101
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Adesnik H, Naka A. Cracking the Function of Layers in the Sensory Cortex. Neuron 2019; 100:1028-1043. [PMID: 30521778 DOI: 10.1016/j.neuron.2018.10.032] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2018] [Revised: 08/08/2018] [Accepted: 10/18/2018] [Indexed: 12/24/2022]
Abstract
Understanding how cortical activity generates sensory perceptions requires a detailed dissection of the function of cortical layers. Despite our relatively extensive knowledge of their anatomy and wiring, we have a limited grasp of what each layer contributes to cortical computation. We need to develop a theory of cortical function that is rooted solidly in each layer's component cell types and fine circuit architecture and produces predictions that can be validated by specific perturbations. Here we briefly review the progress toward such a theory and suggest an experimental road map toward this goal. We discuss new methods for the all-optical interrogation of cortical layers, for correlating in vivo function with precise identification of transcriptional cell type, and for mapping local and long-range activity in vivo with synaptic resolution. The new technologies that can crack the function of cortical layers are finally on the immediate horizon.
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Affiliation(s)
- Hillel Adesnik
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, USA; The Helen Wills Neuroscience Institute, University of California, Berkeley, Berkeley, CA, USA.
| | - Alexander Naka
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, USA; The Helen Wills Neuroscience Institute, University of California, Berkeley, Berkeley, CA, USA
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102
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Kozawa Y, Sato S. Light needle microscopy with spatially transposed detection for axially resolved volumetric imaging. Sci Rep 2019; 9:11687. [PMID: 31406209 PMCID: PMC6690918 DOI: 10.1038/s41598-019-48265-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2019] [Accepted: 08/01/2019] [Indexed: 11/14/2022] Open
Abstract
The demand for rapid three-dimensional volumetric imaging is increasing in various fields, including life science. Laser scanning fluorescence microscopy has been widely employed for this purpose; however, a volumetric image is constructed by two-dimensional image stacking with a varying observation plane, ultimately limiting the acquisition speed. Here we propose a method enabling axially resolved volumetric imaging without a moving observation plane in the framework of laser scanning microscopy. A scanning light needle spot with an extended focal depth provides excitation, which normally produces a deep focus image with a loss of depth information. In our method, the depth information is retrieved from transposed lateral information on an array detector by utilising non-diffracting and self-bending characteristics imposed on fluorescent signals. This technique, implemented in two-photon microscopy, achieves truly volumetric images constructed from a single raster scan of a light needle, which has the capability to significantly reduce the acquisition time.
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Affiliation(s)
- Yuichi Kozawa
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, 2-1-1 Katahira, Aoba-ku, Sendai, 980-8577, Japan.
| | - Shunichi Sato
- Institute of Multidisciplinary Research for Advanced Materials, Tohoku University, 2-1-1 Katahira, Aoba-ku, Sendai, 980-8577, Japan
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103
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Kazemipour A, Novak O, Flickinger D, Marvin JS, Abdelfattah AS, King J, Borden PM, Kim JJ, Al-Abdullatif SH, Deal PE, Miller EW, Schreiter ER, Druckmann S, Svoboda K, Looger LL, Podgorski K. Kilohertz frame-rate two-photon tomography. Nat Methods 2019; 16:778-786. [PMID: 31363222 PMCID: PMC6754705 DOI: 10.1038/s41592-019-0493-9] [Citation(s) in RCA: 81] [Impact Index Per Article: 16.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2019] [Accepted: 06/14/2019] [Indexed: 11/25/2022]
Abstract
Point-scanning two-photon microscopy enables high-resolution imaging within scattering specimens such as the mammalian brain, but sequential acquisition of voxels fundamentally limits its speed. We developed a two-photon imaging technique that scans lines of excitation across a focal plane at multiple angles and computationally recovers high-resolution images, attaining voxel rates of over 1 billion Hz in structured samples. Using a static image as a prior for recording neural activity, we imaged visually evoked and spontaneous glutamate release across hundreds of dendritic spines in mice at depths over 250 µm and frame rates over 1 kHz. Dendritic glutamate transients in anesthetized mice are synchronized within spatially contiguous domains spanning tens of micrometers at frequencies ranging from 1-100 Hz. We demonstrate millisecond-resolved recordings of acetylcholine and voltage indicators, three-dimensional single-particle tracking and imaging in densely labeled cortex. Our method surpasses limits on the speed of raster-scanned imaging imposed by fluorescence lifetime.
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Affiliation(s)
- Abbas Kazemipour
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA
- Department of Neurobiology, Stanford University, Stanford, CA, USA
| | - Ondrej Novak
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA
- Second Medical Faculty, Charles University, Prague, Czech Republic
| | - Daniel Flickinger
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA
| | - Jonathan S Marvin
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA
| | | | | | - Philip M Borden
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA
| | - Jeong Jun Kim
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA
| | | | - Parker E Deal
- Department of Chemistry, University of California, Berkeley, Berkeley, CA, USA
| | - Evan W Miller
- Department of Chemistry, University of California, Berkeley, Berkeley, CA, USA
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, USA
- Helen Wills Neuroscience Institute, University of California, Berkeley, Berkeley, CA, USA
| | - Eric R Schreiter
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA
| | - Shaul Druckmann
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA
- Department of Neurobiology, Stanford University, Stanford, CA, USA
| | - Karel Svoboda
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA
| | - Loren L Looger
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA
| | - Kaspar Podgorski
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA.
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104
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Abstract
Embryonic development is highly complex and dynamic, requiring the coordination of numerous molecular and cellular events at precise times and places. Advances in imaging technology have made it possible to follow developmental processes at cellular, tissue, and organ levels over time as they take place in the intact embryo. Parallel innovations of in vivo probes permit imaging to report on molecular, physiological, and anatomical events of embryogenesis, but the resulting multidimensional data sets pose significant challenges for extracting knowledge. In this review, we discuss recent and emerging advances in imaging technologies, in vivo labeling, and data processing that offer the greatest potential for jointly deciphering the intricate cellular dynamics and the underlying molecular mechanisms. Our discussion of the emerging area of “image-omics” highlights both the challenges of data analysis and the promise of more fully embracing computation and data science for rapidly advancing our understanding of biology.
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Affiliation(s)
- Francesco Cutrale
- Department of Biomedical Engineering, University of Southern California, Los Angeles, California 90089, USA
- Translational Imaging Center, University of Southern California, Los Angeles, California 90089, USA
| | - Scott E. Fraser
- Department of Biomedical Engineering, University of Southern California, Los Angeles, California 90089, USA
- Translational Imaging Center, University of Southern California, Los Angeles, California 90089, USA
- Division of Molecular and Computational Biology, Department of Biological Sciences, University of Southern California, Los Angeles, California 90089, USA
| | - Le A. Trinh
- Translational Imaging Center, University of Southern California, Los Angeles, California 90089, USA
- Division of Molecular and Computational Biology, Department of Biological Sciences, University of Southern California, Los Angeles, California 90089, USA
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105
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Luo L, Callaway EM, Svoboda K. Genetic Dissection of Neural Circuits: A Decade of Progress. Neuron 2019; 98:256-281. [PMID: 29673479 DOI: 10.1016/j.neuron.2018.03.040] [Citation(s) in RCA: 231] [Impact Index Per Article: 46.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2018] [Revised: 03/16/2018] [Accepted: 03/21/2018] [Indexed: 01/24/2023]
Abstract
Tremendous progress has been made since Neuron published our Primer on genetic dissection of neural circuits 10 years ago. Since then, cell-type-specific anatomical, neurophysiological, and perturbation studies have been carried out in a multitude of invertebrate and vertebrate organisms, linking neurons and circuits to behavioral functions. New methods allow systematic classification of cell types and provide genetic access to diverse neuronal types for studies of connectivity and neural coding during behavior. Here we evaluate key advances over the past decade and discuss future directions.
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Affiliation(s)
- Liqun Luo
- Department of Biology, Howard Hughes Medical Institute, Stanford University, Stanford, CA 94305, USA
| | - Edward M Callaway
- Systems Neurobiology Laboratory, The Salk Institute for Biological Studies, 10010 North Torrey Pines Road, La Jolla, CA 92037, USA.
| | - Karel Svoboda
- Howard Hughes Medical Institute, Janelia Research Campus, Ashburn, VA 20147, USA
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106
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Towards High-Throughput Chemobehavioural Phenomics in Neuropsychiatric Drug Discovery. Mar Drugs 2019; 17:md17060340. [PMID: 31174272 PMCID: PMC6627923 DOI: 10.3390/md17060340] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2019] [Revised: 05/19/2019] [Accepted: 06/01/2019] [Indexed: 12/11/2022] Open
Abstract
Identifying novel marine-derived neuroactive chemicals with therapeutic potential is difficult due to inherent complexities of the central nervous system (CNS), our limited understanding of the molecular foundations of neuro-psychiatric conditions, as well as the limited applications of effective high-throughput screening models that recapitulate functionalities of the intact CNS. Furthermore, nearly all neuro-modulating chemicals exhibit poorly characterized pleiotropic activities often referred to as polypharmacology. The latter renders conventional target-based in vitro screening approaches very difficult to accomplish. In this context, chemobehavioural phenotyping using innovative small organism models such as planarians and zebrafish represent powerful and highly integrative approaches to study the impact of new chemicals on central and peripheral nervous systems. In contrast to in vitro bioassays aimed predominantly at identification of chemicals acting on single targets, phenotypic chemobehavioural analysis allows for complex multi-target interactions to occur in combination with studies of polypharmacological effects of chemicals in a context of functional and intact milieu of the whole organism. In this review, we will outline recent advances in high-throughput chemobehavioural phenotyping and provide a future outlook on how those innovative methods can be utilized for rapidly screening and characterizing marine-derived compounds with prospective applications in neuropharmacology and psychosomatic medicine.
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107
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Belmouaddine H, Madugundu GS, Wagner JR, Couairon A, Houde D, Sanche L. DNA Base Modifications Mediated by Femtosecond Laser-Induced Cold Low-Density Plasma in Aqueous Solutions. J Phys Chem Lett 2019; 10:2753-2760. [PMID: 31039309 DOI: 10.1021/acs.jpclett.9b00652] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Applications based on near-infrared femtosecond laser-induced plasma in biological materials involve numerous ionization events that inevitably mediate physicochemical effects. Here, the physical chemistry underlying the action of such plasma is characterized in a system of biological interest. We have implemented wavefront shaping techniques to control the generation of laser-induced low electron density plasma channels in DNA aqueous solutions, which minimize the unwanted thermo-mechanical effects associated with plasma of higher density. The number of DNA base modifications per unit of absolute energy deposited by such cold plasma is compared to those induced by either ultraviolet or standard ionizing radiation (γ-rays). Analyses of various photoinduced, oxidative, and reductive DNA base products show that the effects of laser-induced cold plasma are mainly mediated by reactive radical species produced upon the ionization of water, rather than by the direct interaction of the strong laser field with DNA. In the plasma environment, reactions among densely produced primary radicals result in a dramatic decrease in the yields of DNA damages relative to sparse ionizing radiation. This intense radical production also drives the local depletion of oxygen.
