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Uhlířová H, Stibůrek M, Pikálek T, Gomes A, Turtaev S, Kolbábková P, Čižmár T. "There's plenty of room at the bottom": deep brain imaging with holographic endo-microscopy. NEUROPHOTONICS 2024; 11:S11504. [PMID: 38250297 PMCID: PMC10798506 DOI: 10.1117/1.nph.11.s1.s11504] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/14/2023] [Revised: 12/09/2023] [Accepted: 12/14/2023] [Indexed: 01/23/2024]
Abstract
Significance Over more than 300 years, microscopic imaging keeps providing fundamental insights into the mechanisms of living organisms. Seeing microscopic structures beyond the reach of free-space light-based microscopy, however, requires dissection of the tissue-an intervention seriously disturbing its physiological functions. The hunt for low-invasiveness tools has led a growing community of physicists and engineers into the realm of complex media photonics. One of its activities represents exploiting multimode optical fibers (MMFs) as ultra-thin endoscopic probes. Employing wavefront shaping, these tools only recently facilitated the first peeks at cells and their sub-cellular compartments at the bottom of the mouse brain with the impact of micro-scale tissue damage. Aim Here, we aim to highlight advances in MMF-based holographic endo-microscopy facilitating microscopic imaging throughout the whole depth of the mouse brain. Approach We summarize the important technical and methodological prerequisites for stabile high-resolution imaging in vivo. Results We showcase images of the microscopic building blocks of brain tissue, including neurons, neuronal processes, vessels, intracellular calcium signaling, and red blood cell velocity in individual vessels. Conclusions This perspective article helps to understand the complexity behind the technology of holographic endo-microscopy, summarizes its recent advances and challenges, and stimulates the mind of the reader for further exploitation of this tool in the neuroscience research.
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Affiliation(s)
- Hana Uhlířová
- Institute of Scientific Instruments of the Czech Academy of Sciences, Brno, Czech Republic
| | - Miroslav Stibůrek
- Institute of Scientific Instruments of the Czech Academy of Sciences, Brno, Czech Republic
| | - Tomáš Pikálek
- Institute of Scientific Instruments of the Czech Academy of Sciences, Brno, Czech Republic
| | - André Gomes
- Leibniz Institute of Photonic Technology, Jena, Germany
| | | | - Petra Kolbábková
- Institute of Scientific Instruments of the Czech Academy of Sciences, Brno, Czech Republic
| | - Tomáš Čižmár
- Institute of Scientific Instruments of the Czech Academy of Sciences, Brno, Czech Republic
- Leibniz Institute of Photonic Technology, Jena, Germany
- Friedrich Schiller University Jena, Institute of Applied Optics, Jena, Germany
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2
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Phil Brooks F, Davis HC, Wong-Campos JD, Cohen AE. Optical constraints on two-photon voltage imaging. NEUROPHOTONICS 2024; 11:035007. [PMID: 39139631 PMCID: PMC11321468 DOI: 10.1117/1.nph.11.3.035007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/28/2024] [Revised: 07/23/2024] [Accepted: 07/25/2024] [Indexed: 08/15/2024]
Abstract
Significance Genetically encoded voltage indicators (GEVIs) are a valuable tool for studying neural circuits in vivo, but the relative merits and limitations of one-photon (1P) versus two-photon (2P) voltage imaging are not well characterized. Aim We consider the optical and biophysical constraints particular to 1P and 2P voltage imaging and compare the imaging properties of commonly used GEVIs under 1P and 2P excitation. Approach We measure the brightness and voltage sensitivity of voltage indicators from commonly used classes under 1P and 2P illumination. We also measure the decrease in fluorescence as a function of depth in the mouse brain. We develop a simple model of the number of measurable cells as a function of reporter properties, imaging parameters, and desired signal-to-noise ratio (SNR). We then discuss how the performance of voltage imaging would be affected by sensor improvements and by recently introduced advanced imaging modalities. Results Compared with 1P excitation, 2P excitation requires ∼ 10 4 -fold more illumination power per cell to produce similar photon count rates. For voltage imaging with JEDI-2P in the mouse cortex with a target SNR of 10 (spike height to baseline shot noise), a measurement bandwidth of 1 kHz, a thermally limited laser power of 200 mW, and an imaging depth of > 300 μ m , 2P voltage imaging using an 80-MHz source can record from no more than ∼ 12 neurons simultaneously. Conclusions Due to the stringent photon-count requirements of voltage imaging and the modest voltage sensitivity of existing reporters, 2P voltage imaging in vivo faces a stringent tradeoff between shot noise and tissue photodamage. 2P imaging of hundreds of neurons with high SNR at a depth of > 300 μ m will require either major improvements in 2P GEVIs or qualitatively new approaches to imaging.
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Affiliation(s)
- F. Phil Brooks
- Harvard University, Department of Chemistry and Chemical Biology, Cambridge, Massachusetts, United States
| | - Hunter C. Davis
- Harvard University, Department of Chemistry and Chemical Biology, Cambridge, Massachusetts, United States
| | - J. David Wong-Campos
- Harvard University, Department of Chemistry and Chemical Biology, Cambridge, Massachusetts, United States
| | - Adam E. Cohen
- Harvard University, Department of Chemistry and Chemical Biology, Cambridge, Massachusetts, United States
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Zhang H, Xu Z, Chen N, Ma F, Zheng W, Liu C, Meng J. Simultaneous removal of noise and correction of motion warping in neuron calcium imaging using a pipeline structure of self-supervised deep learning models. BIOMEDICAL OPTICS EXPRESS 2024; 15:4300-4317. [PMID: 39022541 PMCID: PMC11249678 DOI: 10.1364/boe.527919] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/19/2024] [Revised: 06/07/2024] [Accepted: 06/10/2024] [Indexed: 07/20/2024]
Abstract
Calcium imaging is susceptible to motion distortions and background noises, particularly for monitoring active animals under low-dose laser irradiation, and hence unavoidably hinder the critical analysis of neural functions. Current research efforts tend to focus on either denoising or dewarping and do not provide effective methods for videos distorted by both noises and motion artifacts simultaneously. We found that when a self-supervised denoising model of DeepCAD [Nat. Methods18, 1359 (2021)10.1038/s41592-021-01225-0] is used on the calcium imaging contaminated by noise and motion warping, it can remove the motion artifacts effectively but with regenerated noises. To address this issue, we develop a two-level deep-learning (DL) pipeline to dewarp and denoise the calcium imaging video sequentially. The pipeline consists of two 3D self-supervised DL models that do not require warp-free and high signal-to-noise ratio (SNR) observations for network optimization. Specifically, a high-frequency enhancement block is presented in the denoising network to restore more structure information in the denoising process; a hierarchical perception module and a multi-scale attention module are designed in the dewarping network to tackle distortions of various sizes. Experiments conducted on seven videos from two-photon and confocal imaging systems demonstrate that our two-level DL pipeline can restore high-clarity neuron images distorted by both motion warping and background noises. Compared to typical DeepCAD, our denoising model achieves a significant improvement of approximately 30% in image resolution and up to 28% in signal-to-noise ratio; compared to traditional dewarping and denoising methods, our proposed pipeline network recovers more neurons, enhancing signal fidelity and improving data correlation among frames by 35% and 60% respectively. This work may provide an attractive method for long-term neural activity monitoring in awake animals and also facilitate functional analysis of neural circuits.
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Affiliation(s)
- Hongdong Zhang
- School of Computer, Qufu Normal University, Rizhao 276826, China
| | - Zhiqiang Xu
- Institute of Biomedical and Health Engineering, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
| | - Ningbo Chen
- Institute of Biomedical and Health Engineering, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
| | - Fei Ma
- School of Computer, Qufu Normal University, Rizhao 276826, China
| | - Wei Zheng
- Institute of Biomedical and Health Engineering, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
| | - Chengbo Liu
- Institute of Biomedical and Health Engineering, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
| | - Jing Meng
- School of Computer, Qufu Normal University, Rizhao 276826, China
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Liu C, Hao Y, Lei B, Zhong Y, Kong L. Removing crosstalk signals in neuron activity by time multiplexed excitations in a two-photon all-optical physiology system. BIOMEDICAL OPTICS EXPRESS 2024; 15:2708-2718. [PMID: 38633062 PMCID: PMC11019693 DOI: 10.1364/boe.521047] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/06/2024] [Revised: 03/11/2024] [Accepted: 03/11/2024] [Indexed: 04/19/2024]
Abstract
The two-photon all-optical physiology system has attracted great interest in deciphering neuronal circuits in vivo, benefiting from its advantages in recording and modulating neuronal activities at single neuron resolutions. However, the interference, or crosstalk, between the imaging and photostimulation beams introduces a significant challenge and may impede the future application of voltage indicators in two-photon all-optical physiology system. Here, we propose the time multiplexed excitation method to distinguish signals from neuronal activities and crosstalks from photostimulation. In our system, the laser pulses of the imaging beam and photostimulation beam are synchronized, and a time delay is introduced into these pulses to separate the fluorescence signal generated by these two beams. We demonstrate the efficacy of our system in eliminating crosstalk signals from photostimulation and evaluate its influence on both genetically encoded calcium indicators (GECIs) and genetically encoded voltage indicators (GEVIs) through in vivo experiments.
