 3D tracking of fast-moving organisms. RAPID thus provides a flexible autofocus solution that is suitable for traditional automated microscopy tasks as well as for quantitative analysis of large biological specimens.
Collapse
|
61
|
Siegle JH, Ledochowitsch P, Jia X, Millman DJ, Ocker GK, Caldejon S, Casal L, Cho A, Denman DJ, Durand S, Groblewski PA, Heller G, Kato I, Kivikas S, Lecoq J, Nayan C, Ngo K, Nicovich PR, North K, Ramirez TK, Swapp J, Waughman X, Williford A, Olsen SR, Koch C, Buice MA, de Vries SEJ. Reconciling functional differences in populations of neurons recorded with two-photon imaging and electrophysiology. eLife 2021; 10:e69068. [PMID: 34270411 PMCID: PMC8285106 DOI: 10.7554/elife.69068] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2021] [Accepted: 07/02/2021] [Indexed: 11/20/2022] Open
Abstract
Extracellular electrophysiology and two-photon calcium imaging are widely used methods for measuring physiological activity with single-cell resolution across large populations of cortical neurons. While each of these two modalities has distinct advantages and disadvantages, neither provides complete, unbiased information about the underlying neural population. Here, we compare evoked responses in visual cortex recorded in awake mice under highly standardized conditions using either imaging of genetically expressed GCaMP6f or electrophysiology with silicon probes. Across all stimulus conditions tested, we observe a larger fraction of responsive neurons in electrophysiology and higher stimulus selectivity in calcium imaging, which was partially reconciled by applying a spikes-to-calcium forward model to the electrophysiology data. However, the forward model could only reconcile differences in responsiveness when restricted to neurons with low contamination and an event rate above a minimum threshold. This work established how the biases of these two modalities impact functional metrics that are fundamental for characterizing sensory-evoked responses.
Collapse
Affiliation(s)
| | | | - Xiaoxuan Jia
- MindScope Program, Allen InstituteSeattleUnited States
| | | | | | | | - Linzy Casal
- MindScope Program, Allen InstituteSeattleUnited States
| | - Andy Cho
- MindScope Program, Allen InstituteSeattleUnited States
| | - Daniel J Denman
- Allen Institute for Brain Science, Allen InstituteSeattleUnited States
| | | | | | - Gregg Heller
- MindScope Program, Allen InstituteSeattleUnited States
| | - India Kato
- MindScope Program, Allen InstituteSeattleUnited States
| | - Sara Kivikas
- MindScope Program, Allen InstituteSeattleUnited States
| | - Jérôme Lecoq
- MindScope Program, Allen InstituteSeattleUnited States
| | - Chelsea Nayan
- MindScope Program, Allen InstituteSeattleUnited States
| | - Kiet Ngo
- Allen Institute for Brain Science, Allen InstituteSeattleUnited States
| | - Philip R Nicovich
- Allen Institute for Brain Science, Allen InstituteSeattleUnited States
| | - Kat North
- MindScope Program, Allen InstituteSeattleUnited States
| | | | - Jackie Swapp
- MindScope Program, Allen InstituteSeattleUnited States
| | - Xana Waughman
- MindScope Program, Allen InstituteSeattleUnited States
| | - Ali Williford
- MindScope Program, Allen InstituteSeattleUnited States
| | - Shawn R Olsen
- MindScope Program, Allen InstituteSeattleUnited States
| | - Christof Koch
- MindScope Program, Allen InstituteSeattleUnited States
| | | | | |
Collapse
|
62
|
Giampetraglia M, Weigelin B. Recent advances in intravital microscopy for preclinical research. Curr Opin Chem Biol 2021; 63:200-208. [PMID: 34274700 DOI: 10.1016/j.cbpa.2021.05.010] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2020] [Revised: 05/08/2021] [Accepted: 05/14/2021] [Indexed: 12/14/2022]
Abstract
Intravital microscopy (IVM) has revolutionized our understanding of single-cell behavior in complex tissues by enabling real-time observation of molecular and cellular processes in their natural environment. In preclinical research, IVM has emerged as a standard tool for mechanistic studies of therapy response and the rational design of new treatment strategies. Technological developments keep expanding the imaging depth and quality that can be achieved in living tissue, and the maturation of imaging modalities such as fluorescence and phosphorescence lifetime imaging facilitates co-registration of individual cell dynamics with metabolic tissue states. Correlation of IVM with mesoscopic and macroscopic imaging modalities further promotes the translation of mechanistic insights gained by IVM into clinically relevant information. This review highlights some of the recent advances in IVM that have made the transition from experimental optical techniques to practical applications in basic and preclinical research.
Collapse
Affiliation(s)
- Martina Giampetraglia
- David H. Koch Center for Applied Research of Genitourinary Cancers, Department of Genitourinary Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, USA
| | - Bettina Weigelin
- Werner Siemens Imaging Center, Department of Preclinical Imaging and Radiopharmacy, Eberhard Karls University Tübingen, Tübingen, Germany; Cluster of Excellence iFIT (EXC 2180) "Image-Guided and Functionally Instructed Tumor Therapies", University of Tübingen, Germany.
| |
Collapse
|
63
|
Song A, Gauthier JL, Pillow JW, Tank DW, Charles AS. Neural anatomy and optical microscopy (NAOMi) simulation for evaluating calcium imaging methods. J Neurosci Methods 2021; 358:109173. [PMID: 33839190 PMCID: PMC8217135 DOI: 10.1016/j.jneumeth.2021.109173] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2020] [Revised: 03/21/2021] [Accepted: 03/24/2021] [Indexed: 11/20/2022]
Abstract
BACKGROUND The past decade has seen a multitude of new in vivo functional imaging methodologies. However, the lack of ground-truth comparisons or evaluation metrics makes the large-scale, systematic validation vital to the continued development and use of optical microscopy impossible. NEW-METHOD We provide a new framework for evaluating two-photon microscopy methods via in silico Neural Anatomy and Optical Microscopy (NAOMi) simulation. Our computationally efficient model generates large anatomical volumes of mouse cortex, simulates neural activity, and incorporates optical propagation and scanning to create realistic calcium imaging datasets. RESULTS We verify NAOMi simulations against in vivo two-photon recordings from mouse cortex. We leverage this in silico ground truth to directly compare different segmentation algorithms and optical designs. We find modern segmentation algorithms extract strong neural time-courses comparable to estimation using oracle spatial information, but with an increase in the false positive rate. Comparison between optical setups demonstrate improved resilience to motion artifacts in sparsely labeled samples using Bessel beams, increased signal-to-noise ratio and cell-count using low numerical aperture Gaussian beams and nuclear GCaMP, and more uniform spatial sampling with temporal focusing versus multi-plane imaging. COMPARISON WITH EXISTING METHODS NAOMi is a first-of-its kind framework for assessing optical imaging modalities. Existing methods are either anatomical simulations or do not address functional imaging. Thus there is no competing method for simulating realistic functional optical microscopy data. CONCLUSIONS By leveraging the rich accumulated knowledge of neural anatomy and optical physics, we provide a powerful new tool to assess and develop important methods in neural imaging.
Collapse
Affiliation(s)
- Alexander Song
- Princeton Neuroscience Institute, Princeton University, Princeton, 08540 NJ, USA; Department of Physics, Princeton University, Princeton, 08540 NJ, USA
| | - Jeff L Gauthier
- Princeton Neuroscience Institute, Princeton University, Princeton, 08540 NJ, USA
| | - Jonathan W Pillow
- Princeton Neuroscience Institute, Princeton University, Princeton, 08540 NJ, USA; Department of Psychology, Princeton University, Princeton, 08540 NJ, USA
| | - David W Tank
- Princeton Neuroscience Institute, Princeton University, Princeton, 08540 NJ, USA; Bezos Center for Neural Circuit Dynamics, Princeton University, Princeton, 08540 NJ, USA; Department of Molecular Biology, Princeton University, Princeton, 08540 NJ, USA
| | - Adam S Charles
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, 21218, MD, USA; Mathematical Institute for Data Science, Johns Hopkins University, Baltimore, 21218, MD, USA; Center for Imaging Science, Johns Hopkins University, Baltimore, 21218, MD, USA; Kavli Neuroscience Discovery Institute, Johns Hopkins University, Baltimore, 21218, MD, USA
| |
Collapse
|
64
|
Ren C, Komiyama T. Characterizing Cortex-Wide Dynamics with Wide-Field Calcium Imaging. J Neurosci 2021; 41:4160-4168. [PMID: 33893217 PMCID: PMC8143209 DOI: 10.1523/jneurosci.3003-20.2021] [Citation(s) in RCA: 39] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Revised: 03/26/2021] [Accepted: 03/30/2021] [Indexed: 12/27/2022] Open
Abstract
The brain functions through coordinated activity among distributed regions. Wide-field calcium imaging, combined with improved genetically encoded calcium indicators, allows sufficient signal-to-noise ratio and spatiotemporal resolution to afford a unique opportunity to capture cortex-wide dynamics on a moment-by-moment basis in behaving animals. Recent applications of this approach have been uncovering cortical dynamics at unprecedented scales during various cognitive processes, ranging from relatively simple sensorimotor integration to more complex decision-making tasks. In this review, we will highlight recent scientific advances enabled by wide-field calcium imaging in behaving mice. We then summarize several technical considerations and future opportunities for wide-field imaging to uncover large-scale circuit dynamics.