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Affiliation(s)
- Hakim Belmouaddine
- Department of Nuclear Medicine and Radiobiology , Faculty of Medicine and Health Sciences, University of Sherbrooke , Sherbrooke , Quebec J1H 5N4 , Canada
| | - Guru S Madugundu
- Department of Nuclear Medicine and Radiobiology , Faculty of Medicine and Health Sciences, University of Sherbrooke , Sherbrooke , Quebec J1H 5N4 , Canada
| | - J Richard Wagner
- Department of Nuclear Medicine and Radiobiology , Faculty of Medicine and Health Sciences, University of Sherbrooke , Sherbrooke , Quebec J1H 5N4 , Canada
| | - Arnaud Couairon
- CPHT, CNRS, Ecole polytechnique, IP Paris , F-91128 Palaiseau , France
| | - Daniel Houde
- Department of Nuclear Medicine and Radiobiology , Faculty of Medicine and Health Sciences, University of Sherbrooke , Sherbrooke , Quebec J1H 5N4 , Canada
| | - Léon Sanche
- Department of Nuclear Medicine and Radiobiology , Faculty of Medicine and Health Sciences, University of Sherbrooke , Sherbrooke , Quebec J1H 5N4 , Canada
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108
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Multiplexed temporally focused light shaping through a gradient index lens for precise in-depth optogenetic photostimulation. Sci Rep 2019; 9:7603. [PMID: 31110187 PMCID: PMC6527563 DOI: 10.1038/s41598-019-43933-w] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2018] [Accepted: 04/25/2019] [Indexed: 11/08/2022] Open
Abstract
In the past 10 years, the use of light has become irreplaceable for the optogenetic study and control of neurons and neural circuits. Optical techniques are however limited by scattering and can only see through a depth of few hundreds µm in living tissues. GRIN lens based micro-endoscopes represent a powerful solution to reach deeper regions. In this work we demonstrate that cutting edge optical methods for the precise photostimulation of multiple neurons in three dimensions can be performed through a GRIN lens. By spatio-temporally shaping a laser beam in the two-photon regime we project several tens of spatially confined targets in a volume of at least 100 × 150 × 300 µm3. We then apply such approach to the optogenetic stimulation of multiple neurons simultaneously in vivo in mice. Our work paves the way for an all-optical investigation of neural circuits in previously inaccessible brain areas.
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109
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Wagner N, Norlin N, Gierten J, de Medeiros G, Balázs B, Wittbrodt J, Hufnagel L, Prevedel R. Instantaneous isotropic volumetric imaging of fast biological processes. Nat Methods 2019; 16:497-500. [PMID: 31036959 DOI: 10.1038/s41592-019-0393-z] [Citation(s) in RCA: 54] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2018] [Accepted: 03/05/2019] [Indexed: 11/09/2022]
Abstract
To capture highly dynamic biological processes at cellular resolution is a recurring challenge in biology. Here we show that combining selective-volume illumination with simultaneous acquisition of orthogonal light fields yields three-dimensional images with high, isotropic spatial resolution and a significant reduction of reconstruction artefacts, thereby overcoming current limitations of light-field microscopy implementations. We demonstrate medaka heart and blood flow imaging at single-cell resolution and free of motion artefacts at volume rates of up to 200 Hz.
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Affiliation(s)
- Nils Wagner
- Cell Biology and Biophysics Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Nils Norlin
- Cell Biology and Biophysics Unit, European Molecular Biology Laboratory, Heidelberg, Germany.,Department of Medical Biochemistry and Biophysics, Karolinska Institute, Stockholm, Sweden
| | - Jakob Gierten
- Centre for Organismal Studies, Heidelberg University, Heidelberg, Germany.,Department of Pediatric Cardiology, University Hospital Heidelberg, Heidelberg, Germany
| | - Gustavo de Medeiros
- Cell Biology and Biophysics Unit, European Molecular Biology Laboratory, Heidelberg, Germany.,Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
| | - Bálint Balázs
- Cell Biology and Biophysics Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Joachim Wittbrodt
- Centre for Organismal Studies, Heidelberg University, Heidelberg, Germany
| | - Lars Hufnagel
- Cell Biology and Biophysics Unit, European Molecular Biology Laboratory, Heidelberg, Germany.
| | - Robert Prevedel
- Cell Biology and Biophysics Unit, European Molecular Biology Laboratory, Heidelberg, Germany. .,Developmental Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany. .,Epigenetics and Neurobiology Unit, European Molecular Biology Laboratory, Monterotondo, Italy.
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110
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Valle AF, Seelig JD. Two-photon Bessel beam tomography for fast volume imaging. OPTICS EXPRESS 2019; 27:12147-12162. [PMID: 31052759 DOI: 10.1364/oe.27.012147] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/28/2019] [Accepted: 04/01/2019] [Indexed: 06/09/2023]
Abstract
Light microscopy on dynamic samples, for example neural activity in the brain, often requires imaging volumes that extend over several 100 µm in axial direction at a rate of at least several tens of Hertz. Here, we develop a tomography approach for scanning fluorescence microscopy which allows recording a volume image in a single frame scan. Volumes are imaged by simultaneously recording four independent projections at different angles using temporally multiplexed, tilted Bessel beams. From the resulting projections, three-dimensional images are reconstructed using inverse Radon transforms combined with convolutional neural networks (U-net).
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111
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Badon A, Bensussen S, Gritton HJ, Awal MR, Gabel CV, Han X, Mertz J. Video-rate large-scale imaging with Multi-Z confocal microscopy. OPTICA 2019; 6:389-395. [PMID: 34504902 PMCID: PMC8425499 DOI: 10.1364/optica.6.000389] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Fast, volumetric imaging over large scales has been a long-standing challenge in biological microscopy. To address this challenge, we report an augmented variant of confocal microscopy that uses a series of reflecting pinholes axially distributed in the detection space, such that each pinhole probes a different depth within the sample. We thus obtain simultaneous multiplane imaging without the need for axial scanning. Our microscope technique is versatile and configured here to provide two-color fluorescence imaging with a field of view larger than a millimeter at video rate. Its general applicability is demonstrated with neuronal imaging of both Caenorhabditis elegans and mouse brains in vivo.
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Affiliation(s)
- Amaury Badon
- Department of Biomedical Engineering, Boston University, Boston, Massachusetts 02215, USA
- Corresponding author:
| | - Seth Bensussen
- Department of Biomedical Engineering, Boston University, Boston, Massachusetts 02215, USA
| | - Howard J. Gritton
- Department of Biomedical Engineering, Boston University, Boston, Massachusetts 02215, USA
| | - Mehraj R. Awal
- Department of Physiology and Biophysics, Boston University School of Medicine, Boston, Massachusetts 02218, USA
| | - Christopher V. Gabel
- Department of Physiology and Biophysics, Boston University School of Medicine, Boston, Massachusetts 02218, USA
- Boston University Photonics Center, Boston, Massachusetts 02215, USA
| | - Xue Han
- Department of Biomedical Engineering, Boston University, Boston, Massachusetts 02215, USA
- Boston University Photonics Center, Boston, Massachusetts 02215, USA
| | - Jerome Mertz
- Department of Biomedical Engineering, Boston University, Boston, Massachusetts 02215, USA
- Boston University Photonics Center, Boston, Massachusetts 02215, USA
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112
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Weisenburger S, Tejera F, Demas J, Chen B, Manley J, Sparks FT, Martínez Traub F, Daigle T, Zeng H, Losonczy A, Vaziri A. Volumetric Ca 2+ Imaging in the Mouse Brain Using Hybrid Multiplexed Sculpted Light Microscopy. Cell 2019; 177:1050-1066.e14. [PMID: 30982596 DOI: 10.1016/j.cell.2019.03.011] [Citation(s) in RCA: 102] [Impact Index Per Article: 20.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2018] [Revised: 12/19/2018] [Accepted: 03/04/2019] [Indexed: 01/07/2023]
Abstract
Calcium imaging using two-photon scanning microscopy has become an essential tool in neuroscience. However, in its typical implementation, the tradeoffs between fields of view, acquisition speeds, and depth restrictions in scattering brain tissue pose severe limitations. Here, using an integrated systems-wide optimization approach combined with multiple technical innovations, we introduce a new design paradigm for optical microscopy based on maximizing biological information while maintaining the fidelity of obtained neuron signals. Our modular design utilizes hybrid multi-photon acquisition and allows volumetric recording of neuroactivity at single-cell resolution within up to 1 × 1 × 1.22 mm volumes at up to 17 Hz in awake behaving mice. We establish the capabilities and potential of the different configurations of our imaging system at depth and across brain regions by applying it to in vivo recording of up to 12,000 neurons in mouse auditory cortex, posterior parietal cortex, and hippocampus.
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Affiliation(s)
- Siegfried Weisenburger
- Laboratory of Neurotechnology and Biophysics, The Rockefeller University, New York, NY, USA
| | - Frank Tejera
- Laboratory of Neurotechnology and Biophysics, The Rockefeller University, New York, NY, USA
| | - Jeffrey Demas
- Laboratory of Neurotechnology and Biophysics, The Rockefeller University, New York, NY, USA
| | - Brandon Chen
- Laboratory of Neurotechnology and Biophysics, The Rockefeller University, New York, NY, USA
| | - Jason Manley
- Laboratory of Neurotechnology and Biophysics, The Rockefeller University, New York, NY, USA
| | - Fraser T Sparks
- Department of Neuroscience, Columbia University, New York, NY, USA; Mortimer B. Zuckerman Mind Brain Behavior Institute, Columbia University, New York, NY, USA
| | | | - Tanya Daigle
- Allen Institute for Brain Science, Seattle, WA, USA
| | - Hongkui Zeng
- Allen Institute for Brain Science, Seattle, WA, USA
| | - Attila Losonczy
- Department of Neuroscience, Columbia University, New York, NY, USA; The Kavli Institute for Brain Science, Columbia University, New York, NY, USA; Mortimer B. Zuckerman Mind Brain Behavior Institute, Columbia University, New York, NY, USA
| | - Alipasha Vaziri
- Laboratory of Neurotechnology and Biophysics, The Rockefeller University, New York, NY, USA; Research Institute of Molecular Pathology, Vienna, Austria; The Kavli Neural Systems Institute, The Rockefeller University, New York, NY, USA.
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113
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In Vivo Submillisecond Two-Photon Optogenetics with Temporally Focused Patterned Light. J Neurosci 2019; 39:3484-3497. [PMID: 30833505 DOI: 10.1523/jneurosci.1785-18.2018] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2018] [Revised: 12/08/2018] [Accepted: 12/12/2018] [Indexed: 01/09/2023] Open
Abstract
To better examine circuit mechanisms underlying perception and behavior, researchers need tools to enable temporally precise control of action-potential generation of individual cells from neuronal ensembles. Here we demonstrate that such precision can be achieved with two-photon (2P) temporally focused computer-generated holography to control neuronal excitability at the supragranular layers of anesthetized and awake visual cortex in both male and female mice. Using 2P-guided whole-cell or cell-attached recordings in positive neurons expressing any of the three opsins ReaChR, CoChR, or ChrimsonR, we investigated the dependence of spiking activity on the opsin's channel kinetics. We found that in all cases the use of brief illumination (≤10 ms) induces spikes of millisecond temporal resolution and submillisecond precision, which were preserved upon repetitive illuminations up to tens of hertz. To reach high temporal precision, we used a large illumination spot covering the entire cell body and an amplified laser at high peak power and low excitation intensity (on average ≤0.2 mW/μm2), thus minimizing the risk for nonlinear photodamage effects. Finally, by combining 2P holographic excitation with electrophysiological recordings and calcium imaging using GCaMP6s, we investigated the factors, including illumination shape and intensity, opsin distribution in the target cell, and cell morphology, which affect the spatial selectivity of single-cell and multicell holographic activation. Parallel optical control of neuronal activity with cellular resolution and millisecond temporal precision should make it easier to investigate neuronal connections and find further links between connectivity, microcircuit dynamics, and brain functions.SIGNIFICANCE STATEMENT Recent developments in the field of optogenetics has enabled researchers to probe the neuronal microcircuit with light by optically actuating genetically encoded light-sensitive opsins expressed in the target cells. Here, we applied holographic light shaping and temporal focusing to simultaneously deliver axially confined holographic patterns to opsin-positive cells in the living mouse cortex. Parallel illumination efficiently induced action potentials with high temporal resolution and precision for three opsins of different kinetics. We extended the parallel optogenetic activation at low intensity to multiple neurons and concurrently monitored their calcium dynamics. These results demonstrate fast and temporally precise in vivo control of a neuronal subpopulation, opening new opportunities for revealing circuit mechanisms underlying brain functions.