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Affiliation(s)
- Chi Liu
- State Key Laboratory of Precision Measurement Technology and Instruments, Department of Precision Instrument, Tsinghua University, Beijing 100084, China
| | - Yuejun Hao
- IDG/McGovern Institute for Brain Research, Tsinghua University, Beijing 100084, China
- Tsinghua-Peking Center for Life Sciences, Tsinghua University, Beijing 100084, China
- School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Bo Lei
- IDG/McGovern Institute for Brain Research, Tsinghua University, Beijing 100084, China
- Tsinghua-Peking Center for Life Sciences, Tsinghua University, Beijing 100084, China
- Beijing Academy of Artificial Intelligence, Beijing 100084, China
| | - Yi Zhong
- IDG/McGovern Institute for Brain Research, Tsinghua University, Beijing 100084, China
- Tsinghua-Peking Center for Life Sciences, Tsinghua University, Beijing 100084, China
- School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Lingjie Kong
- State Key Laboratory of Precision Measurement Technology and Instruments, Department of Precision Instrument, Tsinghua University, Beijing 100084, China
- IDG/McGovern Institute for Brain Research, Tsinghua University, Beijing 100084, China
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Vilar N, Artigas R, Duocastella M, Carles G. Fast topographic optical imaging using encoded search focal scan. Nat Commun 2024; 15:2065. [PMID: 38453926 PMCID: PMC10920621 DOI: 10.1038/s41467-024-46267-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2023] [Accepted: 02/21/2024] [Indexed: 03/09/2024] Open
Abstract
A central quest in optics is to rapidly extract quantitative information from a sample. Existing topographical imaging tools allow non-contact and three-dimensional measurements at the micro and nanoscales and are essential in applications including precision engineering and optical quality control. However, these techniques involve acquiring a focal stack of images, a time-consuming process that prevents measurement of moving samples. Here, we propose a method for increasing the speed of topographic imaging by orders of magnitude. Our approach involves collecting a reduced set of images, each integrated during the full focal scan, whilst the illumination is synchronously modulated during exposure. By properly designing the modulation sequence for each image, unambiguous reconstruction of the object height map is achieved using far fewer images than conventional methods. We describe the theoretical foundations of our technique, characterise its performance, and demonstrate sub-micrometric topographic imaging over 100 µm range of static and dynamic systems at rates as high as 67 topographies per second, limited by the camera frame rate. The high speed of the technique and its ease of implementation could enable a paradigm shift in optical metrology, allowing the real-time characterisation of large or rapidly moving samples.
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Affiliation(s)
- Narcís Vilar
- Sensofar Tech S.L, Parc audiovisual de Catalunya, BV-1274 km 1, 08225, Terrassa, Spain
- Department of Applied Physics, Universitat de Barcelona, C/Martí i Franquès 1, 08028, Barcelona, Spain
| | - Roger Artigas
- Sensofar Tech S.L, Parc audiovisual de Catalunya, BV-1274 km 1, 08225, Terrassa, Spain
| | - Martí Duocastella
- Department of Applied Physics, Universitat de Barcelona, C/Martí i Franquès 1, 08028, Barcelona, Spain.
| | - Guillem Carles
- Sensofar Tech S.L, Parc audiovisual de Catalunya, BV-1274 km 1, 08225, Terrassa, Spain.
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6
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Kume D, Kozawa Y, Kawakami R, Ishii H, Watakabe Y, Uesugi Y, Imamura T, Nemoto T, Sato S. Graded arc beam in light needle microscopy for axially resolved, rapid volumetric imaging without nonlinear processes. OPTICS EXPRESS 2024; 32:7289-7306. [PMID: 38439413 DOI: 10.1364/oe.516437] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/21/2023] [Accepted: 02/06/2024] [Indexed: 03/06/2024]
Abstract
High-speed three-dimensional (3D) imaging is essential for revealing the structure and functions of biological specimens. Confocal laser scanning microscopy has been widely employed for this purpose. However, it requires a time-consuming image-stacking procedure. As a solution, we previously developed light needle microscopy using a Bessel beam with a wavefront-engineered approach [Biomed. Opt. Express13, 1702 (2022)10.1364/BOE.449329]. However, this method applies only to multiphoton excitation microscopy because of the requirement to reduce the sidelobes of the Bessel beam. Here, we introduce a beam that produces a needle spot while eluding the intractable artifacts due to the sidelobes. This beam can be adopted even in one-photon excitation fluorescence 3D imaging. The proposed method can achieve real-time, rapid 3D observation of 200-nm particles in water at a rate of over 50 volumes per second. In addition, fine structures, such as the spines of neurons in fixed mouse brain tissue, can be visualized in 3D from a single raster scan of the needle spot. The proposed method can be applied to various modalities in biological imaging, enabling rapid 3D image acquisition.
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7
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Giacomelli MG. Optimal real-time resonant scanner linearization using filtered Hermite interpolation. BIOMEDICAL OPTICS EXPRESS 2023; 14:5861-5869. [PMID: 38021131 PMCID: PMC10659797 DOI: 10.1364/boe.504764] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2023] [Revised: 10/11/2023] [Accepted: 10/11/2023] [Indexed: 12/01/2023]
Abstract
High-speed laser scanning microscopy frequently relies on resonant scanners due to their order of magnitude increase in imaging rate compared to conventional galvanometer scanners. However, the use of a nonlinear scan trajectory introduces distortion that must be corrected. This manuscript derives a new algorithm based on filtered Hermite polynomial interpolation that provides the optimal shot-noise-limited SNR for a fixed number of photons and provides higher spatial accuracy than previous methods. An open-source library is presented using the Intel advanced vector instruction set (AVX) to process up to 32 samples in parallel. Using this approach, I simultaneously demonstrate lower shot noise variance, moderately higher spatial accuracy and greater than 1 gigapixel per second interpolation rate on a desktop CPU.
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Affiliation(s)
- Michael G. Giacomelli
- Department of Biomedical Engineering, University of Rochester, 207 Goergen Hall, Box 270168, Rochester, NY 14627, USA
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8
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Platisa J, Ye X, Ahrens AM, Liu C, Chen IA, Davison IG, Tian L, Pieribone VA, Chen JL. High-speed low-light in vivo two-photon voltage imaging of large neuronal populations. Nat Methods 2023; 20:1095-1103. [PMID: 36973547 PMCID: PMC10894646 DOI: 10.1038/s41592-023-01820-3] [Citation(s) in RCA: 24] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2022] [Accepted: 02/16/2023] [Indexed: 03/29/2023]
Abstract
Monitoring spiking activity across large neuronal populations at behaviorally relevant timescales is critical for understanding neural circuit function. Unlike calcium imaging, voltage imaging requires kilohertz sampling rates that reduce fluorescence detection to near shot-noise levels. High-photon flux excitation can overcome photon-limited shot noise, but photobleaching and photodamage restrict the number and duration of simultaneously imaged neurons. We investigated an alternative approach aimed at low two-photon flux, which is voltage imaging below the shot-noise limit. This framework involved developing positive-going voltage indicators with improved spike detection (SpikeyGi and SpikeyGi2); a two-photon microscope ('SMURF') for kilohertz frame rate imaging across a 0.4 mm × 0.4 mm field of view; and a self-supervised denoising algorithm (DeepVID) for inferring fluorescence from shot-noise-limited signals. Through these combined advances, we achieved simultaneous high-speed deep-tissue imaging of more than 100 densely labeled neurons over 1 hour in awake behaving mice. This demonstrates a scalable approach for voltage imaging across increasing neuronal populations.
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Affiliation(s)
- Jelena Platisa
- Department of Cellular and Molecular Physiology, Yale University, New Haven, CT, USA
- The John B. Pierce Laboratory, New Haven, CT, USA
| | - Xin Ye
- Department of Biomedical Engineering, Boston University, Boston, MA, USA
- Neurophotonics Center, Boston University, Boston, MA, USA
| | | | - Chang Liu
- Department of Biomedical Engineering, Boston University, Boston, MA, USA
| | | | - Ian G Davison
- Neurophotonics Center, Boston University, Boston, MA, USA
- Department of Biology, Boston University, Boston, MA, USA
- Center for Systems Neuroscience, Boston University, Boston, MA, USA
| | - Lei Tian
- Department of Biomedical Engineering, Boston University, Boston, MA, USA
- Neurophotonics Center, Boston University, Boston, MA, USA
- Department of Electrical and Computer Engineering, Boston University, Boston, MA, USA
| | - Vincent A Pieribone
- Department of Cellular and Molecular Physiology, Yale University, New Haven, CT, USA.
- The John B. Pierce Laboratory, New Haven, CT, USA.
- Department of Neuroscience, Yale University, New Haven, CT, USA.
| | - Jerry L Chen
- Department of Biomedical Engineering, Boston University, Boston, MA, USA.
- Neurophotonics Center, Boston University, Boston, MA, USA.
- Department of Biology, Boston University, Boston, MA, USA.
- Center for Systems Neuroscience, Boston University, Boston, MA, USA.