Collapse
Affiliation(s)
- Chi Ren
- Neurobiology Section, Center for Neural Circuits and Behavior, Department of Neurosciences, and Halıcıoğlu Data Science Institute, University of California San Diego, La Jolla, California 92093
| | - Takaki Komiyama
- Neurobiology Section, Center for Neural Circuits and Behavior, Department of Neurosciences, and Halıcıoğlu Data Science Institute, University of California San Diego, La Jolla, California 92093
| |
Collapse
|
65
|
Chien MP, Brinks D, Testa-Silva G, Tian H, Phil Brooks F, Adam Y, Bloxham B, Gmeiner B, Kheifets S, Cohen AE. Photoactivated voltage imaging in tissue with an archaerhodopsin-derived reporter. SCIENCE ADVANCES 2021; 7:7/19/eabe3216. [PMID: 33952514 PMCID: PMC8099184 DOI: 10.1126/sciadv.abe3216] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/13/2020] [Accepted: 03/15/2021] [Indexed: 05/19/2023]
Abstract
Photoactivated genetically encoded voltage indicators (GEVIs) have the potential to enable optically sectioned voltage imaging at the intersection of a photoactivation beam and an imaging beam. We developed a pooled high-throughput screen to identify archaerhodopsin mutants with enhanced photoactivation. After screening ~105 cells, we identified a novel GEVI, NovArch, whose one-photon near-infrared fluorescence is reversibly enhanced by weak one-photon blue or two-photon near-infrared excitation. Because the photoactivation leads to fluorescent signals catalytically rather than stoichiometrically, high fluorescence signals, optical sectioning, and high time resolution are achieved simultaneously at modest blue or two-photon laser power. We demonstrate applications of the combined molecular and optical tools to optical mapping of membrane voltage in distal dendrites in acute mouse brain slices and in spontaneously active neurons in vivo.
Collapse
Affiliation(s)
- Miao-Ping Chien
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, USA
- Department of Molecular Genetics, Erasmus University Medical Center, Rotterdam, Netherlands
- Oncode Institute, Utrecht, Netherlands
| | - Daan Brinks
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, USA
- Department of Molecular Genetics, Erasmus University Medical Center, Rotterdam, Netherlands
- Department of Imaging Physics, Delft University of Technology, Delft, Netherlands
| | - Guilherme Testa-Silva
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, USA
- Howard Hughes Medical Institute, Cambridge, MA 02138, USA
| | - He Tian
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, USA
| | - F Phil Brooks
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, USA
| | - Yoav Adam
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, USA
| | - Blox Bloxham
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, USA
| | - Benjamin Gmeiner
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, USA
| | - Simon Kheifets
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, USA
| | - Adam E Cohen
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, USA.
- Howard Hughes Medical Institute, Cambridge, MA 02138, USA
| |
Collapse
|
66
|
Fast, cell-resolution, contiguous-wide two-photon imaging to reveal functional network architectures across multi-modal cortical areas. Neuron 2021; 109:1810-1824.e9. [PMID: 33878295 DOI: 10.1016/j.neuron.2021.03.032] [Citation(s) in RCA: 40] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2020] [Revised: 02/11/2021] [Accepted: 03/25/2021] [Indexed: 02/07/2023]
Abstract
Fast and wide field-of-view imaging with single-cell resolution, high signal-to-noise ratio, and no optical aberrations have the potential to inspire new avenues of investigations in biology. However, such imaging is challenging because of the inevitable tradeoffs among these parameters. Here, we overcome these tradeoffs by combining a resonant scanning system, a large objective with low magnification and high numerical aperture, and highly sensitive large-aperture photodetectors. The result is a practically aberration-free, fast-scanning high optical invariant two-photon microscopy (FASHIO-2PM) that enables calcium imaging from a large network composed of ∼16,000 neurons at 7.5 Hz from a 9 mm2 contiguous image plane, including more than 10 sensory-motor and higher-order areas of the cerebral cortex in awake mice. Network analysis based on single-cell activities revealed that the brain exhibits small-world rather than scale-free behavior. The FASHIO-2PM is expected to enable studies on biological dynamics by simultaneously monitoring macroscopic activities and their compositional elements.
Collapse
|
67
|
Cramer SW, Carter RE, Aronson JD, Kodandaramaiah SB, Ebner TJ, Chen CC. Through the looking glass: A review of cranial window technology for optical access to the brain. J Neurosci Methods 2021; 354:109100. [PMID: 33600850 PMCID: PMC8100903 DOI: 10.1016/j.jneumeth.2021.109100] [Citation(s) in RCA: 41] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2020] [Revised: 02/07/2021] [Accepted: 02/09/2021] [Indexed: 02/07/2023]
Abstract
Deciphering neurologic function is a daunting task, requiring understanding the neuronal networks and emergent properties that arise from the interactions among single neurons. Mechanistic insights into neuronal networks require tools that simultaneously assess both single neuron activity and the consequent mesoscale output. The development of cranial window technologies, in which the skull is thinned or replaced with a synthetic optical interface, has enabled monitoring neuronal activity from subcellular to mesoscale resolution in awake, behaving animals when coupled with advanced microscopy techniques. Here we review recent achievements in cranial window technologies, appraise the relative merits of each design and discuss the future research in cranial window design.
Collapse
Affiliation(s)
- Samuel W Cramer
- Department of Neurosurgery, University of Minnesota, 420 Delaware St SE, Mayo D429, MMC 96, Twin Cities, Minneapolis, MN, 55455, USA
| | - Russell E Carter
- Department of Neuroscience, University of Minnesota, Twin Cities, Room 421, 2001 Sixth Street S.E., Minneapolis, MN, 55455 MN, USA
| | - Justin D Aronson
- Department of Neuroscience, University of Minnesota, Twin Cities, Room 421, 2001 Sixth Street S.E., Minneapolis, MN, 55455 MN, USA
| | - Suhasa B Kodandaramaiah
- Department of Mechanical Engineering, University of Minnesota, Twin Cities, MN, USA; Department of Biomedical Engineering, University of Minnesota, Twin Cities, MN, USA; Graduate Program in Neuroscience, University of Minnesota, Twin Cities, MN, USA
| | - Timothy J Ebner
- Department of Neuroscience, University of Minnesota, Twin Cities, Room 421, 2001 Sixth Street S.E., Minneapolis, MN, 55455 MN, USA.
| | - Clark C Chen
- Department of Neurosurgery, University of Minnesota, 420 Delaware St SE, Mayo D429, MMC 96, Twin Cities, Minneapolis, MN, 55455, USA.
| |
Collapse
|
68
|
Moon J, Lim YS, Yoon S, Choi W. Single-shot multi-depth full-field optical coherence tomography using spatial frequency division multiplexing. OPTICS EXPRESS 2021; 29:7060-7069. [PMID: 33726214 DOI: 10.1364/oe.417950] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Accepted: 02/11/2021] [Indexed: 06/12/2023]
Abstract
Fast 3D volumetric imaging has been essential for biology, medicine and industrial inspections, and various optical coherence tomography (OCT) methods have been developed to meet such needs. Point-scanning based approaches, such as swept-source OCT and spectral domain OCT, can obtain a depth information at once, but they require lateral scan for full 3D imaging. On the contrary, full-field OCT needs the scanning of imaging depth while it records a full lateral information at once. Here, we present a full-field OCT system that can obtain multi-depth information at once by a single-shot recording. We combine a 2D diffraction grating and a custom-made echelon to prepare multiple reference beams having different pathlengths and propagating angles. By recording a single interference image between the reflected wave from a sample and these multiple reference beams, we reconstruct full-field images at multiple depths associated with the pathlengths of the individual reference beams. We demonstrated the single-shot recording of 7 different depth images at 10 µm for biological tissues. Our method can potentially be useful for applications where high-speed recording of multiple en-face images is crucial.
Collapse
|
69
|
Tsang JM, Gritton HJ, Das SL, Weber TD, Chen CS, Han X, Mertz J. Fast, multiplane line-scan confocal microscopy using axially distributed slits. BIOMEDICAL OPTICS EXPRESS 2021; 12:1339-1350. [PMID: 33796357 PMCID: PMC7984773 DOI: 10.1364/boe.417286] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/11/2020] [Revised: 01/28/2021] [Accepted: 01/29/2021] [Indexed: 05/29/2023]
Abstract
The inherent constraints on resolution, speed and field of view have hindered the development of high-speed, three-dimensional microscopy techniques over large scales. Here, we present a multiplane line-scan imaging strategy, which uses a series of axially distributed reflecting slits to probe different depths within a sample volume. Our technique enables the simultaneous imaging of an optically sectioned image stack with a single camera at frame rates of hundreds of hertz, without the need for axial scanning. We demonstrate the applicability of our system to monitor fast dynamics in biological samples by performing calcium imaging of neuronal activity in mouse brains and voltage imaging of cardiomyocytes in cardiac samples.
Collapse
Affiliation(s)
- Jean-Marc Tsang
- Department of Biomedical Engineering, Boston University, 44 Cummington Mall, Boston, MA 02215, USA
| | - Howard J. Gritton
- Department of Biomedical Engineering, Boston University, 44 Cummington Mall, Boston, MA 02215, USA
- Department of Comparative Biosciences, University of Illinois at Urbana-Champaign, Urbana, IL 61802, USA
| | - Shoshana L. Das
- Department of Biomedical Engineering, Boston University, 44 Cummington Mall, Boston, MA 02215, USA
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA 02115, USA
| | - Timothy D. Weber
- Department of Biomedical Engineering, Boston University, 44 Cummington Mall, Boston, MA 02215, USA
| | - Christopher S. Chen
- Department of Biomedical Engineering, Boston University, 44 Cummington Mall, Boston, MA 02215, USA
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA 02115, USA
| | - Xue Han
- Department of Biomedical Engineering, Boston University, 44 Cummington Mall, Boston, MA 02215, USA
- Photonics Center, Boston University, 8 Saint Mary’s Street, Boston, MA 02215, USA
| | - Jerome Mertz
- Department of Biomedical Engineering, Boston University, 44 Cummington Mall, Boston, MA 02215, USA
- Photonics Center, Boston University, 8 Saint Mary’s Street, Boston, MA 02215, USA
| |
Collapse
|
70
|
Hontani Y, Xia F, Xu C. Multicolor three-photon fluorescence imaging with single-wavelength excitation deep in mouse brain. SCIENCE ADVANCES 2021; 7:eabf3531. [PMID: 33731355 PMCID: PMC7968831 DOI: 10.1126/sciadv.abf3531] [Citation(s) in RCA: 58] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/20/2020] [Accepted: 01/27/2021] [Indexed: 05/03/2023]
Abstract
Multiphoton fluorescence microscopy is a powerful technique for deep-tissue observation of living cells. In particular, three-photon microscopy is highly beneficial for deep-tissue imaging because of the long excitation wavelength and the high nonlinear confinement in living tissues. Because of the large spectral separation of fluorophores of different color, multicolor three-photon imaging typically requires multiple excitation wavelengths. Here, we report a new three-photon excitation scheme: excitation to a higher-energy electronic excited state instead of the conventional excitation to the lowest-energy excited state, enabling multicolor three-photon fluorescence imaging with deep-tissue penetration in the living mouse brain using single-wavelength excitation. We further demonstrate that our excitation method results in ≥10-fold signal enhancement for some of the common red fluorescent molecules. The multicolor imaging capability and the possibility of enhanced three-photon excitation cross section will open new opportunities for life science applications of three-photon microscopy.