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114
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Tsyboulski D, Orlova N, Ledochowitsch P, Saggau P. Two-photon frequency division multiplexing for functional in vivo imaging: a feasibility study. OPTICS EXPRESS 2019; 27:4488-4503. [PMID: 30876067 DOI: 10.1364/oe.27.004488] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/22/2018] [Accepted: 01/19/2019] [Indexed: 06/09/2023]
Abstract
Recently, we presented a new approach to create high-speed amplitude modulation of femtosecond laser pulses and tag multiple excitation beams with specific modulation frequencies. In this work, we discuss the utility of this method to record calcium signals in brain tissue with two-photon frequency-division multiplexing (2P-FDM) microscopy. While frequency-multiplexed imaging appears slightly inferior in terms of image quality as compared to conventional two-photon laser scanning microscopy due to shot noise-induced cross-talk between frequency channels, applying this technique to record average signals from regions of interest (ROI) such as neuronal cell bodies was found to be promising. We use phase information associated with each pixel or waveform within a selected ROI to phase-align and recombine the signals into one extended amplitude-modulated waveform. This procedure narrows the frequency detection window, effectively decreasing noise contributions from other frequency channels. Using theoretical analysis, numerical simulations, and in vitro imaging, we demonstrate a reduction of cross-talk by more than an order of magnitude and predict the usefulness of 2P-FDM for functional studies of brain activity.
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115
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Aimon S, Katsuki T, Jia T, Grosenick L, Broxton M, Deisseroth K, Sejnowski TJ, Greenspan RJ. Fast near-whole-brain imaging in adult Drosophila during responses to stimuli and behavior. PLoS Biol 2019; 17:e2006732. [PMID: 30768592 PMCID: PMC6395010 DOI: 10.1371/journal.pbio.2006732] [Citation(s) in RCA: 73] [Impact Index Per Article: 14.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2018] [Revised: 02/28/2019] [Accepted: 01/28/2019] [Indexed: 11/18/2022] Open
Abstract
Whole-brain recordings give us a global perspective of the brain in action. In this study, we describe a method using light field microscopy to record near-whole brain calcium and voltage activity at high speed in behaving adult flies. We first obtained global activity maps for various stimuli and behaviors. Notably, we found that brain activity increased on a global scale when the fly walked but not when it groomed. This global increase with walking was particularly strong in dopamine neurons. Second, we extracted maps of spatially distinct sources of activity as well as their time series using principal component analysis and independent component analysis. The characteristic shapes in the maps matched the anatomy of subneuropil regions and, in some cases, a specific neuron type. Brain structures that responded to light and odor were consistent with previous reports, confirming the new technique's validity. We also observed previously uncharacterized behavior-related activity as well as patterns of spontaneous voltage activity.
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Affiliation(s)
- Sophie Aimon
- Kavli Institute for Brain and Mind, UCSD, La Jolla, California, United States of America
- Computational Neurobiology Laboratory, Salk Institute for Biological Studies, La Jolla, California, United States of America
- Neurobiology Section, University of California, San Diego, La Jolla, California, United States of America
- * E-mail:
| | - Takeo Katsuki
- Kavli Institute for Brain and Mind, UCSD, La Jolla, California, United States of America
| | - Tongqiu Jia
- Computational Neurobiology Laboratory, Salk Institute for Biological Studies, La Jolla, California, United States of America
| | - Logan Grosenick
- Departments of Computer Science and Bioengineering, Stanford University, Stanford, California, United States of America
| | - Michael Broxton
- Departments of Computer Science and Bioengineering, Stanford University, Stanford, California, United States of America
| | - Karl Deisseroth
- Departments of Bioengineering and Psychiatry, Stanford University, Stanford, California, United States of America
- Howard Hughes Medical Institute, Stanford University, Stanford, Stanford, California, United States of America
| | - Terrence J. Sejnowski
- Computational Neurobiology Laboratory, Salk Institute for Biological Studies, La Jolla, California, United States of America
- Division of Biological Sciences, University of California San Diego, La Jolla, California, United States of America
| | - Ralph J. Greenspan
- Kavli Institute for Brain and Mind, UCSD, La Jolla, California, United States of America
- Neurobiology Section, University of California, San Diego, La Jolla, California, United States of America
- Division of Biological Sciences, University of California San Diego, La Jolla, California, United States of America
- Department of Cognitive Science, University of California, San Diego, La Jolla, California, United States of America
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116
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Pnevmatikakis EA. Analysis pipelines for calcium imaging data. Curr Opin Neurobiol 2019; 55:15-21. [PMID: 30529147 DOI: 10.1016/j.conb.2018.11.004] [Citation(s) in RCA: 51] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2018] [Revised: 09/11/2018] [Accepted: 11/19/2018] [Indexed: 11/26/2022]
Abstract
Calcium imaging is a popular tool among neuroscientists because of its capability to monitor in vivo large neural populations across weeks with single neuron and single spike resolution. Before any downstream analysis, the data needs to be pre-processed to extract the location and activity of the neurons and processes in the observed field of view. The ever increasing size of calcium imaging datasets necessitates scalable analysis pipelines that are reproducible and fully automated. This review focuses on recent methods for addressing the pre-processing problems that arise in calcium imaging data analysis, and available software tools for high throughput analysis pipelines.
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117
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Paninski L, Cunningham JP. Neural data science: accelerating the experiment-analysis-theory cycle in large-scale neuroscience. Curr Opin Neurobiol 2019; 50:232-241. [PMID: 29738986 DOI: 10.1016/j.conb.2018.04.007] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2017] [Revised: 03/12/2018] [Accepted: 04/06/2018] [Indexed: 01/01/2023]
Abstract
Modern large-scale multineuronal recording methodologies, including multielectrode arrays, calcium imaging, and optogenetic techniques, produce single-neuron resolution data of a magnitude and precision that were the realm of science fiction twenty years ago. The major bottlenecks in systems and circuit neuroscience no longer lie in simply collecting data from large neural populations, but also in understanding this data: developing novel scientific questions, with corresponding analysis techniques and experimental designs to fully harness these new capabilities and meaningfully interrogate these questions. Advances in methods for signal processing, network analysis, dimensionality reduction, and optimal control-developed in lockstep with advances in experimental neurotechnology-promise major breakthroughs in multiple fundamental neuroscience problems. These trends are clear in a broad array of subfields of modern neuroscience; this review focuses on recent advances in methods for analyzing neural time-series data with single-neuronal precision.
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Affiliation(s)
- L Paninski
- Department of Statistics, Grossman Center for the Statistics of Mind, Zuckerman Mind Brain Behavior Institute, Center for Theoretical Neuroscience, Columbia University, United States; Department of Neuroscience, Grossman Center for the Statistics of Mind, Zuckerman Mind Brain Behavior Institute, Center for Theoretical Neuroscience, Columbia University, United States.
| | - J P Cunningham
- Department of Statistics, Grossman Center for the Statistics of Mind, Zuckerman Mind Brain Behavior Institute, Center for Theoretical Neuroscience, Columbia University, United States
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118
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Wang H, Mu X, Yang J, Liang Y, Zhang XD, Ming D. Brain imaging with near-infrared fluorophores. Coord Chem Rev 2019. [DOI: 10.1016/j.ccr.2018.11.003] [Citation(s) in RCA: 44] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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119
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Xue Y, Berry KP, Boivin JR, Rowlands CJ, Takiguchi Y, Nedivi E, So PTC. Scanless volumetric imaging by selective access multifocal multiphoton microscopy. OPTICA 2019; 6:76-83. [PMID: 31984218 PMCID: PMC6980307 DOI: 10.1364/optica.6.000076] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/12/2018] [Accepted: 12/17/2018] [Indexed: 05/14/2023]
Abstract
Simultaneous, high-resolution imaging across a large number of synaptic and dendritic sites is critical for understanding how neurons receive and integrate signals. Yet, functional imaging that targets a large number of submicrometer-sized synaptic and dendritic locations poses significant technical challenges. We demonstrate a new parallelized approach to address such questions, increasing the signal-to-noise ratio by an order of magnitude compared to previous approaches. This selective access multifocal multiphoton microscopy uses a spatial light modulator to generate multifocal excitation in three dimensions (3D) and a Gaussian-Laguerre phase plate to simultaneously detect fluorescence from these spots throughout the volume. We test the performance of this system by simultaneously recording Ca2+ dynamics from cultured neurons at 98-118 locations distributed throughout a 3D volume. This is the first demonstration of 3D imaging in a "single shot" and permits synchronized monitoring of signal propagation across multiple different dendrites.
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Affiliation(s)
- Yi Xue
- Department of Mechanical Engineering, Massachusetts Institute of Technology, 77 Massachusetts Ave., Cambridge, Massachusetts 02139, USA
- Laser Biomedical Research Center, Massachusetts Institute of Technology, 77 Massachusetts Ave., Cambridge, Massachusetts 02139, USA
| | - Kalen P. Berry
- Department of Biology, Massachusetts Institute of Technology, 77 Massachusetts Ave., Cambridge, Massachusetts 02139, USA
| | - Josiah R. Boivin
- Picower Institute, Massachusetts Institute of Technology, 77 Massachusetts Ave., Cambridge, Massachusetts 02139, USA
| | - Christopher J. Rowlands
- Department of Biological Engineering, Massachusetts Institute of Technology, 77 Massachusetts Ave., Cambridge, Massachusetts 02139, USA
| | - Yu Takiguchi
- Laser Biomedical Research Center, Massachusetts Institute of Technology, 77 Massachusetts Ave., Cambridge, Massachusetts 02139, USA
- Hamamatsu Photonics K.K., Hamamatsu, Japan
| | - Elly Nedivi
- Department of Biology, Massachusetts Institute of Technology, 77 Massachusetts Ave., Cambridge, Massachusetts 02139, USA
- Picower Institute, Massachusetts Institute of Technology, 77 Massachusetts Ave., Cambridge, Massachusetts 02139, USA
- Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, 77 Massachusetts Ave., Cambridge, Massachusetts 02139, USA
| | - Peter T. C. So
- Department of Mechanical Engineering, Massachusetts Institute of Technology, 77 Massachusetts Ave., Cambridge, Massachusetts 02139, USA
- Laser Biomedical Research Center, Massachusetts Institute of Technology, 77 Massachusetts Ave., Cambridge, Massachusetts 02139, USA
- Department of Biological Engineering, Massachusetts Institute of Technology, 77 Massachusetts Ave., Cambridge, Massachusetts 02139, USA
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120
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Meng G, Liang Y, Sarsfield S, Jiang WC, Lu R, Dudman JT, Aponte Y, Ji N. High-throughput synapse-resolving two-photon fluorescence microendoscopy for deep-brain volumetric imaging in vivo. eLife 2019; 8:40805. [PMID: 30604680 PMCID: PMC6338462 DOI: 10.7554/elife.40805] [Citation(s) in RCA: 60] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2018] [Accepted: 12/20/2018] [Indexed: 01/02/2023] Open
Abstract
Optical imaging has become a powerful tool for studying brains in vivo. The opacity of adult brains makes microendoscopy, with an optical probe such as a gradient index (GRIN) lens embedded into brain tissue to provide optical relay, the method of choice for imaging neurons and neural activity in deeply buried brain structures. Incorporating a Bessel focus scanning module into two-photon fluorescence microendoscopy, we extended the excitation focus axially and improved its lateral resolution. Scanning the Bessel focus in 2D, we imaged volumes of neurons at high-throughput while resolving fine structures such as synaptic terminals. We applied this approach to the volumetric anatomical imaging of dendritic spines and axonal boutons in the mouse hippocampus, and functional imaging of GABAergic neurons in the mouse lateral hypothalamus in vivo.