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9
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Hernández IC, Yau J, Rishøj L, Cui N, Minderler S, Jowett N. Tutorial: multiphoton microscopy to advance neuroscience research. Methods Appl Fluoresc 2023; 11. [PMID: 36753763 DOI: 10.1088/2050-6120/acba66] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2022] [Accepted: 02/08/2023] [Indexed: 02/10/2023]
Abstract
Multiphoton microscopy (MPM) employs ultrafast infrared lasers for high-resolution deep three-dimensional imaging of live biological samples. The goal of this tutorial is to provide a practical guide to MPM imaging for novice microscopy developers and life-science users. Principles of MPM, microscope setup, and labeling strategies are discussed. Use of MPM to achieve unprecedented imaging depth of whole mounted explants and intravital imaging via implantable glass windows of the mammalian nervous system is demonstrated.
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Affiliation(s)
- Iván Coto Hernández
- Surgical Photonics & Engineering Laboratory, Mass Eye and Ear, Harvard Medical School, 243 Charles St, Boston, MA, United States of America
| | - Jenny Yau
- Surgical Photonics & Engineering Laboratory, Mass Eye and Ear, Harvard Medical School, 243 Charles St, Boston, MA, United States of America
| | - Lars Rishøj
- Technical University of Denmark, DTU Electro, Ørsteds Plads 343, 2800 Kgs. Lyngby, Denmark
| | - Nanke Cui
- Surgical Photonics & Engineering Laboratory, Mass Eye and Ear, Harvard Medical School, 243 Charles St, Boston, MA, United States of America
| | - Steven Minderler
- Surgical Photonics & Engineering Laboratory, Mass Eye and Ear, Harvard Medical School, 243 Charles St, Boston, MA, United States of America
| | - Nate Jowett
- Surgical Photonics & Engineering Laboratory, Mass Eye and Ear, Harvard Medical School, 243 Charles St, Boston, MA, United States of America
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Bai L, Zhang Z, Ye L, Cong L, Zhao Y, Zhang T, Shi Z, Wang K. Volumetric Imaging of Neural Activity by Light Field Microscopy. Neurosci Bull 2022; 38:1559-1568. [PMID: 35939199 PMCID: PMC9723040 DOI: 10.1007/s12264-022-00923-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2022] [Accepted: 06/10/2022] [Indexed: 10/15/2022] Open
Abstract
Recording the highly diverse and dynamic activities in large populations of neurons in behaving animals is crucial for a better understanding of how the brain works. To meet this challenge, extensive efforts have been devoted to developing functional fluorescent indicators and optical imaging techniques to optically monitor neural activity. Indeed, optical imaging potentially has extremely high throughput due to its non-invasive access to large brain regions and capability to sample neurons at high density, but the readout speed, such as the scanning speed in two-photon scanning microscopy, is often limited by various practical considerations. Among different imaging methods, light field microscopy features a highly parallelized 3D fluorescence imaging scheme and therefore promises a novel and faster strategy for functional imaging of neural activity. Here, we briefly review the working principles of various types of light field microscopes and their recent developments and applications in neuroscience studies. We also discuss strategies and considerations of optimizing light field microscopy for different experimental purposes, with illustrative examples in imaging zebrafish and mouse brains.
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Affiliation(s)
- Lu Bai
- Institute of Neuroscience, State Key Laboratory of Neuroscience, Center for Excellence in Brain Science and Intelligence Technology, Chinese Academy of Sciences, Shanghai, 200031, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Zhenkun Zhang
- Institute of Neuroscience, State Key Laboratory of Neuroscience, Center for Excellence in Brain Science and Intelligence Technology, Chinese Academy of Sciences, Shanghai, 200031, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Lichen Ye
- Institute of Neuroscience, State Key Laboratory of Neuroscience, Center for Excellence in Brain Science and Intelligence Technology, Chinese Academy of Sciences, Shanghai, 200031, China
| | - Lin Cong
- Institute of Neuroscience, State Key Laboratory of Neuroscience, Center for Excellence in Brain Science and Intelligence Technology, Chinese Academy of Sciences, Shanghai, 200031, China
| | - Yuchen Zhao
- Institute of Neuroscience, State Key Laboratory of Neuroscience, Center for Excellence in Brain Science and Intelligence Technology, Chinese Academy of Sciences, Shanghai, 200031, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Tianlei Zhang
- Institute of Neuroscience, State Key Laboratory of Neuroscience, Center for Excellence in Brain Science and Intelligence Technology, Chinese Academy of Sciences, Shanghai, 200031, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Ziqi Shi
- Institute of Neuroscience, State Key Laboratory of Neuroscience, Center for Excellence in Brain Science and Intelligence Technology, Chinese Academy of Sciences, Shanghai, 200031, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Kai Wang
- Institute of Neuroscience, State Key Laboratory of Neuroscience, Center for Excellence in Brain Science and Intelligence Technology, Chinese Academy of Sciences, Shanghai, 200031, China.
- University of Chinese Academy of Sciences, Beijing, 100049, China.
- Shanghai Center for Brain Science and Brain-Inspired Intelligence Technology, Shanghai, 201210, China.
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11
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Zhang Z, Jiang S, Shi K, Li Y, Jin WN, Liu Q, Zhao T, Cheng H, Shi FD. Visualizing Seizure Propagation in Freely-moving Mice via Miniature Two-photon Microscopy. Neurosci Bull 2022; 38:1593-1597. [PMID: 36161581 PMCID: PMC9723026 DOI: 10.1007/s12264-022-00947-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2022] [Accepted: 05/27/2022] [Indexed: 02/07/2023] Open
Affiliation(s)
- Zhuoran Zhang
- Department of Neurology, Tianjin Medical University General Hospital, Tianjin, 300052, China
- Center for Neurological Diseases, China National Clinical Research Center for Neurological Diseases, Beijing Tiantan Hospital, Capital Medical University, Beijing, 100070, China
| | - Shihe Jiang
- Department of Neurology, Tianjin Medical University General Hospital, Tianjin, 300052, China
- Center for Neurological Diseases, China National Clinical Research Center for Neurological Diseases, Beijing Tiantan Hospital, Capital Medical University, Beijing, 100070, China
| | - Kaibin Shi
- Department of Neurology, Tianjin Medical University General Hospital, Tianjin, 300052, China
- Center for Neurological Diseases, China National Clinical Research Center for Neurological Diseases, Beijing Tiantan Hospital, Capital Medical University, Beijing, 100070, China
| | - Yan Li
- Department of Neurology, Tianjin Medical University General Hospital, Tianjin, 300052, China
| | - Wei-Na Jin
- Center for Neurological Diseases, China National Clinical Research Center for Neurological Diseases, Beijing Tiantan Hospital, Capital Medical University, Beijing, 100070, China
| | - Qiang Liu
- Department of Neurology, Tianjin Medical University General Hospital, Tianjin, 300052, China
| | - Ting Zhao
- Nanjing Brain Observatory, PKU-Nanjing Institute of Translational Medicine, Nanjing, 211899, China
| | - Heping Cheng
- State Key Laboratory of Membrane Biology, Institute of Molecular Medicine, Peking-Tsinghua Center for Life Sciences, College of Future Technology, Peking University, Beijing, 100091, China
| | - Fu-Dong Shi
- Department of Neurology, Tianjin Medical University General Hospital, Tianjin, 300052, China.
- Center for Neurological Diseases, China National Clinical Research Center for Neurological Diseases, Beijing Tiantan Hospital, Capital Medical University, Beijing, 100070, China.
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12
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Lin J, Cheng Z, Yang G, Cui M. Optical gearbox enabled versatile multiscale high-throughput multiphoton functional imaging. Nat Commun 2022; 13:6564. [PMID: 36323707 PMCID: PMC9630539 DOI: 10.1038/s41467-022-34472-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2022] [Accepted: 10/19/2022] [Indexed: 11/05/2022] Open
Abstract
To understand the function and mechanism of biological systems, it is crucial to observe the cellular dynamics at high spatiotemporal resolutions within live animals. The recent advances in genetically encoded function indicators have significantly improved the response rate to a near millisecond time scale. However, the widely employed in vivo imaging systems often lack the temporal solution to capture the fast biological dynamics. To broadly enable the capability of high-speed in vivo deep-tissue imaging, we developed an optical gearbox. As an add-on module, the optical gearbox can convert the common multiphoton imaging systems for versatile multiscale high-throughput imaging applications. In this work, we demonstrate in vivo 2D and 3D function imaging in mammalian brains at frame rates ranging from 50 to 1000 Hz. The optical gearbox's versatility and compatibility with the widely employed imaging components will be highly valuable to a variety of deep tissue imaging applications.
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Affiliation(s)
- Jianian Lin
- School of Electrical and Computer Engineering, Purdue University, West Lafayette, IN, 47907, USA
- Bindley Bioscience Center, Purdue University, West Lafayette, IN, 47907, USA
| | - Zongyue Cheng
- School of Electrical and Computer Engineering, Purdue University, West Lafayette, IN, 47907, USA
- Bindley Bioscience Center, Purdue University, West Lafayette, IN, 47907, USA
| | - Guang Yang
- Department of Anesthesiology, Columbia University Irving Medical Center, New York, NY, 10032, USA
| | - Meng Cui
- School of Electrical and Computer Engineering, Purdue University, West Lafayette, IN, 47907, USA.
- Bindley Bioscience Center, Purdue University, West Lafayette, IN, 47907, USA.