Collapse
Affiliation(s)
- Yusaku Hontani
- School of Applied and Engineering Physics, Cornell University, Ithaca, NY 14853, USA.
| | - Fei Xia
- School of Applied and Engineering Physics, Cornell University, Ithaca, NY 14853, USA
- Meinig School of Biomedical Engineering, Cornell University, Ithaca, NY 14853, USA
| | - Chris Xu
- School of Applied and Engineering Physics, Cornell University, Ithaca, NY 14853, USA.
| |
Collapse
|
71
|
Zhang Z, Cong L, Bai L, Wang K. Light-field microscopy for fast volumetric brain imaging. J Neurosci Methods 2021; 352:109083. [PMID: 33484746 DOI: 10.1016/j.jneumeth.2021.109083] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2020] [Revised: 12/23/2020] [Accepted: 01/14/2021] [Indexed: 01/06/2023]
Abstract
Recording neural activities over large populations is critical for a better understanding of the functional mechanisms of animal brains. Traditional optical imaging technologies for in vivo neural activity recording are usually limited in throughput and cannot cover a large imaging volume at high speed. Light-field microscopy features a highly parallelized imaging collection mechanism and can simultaneously record optical signals from different depths. Therefore, it can potentially increase the imaging throughput substantially. Furthermore, its unique instantaneous volumetric imaging capability enables the capture of highly dynamic processes, such as recording whole-animal neural activities in freely moving Caenorhabditis elegans and whole-brain neural activity in freely swimming larval zebrafish during prey capture. Here, we summarize the principles of and considerations in the practical implementation of light-field microscopy as currently applied in biological imaging experiments. We also discuss the strategies that light-field microscopy can employ when imaging thick tissues in the presence of scattering and background interference. Finally, we present a few examples of applying light-field microscopy in neuroscientific studies in several important animal models.
Collapse
Affiliation(s)
- Zhenkun Zhang
- Institute of Neuroscience, State Key Laboratory of Neuroscience, Center for Excellence in Brain Science and Intelligence Technology, Chinese Academy of Sciences, Shanghai, 200031, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Lin Cong
- Institute of Neuroscience, State Key Laboratory of Neuroscience, Center for Excellence in Brain Science and Intelligence Technology, Chinese Academy of Sciences, Shanghai, 200031, China
| | - Lu Bai
- Institute of Neuroscience, State Key Laboratory of Neuroscience, Center for Excellence in Brain Science and Intelligence Technology, Chinese Academy of Sciences, Shanghai, 200031, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Kai Wang
- Institute of Neuroscience, State Key Laboratory of Neuroscience, Center for Excellence in Brain Science and Intelligence Technology, Chinese Academy of Sciences, Shanghai, 200031, China; University of Chinese Academy of Sciences, Beijing, 100049, China; Shanghai Center for Brain Science and Brain-Inspired Intelligence Technology, Shanghai, 201210, China.
| |
Collapse
|
72
|
Fernández A, Straw A, Distel M, Leitgeb R, Baltuska A, Verhoef AJ. Dynamic real-time subtraction of stray-light and background for multiphoton imaging. BIOMEDICAL OPTICS EXPRESS 2021; 12:288-302. [PMID: 33659077 PMCID: PMC7899518 DOI: 10.1364/boe.403255] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/20/2020] [Revised: 10/13/2020] [Accepted: 11/17/2020] [Indexed: 06/12/2023]
Abstract
We introduce a new approach to reduce uncorrelated background signals from fluorescence imaging data, using real-time subtraction of background light. This approach takes advantage of the short fluorescence lifetime of most popular fluorescent activity reporters, and the low duty-cycle of ultrafast lasers. By synchronizing excitation and recording, laser-induced multiphoton fluorescence can be discriminated from background light levels with each laser pulse. We demonstrate the ability of our method to - in real-time - remove image artifacts that in a conventional imaging setup lead to clipping of the signal. In other words, our method enables imaging under conditions that in a conventional setup would yield corrupted data from which no accurate information can be extracted. This is advantageous in experimental setups requiring additional light sources for applications such as optogenetic stimulation.
Collapse
Affiliation(s)
- A Fernández
- IQSE and Department of Soil and Crop Sciences, Texas A&M University, 4242 TAMU, College Station, TX 77843, USA
- Photonics Institute, TU Wien, Gusshausstrasse 27-29/387, 1040 Vienna, Austria
- Centro Regional Universitario de Coclé, Universidad de Panamá, Penonomé, Coclé, Panama
| | - A Straw
- Institute of Biology I and Bernstein Center Freiburg, University of Freiburg, Hauptstrasse 1, 79104 Freiburg, Germany
| | - M Distel
- St. Anna Children's Cancer Research Institute, Zimmermannplatz 10, 1090 Vienna, Austria
| | - R Leitgeb
- Center for Medical Physics and Biomedical Engineering, Medical University of Vienna, Währinger Gürtel 18-20/4L, 1090 Vienna, Austria
| | - A Baltuska
- Photonics Institute, TU Wien, Gusshausstrasse 27-29/387, 1040 Vienna, Austria
| | - A J Verhoef
- IQSE and Department of Soil and Crop Sciences, Texas A&M University, 4242 TAMU, College Station, TX 77843, USA
- Photonics Institute, TU Wien, Gusshausstrasse 27-29/387, 1040 Vienna, Austria
- Centro Regional Universitario de Coclé, Universidad de Panamá, Penonomé, Coclé, Panama
- Center for Medical Physics and Biomedical Engineering, Medical University of Vienna, Währinger Gürtel 18-20/4L, 1090 Vienna, Austria
| |
Collapse
|
73
|
Zong W. New solution for fast axial scanning in fluorescence microscopy. LIGHT, SCIENCE & APPLICATIONS 2020; 9:199. [PMID: 33318466 PMCID: PMC7736891 DOI: 10.1038/s41377-020-00442-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
A novel technique based on the remote-focusing concept, using a galvanometer scanner combined with a self-fabricated "step mirror" or "tilted mirror" to transform fast lateral scanning into axial scanning, was reported as a new solution for fast, subcellular, 3D fluorescence imaging.
Collapse
Affiliation(s)
- Weijian Zong
- Kavli Institute for Systems Neuroscience and Centre for Neural Computation, Norwegian University of Science and Technology, Trondheim, Norway.
| |
Collapse
|
74
|
Sparks FT, Liao Z, Li W, Grosmark A, Soltesz I, Losonczy A. Hippocampal adult-born granule cells drive network activity in a mouse model of chronic temporal lobe epilepsy. Nat Commun 2020; 11:6138. [PMID: 33262339 PMCID: PMC7708476 DOI: 10.1038/s41467-020-19969-2] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2020] [Accepted: 11/10/2020] [Indexed: 02/06/2023] Open
Abstract
Temporal lobe epilepsy (TLE) is characterized by recurrent seizures driven by synchronous neuronal activity. The reorganization of the dentate gyrus (DG) in TLE may create pathological conduction pathways for synchronous discharges in the temporal lobe, though critical microcircuit-level detail is missing from this pathophysiological intuition. In particular, the relative contribution of adult-born (abGC) and mature (mGC) granule cells to epileptiform network events remains unknown. We assess dynamics of abGCs and mGCs during interictal epileptiform discharges (IEDs) in mice with TLE as well as sharp-wave ripples (SPW-Rs) in healthy mice, and find that abGCs and mGCs are desynchronized and differentially recruited by IEDs compared to SPW-Rs. We introduce a neural topic model to explain these observations, and find that epileptic DG networks organize into disjoint, cell-type specific pathological ensembles in which abGCs play an outsized role. Our results characterize identified GC subpopulation dynamics in TLE, and reveal a specific contribution of abGCs to IEDs.
Collapse
Affiliation(s)
- F T Sparks
- Department of Neuroscience, Columbia University, New York, NY, USA
- Mortimer B. Zuckerman Mind Brain Behavior Institute, Columbia University, New York, NY, USA
- The Kavli Institute for Brain Science, Columbia University, New York, NY, USA
| | - Z Liao
- Department of Neuroscience, Columbia University, New York, NY, USA
- Mortimer B. Zuckerman Mind Brain Behavior Institute, Columbia University, New York, NY, USA
- The Kavli Institute for Brain Science, Columbia University, New York, NY, USA
| | - W Li
- Department of Neuroscience, Columbia University, New York, NY, USA
- Mortimer B. Zuckerman Mind Brain Behavior Institute, Columbia University, New York, NY, USA
- The Kavli Institute for Brain Science, Columbia University, New York, NY, USA
| | - A Grosmark
- Department of Neuroscience, Columbia University, New York, NY, USA
- Mortimer B. Zuckerman Mind Brain Behavior Institute, Columbia University, New York, NY, USA
- The Kavli Institute for Brain Science, Columbia University, New York, NY, USA
| | - I Soltesz
- Department of Neurosurgery, Stanford University, Stanford, CA, USA
| | - A Losonczy
- Department of Neuroscience, Columbia University, New York, NY, USA.
- Mortimer B. Zuckerman Mind Brain Behavior Institute, Columbia University, New York, NY, USA.