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Affiliation(s)
- Guanghan Meng
- Department of Molecular and Cell Biology, University of California, Berkeley, United States.,Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, United States.,Solomon H Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, United States.,Department of Physics, University of California, Berkeley, United States.,Helen Wills Neuroscience Institute, University of California, Berkeley, United States
| | - Yajie Liang
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, United States
| | - Sarah Sarsfield
- Intramural Research Program, Neuronal Circuits and Behavior Unit, National Institute on Drug Abuse, National Institutes of Health, Baltimore, United States
| | - Wan-Chen Jiang
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, United States
| | - Rongwen Lu
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, United States
| | - Joshua Tate Dudman
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, United States
| | - Yeka Aponte
- Solomon H Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, United States.,Intramural Research Program, Neuronal Circuits and Behavior Unit, National Institute on Drug Abuse, National Institutes of Health, Baltimore, United States
| | - Na Ji
- Department of Molecular and Cell Biology, University of California, Berkeley, United States.,Department of Physics, University of California, Berkeley, United States.,Helen Wills Neuroscience Institute, University of California, Berkeley, United States.,Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, United States
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121
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Hua X, Guo C, Wang J, Kim-Holzapfel D, Schroeder B, Liu W, Yuan J, French J, Jia S. Depth-extended, high-resolution fluorescence microscopy: whole-cell imaging with double-ring phase (DRiP) modulation. BIOMEDICAL OPTICS EXPRESS 2019; 10:204-214. [PMID: 30775094 PMCID: PMC6363204 DOI: 10.1364/boe.10.000204] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/24/2018] [Revised: 11/09/2018] [Accepted: 11/30/2018] [Indexed: 06/09/2023]
Abstract
We report a depth-extended, high-resolution fluorescence microscopy system based on interfering Bessel beams generated with double-ring phase (DRiP) modulation. The DRiP method effectively suppresses the Bessel side lobes, exhibiting a high resolution of the main lobe throughout a four- to five-fold improved depth of focus (DOF), compared to conventional wide-field microscopy. We showed both theoretically and experimentally the generation and propagation of a DRiP point-spread function (DRiP-PSF) of the imaging system. We further developed an approach for creating an axially-uniform DRiP-PSF and successfully demonstrated diffraction-limited, depth-extended imaging of cellular structures. We expect the DRiP method to contribute to the fast-developing field of non-diffracting-beam-enabled optical microscopy and be useful for various types of imaging modalities.
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Affiliation(s)
- Xuanwen Hua
- Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, Georgia 30332, USA
| | - Changliang Guo
- Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, Georgia 30332, USA
| | - Jian Wang
- Department of Biomedical Engineering, Stony Brook University, Stony Brook, New York 11794, USA
- Department of Physics, Harbin Institute of Technology, Harbin 150001, China
| | - Deborah Kim-Holzapfel
- Department of Biochemistry and Cell Biology and Department of Chemistry, Stony Brook University, Stony Brook, New York 11794, USA
| | - Bryce Schroeder
- Department of Biomedical Engineering, Stony Brook University, Stony Brook, New York 11794, USA
- Medical Scientist Training Program, School of Medicine, Stony Brook University, Stony Brook, New York 11794, USA
| | - Wenhao Liu
- Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, Georgia 30332, USA
| | - Junhua Yuan
- Department of Physics, University of Science and Technology of China, Hefei 230026, China
| | - Jarrod French
- Department of Biochemistry and Cell Biology and Department of Chemistry, Stony Brook University, Stony Brook, New York 11794, USA
| | - Shu Jia
- Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, Georgia 30332, USA
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122
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Ronzitti E, Emiliani V, Papagiakoumou E. Methods for Three-Dimensional All-Optical Manipulation of Neural Circuits. Front Cell Neurosci 2018; 12:469. [PMID: 30618626 PMCID: PMC6304748 DOI: 10.3389/fncel.2018.00469] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2018] [Accepted: 11/19/2018] [Indexed: 12/18/2022] Open
Abstract
Optical means for modulating and monitoring neuronal activity, have provided substantial insights to neurophysiology and toward our understanding of how the brain works. Optogenetic actuators, calcium or voltage imaging probes and other molecular tools, combined with advanced microscopies have allowed an "all-optical" readout and modulation of neural circuits. Completion of this remarkable work is evolving toward a three-dimensional (3D) manipulation of neural ensembles at a high spatiotemporal resolution. Recently, original optical methods have been proposed for both activating and monitoring neurons in a 3D space, mainly through optogenetic compounds. Here, we review these methods and anticipate possible combinations among them.
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Affiliation(s)
| | | | - Eirini Papagiakoumou
- Wavefront Engineering Microscopy Group, Photonics Department, Institut de la Vision, Sorbonne Université, Inserm S968, CNRS UMR7210, Paris, France
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123
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High-Fidelity Imaging in Brain-Wide Structural Studies Using Light-Sheet Microscopy. eNeuro 2018; 5:eN-TMNT-0124-18. [PMID: 30627630 PMCID: PMC6325532 DOI: 10.1523/eneuro.0124-18.2018] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2018] [Revised: 07/26/2018] [Accepted: 08/22/2018] [Indexed: 11/21/2022] Open
Abstract
Light-sheet microscopy (LSM) has proven a useful tool in neuroscience to image whole brains with high frame rates at cellular resolution and, in combination with tissue clearing methods, is often employed to reconstruct the cyto-architecture over the intact mouse brain. Inherently to LSM, however, residual opaque objects, always present to some extent even in extremely well optically cleared samples, cause stripe artifacts, which, in the best case, severely affect image homogeneity and, in the worst case, completely obscure features of interest. Here, demonstrating two example applications in intact optically cleared mouse brains, we report how Bessel beams reduce streaking artifacts and produce high-fidelity structural data for the brain-wide morphology of neuronal and vascular networks. We found that a third of the imaged volume of the brain was affected by strong striated image intensity inhomogeneity and, furthermore, a significant amount of information content lost with Gaussian illumination was accessible when interrogated with Bessel beams. In conclusion, Bessel beams produce high-fidelity structural data of improved image homogeneity and might significantly relax demands placed on the automated tools to count, trace, or segment fluorescent features of interest.
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124
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Grangeteau C, Lepinois F, Winckler P, Perrier-Cornet JM, Dupont S, Beney L. Cell Death Mechanisms Induced by Photo-Oxidation Studied at the Cell Scale in the Yeast Saccharomyces cerevisiae. Front Microbiol 2018; 9:2640. [PMID: 30455675 PMCID: PMC6230929 DOI: 10.3389/fmicb.2018.02640] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2018] [Accepted: 10/16/2018] [Indexed: 12/22/2022] Open
Abstract
Blue light (400–430 nm) is known to induce lethal effects in some species of fungi by photo-oxidation caused by the excitation of porphyrins but the mechanisms involved remain poorly understood. In this work, we exposed the yeast Saccharomyces cerevisiae to a high density light flux with two-photon excitation (830 nm equivalent to a one-photon excitation around 415 nm) and used quasi real-time visualization with confocal microscopy to study the initiation and dynamics of photo-oxidation in subcellular structures. Our results show that the oxidation generated by light treatments led to the permeabilization of the plasma membrane accompanied by the sudden expulsion of the cellular content, corresponding to cell death by necrosis. Moreover, excitation in the plasma membrane led to very fast oxidation and membrane permeabilization (<60 s) while excitation at the center of the cell did not induce permeabilization even after a period exceeding 600 s. Finally, our study shows that the relationship between the laser power used for two-photon excitation and the time required to permeabilize the plasma membrane was not linear. Thus, the higher the power used, the lower the energy required to permeabilize the plasma membrane. We conclude that fungal destruction can be generated very quickly using a high density light flux. Better knowledge of the intracellular processes and the conditions necessary to induce necrosis should make it possible in the future to improve the efficiency of antimicrobial strategies photo-oxidation-based.
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Affiliation(s)
- Cédric Grangeteau
- Univ. Bourgogne Franche-Comté, AgroSup Dijon, PAM UMR A 02.102, Dijon, France
| | - Florine Lepinois
- Univ. Bourgogne Franche-Comté, AgroSup Dijon, PAM UMR A 02.102, Dijon, France
| | - Pascale Winckler
- Univ. Bourgogne Franche-Comté, AgroSup Dijon, PAM UMR A 02.102, Dijon, France
| | | | - Sebastien Dupont
- Univ. Bourgogne Franche-Comté, AgroSup Dijon, PAM UMR A 02.102, Dijon, France
| | - Laurent Beney
- Univ. Bourgogne Franche-Comté, AgroSup Dijon, PAM UMR A 02.102, Dijon, France
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125
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Imaging neural activity in the ventral nerve cord of behaving adult Drosophila. Nat Commun 2018; 9:4390. [PMID: 30348941 PMCID: PMC6197219 DOI: 10.1038/s41467-018-06857-z] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2018] [Accepted: 10/02/2018] [Indexed: 12/11/2022] Open
Abstract
To understand neural circuits that control limbs, one must measure their activity during behavior. Until now this goal has been challenging, because limb premotor and motor circuits have been largely inaccessible for large-scale recordings in intact, moving animals—a constraint that is true for both vertebrate and invertebrate models. Here, we introduce a method for 2-photon functional imaging from the ventral nerve cord (VNC) of behaving adult Drosophila melanogaster. We use this method to reveal patterns of activity across nerve cord populations during grooming and walking and to uncover the functional encoding of moonwalker ascending neurons (MANs), moonwalker descending neurons (MDNs), and a previously uncharacterized class of locomotion-associated A1 descending neurons. Finally, we develop a genetic reagent to destroy the indirect flight muscles and to facilitate experimental access to the VNC. Taken together, these approaches enable the direct investigation of circuits associated with complex limb movements. The Drosophila ventral nerve cord (VNC) is functionally equivalent to the vertebrate spinal cord. This study reports a 2-photon imaging approach for recording neural activity in the VNC of walking and grooming adult flies.