- Department of Biology, Purdue University, West Lafayette, IN, 47907, USA.
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13
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Grienberger C, Giovannucci A, Zeiger W, Portera-Cailliau C. Two-photon calcium imaging of neuronal activity. NATURE REVIEWS. METHODS PRIMERS 2022; 2:67. [PMID: 38124998 PMCID: PMC10732251 DOI: 10.1038/s43586-022-00147-1] [Citation(s) in RCA: 37] [Impact Index Per Article: 18.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 07/07/2022] [Indexed: 12/23/2023]
Abstract
In vivo two-photon calcium imaging (2PCI) is a technique used for recording neuronal activity in the intact brain. It is based on the principle that, when neurons fire action potentials, intracellular calcium levels rise, which can be detected using fluorescent molecules that bind to calcium. This Primer is designed for scientists who are considering embarking on experiments with 2PCI. We provide the reader with a background on the basic concepts behind calcium imaging and on the reasons why 2PCI is an increasingly powerful and versatile technique in neuroscience. The Primer explains the different steps involved in experiments with 2PCI, provides examples of what ideal preparations should look like and explains how data are analysed. We also discuss some of the current limitations of the technique, and the types of solutions to circumvent them. Finally, we conclude by anticipating what the future of 2PCI might look like, emphasizing some of the analysis pipelines that are being developed and international efforts for data sharing.
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Affiliation(s)
- Christine Grienberger
- Department of Biology and Volen National Center for Complex Systems, Brandeis University, Waltham, MA, USA
| | - Andrea Giovannucci
- Joint Department of Biomedical Engineering University of North Carolina at Chapel Hill and North Carolina State University, Chapel Hill, NC, USA
- UNC Neuroscience Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - William Zeiger
- Department of Neurology, David Geffen School of Medicine at UCLA, Los Angeles, CA, USA
| | - Carlos Portera-Cailliau
- Department of Neurology, David Geffen School of Medicine at UCLA, Los Angeles, CA, USA
- Department of Neurobiology, David Geffen School of Medicine at UCLA, Los Angeles, CA, USA
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14
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Xu D, Ding JB, Peng L. Depth random-access two-photon Bessel light-sheet imaging in brain tissue. OPTICS EXPRESS 2022; 30:26396-26406. [PMID: 36236832 PMCID: PMC9363024 DOI: 10.1364/oe.456871] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/22/2022] [Revised: 05/27/2022] [Accepted: 06/07/2022] [Indexed: 06/16/2023]
Abstract
Two-photon light-sheet fluorescence microscopy enables high-resolution imaging of neural activity in brain tissue at a high frame rate. Traditionally, light-sheet microscopy builds up a 3D stack by multiple depth scans with uniform spatial intervals, which substantially limits the volumetric imaging speed. Here, we introduce the depth random-access light-sheet microscopy, allowing rapid switching scanning depth for light-sheet imaging. With a low-cost electrically tunable lens and minimum modification of an existing two-photon light-sheet imaging instrument, we demonstrated fast random depth hopping light-sheet imaging at 100 frames per second in the live brain slice. Through depth random-access, calcium activities for an astrocyte were recorded on four user-selected detection planes at a refreshing rate of 25 Hz.
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Affiliation(s)
- Dongli Xu
- College of Optical Science, The University of Arizona, Tucson, AZ 85721, USA
- Department of Neurosurgery, Department of Neurology and Neurological Sciences, Wu-Tsai Neuroscience Institute, Stanford University, Stanford, CA 94305, USA
| | - Jun B. Ding
- Department of Neurosurgery, Department of Neurology and Neurological Sciences, Wu-Tsai Neuroscience Institute, Stanford University, Stanford, CA 94305, USA
| | - Leilei Peng
- College of Optical Science, The University of Arizona, Tucson, AZ 85721, USA
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15
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Generation of A Space-Variant Vector Beam with Catenary-Shaped Polarization States. MATERIALS 2022; 15:ma15082940. [PMID: 35454633 PMCID: PMC9026301 DOI: 10.3390/ma15082940] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/11/2022] [Revised: 04/12/2022] [Accepted: 04/15/2022] [Indexed: 11/17/2022]
Abstract
We demonstrate the generation of a space-variant vector beam with catenary-shaped polarization states based on the polarization interferometry. With a spatial light modulator and a common path interferometric configuration, two orthogonally circularly polarized beams with different phase modulation overlap each other, yielding the vector beams. In addition, the polarization states of this vector beam are scalable to the arbitrary spatial distribution because of its great flexibility and universal applicability. It is expected that this vector beam may have many potential and intriguing applications in the micro/nano material processing, liquid crystal elements fabrication and optical micro-manipulation, and so on.
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16
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Flores-Valle A, Seelig JD. Axial motion estimation and correction for simultaneous multi-plane two-photon calcium imaging. BIOMEDICAL OPTICS EXPRESS 2022; 13:2035-2049. [PMID: 35519241 PMCID: PMC9045928 DOI: 10.1364/boe.445775] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/13/2021] [Revised: 12/16/2021] [Accepted: 02/01/2022] [Indexed: 06/14/2023]
Abstract
Two-photon imaging in behaving animals is typically accompanied by brain motion. For functional imaging experiments, for example with genetically encoded calcium indicators, such brain motion induces changes in fluorescence intensity. These motion-related intensity changes or motion artifacts can typically not be separated from neural activity-induced signals. While lateral motion, within the focal plane, can be corrected by computationally aligning images, axial motion, out of the focal plane, cannot easily be corrected. Here, we developed an algorithm for axial motion correction for non-ratiometric calcium indicators taking advantage of simultaneous multi-plane imaging. Using temporally multiplexed beams, recording simultaneously from at least two focal planes at different z positions, and recording a z-stack for each beam as a calibration step, the algorithm separates motion-related and neural activity-induced changes in fluorescence intensity. The algorithm is based on a maximum likelihood optimisation approach; it assumes (as a first order approximation) that no distortions of the sample occurs during axial motion and that neural activity increases uniformly along the optical axis in each region of interest. The developed motion correction approach allows axial motion estimation and correction at high frame rates for isolated structures in the imaging volume in vivo, such as sparse expression patterns in the fruit fly brain.
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Affiliation(s)
- Andres Flores-Valle
- Max Planck Institute for Neurobiology of Behavior - caesar (MPINB), Bonn, Germany
- International Max Planck Research School for Brain and Behavior, Bonn, Germany
| | - Johannes D Seelig
- Max Planck Institute for Neurobiology of Behavior - caesar (MPINB), Bonn, Germany
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17
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Ito KN, Isobe K, Osakada F. Fast z-focus controlling and multiplexing strategies for multiplane two-photon imaging of neural dynamics. Neurosci Res 2022; 179:15-23. [DOI: 10.1016/j.neures.2022.03.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2022] [Accepted: 03/18/2022] [Indexed: 10/18/2022]
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18
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Janiak FK, Bartel P, Bale MR, Yoshimatsu T, Komulainen E, Zhou M, Staras K, Prieto-Godino LL, Euler T, Maravall M, Baden T. Non-telecentric two-photon microscopy for 3D random access mesoscale imaging. Nat Commun 2022; 13:544. [PMID: 35087041 PMCID: PMC8795402 DOI: 10.1038/s41467-022-28192-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2020] [Accepted: 01/04/2022] [Indexed: 01/07/2023] Open
Abstract
Diffraction-limited two-photon microscopy permits minimally invasive optical monitoring of neuronal activity. However, most conventional two-photon microscopes impose significant constraints on the size of the imaging field-of-view and the specific shape of the effective excitation volume, thus limiting the scope of biological questions that can be addressed and the information obtainable. Here, employing a non-telecentric optical design, we present a low-cost, easily implemented and flexible solution to address these limitations, offering a several-fold expanded three-dimensional field of view. Moreover, rapid laser-focus control via an electrically tunable lens allows near-simultaneous imaging of remote regions separated in three dimensions and permits the bending of imaging planes to follow natural curvatures in biological structures. Crucially, our core design is readily implemented (and reversed) within a matter of hours, making it highly suitable as a base platform for further development. We demonstrate the application of our system for imaging neuronal activity in a variety of examples in zebrafish, mice and fruit flies.
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Affiliation(s)
- F K Janiak
- Sussex Neuroscience, School of Life Sciences, University of Sussex, Brighton, UK.
| | - P Bartel
- Sussex Neuroscience, School of Life Sciences, University of Sussex, Brighton, UK
| | - M R Bale
- Sussex Neuroscience, School of Life Sciences, University of Sussex, Brighton, UK
| | - T Yoshimatsu
- Sussex Neuroscience, School of Life Sciences, University of Sussex, Brighton, UK
| | - E Komulainen
- Sussex Neuroscience, School of Life Sciences, University of Sussex, Brighton, UK
| | - M Zhou
- Sussex Neuroscience, School of Life Sciences, University of Sussex, Brighton, UK
| | - K Staras
- Sussex Neuroscience, School of Life Sciences, University of Sussex, Brighton, UK
| | | | - T Euler
- Institute of Ophthalmic Research, University of Tübingen, Tübingen, Germany
- Centre for Integrative Neuroscience, University of Tübingen, Tübingen, Germany
| | - M Maravall
- Sussex Neuroscience, School of Life Sciences, University of Sussex, Brighton, UK
| | - T Baden
- Sussex Neuroscience, School of Life Sciences, University of Sussex, Brighton, UK.