- The Kavli Institute for Brain Science, Columbia University, New York, NY, USA.
| |
Collapse
|
75
|
Shipley FB, Dani N, Xu H, Deister C, Cui J, Head JP, Sadegh C, Fame RM, Shannon ML, Flores VI, Kishkovich T, Jang E, Klein EM, Goldey GJ, He K, Zhang Y, Holtzman MJ, Kirchhausen T, Wyart C, Moore CI, Andermann ML, Lehtinen MK. Tracking Calcium Dynamics and Immune Surveillance at the Choroid Plexus Blood-Cerebrospinal Fluid Interface. Neuron 2020; 108:623-639.e10. [PMID: 32961128 PMCID: PMC7847245 DOI: 10.1016/j.neuron.2020.08.024] [Citation(s) in RCA: 48] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2019] [Revised: 05/18/2020] [Accepted: 08/25/2020] [Indexed: 12/26/2022]
Abstract
The choroid plexus (ChP) epithelium is a source of secreted signaling factors in cerebrospinal fluid (CSF) and a key barrier between blood and brain. Here, we develop imaging tools to interrogate these functions in adult lateral ventricle ChP in whole-mount explants and in awake mice. By imaging epithelial cells in intact ChP explants, we observed calcium activity and secretory events that increased in frequency following delivery of serotonergic agonists. Using chronic two-photon imaging in awake mice, we observed spontaneous subcellular calcium events as well as strong agonist-evoked calcium activation and cytoplasmic secretion into CSF. Three-dimensional imaging of motility and mobility of multiple types of ChP immune cells at baseline and following immune challenge or focal injury revealed a range of surveillance and defensive behaviors. Together, these tools should help illuminate the diverse functions of this understudied body-brain interface.
Collapse
Affiliation(s)
- Frederick B Shipley
- Department of Pathology, Boston Children's Hospital, Boston, MA 02115, USA; Graduate Program in Biophysics, Harvard University, Cambridge, MA 02138, USA
| | - Neil Dani
- Department of Pathology, Boston Children's Hospital, Boston, MA 02115, USA
| | - Huixin Xu
- Department of Pathology, Boston Children's Hospital, Boston, MA 02115, USA
| | - Christopher Deister
- Carney Institute for Brain Science, Brown University, Providence, RI 02912, USA
| | - Jin Cui
- Department of Pathology, Boston Children's Hospital, Boston, MA 02115, USA
| | - Joshua P Head
- Department of Pathology, Boston Children's Hospital, Boston, MA 02115, USA
| | - Cameron Sadegh
- Department of Pathology, Boston Children's Hospital, Boston, MA 02115, USA; Department of Neurosurgery, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA
| | - Ryann M Fame
- Department of Pathology, Boston Children's Hospital, Boston, MA 02115, USA
| | - Morgan L Shannon
- Department of Pathology, Boston Children's Hospital, Boston, MA 02115, USA
| | - Vanessa I Flores
- Division of Endocrinology, Diabetes, and Metabolism, Department of Medicine, Beth Israel Deaconess Medical Center, Boston, MA 02115, USA
| | - Thomas Kishkovich
- Carney Institute for Brain Science, Brown University, Providence, RI 02912, USA
| | - Emily Jang
- Carney Institute for Brain Science, Brown University, Providence, RI 02912, USA
| | - Eric M Klein
- Carney Institute for Brain Science, Brown University, Providence, RI 02912, USA
| | - Glenn J Goldey
- Division of Endocrinology, Diabetes, and Metabolism, Department of Medicine, Beth Israel Deaconess Medical Center, Boston, MA 02115, USA
| | - Kangmin He
- Department of Cell Biology and Department of Pediatrics, Harvard Medical School, Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA 02115, USA
| | - Yong Zhang
- Pulmonary and Critical Care Medicine, Department of Medicine, Washington University, St. Louis, MO 63110, USA
| | - Michael J Holtzman
- Pulmonary and Critical Care Medicine, Department of Medicine, Washington University, St. Louis, MO 63110, USA
| | - Tomas Kirchhausen
- Department of Cell Biology and Department of Pediatrics, Harvard Medical School, Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA 02115, USA
| | - Claire Wyart
- Institut du Cerveau et de la Moelle Épinière (ICM), Sorbonne Université, Inserm U1127, CNRS UMR 7225, 75013 Paris, France
| | - Christopher I Moore
- Carney Institute for Brain Science, Brown University, Providence, RI 02912, USA
| | - Mark L Andermann
- Graduate Program in Biophysics, Harvard University, Cambridge, MA 02138, USA; Division of Endocrinology, Diabetes, and Metabolism, Department of Medicine, Beth Israel Deaconess Medical Center, Boston, MA 02115, USA.
| | - Maria K Lehtinen
- Department of Pathology, Boston Children's Hospital, Boston, MA 02115, USA; Graduate Program in Biophysics, Harvard University, Cambridge, MA 02138, USA.
| |
Collapse
|
76
|
Malkemper EP, Nimpf S, Nordmann GC, Keays DA. Neuronal circuits and the magnetic sense: central questions. ACTA ACUST UNITED AC 2020; 223:223/21/jeb232371. [PMID: 33168544 DOI: 10.1242/jeb.232371] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Magnetoreception is the ability to sense the Earth's magnetic field, which is used for orientation and navigation. Behavioural experiments have shown that it is employed by many species across all vertebrate classes; however, our understanding of how magnetic information is processed and integrated within the central nervous system is limited. In this Commentary, we review the progress in birds and rodents, highlighting the role of the vestibular and trigeminal systems as well as that of the hippocampus. We reflect on the strengths and weaknesses of the methodologies currently at our disposal, the utility of emerging technologies and identify questions that we feel are critical for the advancement of the field. We expect that magnetic circuits are likely to share anatomical motifs with other senses, which culminates in the formation of spatial maps in telencephalic areas of the brain. Specifically, we predict the existence of spatial cells that encode defined components of the Earth's magnetic field.
Collapse
Affiliation(s)
- E Pascal Malkemper
- Max Planck Research Group Neurobiology of Magnetoreception, Center of Advanced European Studies and Research (caesar), Ludwig-Erhard-Allee 2, Bonn 53175, Germany
| | - Simon Nimpf
- Research Institute of Molecular Pathology (IMP), Vienna Biocenter (VBC), Campus Vienna Biocenter 1, Vienna 1030, Austria
| | - Gregory C Nordmann
- Research Institute of Molecular Pathology (IMP), Vienna Biocenter (VBC), Campus Vienna Biocenter 1, Vienna 1030, Austria
| | - David A Keays
- Research Institute of Molecular Pathology (IMP), Vienna Biocenter (VBC), Campus Vienna Biocenter 1, Vienna 1030, Austria .,Department of Anatomy and Neuroscience, University of Melbourne, Parkville, VIC 3010, Australia.,Division of Neurobiology, Department Biology II, Ludwig-Maximilians-University Munich, Planegg-Martinsried 82152, Germany
| |
Collapse
|
77
|
Akondi V, Kowalski B, Burns SA, Dubra A. Dynamic distortion in resonant galvanometric optical scanners. OPTICA 2020; 7:1506-1513. [PMID: 34368405 PMCID: PMC8345821 DOI: 10.1364/optica.405187] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
High-speed optical systems are revolutionizing biomedical imaging in microscopy, DNA sequencing, and flow cytometry, as well as numerous other applications, including data storage, display technologies, printing, and autonomous vehicles. These systems often achieve the necessary imaging or sensing speed through the use of resonant galvanometric optical scanners. Here, we show that the optical performance of these devices suffers due to the dynamic mirror distortion that arises from the variation in torque with angular displacement. In one of two scanners tested, these distortions result in a variation of signal-to-noise (Strehl) ratio by an order of magnitude across the field of view, degrading transverse resolution by more than a factor of 2. This mirror distortion could be mitigated through the use of stiffer materials, such as beryllium or silicon carbide, at the expense of surface roughness, as these cannot be polished to the same degree of smoothness as common optical glasses. The repeatability of the dynamic distortion indicates that computational and optical corrective methods are also possible.
Collapse
Affiliation(s)
- Vyas Akondi
- Byers Eye Institute, Stanford University, Palo Alto, California 94303, USA
- Corresponding author:
| | | | - Stephen A. Burns
- Indiana University School of Optometry, Bloomington, Indiana 47405, USA
| | - Alfredo Dubra
- Byers Eye Institute, Stanford University, Palo Alto, California 94303, USA
| |
Collapse
|
78
|
Chen S, Wang Z, Zhang D, Wang A, Chen L, Cheng H, Wu R. Miniature Fluorescence Microscopy for Imaging Brain Activity in Freely-Behaving Animals. Neurosci Bull 2020; 36:1182-1190. [PMID: 32797396 PMCID: PMC7532237 DOI: 10.1007/s12264-020-00561-z] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2020] [Accepted: 05/11/2020] [Indexed: 12/11/2022] Open
Abstract
An ultimate goal of neuroscience is to decipher the principles underlying neuronal information processing at the molecular, cellular, circuit, and system levels. The advent of miniature fluorescence microscopy has furthered the quest by visualizing brain activities and structural dynamics in animals engaged in self-determined behaviors. In this brief review, we summarize recent advances in miniature fluorescence microscopy for neuroscience, focusing mostly on two mainstream solutions - miniature single-photon microscopy, and miniature two-photon microscopy. We discuss their technical advantages and limitations as well as unmet challenges for future improvement. Examples of preliminary applications are also presented to reflect on a new trend of brain imaging in experimental paradigms involving body movements, long and complex protocols, and even disease progression and aging.