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126
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Hu Q, Li P, Xiong Y, Wang Y, Lv X, Zeng S. Simultaneous two-plane, two-photon imaging based on spatial multiplexing. OPTICS LETTERS 2018; 43:4598-4601. [PMID: 30272692 DOI: 10.1364/ol.43.004598] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/04/2018] [Accepted: 08/24/2018] [Indexed: 06/08/2023]
Abstract
The two-photon microscope is a powerful tool in life science. Conventional two-photon microscopy can image only a plane of a particular axial position at a time. Axial scanning can get the volumetric information, but it gets signals from different axial positions serially, which means that the exposure time at every plane is limited. Here we demonstrate a novel method, to the best of our knowledge, that can simultaneously record images from two planes at different xyz positions. The demultiplexing of the signal is realized using a confocal strategy. The experimental results show that it can be used for simultaneous two-photon imaging at two focal planes with little cross talk.
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127
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Müllenbroich MC, Turrini L, Silvestri L, Alterini T, Gheisari A, Tiso N, Vanzi F, Sacconi L, Pavone FS. Bessel Beam Illumination Reduces Random and Systematic Errors in Quantitative Functional Studies Using Light-Sheet Microscopy. Front Cell Neurosci 2018; 12:315. [PMID: 30294262 PMCID: PMC6158350 DOI: 10.3389/fncel.2018.00315] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2018] [Accepted: 08/29/2018] [Indexed: 11/24/2022] Open
Abstract
Light-sheet microscopy (LSM), in combination with intrinsically transparent zebrafish larvae, is a method of choice to observe brain function with high frame rates at cellular resolution. Inherently to LSM, however, residual opaque objects cause stripe artifacts, which obscure features of interest and, during functional imaging, modulate fluorescence variations related to neuronal activity. Here, we report how Bessel beams reduce streaking artifacts and produce high-fidelity quantitative data demonstrating a fivefold increase in sensitivity to calcium transients and a 20-fold increase in accuracy in the detection of activity correlations in functional imaging. Furthermore, using principal component analysis, we show that measurements obtained with Bessel beams are clean enough to reveal in one-shot experiments correlations that can not be averaged over trials after stimuli as is the case when studying spontaneous activity. Our results not only demonstrate the contamination of data by systematic and random errors through conventional Gaussian illumination and but,furthermore, quantify the increase in fidelity of such data when using Bessel beams.
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Affiliation(s)
- M Caroline Müllenbroich
- National Institute of Optics, National Research Council, Sesto Fiorentino, Italy.,European Laboratory for Non-linear Spectroscopy, LENS, Sesto Fiorentino, Italy
| | - Lapo Turrini
- European Laboratory for Non-linear Spectroscopy, LENS, Sesto Fiorentino, Italy
| | - Ludovico Silvestri
- National Institute of Optics, National Research Council, Sesto Fiorentino, Italy.,European Laboratory for Non-linear Spectroscopy, LENS, Sesto Fiorentino, Italy
| | - Tommaso Alterini
- European Laboratory for Non-linear Spectroscopy, LENS, Sesto Fiorentino, Italy
| | - Ali Gheisari
- European Laboratory for Non-linear Spectroscopy, LENS, Sesto Fiorentino, Italy
| | - Natascia Tiso
- Department of Biology, University of Padova, Padua, Italy
| | - Francesco Vanzi
- European Laboratory for Non-linear Spectroscopy, LENS, Sesto Fiorentino, Italy.,Department of Biology, University of Florence, Sesto Fiorentino, Italy
| | - Leonardo Sacconi
- National Institute of Optics, National Research Council, Sesto Fiorentino, Italy.,European Laboratory for Non-linear Spectroscopy, LENS, Sesto Fiorentino, Italy
| | - Francesco S Pavone
- National Institute of Optics, National Research Council, Sesto Fiorentino, Italy.,European Laboratory for Non-linear Spectroscopy, LENS, Sesto Fiorentino, Italy.,Department of Physics and Astronomy, University of Florence, Sesto Fiorentino, Italy
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128
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Weisenburger S, Vaziri A. A Guide to Emerging Technologies for Large-Scale and Whole-Brain Optical Imaging of Neuronal Activity. Annu Rev Neurosci 2018; 41:431-452. [PMID: 29709208 PMCID: PMC6037565 DOI: 10.1146/annurev-neuro-072116-031458] [Citation(s) in RCA: 66] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
The mammalian brain is a densely interconnected network that consists of millions to billions of neurons. Decoding how information is represented and processed by this neural circuitry requires the ability to capture and manipulate the dynamics of large populations at high speed and high resolution over a large area of the brain. Although the use of optical approaches by the neuroscience community has rapidly increased over the past two decades, most microscopy approaches are unable to record the activity of all neurons comprising a functional network across the mammalian brain at relevant temporal and spatial resolutions. In this review, we survey the recent development in optical technologies for Ca2+ imaging in this regard and provide an overview of the strengths and limitations of each modality and its potential for scalability. We provide guidance from the perspective of a biological user driven by the typical biological applications and sample conditions. We also discuss the potential for future advances and synergies that could be obtained through hybrid approaches or other modalities.
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Affiliation(s)
- Siegfried Weisenburger
- Laboratory of Neurotechnology and Biophysics, The Rockefeller University, New York, New York 10065, USA
| | - Alipasha Vaziri
- Laboratory of Neurotechnology and Biophysics, The Rockefeller University, New York, New York 10065, USA
- Kavli Neural Systems Institute, The Rockefeller University, New York, New York 10065, USA
- Research Institute of Molecular Pathology, 1030 Vienna, Austria;
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129
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Lee AK, Brecht M. Elucidating Neuronal Mechanisms Using Intracellular Recordings during Behavior. Trends Neurosci 2018; 41:385-403. [DOI: 10.1016/j.tins.2018.03.014] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2017] [Revised: 03/19/2018] [Accepted: 03/23/2018] [Indexed: 12/17/2022]
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130
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Hillman EM, Voleti V, Patel K, Li W, Yu H, Perez-Campos C, Benezra SE, Bruno RM, Galwaduge PT. High-speed 3D imaging of cellular activity in the brain using axially-extended beams and light sheets. Curr Opin Neurobiol 2018; 50:190-200. [PMID: 29642044 PMCID: PMC6002850 DOI: 10.1016/j.conb.2018.03.007] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2017] [Revised: 03/19/2018] [Accepted: 03/21/2018] [Indexed: 10/17/2022]
Abstract
As optical reporters and modulators of cellular activity have become increasingly sophisticated, the amount that can be learned about the brain via high-speed cellular imaging has increased dramatically. However, despite fervent innovation, point-scanning microscopy is facing a fundamental limit in achievable 3D imaging speeds and fields of view. A range of alternative approaches are emerging, some of which are moving away from point-scanning to use axially-extended beams or sheets of light, for example swept confocally aligned planar excitation (SCAPE) microscopy. These methods are proving effective for high-speed volumetric imaging of the nervous system of small organisms such as Drosophila (fruit fly) and D. Rerio (Zebrafish), and are showing promise for imaging activity in the living mammalian brain using both single and two-photon excitation. This article describes these approaches and presents a simple model that demonstrates key advantages of axially-extended illumination over point-scanning strategies for high-speed volumetric imaging, including longer integration times per voxel, improved photon efficiency and reduced photodamage.
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Affiliation(s)
- Elizabeth Mc Hillman
- Laboratory for Functional Optical Imaging, Departments of Biomedical Engineering and Radiology, Columbia University, New York, NY, USA; Mortimer B. Zuckerman Mind Brain Behavior Institute, Columbia University, New York, NY, USA.
| | - Venkatakaushik Voleti
- Laboratory for Functional Optical Imaging, Departments of Biomedical Engineering and Radiology, Columbia University, New York, NY, USA; Mortimer B. Zuckerman Mind Brain Behavior Institute, Columbia University, New York, NY, USA
| | - Kripa Patel
- Laboratory for Functional Optical Imaging, Departments of Biomedical Engineering and Radiology, Columbia University, New York, NY, USA; Mortimer B. Zuckerman Mind Brain Behavior Institute, Columbia University, New York, NY, USA
| | - Wenze Li
- Laboratory for Functional Optical Imaging, Departments of Biomedical Engineering and Radiology, Columbia University, New York, NY, USA; Mortimer B. Zuckerman Mind Brain Behavior Institute, Columbia University, New York, NY, USA
| | - Hang Yu
- Laboratory for Functional Optical Imaging, Departments of Biomedical Engineering and Radiology, Columbia University, New York, NY, USA; Mortimer B. Zuckerman Mind Brain Behavior Institute, Columbia University, New York, NY, USA
| | - Citlali Perez-Campos
- Laboratory for Functional Optical Imaging, Departments of Biomedical Engineering and Radiology, Columbia University, New York, NY, USA; Mortimer B. Zuckerman Mind Brain Behavior Institute, Columbia University, New York, NY, USA
| | - Sam E Benezra
- Mortimer B. Zuckerman Mind Brain Behavior Institute, Columbia University, New York, NY, USA; Bruno Lab, Department of Neuroscience, Columbia University, New York, NY, USA
| | - Randy M Bruno
- Mortimer B. Zuckerman Mind Brain Behavior Institute, Columbia University, New York, NY, USA; Bruno Lab, Department of Neuroscience, Columbia University, New York, NY, USA
| | - Pubudu T Galwaduge
- Laboratory for Functional Optical Imaging, Departments of Biomedical Engineering and Radiology, Columbia University, New York, NY, USA; Mortimer B. Zuckerman Mind Brain Behavior Institute, Columbia University, New York, NY, USA
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131
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Yoshida E, Terada SI, Tanaka YH, Kobayashi K, Ohkura M, Nakai J, Matsuzaki M. In vivo wide-field calcium imaging of mouse thalamocortical synapses with an 8 K ultra-high-definition camera. Sci Rep 2018; 8:8324. [PMID: 29844612 PMCID: PMC5974322 DOI: 10.1038/s41598-018-26566-3] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2017] [Accepted: 05/15/2018] [Indexed: 12/12/2022] Open
Abstract
In vivo wide-field imaging of neural activity with a high spatio-temporal resolution is a challenge in modern neuroscience. Although two-photon imaging is very powerful, high-speed imaging of the activity of individual synapses is mostly limited to a field of approximately 200 µm on a side. Wide-field one-photon epifluorescence imaging can reveal neuronal activity over a field of ≥1 mm2 at a high speed, but is not able to resolve a single synapse. Here, to achieve a high spatio-temporal resolution, we combine an 8 K ultra-high-definition camera with spinning-disk one-photon confocal microscopy. This combination allowed us to image a 1 mm2 field with a pixel resolution of 0.21 µm at 60 fps. When we imaged motor cortical layer 1 in a behaving head-restrained mouse, calcium transients were detected in presynaptic boutons of thalamocortical axons sparsely labeled with GCaMP6s, although their density was lower than when two-photon imaging was used. The effects of out-of-focus fluorescence changes on calcium transients in individual boutons appeared minimal. Axonal boutons with highly correlated activity were detected over the 1 mm2 field, and were probably distributed on multiple axonal arbors originating from the same thalamic neuron. This new microscopy with an 8 K ultra-high-definition camera should serve to clarify the activity and plasticity of widely distributed cortical synapses.
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Affiliation(s)
- Eriko Yoshida
- Department of Physiology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Shin-Ichiro Terada
- Department of Physiology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Yasuyo H Tanaka
- Department of Physiology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Kenta Kobayashi
- Section of Viral Vector Development, National Institute for Physiological Sciences, Aichi, Japan
| | - Masamichi Ohkura
- Brain and Body System Science Institute, Saitama University, Saitama, Japan
| | - Junichi Nakai
- Brain and Body System Science Institute, Saitama University, Saitama, Japan
| | - Masanori Matsuzaki
- Department of Physiology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan.