- Institute of Ophthalmic Research, University of Tübingen, Tübingen, Germany.
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19
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Kim TH, Schnitzer MJ. Fluorescence imaging of large-scale neural ensemble dynamics. Cell 2022; 185:9-41. [PMID: 34995519 PMCID: PMC8849612 DOI: 10.1016/j.cell.2021.12.007] [Citation(s) in RCA: 75] [Impact Index Per Article: 37.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2021] [Revised: 12/06/2021] [Accepted: 12/07/2021] [Indexed: 12/14/2022]
Abstract
Recent progress in fluorescence imaging allows neuroscientists to observe the dynamics of thousands of individual neurons, identified genetically or by their connectivity, across multiple brain areas and for extended durations in awake behaving mammals. We discuss advances in fluorescent indicators of neural activity, viral and genetic methods to express these indicators, chronic animal preparations for long-term imaging studies, and microscopes to monitor and manipulate the activity of large neural ensembles. Ca2+ imaging studies of neural activity can track brain area interactions and distributed information processing at cellular resolution. Across smaller spatial scales, high-speed voltage imaging reveals the distinctive spiking patterns and coding properties of targeted neuron types. Collectively, these innovations will propel studies of brain function and dovetail with ongoing neuroscience initiatives to identify new neuron types and develop widely applicable, non-human primate models. The optical toolkit's growing sophistication also suggests that "brain observatory" facilities would be useful open resources for future brain-imaging studies.
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Affiliation(s)
- Tony Hyun Kim
- James Clark Center for Biomedical Engineering & Sciences, Stanford University, Stanford, CA 94305, USA; CNC Program, Stanford University, Stanford, CA 94305, USA; Howard Hughes Medical Institute, Stanford University, Stanford, CA 94305, USA.
| | - Mark J Schnitzer
- James Clark Center for Biomedical Engineering & Sciences, Stanford University, Stanford, CA 94305, USA; CNC Program, Stanford University, Stanford, CA 94305, USA; Howard Hughes Medical Institute, Stanford University, Stanford, CA 94305, USA.
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20
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Akemann W, Wolf S, Villette V, Mathieu B, Tangara A, Fodor J, Ventalon C, Léger JF, Dieudonné S, Bourdieu L. Fast optical recording of neuronal activity by three-dimensional custom-access serial holography. Nat Methods 2022; 19:100-110. [PMID: 34949810 DOI: 10.1038/s41592-021-01329-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2019] [Accepted: 10/25/2021] [Indexed: 11/08/2022]
Abstract
Optical recording of neuronal activity in three-dimensional (3D) brain circuits at cellular and millisecond resolution in vivo is essential for probing information flow in the brain. While random-access multiphoton microscopy permits fast optical access to neuronal targets in three dimensions, the method is challenged by motion artifacts when recording from behaving animals. Therefore, we developed three-dimensional custom-access serial holography (3D-CASH). Built on a fast acousto-optic light modulator, 3D-CASH performs serial sampling at 40 kHz from neurons at freely selectable 3D locations. Motion artifacts are eliminated by targeting each neuron with a size-optimized pattern of excitation light covering the cell body and its anticipated displacement field. Spike rates inferred from GCaMP6f recordings in visual cortex of awake mice tracked the phase of a moving bar stimulus with higher spike correlation between intra compared to interlaminar neuron pairs. 3D-CASH offers access to the millisecond correlation structure of in vivo neuronal activity in 3D microcircuits.
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Affiliation(s)
- Walther Akemann
- Institut de Biologie de l'ENS (IBENS), École Normale Supérieure, CNRS, INSERM, Université PSL, Paris, France
| | - Sébastien Wolf
- Institut de Biologie de l'ENS (IBENS), École Normale Supérieure, CNRS, INSERM, Université PSL, Paris, France
- Laboratoire de Physique de l'ENS (LPENS), École Normale Supérieure, CNRS, Université PSL, Paris, France
| | - Vincent Villette
- Institut de Biologie de l'ENS (IBENS), École Normale Supérieure, CNRS, INSERM, Université PSL, Paris, France
| | - Benjamin Mathieu
- Institut de Biologie de l'ENS (IBENS), École Normale Supérieure, CNRS, INSERM, Université PSL, Paris, France
| | - Astou Tangara
- Institut de Biologie de l'ENS (IBENS), École Normale Supérieure, CNRS, INSERM, Université PSL, Paris, France
| | - Jozsua Fodor
- Institut de Biologie de l'ENS (IBENS), École Normale Supérieure, CNRS, INSERM, Université PSL, Paris, France
| | - Cathie Ventalon
- Institut de Biologie de l'ENS (IBENS), École Normale Supérieure, CNRS, INSERM, Université PSL, Paris, France
| | - Jean-François Léger
- Institut de Biologie de l'ENS (IBENS), École Normale Supérieure, CNRS, INSERM, Université PSL, Paris, France
| | - Stéphane Dieudonné
- Institut de Biologie de l'ENS (IBENS), École Normale Supérieure, CNRS, INSERM, Université PSL, Paris, France.
| | - Laurent Bourdieu
- Institut de Biologie de l'ENS (IBENS), École Normale Supérieure, CNRS, INSERM, Université PSL, Paris, France.
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21
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Abdelfattah AS, Ahuja S, Akkin T, Allu SR, Brake J, Boas DA, Buckley EM, Campbell RE, Chen AI, Cheng X, Čižmár T, Costantini I, De Vittorio M, Devor A, Doran PR, El Khatib M, Emiliani V, Fomin-Thunemann N, Fainman Y, Fernandez-Alfonso T, Ferri CGL, Gilad A, Han X, Harris A, Hillman EMC, Hochgeschwender U, Holt MG, Ji N, Kılıç K, Lake EMR, Li L, Li T, Mächler P, Miller EW, Mesquita RC, Nadella KMNS, Nägerl UV, Nasu Y, Nimmerjahn A, Ondráčková P, Pavone FS, Perez Campos C, Peterka DS, Pisano F, Pisanello F, Puppo F, Sabatini BL, Sadegh S, Sakadzic S, Shoham S, Shroff SN, Silver RA, Sims RR, Smith SL, Srinivasan VJ, Thunemann M, Tian L, Tian L, Troxler T, Valera A, Vaziri A, Vinogradov SA, Vitale F, Wang LV, Uhlířová H, Xu C, Yang C, Yang MH, Yellen G, Yizhar O, Zhao Y. Neurophotonic tools for microscopic measurements and manipulation: status report. NEUROPHOTONICS 2022; 9:013001. [PMID: 35493335 PMCID: PMC9047450 DOI: 10.1117/1.nph.9.s1.013001] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
Neurophotonics was launched in 2014 coinciding with the launch of the BRAIN Initiative focused on development of technologies for advancement of neuroscience. For the last seven years, Neurophotonics' agenda has been well aligned with this focus on neurotechnologies featuring new optical methods and tools applicable to brain studies. While the BRAIN Initiative 2.0 is pivoting towards applications of these novel tools in the quest to understand the brain, this status report reviews an extensive and diverse toolkit of novel methods to explore brain function that have emerged from the BRAIN Initiative and related large-scale efforts for measurement and manipulation of brain structure and function. Here, we focus on neurophotonic tools mostly applicable to animal studies. A companion report, scheduled to appear later this year, will cover diffuse optical imaging methods applicable to noninvasive human studies. For each domain, we outline the current state-of-the-art of the respective technologies, identify the areas where innovation is needed, and provide an outlook for the future directions.