Collapse
Affiliation(s)
- Shiyuan Chen
- State Key Laboratory of Membrane Biology, Institute of Molecular Medicine, Peking-Tsinghua Center for Life Sciences, PKU-Nanjing Institute of Translational Medicine, Peking University, Beijing, 100871, China
| | - Zichen Wang
- State Key Laboratory of Membrane Biology, Institute of Molecular Medicine, Peking-Tsinghua Center for Life Sciences, PKU-Nanjing Institute of Translational Medicine, Peking University, Beijing, 100871, China
| | - Dong Zhang
- Academy of Advanced Interdisciplinary Study, Peking University, Beijing, 100871, China
| | - Aiming Wang
- Department of Electronics, Peking University, Beijing, 100871, China
- State Key Laboratory of Advanced Optical Communication System and Networks, Peking University, Beijing, 100871, China
| | - Liangyi Chen
- State Key Laboratory of Membrane Biology, Institute of Molecular Medicine, Peking-Tsinghua Center for Life Sciences, PKU-Nanjing Institute of Translational Medicine, Peking University, Beijing, 100871, China
| | - Heping Cheng
- State Key Laboratory of Membrane Biology, Institute of Molecular Medicine, Peking-Tsinghua Center for Life Sciences, PKU-Nanjing Institute of Translational Medicine, Peking University, Beijing, 100871, China
| | - Runlong Wu
- State Key Laboratory of Membrane Biology, Institute of Molecular Medicine, Peking-Tsinghua Center for Life Sciences, PKU-Nanjing Institute of Translational Medicine, Peking University, Beijing, 100871, China.
| |
Collapse
|
79
|
Milosevic MM, Jang J, McKimm EJ, Zhu MH, Antic SD. In Vitro Testing of Voltage Indicators: Archon1, ArcLightD, ASAP1, ASAP2s, ASAP3b, Bongwoori-Pos6, BeRST1, FlicR1, and Chi-VSFP-Butterfly. eNeuro 2020; 7:ENEURO.0060-20.2020. [PMID: 32817120 PMCID: PMC7540930 DOI: 10.1523/eneuro.0060-20.2020] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2020] [Revised: 08/03/2020] [Accepted: 08/09/2020] [Indexed: 01/04/2023] Open
Abstract
Genetically encoded voltage indicators (GEVIs) could potentially be used for mapping neural circuits at the plane of synaptic potentials and plateau potentials-two blind spots of GCaMP-based imaging. In the last year alone, several laboratories reported significant breakthroughs in the quality of GEVIs and the efficacy of the voltage imaging equipment. One major obstacle of using well performing GEVIs in the pursuit of interesting biological data is the process of transferring GEVIs between laboratories, as their reported qualities (e.g., membrane targeting, brightness, sensitivity, optical signal quality) are often difficult to reproduce outside of the laboratory of the GEVI origin. We have tested eight available GEVIs (Archon1, ArcLightD, ASAP1, ASAP2s, ASAP3b, Bongwoori-Pos6, FlicR1, and chi-VSFP-Butterfly) and two voltage-sensitive dyes (BeRST1 and di-4-ANEPPS). We used the same microscope, lens, and optical detector, while the light sources were interchanged. GEVI voltage imaging was attempted in the following three preparations: (1) cultured neurons, (2) HEK293 cells, and (3) mouse brain slices. Systematic measurements were successful only in HEK293 cells and brain slices. Despite the significant differences in brightness and dynamic response (ON rate), all tested indicators produced reasonable optical signals in brain slices and solid in vitro quality properties, in the range initially reported by the creator laboratories. Side-by-side comparisons between GEVIs and organic dyes obtained in HEK293 cells and brain slices by a "third party" (current data) will be useful for determining the right voltage indicator for a given research application.
Collapse
Affiliation(s)
- Milena M Milosevic
- Institute for Systems Genomics, Department of Neuroscience, UConn School of Medicine, Farmington, Connecticut 06030
- Center for Laser Microscopy, Faculty of Biology, University of Belgrade, Belgrade, Serbia
| | - Jinyoung Jang
- Institute for Systems Genomics, Department of Neuroscience, UConn School of Medicine, Farmington, Connecticut 06030
| | - Eric J McKimm
- Institute for Systems Genomics, Department of Neuroscience, UConn School of Medicine, Farmington, Connecticut 06030
| | - Mei Hong Zhu
- Institute for Systems Genomics, Department of Neuroscience, UConn School of Medicine, Farmington, Connecticut 06030
| | - Srdjan D Antic
- Institute for Systems Genomics, Department of Neuroscience, UConn School of Medicine, Farmington, Connecticut 06030
| |
Collapse
|
80
|
Set lasers to image. Lab Anim (NY) 2020; 49:245-248. [DOI: 10.1038/s41684-020-0623-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
|
81
|
Functional interrogation of neural circuits with virally transmitted optogenetic tools. J Neurosci Methods 2020; 345:108905. [PMID: 32795553 DOI: 10.1016/j.jneumeth.2020.108905] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2020] [Revised: 08/03/2020] [Accepted: 08/06/2020] [Indexed: 12/12/2022]
Abstract
The vertebrate brain comprises a plethora of cell types connected by intertwined pathways. Optogenetics enriches the neuroscientific tool set for disentangling these neuronal circuits in a manner which exceeds the spatio-temporal precision of previously existing techniques. Technically, optogenetics can be divided in three types of optical and genetic combinations: (1) it is primarily understood as the manipulation of the activity of genetically modified cells (typically neurons) with light, i.e. optical actuators. (2) A second combination refers to visualizing the activity of genetically modified cells (again typically neurons), i.e. optical sensors. (3) A completely different interpretation of optogenetics refers to the light activated expression of a genetically induced construct. Here, we focus on the first two types of optogenetics, i.e. the optical actuators and sensors in an attempt to give an overview into the topic. We first cover methods to express opsins into neurons and introduce strategies of targeting specific neuronal populations in different animal species. We then summarize combinations of optogenetics with behavioral read out and neuronal imaging. Finally, we give an overview of the current state-of-the-art and an outlook on future perspectives.
Collapse
|
82
|
Quicke P, Howe CL, Song P, Jadan HV, Song C, Knöpfel T, Neil M, Dragotti PL, Schultz SR, Foust AJ. Subcellular resolution three-dimensional light-field imaging with genetically encoded voltage indicators. NEUROPHOTONICS 2020; 7:035006. [PMID: 32904628 PMCID: PMC7456658 DOI: 10.1117/1.nph.7.3.035006] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/26/2020] [Accepted: 08/07/2020] [Indexed: 05/13/2023]
Abstract
Significance: Light-field microscopy (LFM) enables high signal-to-noise ratio (SNR) and light efficient volume imaging at fast frame rates. Voltage imaging with genetically encoded voltage indicators (GEVIs) stands to particularly benefit from LFM's volumetric imaging capability due to high required sampling rates and limited probe brightness and functional sensitivity. Aim: We demonstrate subcellular resolution GEVI light-field imaging in acute mouse brain slices resolving dendritic voltage signals in three spatial dimensions. Approach: We imaged action potential-induced fluorescence transients in mouse brain slices sparsely expressing the GEVI VSFP-Butterfly 1.2 in wide-field microscopy (WFM) and LFM modes. We compared functional signal SNR and localization between different LFM reconstruction approaches and between LFM and WFM. Results: LFM enabled three-dimensional (3-D) localization of action potential-induced fluorescence transients in neuronal somata and dendrites. Nonregularized deconvolution decreased SNR with increased iteration number compared to synthetic refocusing but increased axial and lateral signal localization. SNR was unaffected for LFM compared to WFM. Conclusions: LFM enables 3-D localization of fluorescence transients, therefore eliminating the need for structures to lie in a single focal plane. These results demonstrate LFM's potential for studying dendritic integration and action potential propagation in three spatial dimensions.
Collapse
Affiliation(s)
- Peter Quicke
- Imperial College London, Department of Bioengineering, London, United Kingdom
- Imperial College London, Centre for Neurotechnology, London, United Kingdom
| | - Carmel L. Howe
- Imperial College London, Department of Bioengineering, London, United Kingdom
- Imperial College London, Centre for Neurotechnology, London, United Kingdom
| | - Pingfan Song
- Imperial College London, Department of Electrical and Electronic Engineering, London, United Kingdom
| | - Herman V. Jadan
- Imperial College London, Department of Electrical and Electronic Engineering, London, United Kingdom
| | - Chenchen Song
- Imperial College London, Department of Brain Sciences, London, United Kingdom
| | - Thomas Knöpfel
- Imperial College London, Centre for Neurotechnology, London, United Kingdom
- Imperial College London, Department of Brain Sciences, London, United Kingdom
| | - Mark Neil
- Imperial College London, Centre for Neurotechnology, London, United Kingdom
- Imperial College London, Department of Physics, London, United Kingdom
| | - Pier L. Dragotti
- Imperial College London, Department of Electrical and Electronic Engineering, London, United Kingdom
| | - Simon R. Schultz
- Imperial College London, Department of Bioengineering, London, United Kingdom
- Imperial College London, Centre for Neurotechnology, London, United Kingdom
- Address all correspondence to Simon R. Schultz, E-mail: ; Amanda J. Foust, E-mail:
| | - Amanda J. Foust
- Imperial College London, Department of Bioengineering, London, United Kingdom
- Imperial College London, Centre for Neurotechnology, London, United Kingdom
- Address all correspondence to Simon R. Schultz, E-mail: ; Amanda J. Foust, E-mail:
| |
Collapse
|
83
|
Delestro F, Scheunemann L, Pedrazzani M, Tchenio P, Preat T, Genovesio A. In vivo large-scale analysis of Drosophila neuronal calcium traces by automated tracking of single somata. Sci Rep 2020; 10:7153. [PMID: 32346011 PMCID: PMC7188892 DOI: 10.1038/s41598-020-64060-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2019] [Accepted: 04/07/2020] [Indexed: 01/30/2023] Open
Abstract
How does the concerted activity of neuronal populations shape behavior? Impediments to address this question are primarily due to critical experimental barriers. An integrated perspective on large scale neural information processing requires an in vivo approach that can combine the advantages of exhaustively observing all neurons dedicated to a given type of stimulus, and simultaneously achieve a resolution that is precise enough to capture individual neuron activity. Current experimental data from in vivo observations are either restricted to a small fraction of the total number of neurons, or are based on larger brain volumes but at a low spatial and temporal resolution. Consequently, fundamental questions as to how sensory information is represented on a population scale remain unanswered. In Drosophila melanogaster, the mushroom body (MB) represents an excellent model to analyze sensory coding and memory plasticity. In this work, we present an experimental setup coupled with a dedicated computational method that provides in vivo measurements of the activity of hundreds of densely packed somata uniformly spread in the MB. We exploit spinning-disk confocal 3D imaging over time of the whole MB cell body layer in vivo while it is exposed to olfactory stimulation. Importantly, to derive individual signal from densely packed somata, we have developed a fully automated image analysis procedure that takes advantage of the specificities of our data. After anisotropy correction, our approach operates a dedicated spot detection and registration over the entire time sequence to transform trajectories to identifiable clusters. This enabled us to discard spurious detections and reconstruct missing ones in a robust way. We demonstrate that this approach outperformed existing methods in this specific context and made possible high-throughput analysis of approximately 500 single somata uniformly spread over the MB in various conditions. Applying this approach, we find that learned experiences change the population code of odor representations in the MB. After long-term memory (LTM) formation, we quantified an increase in responsive somata count and a stable single neuron signal. We predict that this method, which should further enable studying the population pattern of neuronal activity, has the potential to uncover fine details of sensory processing and memory plasticity.