- International Research Center for Neurointelligence (WPI-IRCN), The University of Tokyo Institutes for Advanced Study, Tokyo, 113-0033, Japan.
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132
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Xiao S, Tseng HA, Gritton H, Han X, Mertz J. Video-rate volumetric neuronal imaging using 3D targeted illumination. Sci Rep 2018; 8:7921. [PMID: 29784920 PMCID: PMC5962542 DOI: 10.1038/s41598-018-26240-8] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2018] [Accepted: 05/03/2018] [Indexed: 12/28/2022] Open
Abstract
Fast volumetric microscopy is required to monitor large-scale neural ensembles with high spatio-temporal resolution. Widefield fluorescence microscopy can image large 2D fields of view at high resolution and speed while remaining simple and costeffective. A focal sweep add-on can further extend the capacity of widefield microscopy by enabling extended-depth-of-field (EDOF) imaging, but suffers from an inability to reject out-of-focus fluorescence background. Here, by using a digital micromirror device to target only in-focus sample features, we perform EDOF imaging with greatly enhanced contrast and signal-to-noise ratio, while reducing the light dosage delivered to the sample. Image quality is further improved by the application of a robust deconvolution algorithm. We demonstrate the advantages of our technique for in vivo calcium imaging in the mouse brain.
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Affiliation(s)
- Sheng Xiao
- Department of Electrical & Computer Engineering, Boston University, 8 Saint Mary's St., Boston, Massachusetts, 02215, USA.
| | - Hua-An Tseng
- Department of Biomedical Engineering, Boston University, 44 Cummington Mall, Boston, Massachusetts, 02215, USA
| | - Howard Gritton
- Department of Biomedical Engineering, Boston University, 44 Cummington Mall, Boston, Massachusetts, 02215, USA
| | - Xue Han
- Department of Biomedical Engineering, Boston University, 44 Cummington Mall, Boston, Massachusetts, 02215, USA
| | - Jerome Mertz
- Department of Biomedical Engineering, Boston University, 44 Cummington Mall, Boston, Massachusetts, 02215, USA
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133
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Skocek O, Nöbauer T, Weilguny L, Martínez Traub F, Xia CN, Molodtsov MI, Grama A, Yamagata M, Aharoni D, Cox DD, Golshani P, Vaziri A. High-speed volumetric imaging of neuronal activity in freely moving rodents. Nat Methods 2018; 15:429-432. [PMID: 29736000 DOI: 10.1038/s41592-018-0008-0] [Citation(s) in RCA: 109] [Impact Index Per Article: 18.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2017] [Accepted: 03/09/2018] [Indexed: 11/09/2022]
Abstract
Thus far, optical recording of neuronal activity in freely behaving animals has been limited to a thin axial range. We present a head-mounted miniaturized light-field microscope (MiniLFM) capable of capturing neuronal network activity within a volume of 700 × 600 × 360 µm3 at 16 Hz in the hippocampus of freely moving mice. We demonstrate that neurons separated by as little as ~15 µm and at depths up to 360 µm can be discriminated.
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Affiliation(s)
- Oliver Skocek
- Laboratory of Neurotechnology and Biophysics, The Rockefeller University, New York, NY, USA
| | - Tobias Nöbauer
- Laboratory of Neurotechnology and Biophysics, The Rockefeller University, New York, NY, USA
| | - Lukas Weilguny
- Research Institute of Molecular Pathology, Vienna, Austria
| | | | - Chuying Naomi Xia
- Laboratory of Neurotechnology and Biophysics, The Rockefeller University, New York, NY, USA
| | | | - Abhinav Grama
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA, USA.,Center for Brain Science, Harvard University, Cambridge, MA, USA
| | - Masahito Yamagata
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA, USA.,Center for Brain Science, Harvard University, Cambridge, MA, USA
| | - Daniel Aharoni
- Department of Neurology, Integrative Center for Learning and Memory, Brain Research Institute, University of California, Los Angeles, Los Angeles, CA, USA
| | - David D Cox
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA, USA.,Center for Brain Science, Harvard University, Cambridge, MA, USA
| | - Peyman Golshani
- Department of Neurology, Integrative Center for Learning and Memory, Brain Research Institute, University of California, Los Angeles, Los Angeles, CA, USA.,Department of Psychiatry & Biobehavioral Sciences, Integrative Center for Learning and Memory, Brain Research Institute, University of California, Los Angeles, Los Angeles, CA, USA.,West Los Angeles Virginia Medical Center, Los Angeles, CA, USA
| | - Alipasha Vaziri
- Laboratory of Neurotechnology and Biophysics, The Rockefeller University, New York, NY, USA. .,Research Institute of Molecular Pathology, Vienna, Austria. .,The Kavli Neural Systems Institute, The Rockefeller University, New York, NY, USA.
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134
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Rodríguez C, Liang Y, Lu R, Ji N. Three-photon fluorescence microscopy with an axially elongated Bessel focus. OPTICS LETTERS 2018; 43:1914-1917. [PMID: 29652397 PMCID: PMC5986555 DOI: 10.1364/ol.43.001914] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
Volumetric imaging tools that are simple to adopt, flexible, and robust are in high demand in the field of neuroscience, where the ability to image neurons and their networks with high spatiotemporal resolution is essential. Using an axially elongated focus approximating a Bessel beam, in combination with two-photon fluorescence microscopy, has proven successful at such an endeavor. Here, we demonstrate three-photon fluorescence imaging with an axially extended Bessel focus. We use an axicon-based module that allowed for the generation of Bessel foci of varying numerical apertures and axial lengths, and apply this volumetric imaging tool to image mouse brain slices and for in vivo imaging of the mouse brain.
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Affiliation(s)
- Cristina Rodríguez
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, Virginia 20147, USA
| | - Yajie Liang
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, Virginia 20147, USA
| | - Rongwen Lu
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, Virginia 20147, USA
| | - Na Ji
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, Virginia 20147, USA
- Department of Physics, Department of Molecular & Cellular Biology, University of California, Berkeley, California 94720, USA
- Corresponding author:
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135
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Yang W, Yuste R. Holographic imaging and photostimulation of neural activity. Curr Opin Neurobiol 2018; 50:211-221. [PMID: 29660600 DOI: 10.1016/j.conb.2018.03.006] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2017] [Revised: 02/10/2018] [Accepted: 03/21/2018] [Indexed: 10/17/2022]
Abstract
Optical imaging methods are powerful tools in neuroscience as they can systematically monitor the activity of neuronal populations with high spatiotemporal resolution using calcium or voltage indicators. Moreover, caged compounds and optogenetic actuators enable to optically manipulate neural activity. Among optical methods, computer-generated holography offers an enormous flexibility to sculpt the excitation light in three-dimensions (3D), particularly when combined with two-photon light sources. By projecting holographic light patterns on the sample, the activity of multiple neurons across a 3D brain volume can be simultaneously imaged or optically manipulated with single-cell precision. This flexibility makes two-photon holographic microscopy an ideal all-optical platform to simultaneously read and write activity in neuronal populations in vivo in 3D, a critical ability to dissect the function of neural circuits.
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Affiliation(s)
- Weijian Yang
- Neurotechnology Center, Department of Biological Sciences, Columbia University, New York, NY 10027, USA
| | - Rafael Yuste
- Neurotechnology Center, Department of Biological Sciences, Columbia University, New York, NY 10027, USA.
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136
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Chen B, Huang X, Gou D, Zeng J, Chen G, Pang M, Hu Y, Zhao Z, Zhang Y, Zhou Z, Wu H, Cheng H, Zhang Z, Xu C, Li Y, Chen L, Wang A. Rapid volumetric imaging with Bessel-Beam three-photon microscopy. BIOMEDICAL OPTICS EXPRESS 2018; 9:1992-2000. [PMID: 29675334 PMCID: PMC5905939 DOI: 10.1364/boe.9.001992] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/09/2018] [Revised: 03/22/2018] [Accepted: 03/23/2018] [Indexed: 05/05/2023]
Abstract
Owing to its tissue-penetration ability, multi-photon fluorescence microscopy allows for the high-resolution, non-invasive imaging of deep tissue in vivo; the recently developed three-photon microscopy (3PM) has extended the depth of high-resolution, non-invasive functional imaging of mouse brains to beyond 1.0 mm. However, the low repetition rate of femtosecond lasers that are normally used in 3PM limits the temporal resolution of point-scanning three-photon microscopy. To increase the volumetric imaging speed of 3PM, we propose a combination of an axially elongated needle-like Bessel-beam with three-photon excitation (3PE) to image biological samples with an extended depth of focus. We demonstrate the higher signal-to-background ratio (SBR) of the Bessel-beam 3PM compared to the two-photon version both theoretically and experimentally. Finally, we perform simultaneous calcium imaging of brain regions at different axial locations in live fruit flies and rapid volumetric imaging of neuronal structures in live mouse brains. These results highlight the unique advantage of conducting rapid volumetric imaging with a high SBR in the deep brain in vivo using scanning Bessel-3PM.