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Affiliation(s)
- Ahmed S. Abdelfattah
- Brown University, Department of Neuroscience, Providence, Rhode Island, United States
| | - Sapna Ahuja
- University of Pennsylvania, Perelman School of Medicine, Department of Biochemistry and Biophysics, Philadelphia, Pennsylvania, United States
- University of Pennsylvania, School of Arts and Sciences, Department of Chemistry, Philadelphia, Pennsylvania, United States
| | - Taner Akkin
- University of Minnesota, Department of Biomedical Engineering, Minneapolis, Minnesota, United States
| | - Srinivasa Rao Allu
- University of Pennsylvania, Perelman School of Medicine, Department of Biochemistry and Biophysics, Philadelphia, Pennsylvania, United States
- University of Pennsylvania, School of Arts and Sciences, Department of Chemistry, Philadelphia, Pennsylvania, United States
| | - Joshua Brake
- Harvey Mudd College, Department of Engineering, Claremont, California, United States
| | - David A. Boas
- Boston University, Department of Biomedical Engineering, Boston, Massachusetts, United States
| | - Erin M. Buckley
- Georgia Institute of Technology and Emory University, Wallace H. Coulter Department of Biomedical Engineering, Atlanta, Georgia, United States
- Emory University, Department of Pediatrics, Atlanta, Georgia, United States
| | - Robert E. Campbell
- University of Tokyo, Department of Chemistry, Tokyo, Japan
- University of Alberta, Department of Chemistry, Edmonton, Alberta, Canada
| | - Anderson I. Chen
- Boston University, Department of Biomedical Engineering, Boston, Massachusetts, United States
| | - Xiaojun Cheng
- Boston University, Department of Biomedical Engineering, Boston, Massachusetts, United States
| | - Tomáš Čižmár
- Institute of Scientific Instruments of the Czech Academy of Sciences, Brno, Czech Republic
| | - Irene Costantini
- University of Florence, European Laboratory for Non-Linear Spectroscopy, Department of Biology, Florence, Italy
- National Institute of Optics, National Research Council, Rome, Italy
| | - Massimo De Vittorio
- Istituto Italiano di Tecnologia, Center for Biomolecular Nanotechnologies, Arnesano, Italy
| | - Anna Devor
- Boston University, Department of Biomedical Engineering, Boston, Massachusetts, United States
- Massachusetts General Hospital, Harvard Medical School, Athinoula A. Martinos Center for Biomedical Imaging, Charlestown, Massachusetts, United States
| | - Patrick R. Doran
- Boston University, Department of Biomedical Engineering, Boston, Massachusetts, United States
| | - Mirna El Khatib
- University of Pennsylvania, Perelman School of Medicine, Department of Biochemistry and Biophysics, Philadelphia, Pennsylvania, United States
- University of Pennsylvania, School of Arts and Sciences, Department of Chemistry, Philadelphia, Pennsylvania, United States
| | | | - Natalie Fomin-Thunemann
- Boston University, Department of Biomedical Engineering, Boston, Massachusetts, United States
| | - Yeshaiahu Fainman
- University of California San Diego, Department of Electrical and Computer Engineering, La Jolla, California, United States
| | - Tomas Fernandez-Alfonso
- University College London, Department of Neuroscience, Physiology and Pharmacology, London, United Kingdom
| | - Christopher G. L. Ferri
- University of California San Diego, Departments of Neurosciences, La Jolla, California, United States
| | - Ariel Gilad
- The Hebrew University of Jerusalem, Institute for Medical Research Israel–Canada, Department of Medical Neurobiology, Faculty of Medicine, Jerusalem, Israel
| | - Xue Han
- Boston University, Department of Biomedical Engineering, Boston, Massachusetts, United States
| | - Andrew Harris
- Weizmann Institute of Science, Department of Brain Sciences, Rehovot, Israel
| | | | - Ute Hochgeschwender
- Central Michigan University, Department of Neuroscience, Mount Pleasant, Michigan, United States
| | - Matthew G. Holt
- University of Porto, Instituto de Investigação e Inovação em Saúde (i3S), Porto, Portugal
| | - Na Ji
- University of California Berkeley, Department of Physics, Berkeley, California, United States
| | - Kıvılcım Kılıç
- Boston University, Department of Biomedical Engineering, Boston, Massachusetts, United States
| | - Evelyn M. R. Lake
- Yale School of Medicine, Department of Radiology and Biomedical Imaging, New Haven, Connecticut, United States
| | - Lei Li
- California Institute of Technology, Andrew and Peggy Cherng Department of Medical Engineering, Department of Electrical Engineering, Pasadena, California, United States
| | - Tianqi Li
- University of Minnesota, Department of Biomedical Engineering, Minneapolis, Minnesota, United States
| | - Philipp Mächler
- Boston University, Department of Biomedical Engineering, Boston, Massachusetts, United States
| | - Evan W. Miller
- University of California Berkeley, Departments of Chemistry and Molecular & Cell Biology and Helen Wills Neuroscience Institute, Berkeley, California, United States
| | | | | | - U. Valentin Nägerl
- Interdisciplinary Institute for Neuroscience University of Bordeaux & CNRS, Bordeaux, France
| | - Yusuke Nasu
- University of Tokyo, Department of Chemistry, Tokyo, Japan
| | - Axel Nimmerjahn
- Salk Institute for Biological Studies, Waitt Advanced Biophotonics Center, La Jolla, California, United States
| | - Petra Ondráčková
- Institute of Scientific Instruments of the Czech Academy of Sciences, Brno, Czech Republic
| | - Francesco S. Pavone
- National Institute of Optics, National Research Council, Rome, Italy
- University of Florence, European Laboratory for Non-Linear Spectroscopy, Department of Physics, Florence, Italy
| | - Citlali Perez Campos
- Columbia University, Zuckerman Mind Brain Behavior Institute, New York, United States
| | - Darcy S. Peterka
- Columbia University, Zuckerman Mind Brain Behavior Institute, New York, United States
| | - Filippo Pisano
- Istituto Italiano di Tecnologia, Center for Biomolecular Nanotechnologies, Arnesano, Italy
| | - Ferruccio Pisanello
- Istituto Italiano di Tecnologia, Center for Biomolecular Nanotechnologies, Arnesano, Italy
| | - Francesca Puppo
- University of California San Diego, Departments of Neurosciences, La Jolla, California, United States
| | - Bernardo L. Sabatini
- Harvard Medical School, Howard Hughes Medical Institute, Department of Neurobiology, Boston, Massachusetts, United States
| | - Sanaz Sadegh
- University of California San Diego, Departments of Neurosciences, La Jolla, California, United States
| | - Sava Sakadzic
- Massachusetts General Hospital, Harvard Medical School, Athinoula A. Martinos Center for Biomedical Imaging, Charlestown, Massachusetts, United States
| | - Shy Shoham
- New York University Grossman School of Medicine, Tech4Health and Neuroscience Institutes, New York, New York, United States
| | - Sanaya N. Shroff
- Boston University, Department of Biomedical Engineering, Boston, Massachusetts, United States
| | - R. Angus Silver
- University College London, Department of Neuroscience, Physiology and Pharmacology, London, United Kingdom
| | - Ruth R. Sims
- Sorbonne University, INSERM, CNRS, Institut de la Vision, Paris, France
| | - Spencer L. Smith
- University of California Santa Barbara, Department of Electrical and Computer Engineering, Santa Barbara, California, United States
| | - Vivek J. Srinivasan
- New York University Langone Health, Departments of Ophthalmology and Radiology, New York, New York, United States
| | - Martin Thunemann
- Boston University, Department of Biomedical Engineering, Boston, Massachusetts, United States
| | - Lei Tian
- Boston University, Departments of Electrical Engineering and Biomedical Engineering, Boston, Massachusetts, United States
| | - Lin Tian
- University of California Davis, Department of Biochemistry and Molecular Medicine, Davis, California, United States
| | - Thomas Troxler
- University of Pennsylvania, Perelman School of Medicine, Department of Biochemistry and Biophysics, Philadelphia, Pennsylvania, United States
- University of Pennsylvania, School of Arts and Sciences, Department of Chemistry, Philadelphia, Pennsylvania, United States
| | - Antoine Valera
- University College London, Department of Neuroscience, Physiology and Pharmacology, London, United Kingdom
| | - Alipasha Vaziri
- Rockefeller University, Laboratory of Neurotechnology and Biophysics, New York, New York, United States
- The Rockefeller University, The Kavli Neural Systems Institute, New York, New York, United States
| | - Sergei A. Vinogradov
- University of Pennsylvania, Perelman School of Medicine, Department of Biochemistry and Biophysics, Philadelphia, Pennsylvania, United States
- University of Pennsylvania, School of Arts and Sciences, Department of Chemistry, Philadelphia, Pennsylvania, United States
| | - Flavia Vitale
- Center for Neuroengineering and Therapeutics, Departments of Neurology, Bioengineering, Physical Medicine and Rehabilitation, Philadelphia, Pennsylvania, United States
| | - Lihong V. Wang
- California Institute of Technology, Andrew and Peggy Cherng Department of Medical Engineering, Department of Electrical Engineering, Pasadena, California, United States
| | - Hana Uhlířová
- Institute of Scientific Instruments of the Czech Academy of Sciences, Brno, Czech Republic
| | - Chris Xu
- Cornell University, School of Applied and Engineering Physics, Ithaca, New York, United States
| | - Changhuei Yang
- California Institute of Technology, Departments of Electrical Engineering, Bioengineering and Medical Engineering, Pasadena, California, United States
| | - Mu-Han Yang
- University of California San Diego, Department of Electrical and Computer Engineering, La Jolla, California, United States
| | - Gary Yellen
- Harvard Medical School, Department of Neurobiology, Boston, Massachusetts, United States
| | - Ofer Yizhar
- Weizmann Institute of Science, Department of Brain Sciences, Rehovot, Israel
| | - Yongxin Zhao
- Carnegie Mellon University, Department of Biological Sciences, Pittsburgh, Pennsylvania, United States
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22
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Yu CH, Stirman JN, Yu Y, Hira R, Smith SL. Diesel2p mesoscope with dual independent scan engines for flexible capture of dynamics in distributed neural circuitry. Nat Commun 2021; 12:6639. [PMID: 34789723 PMCID: PMC8599518 DOI: 10.1038/s41467-021-26736-4] [Citation(s) in RCA: 51] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2021] [Accepted: 10/05/2021] [Indexed: 11/09/2022] Open
Abstract
Imaging the activity of neurons that are widely distributed across brain regions deep in scattering tissue at high speed remains challenging. Here, we introduce an open-source system with Dual Independent Enhanced Scan Engines for Large field-of-view Two-Photon imaging (Diesel2p). Combining optical design, adaptive optics, and temporal multiplexing, the system offers subcellular resolution over a large field-of-view of ~25 mm2, encompassing distances up to 7 mm, with independent scan engines. We demonstrate the flexibility and various use cases of this system for calcium imaging of neurons in the living brain.