Collapse
Affiliation(s)
- Felipe Delestro
- Computational Bioimaging and Bioinformatics, IBENS, ENS, INSERM, CNRS, PSL, 46 rue d'Ulm, 75005, Paris, France
| | - Lisa Scheunemann
- Genes and Dynamics of Memory Systems, Brain Plasticity Unit, CNRS, ESPCI Paris, PSL, 10 Rue Vauquelin, 75005, Paris, France
| | - Mélanie Pedrazzani
- Genes and Dynamics of Memory Systems, Brain Plasticity Unit, CNRS, ESPCI Paris, PSL, 10 Rue Vauquelin, 75005, Paris, France
| | - Paul Tchenio
- Genes and Dynamics of Memory Systems, Brain Plasticity Unit, CNRS, ESPCI Paris, PSL, 10 Rue Vauquelin, 75005, Paris, France
| | - Thomas Preat
- Genes and Dynamics of Memory Systems, Brain Plasticity Unit, CNRS, ESPCI Paris, PSL, 10 Rue Vauquelin, 75005, Paris, France.
| | - Auguste Genovesio
- Computational Bioimaging and Bioinformatics, IBENS, ENS, INSERM, CNRS, PSL, 46 rue d'Ulm, 75005, Paris, France.
| |
Collapse
|
84
|
Papagiakoumou E, Ronzitti E, Emiliani V. Scanless two-photon excitation with temporal focusing. Nat Methods 2020; 17:571-581. [PMID: 32284609 DOI: 10.1038/s41592-020-0795-y] [Citation(s) in RCA: 60] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2019] [Accepted: 02/28/2020] [Indexed: 11/09/2022]
Abstract
Temporal focusing, with its ability to focus light in time, enables scanless illumination of large surface areas at the sample with micrometer axial confinement and robust propagation through scattering tissue. In conventional two-photon microscopy, widely used for the investigation of intact tissue in live animals, images are formed by point scanning of a spatially focused pulsed laser beam, resulting in limited temporal resolution of the excitation. Replacing point scanning with temporally focused widefield illumination removes this limitation and represents an important milestone in two-photon microscopy. Temporal focusing uses a diffusive or dispersive optical element placed in a plane conjugate to the objective focal plane to generate position-dependent temporal pulse broadening that enables axially confined multiphoton absorption, without the need for tight spatial focusing. Many techniques have benefitted from temporal focusing, including scanless imaging, super-resolution imaging, photolithography, uncaging of caged neurotransmitters and control of neuronal activity via optogenetics.
Collapse
Affiliation(s)
- Eirini Papagiakoumou
- Wavefront-Engineering Microscopy Group, Photonics Department, Institut de la Vision, Sorbonne University, Inserm S968, CNRS UMR7210, Fondation Voir et Entendre, Paris, France
| | - Emiliano Ronzitti
- Wavefront-Engineering Microscopy Group, Photonics Department, Institut de la Vision, Sorbonne University, Inserm S968, CNRS UMR7210, Fondation Voir et Entendre, Paris, France
| | - Valentina Emiliani
- Wavefront-Engineering Microscopy Group, Photonics Department, Institut de la Vision, Sorbonne University, Inserm S968, CNRS UMR7210, Fondation Voir et Entendre, Paris, France.
| |
Collapse
|
85
|
Simultaneous multiplane imaging with reverberation two-photon microscopy. Nat Methods 2020; 17:283-286. [PMID: 32042186 DOI: 10.1038/s41592-019-0728-9] [Citation(s) in RCA: 50] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2019] [Accepted: 12/19/2019] [Indexed: 11/08/2022]
Abstract
Multiphoton microscopy has gained enormous popularity because of its unique capacity to provide high-resolution images from deep within scattering tissue. Here, we demonstrate video-rate multiplane imaging with two-photon microscopy by performing near-instantaneous axial scanning while maintaining three-dimensional micrometer-scale resolution. Our technique, termed reverberation microscopy, enables the monitoring of neuronal populations over large depth ranges and can be implemented as a simple add-on to a conventional design.
Collapse
|
86
|
Montague SJ, Lim YJ, Lee WM, Gardiner EE. Imaging Platelet Processes and Function-Current and Emerging Approaches for Imaging in vitro and in vivo. Front Immunol 2020; 11:78. [PMID: 32082328 PMCID: PMC7005007 DOI: 10.3389/fimmu.2020.00078] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2019] [Accepted: 01/13/2020] [Indexed: 12/22/2022] Open
Abstract
Platelets are small anucleate cells that are essential for many biological processes including hemostasis, thrombosis, inflammation, innate immunity, tumor metastasis, and wound healing. Platelets circulate in the blood and in order to perform all of their biological roles, platelets must be able to arrest their movement at an appropriate site and time. Our knowledge of how platelets achieve this has expanded as our ability to visualize and quantify discreet platelet events has improved. Platelets are exquisitely sensitive to changes in blood flow parameters and so the visualization of rapid intricate platelet processes under conditions found in flowing blood provides a substantial challenge to the platelet imaging field. The platelet's size (~2 μm), rapid activation (milliseconds), and unsuitability for genetic manipulation, means that appropriate imaging tools are limited. However, with the application of modern imaging systems to study platelet function, our understanding of molecular events mediating platelet adhesion from a single-cell perspective, to platelet recruitment and activation, leading to thrombus (clot) formation has expanded dramatically. This review will discuss current platelet imaging techniques in vitro and in vivo, describing how the advancements in imaging have helped answer/expand on platelet biology with a particular focus on hemostasis. We will focus on platelet aggregation and thrombus formation, and how platelet imaging has enhanced our understanding of key events, highlighting the knowledge gained through the application of imaging modalities to experimental models in vitro and in vivo. Furthermore, we will review the limitations of current imaging techniques, and questions in thrombosis research that remain to be addressed. Finally, we will speculate how the same imaging advancements might be applied to the imaging of other vascular cell biological functions and visualization of dynamic cell-cell interactions.
Collapse
Affiliation(s)
- Samantha J. Montague
- ACRF Department of Cancer Biology and Therapeutics, The John Curtin School of Medical Research, The Australian National University, Canberra, ACT, Australia
| | - Yean J. Lim
- ACRF Department of Cancer Biology and Therapeutics, The John Curtin School of Medical Research, The Australian National University, Canberra, ACT, Australia
- Research School of Electrical, Energy and Materials Engineering, The Australian National University, Canberra, ACT, Australia
| | - Woei M. Lee
- ACRF Department of Cancer Biology and Therapeutics, The John Curtin School of Medical Research, The Australian National University, Canberra, ACT, Australia
- Research School of Electrical, Energy and Materials Engineering, The Australian National University, Canberra, ACT, Australia
| | - Elizabeth E. Gardiner
- ACRF Department of Cancer Biology and Therapeutics, The John Curtin School of Medical Research, The Australian National University, Canberra, ACT, Australia
| |
Collapse
|
87
|
Wang T, Wu C, Ouzounov DG, Gu W, Xia F, Kim M, Yang X, Warden MR, Xu C. Quantitative analysis of 1300-nm three-photon calcium imaging in the mouse brain. eLife 2020; 9:53205. [PMID: 31999253 PMCID: PMC7028383 DOI: 10.7554/elife.53205] [Citation(s) in RCA: 60] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2019] [Accepted: 01/29/2020] [Indexed: 12/12/2022] Open
Abstract
1300 nm three-photon calcium imaging has emerged as a useful technique to allow calcium imaging in deep brain regions. Application to large-scale neural activity imaging entails a careful balance between recording fidelity and perturbation to the sample. We calculated and experimentally verified the excitation pulse energy to achieve the minimum photon count required for the detection of calcium transients in GCaMP6s-expressing neurons for 920 nm two-photon and 1320 nm three-photon excitation. By considering the combined effects of in-focus signal attenuation and out-of-focus background generation, we quantified the cross-over depth beyond which three-photon microscopy outpeforms two-photon microscopy in recording fidelity. Brain tissue heating by continuous three-photon imaging was simulated with Monte Carlo method and experimentally validated with immunohistochemistry. Increased immunoreactivity was observed with 150 mW excitation power at 1 and 1.2 mm imaging depths. Our analysis presents a translatable model for the optimization of three-photon calcium imaging based on experimentally tractable parameters.