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Affiliation(s)
- Bingying Chen
- State Key Laboratory of Advanced Optical Communication System and Networks, School of Electronics Engineering and Computer Science, Peking University, Beijing 100871, China
- These authors contributed equally to this work
| | - Xiaoshuai Huang
- State Key Laboratory of Membrane Biology, Beijing Key Laboratory of Cardiometabolic Molecular Medicine, Institute of Molecular Medicine, Peking University, Beijing 100871, China
- These authors contributed equally to this work
| | - Dongzhou Gou
- State Key Laboratory of Membrane Biology, Beijing Key Laboratory of Cardiometabolic Molecular Medicine, Institute of Molecular Medicine, Peking University, Beijing 100871, China
| | - Jianzhi Zeng
- State Key Laboratory of Membrane Biology, School of Life Sciences, PKU-IDG/McGovern Institute for Brain Research, Peking University, Beijing 100871, China
| | - Guoqing Chen
- State Key Laboratory of Membrane Biology, Beijing Key Laboratory of Cardiometabolic Molecular Medicine, Institute of Molecular Medicine, Peking University, Beijing 100871, China
| | - Meijun Pang
- State Key Laboratory of Membrane Biology, Beijing Key Laboratory of Cardiometabolic Molecular Medicine, Institute of Molecular Medicine, Peking University, Beijing 100871, China
| | - Yanhui Hu
- School of Electronics Engineering and Computer Science, Peking University, Beijing 100871, China
| | - Zhe Zhao
- Department of Neurobiology, Institute of Basic Medical Sciences, Beijing, China
| | - Yunfeng Zhang
- School of Electronics Engineering and Computer Science, Peking University, Beijing 100871, China
| | - Zhuan Zhou
- State Key Laboratory of Membrane Biology, Beijing Key Laboratory of Cardiometabolic Molecular Medicine, Institute of Molecular Medicine, Peking University, Beijing 100871, China
| | - Haitao Wu
- Department of Neurobiology, Institute of Basic Medical Sciences, Beijing, China
| | - Heping Cheng
- State Key Laboratory of Membrane Biology, Beijing Key Laboratory of Cardiometabolic Molecular Medicine, Institute of Molecular Medicine, Peking University, Beijing 100871, China
| | - Zhigang Zhang
- State Key Laboratory of Advanced Optical Communication System and Networks, School of Electronics Engineering and Computer Science, Peking University, Beijing 100871, China
| | - Chris Xu
- State Key Laboratory of Membrane Biology, Beijing Key Laboratory of Cardiometabolic Molecular Medicine, Institute of Molecular Medicine, Peking University, Beijing 100871, China
- School of Applied and Engineering Physics, Cornell University, Ithaca, NY 14853, USA
| | - Yulong Li
- State Key Laboratory of Membrane Biology, School of Life Sciences, PKU-IDG/McGovern Institute for Brain Research, Peking University, Beijing 100871, China
| | - Liangyi Chen
- State Key Laboratory of Membrane Biology, Beijing Key Laboratory of Cardiometabolic Molecular Medicine, Institute of Molecular Medicine, Peking University, Beijing 100871, China
| | - Aimin Wang
- State Key Laboratory of Advanced Optical Communication System and Networks, School of Electronics Engineering and Computer Science, Peking University, Beijing 100871, China
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137
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Bumstead JR, Park JJ, Rosen IA, Kraft AW, Wright PW, Reisman MD, Côté DC, Culver JP. Designing a large field-of-view two-photon microscope using optical invariant analysis. NEUROPHOTONICS 2018; 5:025001. [PMID: 29487876 PMCID: PMC5818100 DOI: 10.1117/1.nph.5.2.025001] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/25/2017] [Accepted: 01/22/2018] [Indexed: 05/18/2023]
Abstract
Conventional two-photon microscopy (TPM) is capable of imaging neural dynamics with subcellular resolution, but it is limited to a field-of-view (FOV) diameter [Formula: see text]. Although there has been recent progress in extending the FOV in TPM, a principled design approach for developing large FOV TPM (LF-TPM) with off-the-shelf components has yet to be established. Therefore, we present a design strategy that depends on analyzing the optical invariant of commercially available objectives, relay lenses, mirror scanners, and emission collection systems in isolation. Components are then selected to maximize the space-bandwidth product of the integrated microscope. In comparison with other LF-TPM systems, our strategy simplifies the sequence of design decisions and is applicable to extending the FOV in any microscope with an optical relay. The microscope we constructed with this design approach can image [Formula: see text] lateral and [Formula: see text] axial resolution over a 7-mm diameter FOV, which is a 100-fold increase in FOV compared with conventional TPM. As a demonstration of the potential that LF-TPM has on understanding the microarchitecture of the mouse brain across interhemispheric regions, we performed in vivo imaging of both the cerebral vasculature and microglia cell bodies over the mouse cortex.
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Affiliation(s)
- Jonathan R. Bumstead
- Washington University in Saint Louis, Department of Biomedical Engineering, St. Louis, Missouri, United States
| | - Jasmine J. Park
- Washington University School of Medicine, Department of Radiology, St. Louis, Missouri, United States
| | - Isaac A. Rosen
- Washington University in Saint Louis, Department of Biology, St. Louis, Missouri, United States
| | - Andrew W. Kraft
- Washington University School of Medicine, Department of Neurology, St. Louis, Missouri, United States
| | - Patrick W. Wright
- Washington University in Saint Louis, Department of Biomedical Engineering, St. Louis, Missouri, United States
| | - Matthew D. Reisman
- Washington University in Saint Louis, Department of Physics, St. Louis, Missouri, United States
| | - Daniel C. Côté
- Université Laval, Génie Physique et Optique, Département de Physique, Ville de Québec, Quebec, Canada
| | - Joseph P. Culver
- Washington University in Saint Louis, Department of Biomedical Engineering, St. Louis, Missouri, United States
- Washington University School of Medicine, Department of Radiology, St. Louis, Missouri, United States
- Washington University in Saint Louis, Department of Physics, St. Louis, Missouri, United States
- Address all correspondence to: Joseph P. Culver, E-mail:
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138
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Shain WJ, Vickers NA, Li J, Han X, Bifano T, Mertz J. Axial localization with modulated-illumination extended-depth-of-field microscopy. BIOMEDICAL OPTICS EXPRESS 2018; 9:1771-1782. [PMID: 29675318 PMCID: PMC5905922 DOI: 10.1364/boe.9.001771] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/13/2017] [Revised: 03/07/2018] [Accepted: 03/07/2018] [Indexed: 05/05/2023]
Abstract
High-speed volumetric imaging represents a challenge in microscopy applications. We demonstrate a technique for acquiring volumetric images based on the extended depth of field microscopy with a fast focal scan and modulated illumination. By combining two frames with different illumination ramps, we can perform local depth ranging of the sample at speeds of up to half the camera frame rate. Our technique is light efficient, provides diffraction-limited resolution, enables axial localization that is largely independent of sample size, and can be operated with any standard widefield microscope based on fluorescence or darkfield contrast as a simple add-on. We demonstrate the accuracy of axial localization and applications of the technique to various dynamic extended samples, including in-vivo mouse brain.
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Affiliation(s)
- William J. Shain
- Dept. of Physics, Boston University, 590 Commonwealth Avenue, Boston, MA 02215,
USA
- Photonics Center, Boston University, 8 Saint Mary’s St. Boston, MA 02215,
USA
| | - Nicholas A. Vickers
- Photonics Center, Boston University, 8 Saint Mary’s St. Boston, MA 02215,
USA
- Dept. of Mechanical Engineering, Boston University, 110 Cummington Mall, Boston, MA 02215,
USA
| | - Jiang Li
- Dept. of Physics, Boston University, 590 Commonwealth Avenue, Boston, MA 02215,
USA
- Photonics Center, Boston University, 8 Saint Mary’s St. Boston, MA 02215,
USA
| | - Xue Han
- Photonics Center, Boston University, 8 Saint Mary’s St. Boston, MA 02215,
USA
- Dept. of Biomedical Engineering, Boston University, 44 Cummington Mall, Boston, MA 02215,
USA
| | - Thomas Bifano
- Photonics Center, Boston University, 8 Saint Mary’s St. Boston, MA 02215,
USA
- Dept. of Mechanical Engineering, Boston University, 110 Cummington Mall, Boston, MA 02215,
USA
| | - Jerome Mertz
- Photonics Center, Boston University, 8 Saint Mary’s St. Boston, MA 02215,
USA
- Dept. of Biomedical Engineering, Boston University, 44 Cummington Mall, Boston, MA 02215,
USA
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139
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Lu R, Tanimoto M, Koyama M, Ji N. 50 Hz volumetric functional imaging with continuously adjustable depth of focus. BIOMEDICAL OPTICS EXPRESS 2018; 9:1964-1976. [PMID: 29675332 PMCID: PMC5905937 DOI: 10.1364/boe.9.001964] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/12/2017] [Revised: 03/08/2018] [Accepted: 03/16/2018] [Indexed: 05/22/2023]
Abstract
Understanding how neural circuits control behavior requires monitoring a large population of neurons with high spatial resolution and volume rate. Here we report an axicon-based Bessel beam module with continuously adjustable depth of focus (CADoF), that turns frame rate into volume rate by extending the excitation focus in the axial direction while maintaining high lateral resolutions. Cost-effective and compact, this CADoF Bessel module can be easily integrated into existing two-photon fluorescence microscopes. Simply translating one of the relay lenses along its optical axis enabled continuous adjustment of the axial length of the Bessel focus. We used this module to simultaneously monitor activity of spinal projection neurons extending over 60 µm depth in larval zebrafish at 50 Hz volume rate with adjustable axial extent of the imaged volume.
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Affiliation(s)
- Rongwen Lu
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA
- Contributed equally
| | - Masashi Tanimoto
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA
- Division of Biological Science, Graduate School of Science, Nagoya University, Nagoya, Japan
- Contributed equally
| | - Minoru Koyama
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA
| | - Na Ji
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA
- Department of Physics and Department of Molecular & Cellular Biology, University of California, Berkeley, CA, USA
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140
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Lu R, Tanimoto M, Koyama M, Ji N. 50 Hz volumetric functional imaging with continuously adjustable depth of focus. BIOMEDICAL OPTICS EXPRESS 2018; 9:1964-1976. [PMID: 29675332 DOI: 10.1101/240069] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/12/2017] [Revised: 03/08/2018] [Accepted: 03/16/2018] [Indexed: 05/22/2023]
Abstract
Understanding how neural circuits control behavior requires monitoring a large population of neurons with high spatial resolution and volume rate. Here we report an axicon-based Bessel beam module with continuously adjustable depth of focus (CADoF), that turns frame rate into volume rate by extending the excitation focus in the axial direction while maintaining high lateral resolutions. Cost-effective and compact, this CADoF Bessel module can be easily integrated into existing two-photon fluorescence microscopes. Simply translating one of the relay lenses along its optical axis enabled continuous adjustment of the axial length of the Bessel focus. We used this module to simultaneously monitor activity of spinal projection neurons extending over 60 µm depth in larval zebrafish at 50 Hz volume rate with adjustable axial extent of the imaged volume.
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Affiliation(s)
- Rongwen Lu
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA
- Contributed equally
| | - Masashi Tanimoto
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA
- Division of Biological Science, Graduate School of Science, Nagoya University, Nagoya, Japan
- Contributed equally
| | - Minoru Koyama
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA
| | - Na Ji
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA
- Department of Physics and Department of Molecular & Cellular Biology, University of California, Berkeley, CA, USA
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141
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King SV, Yuan S, Preza C. Performance evaluation of extended depth of field microscopy in the presence of spherical aberration and noise. JOURNAL OF BIOMEDICAL OPTICS 2018; 23:1-15. [PMID: 29600602 DOI: 10.1117/1.jbo.23.3.036016] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/19/2017] [Accepted: 03/08/2018] [Indexed: 06/08/2023]
Abstract
Effectiveness of extended depth of field microscopy (EDFM) implementation with wavefront encoding methods is reduced by depth-induced spherical aberration (SA) due to reliance of this approach on a defined point spread function (PSF). Evaluation of the engineered PSF's robustness to SA, when a specific phase mask design is used, is presented in terms of the final restored image quality. Synthetic intermediate images were generated using selected generalized cubic and cubic phase mask designs. Experimental intermediate images were acquired using the same phase mask designs projected from a liquid crystal spatial light modulator. Intermediate images were restored using the penalized space-invariant expectation maximization and the regularized linear least squares algorithms. In the presence of depth-induced SA, systems characterized by radially symmetric PSFs, coupled with model-based computational methods, achieve microscope imaging performance with fewer deviations in structural fidelity (e.g., artifacts) in simulation and experiment and 50% more accurate positioning of 1-μm beads at 10-μm depth in simulation than those with radially asymmetric PSFs. Despite a drop in the signal-to-noise ratio after processing, EDFM is shown to achieve the conventional resolution limit when a model-based reconstruction algorithm with appropriate regularization is used. These trends are also found in images of fixed fluorescently labeled brine shrimp, not adjacent to the coverslip, and fluorescently labeled mitochondria in live cells.