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Affiliation(s)
- Che-Hang Yu
- Department of Electrical and Computer Engineering, University of California, Santa Barbara, CA, USA
| | | | - Yiyi Yu
- Department of Electrical and Computer Engineering, University of California, Santa Barbara, CA, USA
| | - Riichiro Hira
- Department of Electrical and Computer Engineering, University of California, Santa Barbara, CA, USA
| | - Spencer L Smith
- Department of Electrical and Computer Engineering, University of California, Santa Barbara, CA, USA.
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23
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Clough M, Chen IA, Park SW, Ahrens AM, Stirman JN, Smith SL, Chen JL. Flexible simultaneous mesoscale two-photon imaging of neural activity at high speeds. Nat Commun 2021; 12:6638. [PMID: 34789730 PMCID: PMC8599611 DOI: 10.1038/s41467-021-26737-3] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2021] [Accepted: 10/05/2021] [Indexed: 12/02/2022] Open
Abstract
Understanding brain function requires monitoring local and global brain dynamics. Two-photon imaging of the brain across mesoscopic scales has presented trade-offs between imaging area and acquisition speed. We describe a flexible cellular resolution two-photon microscope capable of simultaneous video rate acquisition of four independently targetable brain regions spanning an approximate five-millimeter field of view. With this system, we demonstrate the ability to measure calcium activity across mouse sensorimotor cortex at behaviorally relevant timescales.
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Affiliation(s)
- Mitchell Clough
- Department of Biomedical Engineering, Boston University, Boston, MA, 02215, USA
| | - Ichun Anderson Chen
- Department of Biomedical Engineering, Boston University, Boston, MA, 02215, USA
- Center for Neurophotonics, Boston University, Boston, MA, 02215, USA
| | - Seong-Wook Park
- Department of Biomedical Engineering, Boston University, Boston, MA, 02215, USA
- Center for Neurophotonics, Boston University, Boston, MA, 02215, USA
| | - Allison M Ahrens
- Department of Biology, Boston University, Boston, MA, 02215, USA
| | - Jeffrey N Stirman
- Neuroscience Center, University of North Carolina School of Medicine, Chapel Hill, NC, 27599, USA
| | - Spencer L Smith
- Department of Electrical and Computer Engineering, University of California Santa Barbara, Santa Barbara, CA, 93106, USA
| | - Jerry L Chen
- Department of Biomedical Engineering, Boston University, Boston, MA, 02215, USA.
- Center for Neurophotonics, Boston University, Boston, MA, 02215, USA.
- Department of Biology, Boston University, Boston, MA, 02215, USA.
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24
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High-speed, cortex-wide volumetric recording of neuroactivity at cellular resolution using light beads microscopy. Nat Methods 2021; 18:1103-1111. [PMID: 34462592 PMCID: PMC8958902 DOI: 10.1038/s41592-021-01239-8] [Citation(s) in RCA: 81] [Impact Index Per Article: 27.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2020] [Accepted: 07/09/2021] [Indexed: 02/07/2023]
Abstract
Two-photon microscopy has enabled high-resolution imaging of neuroactivity at depth within scattering brain tissue. However, its various realizations have not overcome the tradeoffs between speed and spatiotemporal sampling that would be necessary to enable mesoscale volumetric recording of neuroactivity at cellular resolution and speed compatible with resolving calcium transients. Here, we introduce light beads microscopy (LBM), a scalable and spatiotemporally optimal acquisition approach limited only by fluorescence lifetime, where a set of axially separated and temporally distinct foci record the entire axial imaging range near-simultaneously, enabling volumetric recording at 1.41 × 108 voxels per second. Using LBM, we demonstrate mesoscopic and volumetric imaging at multiple scales in the mouse cortex, including cellular-resolution recordings within ~3 × 5 × 0.5 mm volumes containing >200,000 neurons at ~5 Hz and recordings of populations of ~1 million neurons within ~5.4 × 6 × 0.5 mm volumes at ~2 Hz, as well as higher speed (9.6 Hz) subcellular-resolution volumetric recordings. LBM provides an opportunity for discovering the neurocomputations underlying cortex-wide encoding and processing of information in the mammalian brain.
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25
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Hua S, Zhang W. Anisotropy of 2PA, 3PA, and Kerr effect in nonpolar ZnO. OPTICS LETTERS 2021; 46:4065-4068. [PMID: 34388812 DOI: 10.1364/ol.432882] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/31/2021] [Accepted: 07/12/2021] [Indexed: 06/13/2023]
Abstract
Anisotropic optical nonlinearity plays an important role in polarization-dependent optoelectronic devices. Taking the advantage of in-plane crystallographic axis, the polarization dependence of third- and fifth-order nonlinearity in nonpolar ZnO has been investigated by z scan. Here, we established the theory model of anisotropic relation of fifth-order nonlinearity in hexagonal wurtzite crystal. Both two-photon absorption (2PA) and three-photon absorption (3PA) coefficients exhibit anisotropic oscillations with a period of 180°, and the polarization modulation factor and anisotropy coefficient (rp,σ) are measured as (2.10, 1.84) for β2, and (1.66, 1.33) for β3, respectively. This is the first time, to the best of our knowledge, that the anisotropy of the fifth-order optical nonlinear effect has been characterized and confirmed. It is verified that the self-defocusing effect at 500 nm is isotropy, while the self-focusing effect at 800 nm exhibits significant anisotropy. The maximum value of the nonlinear figure of merit is 5.84 along the [0010] crystalline direction, nearly 1.6 times the minimum value, revealing that ZnO exhibits potential for nonlinear applications containing polarization-related all-optical switching components.
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26
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Miller ADC, Ozbakir HF, Mukherjee A. Calcium-responsive contrast agents for functional magnetic resonance imaging. ACTA ACUST UNITED AC 2021; 2:021301. [PMID: 34085055 DOI: 10.1063/5.0041394] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Accepted: 03/15/2021] [Indexed: 02/07/2023]
Abstract
Calcium ions represent one of the key second messengers accompanying neural activity and synaptic signaling. Accordingly, dynamic imaging of calcium fluctuations in living organisms represents a cornerstone technology for discovering neural mechanisms that underlie memory, determine behavior, and modulate emotional states as well as how these mechanisms are perturbed by neurological disease and brain injury. While optical technologies are well established for high resolution imaging of calcium dynamics, physical limits on light penetration hinder their application for whole-brain imaging in intact vertebrates. Unlike optics, magnetic resonance imaging (MRI) enables noninvasive large-scale imaging across vertebrates of all sizes. This has motivated the development of several sensors that leverage innovative physicochemical mechanisms to sensitize MRI contrast to intracellular and extracellular changes in calcium. Here, we review the current state-of-the-art in MRI-based calcium sensors, focusing on fundamental aspects of sensor performance, in vivo applications, and challenges related to sensitivity. We also highlight how innovations at the intersection of reporter gene technology and gene delivery open potential opportunities for mapping calcium activity in genetically targeted cells, complementing the benefits of small molecule probes and nanoparticle sensors.
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Affiliation(s)
- Austin D C Miller
- Biomolecular Science and Engineering, University of California, Santa Barbara, California 93106, USA
| | - Harun F Ozbakir
- Department of Chemical Engineering, University of California, Santa Barbara, California 93106, USA
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27
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Valera AM, Neufeldt FC, Kirkby PA, Mitchell JE, Silver RA. Precompensation of 3D field distortions in remote focus two-photon microscopy. BIOMEDICAL OPTICS EXPRESS 2021; 12:3717-3728. [PMID: 34221690 PMCID: PMC8221938 DOI: 10.1364/boe.425588] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/19/2021] [Revised: 05/07/2021] [Accepted: 05/14/2021] [Indexed: 06/13/2023]
Abstract
Remote focusing is widely used in 3D two-photon microscopy and 3D photostimulation because it enables fast axial scanning without moving the objective lens or specimen. However, due to the design constraints of microscope optics, remote focus units are often located in non-telecentric positions in the optical path, leading to significant depth-dependent 3D field distortions in the imaging volume. To address this limitation, we characterized 3D field distortions arising from non-telecentric remote focusing and present a method for distortion precompensation. We demonstrate its applicability for a 3D two-photon microscope that uses an acousto-optic lens (AOL) for remote focusing and scanning. We show that the distortion precompensation method improves the pointing precision of the AOL microscope to < 0.5 µm throughout the 400 × 400 × 400 µm imaging volume.