Collapse
Affiliation(s)
- Tianyu Wang
- School of Applied and Engineering Physics, Cornell University, Ithaca, United States
| | - Chunyan Wu
- School of Applied and Engineering Physics, Cornell University, Ithaca, United States.,College of Veterinary Medicine, Cornell University, Ithaca, United States
| | - Dimitre G Ouzounov
- School of Applied and Engineering Physics, Cornell University, Ithaca, United States
| | - Wenchao Gu
- Department of Neurobiology and Behavior, Cornell University, Ithaca, United States
| | - Fei Xia
- Meining School of Biomedical Engineering, Cornell University, Ithaca, United States
| | - Minsu Kim
- College of Human Ecology, Cornell University, Ithaca, United States
| | - Xusan Yang
- School of Applied and Engineering Physics, Cornell University, Ithaca, United States
| | - Melissa R Warden
- Department of Neurobiology and Behavior, Cornell University, Ithaca, United States
| | - Chris Xu
- School of Applied and Engineering Physics, Cornell University, Ithaca, United States
| |
Collapse
|
88
|
Chakraborty T, Chen B, Daetwyler S, Chang BJ, Vanderpoorten O, Sapoznik E, Kaminski CF, Knowles TPJ, Dean KM, Fiolka R. Converting lateral scanning into axial focusing to speed up three-dimensional microscopy. LIGHT, SCIENCE & APPLICATIONS 2020; 9:165. [PMID: 33024553 PMCID: PMC7501866 DOI: 10.1038/s41377-020-00401-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/18/2020] [Revised: 08/25/2020] [Accepted: 09/02/2020] [Indexed: 05/04/2023]
Abstract
In optical microscopy, the slow axial scanning rate of the objective or the sample has traditionally limited the speed of volumetric imaging. Recently, by conjugating either a movable mirror to the image plane in a remote-focusing geometry or an electrically tuneable lens (ETL) to the back focal plane, rapid axial scanning has been achieved. However, mechanical actuation of a mirror limits the axial scanning rate (usually only 10-100 Hz for piezoelectric or voice coil-based actuators), while ETLs introduce spherical and higher-order aberrations that prevent high-resolution imaging. In an effort to overcome these limitations, we introduce a novel optical design that transforms a lateral-scan motion into a spherical aberration-free axial scan that can be used for high-resolution imaging. Using a galvanometric mirror, we scan a laser beam laterally in a remote-focusing arm, which is then back-reflected from different heights of a mirror in the image space. We characterize the optical performance of this remote-focusing technique and use it to accelerate axially swept light-sheet microscopy by an order of magnitude, allowing the quantification of rapid vesicular dynamics in three dimensions. We also demonstrate resonant remote focusing at 12 kHz with a two-photon raster-scanning microscope, which allows rapid imaging of brain tissues and zebrafish cardiac dynamics with diffraction-limited resolution.
Collapse
Affiliation(s)
- Tonmoy Chakraborty
- Department of Cell Biology, UT Southwestern Medical Center, Dallas, TX USA
- Department of Physics and Astronomy, University of New Mexico, Albuquerque, NM USA
| | - Bingying Chen
- Department of Cell Biology, UT Southwestern Medical Center, Dallas, TX USA
| | - Stephan Daetwyler
- Department of Cell Biology, UT Southwestern Medical Center, Dallas, TX USA
| | - Bo-Jui Chang
- Department of Cell Biology, UT Southwestern Medical Center, Dallas, TX USA
| | - Oliver Vanderpoorten
- Department of Chemical Engineering and Biotechnology, University of Cambridge, Cambridge, CB3 0AS UK
| | - Etai Sapoznik
- Department of Cell Biology, UT Southwestern Medical Center, Dallas, TX USA
| | - Clemens F. Kaminski
- Department of Chemical Engineering and Biotechnology, University of Cambridge, Cambridge, CB3 0AS UK
| | - Tuomas P. J. Knowles
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW UK
| | - Kevin M. Dean
- Department of Cell Biology, UT Southwestern Medical Center, Dallas, TX USA
| | - Reto Fiolka
- Department of Cell Biology, UT Southwestern Medical Center, Dallas, TX USA
- Lyda Hill Department of Bioinformatics, UT Southwestern Medical Center, Dallas, TX USA
| |
Collapse
|
89
|
Zhang Y, Yao L, Yang F, Yang S, Edathodathil A, Xi W, Roe AW, Li P. INS-fOCT: a label-free, all-optical method for simultaneously manipulating and mapping brain function. NEUROPHOTONICS 2020; 7:015014. [PMID: 32258220 PMCID: PMC7108754 DOI: 10.1117/1.nph.7.1.015014] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/31/2019] [Accepted: 03/18/2020] [Indexed: 06/11/2023]
Abstract
Significance: Current approaches to stimulating and recording from the brain have combined electrical or optogenetic stimulation with recording approaches, such as two-photon, electrophysiology (EP), and optical intrinsic signal imaging (OISI). However, we lack a label-free, all-optical approach with high spatial and temporal resolution. Aim: To develop a label-free, all-optical method that simultaneously manipulates and images brain function using pulsed near-infrared light (INS) and functional optical coherence tomography (fOCT), respectively. Approach: We built a coregistered INS, fOCT, and OISI system. OISI and EP recordings were employed to validate the fOCT signals. Results: The fOCT signal was reliable and regional, and the area of fOCT signal corresponded with the INS-activated region. The fOCT signal was in synchrony with the INS onset time with a delay of ∼ 30 ms . The magnitude of fOCT signal exhibited a linear correlation with the INS radiant exposure. The significant correlation between the fOCT signal and INS was further supported by OISI and EP recordings. Conclusions: The proposed fiber-based, all-optical INS-fOCT method allows simultaneous stimulation and mapping without the risk of interchannel cross-talk and the requirement of contrast injection and viral transfection and offers a deep penetration depth and high resolution.
Collapse
Affiliation(s)
- Ying Zhang
- Zhejiang University, College of Optical Science and Engineering, State Key Lab of Modern Optical Instrumentation, Hangzhou, China
- Zhejiang University, Interdisciplinary Institute of Neuroscience and Technology, School of Medicine, Hangzhou, Zhejiang, China
| | - Lin Yao
- Zhejiang University, College of Optical Science and Engineering, State Key Lab of Modern Optical Instrumentation, Hangzhou, China
| | - Fen Yang
- Zhejiang University, Interdisciplinary Institute of Neuroscience and Technology, School of Medicine, Hangzhou, Zhejiang, China
| | - Shanshan Yang
- Zhejiang University, College of Optical Science and Engineering, State Key Lab of Modern Optical Instrumentation, Hangzhou, China
| | - Akshay Edathodathil
- Zhejiang University, Interdisciplinary Institute of Neuroscience and Technology, School of Medicine, Hangzhou, Zhejiang, China
| | - Wang Xi
- Zhejiang University, Interdisciplinary Institute of Neuroscience and Technology, School of Medicine, Hangzhou, Zhejiang, China
| | - Anna Wang Roe
- Zhejiang University, Interdisciplinary Institute of Neuroscience and Technology, School of Medicine, Hangzhou, Zhejiang, China
- Zhejiang University, Key Laboratory of Biomedical Engineering of Ministry of Education, Hangzhou, Zhejiang, China
- Oregon Health & Sciences University, Oregon National Primate Research Center, Division of Neuroscience, Beaverton, Oregon, United States
| | - Peng Li
- Zhejiang University, College of Optical Science and Engineering, State Key Lab of Modern Optical Instrumentation, Hangzhou, China
- Zhejiang University, International Research Center for Advanced Photonics, Hangzhou, Zhejiang, China
| |
Collapse
|
90
|
An adaptive excitation source for high-speed multiphoton microscopy. Nat Methods 2019; 17:163-166. [PMID: 31792434 PMCID: PMC7004891 DOI: 10.1038/s41592-019-0663-9] [Citation(s) in RCA: 52] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2018] [Accepted: 10/24/2019] [Indexed: 11/25/2022]
Abstract
Optical imaging at high spatial and temporal resolution is important to understand brain function. We demonstrate an adaptive femtosecond excitation source that only illuminates the region of interest. We show that the source reduces the power requirement for two- or three-photon imaging of brain activity in awake mice by more than 30 times. The adaptive excitation source represents a new direction in the development of high speed imaging systems.
Collapse
|
91
|
Brain mapping at high resolutions: Challenges and opportunities. CURRENT OPINION IN BIOMEDICAL ENGINEERING 2019. [DOI: 10.1016/j.cobme.2019.10.009] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
|
92
|
Clough M, Chen JL. CELLULAR RESOLUTION IMAGING OF NEURONAL ACTIVITY ACROSS SPACE AND TIME IN THE MAMMALIAN BRAIN. CURRENT OPINION IN BIOMEDICAL ENGINEERING 2019; 12:95-101. [PMID: 32104747 DOI: 10.1016/j.cobme.2019.11.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
While the action potential has long been understood to be the fundamental bit of information in brain, how these spikes encode representations of stimuli and drive behavior remains unclear. Large-scale neuronal recordings with cellular and spike-time resolution spanning multiple brain regions are needed to capture relevant network dynamics that can be sparse and distributed across the population. This review focuses on recent advancements in optical methods that have pushed the boundaries for simultaneous population recordings at increasing volumes, distances, depths, and speeds. The integration of these technologies will be critical for overcoming fundamental limits in the pursuit of whole brain imaging in mammalian species.
Collapse
Affiliation(s)
- Mitchell Clough
- Department of Biomedical Engineering, Boston University, Boston, USA.,Department of Biology, Boston University, Boston, USA
| | - Jerry L Chen
- Department of Biomedical Engineering, Boston University, Boston, USA.,Department of Biology, Boston University, Boston, USA.,Center for Neurophotonics, Boston University, Boston, USA
| |
Collapse
|
93
|
Lecoq J, Orlova N, Grewe BF. Wide. Fast. Deep: Recent Advances in Multiphoton Microscopy of In Vivo Neuronal Activity. J Neurosci 2019; 39:9042-9052. [PMID: 31578235 PMCID: PMC6855689 DOI: 10.1523/jneurosci.1527-18.2019] [Citation(s) in RCA: 60] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2019] [Revised: 09/27/2019] [Accepted: 09/27/2019] [Indexed: 01/04/2023] Open
Abstract
Multiphoton microscopy (MPM) has emerged as one of the most powerful and widespread technologies to monitor the activity of neuronal networks in awake, behaving animals over long periods of time. MPM development spanned across decades and crucially depended on the concurrent improvement of calcium indicators that report neuronal activity as well as surgical protocols, head fixation approaches, and innovations in optics and microscopy technology. Here we review the last decade of MPM development and highlight how in vivo imaging has matured and diversified, making it now possible to concurrently monitor thousands of neurons across connected brain areas or, alternatively, small local networks with sampling rates in the kilohertz range. This review includes different laser scanning approaches, such as multibeam technologies as well as recent developments to image deeper into neuronal tissues using new, long-wavelength laser sources. As future development will critically depend on our ability to resolve and discriminate individual neuronal spikes, we will also describe a simple framework that allows performing quantitative comparisons between the reviewed MPM instruments. Finally, we provide our own opinion on how the most recent MPM developments can be leveraged at scale to enable the next generation of discoveries in brain function.