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Affiliation(s)
- Sharon V King
- University of Memphis, Department of Electrical and Computer Engineering, Memphis, Tennessee, United States
| | - Shuai Yuan
- University of Memphis, Department of Electrical and Computer Engineering, Memphis, Tennessee, United States
| | - Chrysanthe Preza
- University of Memphis, Department of Electrical and Computer Engineering, Memphis, Tennessee, United States
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142
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Robinson JE, Gradinaru V. Dopaminergic dysfunction in neurodevelopmental disorders: recent advances and synergistic technologies to aid basic research. Curr Opin Neurobiol 2018; 48:17-29. [PMID: 28850815 PMCID: PMC5825239 DOI: 10.1016/j.conb.2017.08.003] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2017] [Accepted: 08/03/2017] [Indexed: 12/19/2022]
Abstract
Neurodevelopmental disorders (NDDs) represent a diverse group of syndromes characterized by abnormal development of the central nervous system and whose symptomatology includes cognitive, emotional, sensory, and motor impairments. The identification of causative genetic defects has allowed for creation of transgenic NDD mouse models that have revealed pathophysiological mechanisms of disease phenotypes in a neural circuit- and cell type-specific manner. Mouse models of several syndromes, including Rett syndrome, Fragile X syndrome, Angelman syndrome, Neurofibromatosis type 1, etc., exhibit abnormalities in the structure and function of dopaminergic circuitry, which regulates motivation, motor behavior, sociability, attention, and executive function. Recent advances in technologies for functional circuit mapping, including tissue clearing, viral vector-based tracing methods, and optical readouts of neural activity, have refined our knowledge of dopaminergic circuits in unperturbed states, yet these tools have not been widely applied to NDD research. Here, we will review recent findings exploring dopaminergic function in NDD models and discuss the promise of new tools to probe NDD pathophysiology in these circuits.
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Affiliation(s)
- J Elliott Robinson
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Viviana Gradinaru
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA.
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143
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Dylda E, Pakan JM, Rochefort NL. Chronic Two-Photon Calcium Imaging in the Visual Cortex of Awake Behaving Mice. ACTA ACUST UNITED AC 2018. [DOI: 10.1016/b978-0-12-812028-6.00013-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/29/2023]
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144
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Back to Pupillometry: How Cortical Network State Fluctuations Tracked by Pupil Dynamics Could Explain Neural Signal Variability in Human Cognitive Neuroscience. eNeuro 2017; 4:eN-OPN-0293-16. [PMID: 29379876 PMCID: PMC5788057 DOI: 10.1523/eneuro.0293-16.2017] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2016] [Revised: 11/12/2017] [Accepted: 11/20/2017] [Indexed: 01/01/2023] Open
Abstract
The mammalian thalamocortical system generates intrinsic activity reflecting different states of excitability, arising from changes in the membrane potentials of underlying neuronal networks. Fluctuations between these states occur spontaneously, regularly, and frequently throughout awake periods and influence stimulus encoding, information processing, and neuronal and behavioral responses. Changes of pupil size have recently been identified as a reliable marker of underlying neuronal membrane potential and thus can encode associated network state changes in rodent cortex. This suggests that pupillometry, a ubiquitous measure of pupil dilation in cognitive neuroscience, could be used as an index for network state fluctuations also for human brain signals. Considering this variable may explain task-independent variance in neuronal and behavioral signals that were previously disregarded as noise.
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Chen B, Rong H, Huang X, Wu R, Wu D, Li Y, Feng L, Zhang Z, Chen L, Wang A. Robust hollow-fiber-pigtailed 930 nm femtosecond Nd:fiber laser for volumetric two-photon imaging. OPTICS EXPRESS 2017; 25:22704-22709. [PMID: 29041577 DOI: 10.1364/oe.25.022704] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/06/2023]
Abstract
We demonstrate a robust high power 930 nm femtosecond Nd:fiber laser system with hollow-core photonic bandgap fiber (HC-PBGF) as the output delivery, which can be easily integrated into compact two-photon microscopy system for bio-imaging. The whole laser system can deliver up to 17.4 nJ, 220-fs pulses at 930 nm with repetition rate of 46 MHz. In this paper, this laser was demonstrated as the light source for volumetric imaging of zebrafish blood vessel.
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146
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Palazzolo G, Moroni M, Soloperto A, Aletti G, Naldi G, Vassalli M, Nieus T, Difato F. Fast wide-volume functional imaging of engineered in vitro brain tissues. Sci Rep 2017; 7:8499. [PMID: 28819205 PMCID: PMC5561227 DOI: 10.1038/s41598-017-08979-8] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2017] [Accepted: 07/20/2017] [Indexed: 12/14/2022] Open
Abstract
The need for in vitro models that mimic the human brain to replace animal testing and allow high-throughput screening has driven scientists to develop new tools that reproduce tissue-like features on a chip. Three-dimensional (3D) in vitro cultures are emerging as an unmatched platform that preserves the complexity of cell-to-cell connections within a tissue, improves cell survival, and boosts neuronal differentiation. In this context, new and flexible imaging approaches are required to monitor the functional states of 3D networks. Herein, we propose an experimental model based on 3D neuronal networks in an alginate hydrogel, a tunable wide-volume imaging approach, and an efficient denoising algorithm to resolve, down to single cell resolution, the 3D activity of hundreds of neurons expressing the calcium sensor GCaMP6s. Furthermore, we implemented a 3D co-culture system mimicking the contiguous interfaces of distinct brain tissues such as the cortical-hippocampal interface. The analysis of the network activity of single and layered neuronal co-cultures revealed cell-type-specific activities and an organization of neuronal subpopulations that changed in the two culture configurations. Overall, our experimental platform represents a simple, powerful and cost-effective platform for developing and monitoring living 3D layered brain tissue on chip structures with high resolution and high throughput.
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Affiliation(s)
- G Palazzolo
- Department of Neuroscience and Brain Technologies, Fondazione Istituto Italiano di Tecnologia, Genoa, Italy
| | - M Moroni
- Department of Neuroscience and Brain Technologies, Fondazione Istituto Italiano di Tecnologia, Genoa, Italy.,Center for Neuroscience and Cognitive Systems @UniTn, Istituto Italiano di Tecnologia, Rovereto, Italy.,Center for Mind/Brain Sciences, University of Trento, Rovereto, Italy
| | - A Soloperto
- Department of Neuroscience and Brain Technologies, Fondazione Istituto Italiano di Tecnologia, Genoa, Italy
| | - G Aletti
- Dipartimento di Matematica, Università degli studi di Milano, Milano, Italy
| | - G Naldi
- Dipartimento di Matematica, Università degli studi di Milano, Milano, Italy
| | - M Vassalli
- Institute of Biophysics, National Research Council of Italy, Genoa, Italy
| | - T Nieus
- Department of Biomedical and Clinical Sciences "L. Sacco", Università degli Studi di Milano, Milano, Italy.
| | - F Difato
- Department of Neuroscience and Brain Technologies, Fondazione Istituto Italiano di Tecnologia, Genoa, Italy.
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147
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Friedrich J, Yang W, Soudry D, Mu Y, Ahrens MB, Yuste R, Peterka DS, Paninski L. Multi-scale approaches for high-speed imaging and analysis of large neural populations. PLoS Comput Biol 2017; 13:e1005685. [PMID: 28771570 PMCID: PMC5557609 DOI: 10.1371/journal.pcbi.1005685] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2016] [Revised: 08/15/2017] [Accepted: 07/14/2017] [Indexed: 11/19/2022] Open
Abstract
Progress in modern neuroscience critically depends on our ability to observe the activity of large neuronal populations with cellular spatial and high temporal resolution. However, two bottlenecks constrain efforts towards fast imaging of large populations. First, the resulting large video data is challenging to analyze. Second, there is an explicit tradeoff between imaging speed, signal-to-noise, and field of view: with current recording technology we cannot image very large neuronal populations with simultaneously high spatial and temporal resolution. Here we describe multi-scale approaches for alleviating both of these bottlenecks. First, we show that spatial and temporal decimation techniques based on simple local averaging provide order-of-magnitude speedups in spatiotemporally demixing calcium video data into estimates of single-cell neural activity. Second, once the shapes of individual neurons have been identified at fine scale (e.g., after an initial phase of conventional imaging with standard temporal and spatial resolution), we find that the spatial/temporal resolution tradeoff shifts dramatically: after demixing we can accurately recover denoised fluorescence traces and deconvolved neural activity of each individual neuron from coarse scale data that has been spatially decimated by an order of magnitude. This offers a cheap method for compressing this large video data, and also implies that it is possible to either speed up imaging significantly, or to "zoom out" by a corresponding factor to image order-of-magnitude larger neuronal populations with minimal loss in accuracy or temporal resolution.
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Affiliation(s)
- Johannes Friedrich
- Department of Statistics, Grossman Center for the Statistics of Mind, and Center for Theoretical Neuroscience, Columbia University, New York, New York, United States of America
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, Virginia, United States of America
- * E-mail: (JF); (LP)
| | - Weijian Yang
- NeuroTechnology Center, Department of Biological Sciences, Columbia University, New York, New York, United States of America
| | - Daniel Soudry
- Department of Statistics, Grossman Center for the Statistics of Mind, and Center for Theoretical Neuroscience, Columbia University, New York, New York, United States of America
| | - Yu Mu
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, Virginia, United States of America
| | - Misha B. Ahrens
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, Virginia, United States of America
| | - Rafael Yuste
- NeuroTechnology Center, Department of Biological Sciences, Columbia University, New York, New York, United States of America
- Kavli Institute of Brain Science, Columbia University, New York, New York, United States of America
| | - Darcy S. Peterka
- NeuroTechnology Center, Department of Biological Sciences, Columbia University, New York, New York, United States of America
- Zuckerman Mind Brain Behavior Institute, Columbia University, New York, New York, United States of America
| | - Liam Paninski
- Department of Statistics, Grossman Center for the Statistics of Mind, and Center for Theoretical Neuroscience, Columbia University, New York, New York, United States of America
- NeuroTechnology Center, Department of Biological Sciences, Columbia University, New York, New York, United States of America
- Kavli Institute of Brain Science, Columbia University, New York, New York, United States of America
- Zuckerman Mind Brain Behavior Institute, Columbia University, New York, New York, United States of America
- * E-mail: (JF); (LP)
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148
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Neuronal cell-type classification: challenges, opportunities and the path forward. Nat Rev Neurosci 2017; 18:530-546. [PMID: 28775344 DOI: 10.1038/nrn.2017.85] [Citation(s) in RCA: 471] [Impact Index Per Article: 67.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Neurons have diverse molecular, morphological, connectional and functional properties. We believe that the only realistic way to manage this complexity - and thereby pave the way for understanding the structure, function and development of brain circuits - is to group neurons into types, which can then be analysed systematically and reproducibly. However, neuronal classification has been challenging both technically and conceptually. New high-throughput methods have created opportunities to address the technical challenges associated with neuronal classification by collecting comprehensive information about individual cells. Nonetheless, conceptual difficulties persist. Borrowing from the field of species taxonomy, we propose principles to be followed in the cell-type classification effort, including the incorporation of multiple, quantitative features as criteria, the use of discontinuous variation to define types and the creation of a hierarchical system to represent relationships between cells. We review the progress of classifying cell types in the retina and cerebral cortex and propose a staged approach for moving forward with a systematic cell-type classification in the nervous system.
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149
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Nöbauer T, Skocek O, Pernía-Andrade AJ, Weilguny L, Traub FM, Molodtsov MI, Vaziri A. Video rate volumetric Ca2+ imaging across cortex using seeded iterative demixing (SID) microscopy. Nat Methods 2017. [DOI: 10.1038/nmeth.4341] [Citation(s) in RCA: 102] [Impact Index Per Article: 14.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
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150
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Shaping up two-photon imaging in vivo. Lab Anim (NY) 2017. [DOI: 10.1038/laban.1266] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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