Collapse
Affiliation(s)
- Jérôme Lecoq
- Allen Institute for Brain Science, Seattle 98109, Washington,
| | - Natalia Orlova
- Allen Institute for Brain Science, Seattle 98109, Washington
| | - Benjamin F Grewe
- Institute of Neuroinformatics, UZH and ETH Zurich, Zurich 8057, Switzerland
- Department of Electrical Engineering and Information Technology, ETH Zurich, Zurich 8092, Switzerland, and
- Faculty of Sciences, University of Zurich, Zurich 8057, Switzerland
| |
Collapse
|
94
|
Optical voltage imaging in neurons: moving from technology development to practical tool. Nat Rev Neurosci 2019; 20:719-727. [PMID: 31705060 DOI: 10.1038/s41583-019-0231-4] [Citation(s) in RCA: 94] [Impact Index Per Article: 18.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/30/2019] [Indexed: 12/13/2022]
Abstract
A central goal in neuroscience is to determine how the brain's neuronal circuits generate perception, cognition and emotions and how these lead to appropriate behavioural actions. A methodological platform based on genetically encoded voltage indicators (GEVIs) that enables the monitoring of large-scale circuit dynamics has brought us closer to this ambitious goal. This Review provides an update on the current state of the art and the prospects of emerging optical GEVI imaging technologies.
Collapse
|
95
|
|
96
|
Choi J, Taal AJ, Pollmann EH, Lee C, Kim K, Moreaux LC, Roukes ML, Shepard KL. A 512-Pixel, 51-kHz-Frame-Rate, Dual-Shank, Lens-less, Filter-less Single Photon Avalanche Diode CMOS Neural Imaging Probe. IEEE JOURNAL OF SOLID-STATE CIRCUITS 2019; 54:2957-2968. [PMID: 31798187 PMCID: PMC6886722 DOI: 10.1109/jssc.2019.2941529] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
We present an implantable single photon shank-based imager, monolithically integrated onto a single CMOS IC. The imager comprises of 512 single photon avalanche diodes distributed along two shanks, with a 6-bit depth in-pixel memory and an on-chip digital-to-time converter. To scale down the system to a minimally invasive form factor, we substitute optical filtering and focusing elements with a time-gated, angle-sensitive detection system. The imager computationally reconstructs the position of fluorescent sources within a three-dimensional volume of 3.4 mm × 600 µm × 400 µm.
Collapse
Affiliation(s)
- Jaebin Choi
- Electrical Engineering Department, Columbia University, New York, NY, USA
| | - Adriaan J Taal
- Electrical Engineering Department, Columbia University, New York, NY, USA
| | - Eric H Pollmann
- Electrical Engineering Department, Columbia University, New York, NY, USA
| | - Changhyuk Lee
- Brain Science Institute, Korea Institute of Science and Technology, Seoul, South Korea
| | - Kukjoo Kim
- Electronics and Telecommunications Research Institute, Daejeon, South Korea
| | | | | | - Kenneth L Shepard
- Bioelectronic Systems Laboratories, Columbia University, New York, NY, USA
| |
Collapse
|
97
|
Takasaki KT, Tsyboulski D, Waters J. Dual-plane 3-photon microscopy with remote focusing. BIOMEDICAL OPTICS EXPRESS 2019; 10:5585-5599. [PMID: 31799032 PMCID: PMC6865092 DOI: 10.1364/boe.10.005585] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/09/2019] [Revised: 09/06/2019] [Accepted: 09/27/2019] [Indexed: 05/04/2023]
Abstract
3-photon excitation enables in vivo fluorescence microscopy deep in densely labeled and highly scattering samples. To date, 3-photon excitation has been restricted to scanning a single focus, limiting the speed of volume acquisition. Here, for the first time to our knowledge, we implemented and characterized dual-plane 3-photon microscopy with temporal multiplexing and remote focusing, and performed simultaneous in vivo calcium imaging of two planes beyond 600 µm deep in the cortex of a pan-excitatory GCaMP6s transgenic mouse with a per-plane framerate of 7 Hz and an effective 2 MHz laser repetition rate. This method is a straightforward and generalizable modification to single-focus 3PE systems, doubling the rate of volume (column) imaging with off-the-shelf components and minimal technical constraints.
Collapse
Affiliation(s)
- Kevin T. Takasaki
- Allen Institute for Brain Science, 615 Westlake Ave N, Seattle, WA 98109, USA
| | - Dmitri Tsyboulski
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA 20147, USA
| | - Jack Waters
- Allen Institute for Brain Science, 615 Westlake Ave N, Seattle, WA 98109, USA
| |
Collapse
|
98
|
Wijesinghe P, Escobet-Montalbán A, Chen M, Munro PRT, Dholakia K. Optimal compressive multiphoton imaging at depth using single-pixel detection. OPTICS LETTERS 2019; 44:4981-4984. [PMID: 31613244 DOI: 10.1364/ol.44.004981] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/03/2019] [Accepted: 08/01/2019] [Indexed: 06/10/2023]
Abstract
Compressive sensing can overcome the Nyquist criterion and record images with a fraction of the usual number of measurements required. However, conventional measurement bases are susceptible to diffraction and scattering, prevalent in high-resolution microscopy. In this Letter, we explore the random Morlet basis as an optimal set for compressive multiphoton imaging, based on its ability to minimize the space-frequency uncertainty. We implement this approach for wide-field multiphoton microscopy with single-pixel detection, which allows imaging through turbid media without correction. The Morlet basis promises a route for rapid acquisition with lower photodamage.
Collapse
|
99
|
Liu R, Ball N, Brockill J, Kuan L, Millman D, White C, Leon A, Williams D, Nishiwaki S, de Vries S, Larkin J, Sullivan D, Slaughterbeck C, Farrell C, Saggau P. Aberration-free multi-plane imaging of neural activity from the mammalian brain using a fast-switching liquid crystal spatial light modulator. BIOMEDICAL OPTICS EXPRESS 2019; 10:5059-5080. [PMID: 31646030 PMCID: PMC6788611 DOI: 10.1364/boe.10.005059] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/02/2019] [Accepted: 09/03/2019] [Indexed: 05/27/2023]
Abstract
We report a novel two-photon fluorescence microscope based on a fast-switching liquid crystal spatial light modulator and a pair of galvo-resonant scanners for large-scale recording of neural activity from the mammalian brain. The spatial light modulator is used to achieve fast switching between different imaging planes in multi-plane imaging and correct for intrinsic optical aberrations associated with this imaging scheme. The utilized imaging technique is capable of monitoring the neural activity from large populations of neurons with known coordinates spread across different layers of the neocortex in awake and behaving mice, regardless of the fluorescent labeling strategy. During each imaging session, all visual stimulus driven somatic activity could be recorded in the same behavior state. We observed heterogeneous response to different types of visual stimuli from ∼ 3,300 excitatory neurons reaching from layer II/III to V of the striate cortex.
Collapse
Affiliation(s)
- Rui Liu
- Allen Institute for Brain Science, 615 Westlake Ave, Seattle, WA 98109, USA
- Now with GE Healthcare Bio-Sciences Corp, 1040 12th Ave NW, Issaquah, WA, 98027, USA
| | - Neil Ball
- Allen Institute for Brain Science, 615 Westlake Ave, Seattle, WA 98109, USA
| | - James Brockill
- Allen Institute for Brain Science, 615 Westlake Ave, Seattle, WA 98109, USA
| | - Leonard Kuan
- Allen Institute for Brain Science, 615 Westlake Ave, Seattle, WA 98109, USA
| | - Daniel Millman
- Allen Institute for Brain Science, 615 Westlake Ave, Seattle, WA 98109, USA
| | - Cassandra White
- Allen Institute for Brain Science, 615 Westlake Ave, Seattle, WA 98109, USA
| | - Arielle Leon
- Allen Institute for Brain Science, 615 Westlake Ave, Seattle, WA 98109, USA
| | - Derric Williams
- Allen Institute for Brain Science, 615 Westlake Ave, Seattle, WA 98109, USA
| | - Shig Nishiwaki
- Allen Institute for Brain Science, 615 Westlake Ave, Seattle, WA 98109, USA
| | - Saskia de Vries
- Allen Institute for Brain Science, 615 Westlake Ave, Seattle, WA 98109, USA
| | - Josh Larkin
- Allen Institute for Brain Science, 615 Westlake Ave, Seattle, WA 98109, USA
| | - David Sullivan
- Allen Institute for Brain Science, 615 Westlake Ave, Seattle, WA 98109, USA
| | | | - Colin Farrell
- Allen Institute for Brain Science, 615 Westlake Ave, Seattle, WA 98109, USA
| | - Peter Saggau
- Allen Institute for Brain Science, 615 Westlake Ave, Seattle, WA 98109, USA
- Now with Italian Institute of Technology, Via Morego 30, 16163 Genoa, Italy
| |
Collapse
|
100
|
WANG X, LI P, ZHANG W, TANG B. Recent Advances in Fluorescence Imaging of Bioactive Molecules in Neurons and in Vivo. CHINESE JOURNAL OF ANALYTICAL CHEMISTRY 2019. [DOI: 10.1016/s1872-2040(19)61191-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
|