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Affiliation(s)
- Antoine M. Valera
- Department of Neuroscience, Physiology and Pharmacology, University College London, Gower Street, London WC1E 6BT, UK
- These authors contributed equally
| | - Fiona C. Neufeldt
- Department of Neuroscience, Physiology and Pharmacology, University College London, Gower Street, London WC1E 6BT, UK
- Department of Electronic and Electrical Engineering, University College London, Malet Place, London WC1E 7JE, UK
- These authors contributed equally
| | - Paul A. Kirkby
- Department of Neuroscience, Physiology and Pharmacology, University College London, Gower Street, London WC1E 6BT, UK
| | - John E. Mitchell
- Department of Electronic and Electrical Engineering, University College London, Malet Place, London WC1E 7JE, UK
| | - R. Angus Silver
- Department of Neuroscience, Physiology and Pharmacology, University College London, Gower Street, London WC1E 6BT, UK
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28
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Stringer C, Michaelos M, Tsyboulski D, Lindo SE, Pachitariu M. High-precision coding in visual cortex. Cell 2021; 184:2767-2778.e15. [PMID: 33857423 DOI: 10.1016/j.cell.2021.03.042] [Citation(s) in RCA: 57] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Revised: 03/04/2021] [Accepted: 03/19/2021] [Indexed: 01/18/2023]
Abstract
Individual neurons in visual cortex provide the brain with unreliable estimates of visual features. It is not known whether the single-neuron variability is correlated across large neural populations, thus impairing the global encoding of stimuli. We recorded simultaneously from up to 50,000 neurons in mouse primary visual cortex (V1) and in higher order visual areas and measured stimulus discrimination thresholds of 0.35° and 0.37°, respectively, in an orientation decoding task. These neural thresholds were almost 100 times smaller than the behavioral discrimination thresholds reported in mice. This discrepancy could not be explained by stimulus properties or arousal states. Furthermore, behavioral variability during a sensory discrimination task could not be explained by neural variability in V1. Instead, behavior-related neural activity arose dynamically across a network of non-sensory brain areas. These results imply that perceptual discrimination in mice is limited by downstream decoders, not by neural noise in sensory representations.
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Affiliation(s)
| | | | | | - Sarah E Lindo
- HHMI Janelia Research Campus, Ashburn, VA 20147, USA
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29
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Ching-Roa VD, Olson EM, Ibrahim SF, Torres R, Giacomelli MG. Ultrahigh-speed point scanning two-photon microscopy using high dynamic range silicon photomultipliers. Sci Rep 2021; 11:5248. [PMID: 33664354 PMCID: PMC7933192 DOI: 10.1038/s41598-021-84522-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2020] [Accepted: 02/17/2021] [Indexed: 11/09/2022] Open
Abstract
Conventional two-photon microscopes use photomultiplier tubes, which enable high sensitivity but can detect relatively few photons per second, forcing longer pixel integration times and limiting maximum imaging rates. We introduce novel detection electronics using silicon photomultipliers that greatly extend dynamic range, enabling more than an order of magnitude increased photon detection rate as compared to state-of-the-art photomultiplier tubes. We demonstrate that this capability can dramatically improve both imaging rates and signal-to-noise ratio (SNR) in two-photon microscopy using human surgical specimens. Finally, to enable wider use of more advanced detection technology, we have formed the OpenSiPM project, which aims to provide open source detector designs for high-speed two-photon and confocal microscopy.
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Affiliation(s)
- Vincent D Ching-Roa
- Department of Biomedical Engineering, University of Rochester, 207 Goergen Hall, BOX 270168, Rochester, NY, 14627, USA
| | - Eben M Olson
- Department of Laboratory Medicine, Yale University, New Haven, CT, USA
| | - Sherrif F Ibrahim
- Department of Dermatology, University of Rochester Medical Center, Rochester, NY, USA
- Rochester Dermatologic Surgery, PC,, Victor, NY, USA
| | - Richard Torres
- Department of Laboratory Medicine, Yale University, New Haven, CT, USA
| | - Michael G Giacomelli
- Department of Biomedical Engineering, University of Rochester, 207 Goergen Hall, BOX 270168, Rochester, NY, 14627, USA.
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30
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Tsang JM, Gritton HJ, Das SL, Weber TD, Chen CS, Han X, Mertz J. Fast, multiplane line-scan confocal microscopy using axially distributed slits. BIOMEDICAL OPTICS EXPRESS 2021; 12:1339-1350. [PMID: 33796357 PMCID: PMC7984773 DOI: 10.1364/boe.417286] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/11/2020] [Revised: 01/28/2021] [Accepted: 01/29/2021] [Indexed: 05/29/2023]
Abstract
The inherent constraints on resolution, speed and field of view have hindered the development of high-speed, three-dimensional microscopy techniques over large scales. Here, we present a multiplane line-scan imaging strategy, which uses a series of axially distributed reflecting slits to probe different depths within a sample volume. Our technique enables the simultaneous imaging of an optically sectioned image stack with a single camera at frame rates of hundreds of hertz, without the need for axial scanning. We demonstrate the applicability of our system to monitor fast dynamics in biological samples by performing calcium imaging of neuronal activity in mouse brains and voltage imaging of cardiomyocytes in cardiac samples.
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Affiliation(s)
- Jean-Marc Tsang
- Department of Biomedical Engineering, Boston University, 44 Cummington Mall, Boston, MA 02215, USA
| | - Howard J. Gritton
- Department of Biomedical Engineering, Boston University, 44 Cummington Mall, Boston, MA 02215, USA
- Department of Comparative Biosciences, University of Illinois at Urbana-Champaign, Urbana, IL 61802, USA
| | - Shoshana L. Das
- Department of Biomedical Engineering, Boston University, 44 Cummington Mall, Boston, MA 02215, USA
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA 02115, USA
| | - Timothy D. Weber
- Department of Biomedical Engineering, Boston University, 44 Cummington Mall, Boston, MA 02215, USA
| | - Christopher S. Chen
- Department of Biomedical Engineering, Boston University, 44 Cummington Mall, Boston, MA 02215, USA
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA 02115, USA
| | - Xue Han
- Department of Biomedical Engineering, Boston University, 44 Cummington Mall, Boston, MA 02215, USA
- Photonics Center, Boston University, 8 Saint Mary’s Street, Boston, MA 02215, USA
| | - Jerome Mertz
- Department of Biomedical Engineering, Boston University, 44 Cummington Mall, Boston, MA 02215, USA
- Photonics Center, Boston University, 8 Saint Mary’s Street, Boston, MA 02215, USA
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31
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Temporally multiplexed dual-plane imaging of neural activity with four-dimensional precision. Neurosci Res 2021; 171:9-18. [PMID: 33607170 DOI: 10.1016/j.neures.2021.02.001] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2021] [Revised: 02/05/2021] [Accepted: 02/07/2021] [Indexed: 11/20/2022]
Abstract
Spatiotemporal patterns of neural activity generate brain functions, such as perception, memory, and behavior. Four-dimensional (4-D: x, y, z, t) analyses of such neural activity will facilitate understanding of brain functions. However, conventional two-photon microscope systems observe single-plane brain tissue alone at a time with cellular resolution. It faces a trade-off between the spatial resolution in the x-, y-, and z-axes and the temporal resolution by a limited point-by-point scan speed. To overcome this trade-off in 4-D imaging, we developed a holographic two-photon microscope for dual-plane imaging. A spatial light modulator (SLM) provided an additional focal plane at a different depth. Temporal multiplexing of split lasers with an optical chopper allowed fast imaging of two different focal planes. We simultaneously recorded the activities of neurons on layers 2/3 and 5 of the cerebral cortex in awake mice in vivo. The present study demonstrated the proof-of-concept of dual-plane two-photon imaging of neural circuits by using the temporally multiplexed SLM-based microscope. The temporally multiplexed holographic microscope, combined with in vivo labeling with genetically encoded probes, enabled 4-D imaging and analysis of neural activities at cellular resolution and physiological timescales. Large-scale 4-D imaging and analysis will facilitate studies of not only the nervous system but also of various biological systems.
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32
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Identification and quantification of neuronal ensembles in optical imaging experiments. J Neurosci Methods 2020; 351:109046. [PMID: 33359231 DOI: 10.1016/j.jneumeth.2020.109046] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2020] [Revised: 12/12/2020] [Accepted: 12/15/2020] [Indexed: 12/30/2022]
Abstract
Recent technical advances in molecular biology and optical imaging have made it possible to record from up to thousands of densely packed neurons in superficial and deep brain regions in vivo, with cellular subtype specificity and high spatiotemporal fidelity. Such optical neurotechnologies are enabling increasingly fine-scaled studies of neuronal circuits and reliably co-active groups of neurons, so-called ensembles. Neuronal ensembles are thought to constitute the basic functional building blocks of brain systems, potentially exhibiting collective computational properties. While the technical framework of in vivo optical imaging and quantification of neuronal activity follows certain widely held standards, analytical methods for study of neuronal co-activity and ensembles lack consensus and are highly varied across the field. Here we provide a comprehensive step-by-step overview of theoretical, experimental, and analytical considerations for the identification and quantification of neuronal ensemble dynamics in high-resolution in vivo optical imaging studies.
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33
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Chan RKY, He H, Ren YX, Lai CSW, Lam EY, Wong KKY. Axially resolved volumetric two-photon microscopy with an extended field of view using depth localization under mirrored Airy beams. OPTICS EXPRESS 2020; 28:39563-39573. [PMID: 33379502 DOI: 10.1364/oe.412453] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/16/2020] [Accepted: 12/08/2020] [Indexed: 06/12/2023]
Abstract
It is a great challenge in two-photon microscopy (2PM) to have a high volumetric imaging speed without sacrificing the spatial and temporal resolution in three dimensions (3D). The structure in 2PM images could be reconstructed with better spatial and temporal resolution by the proper choice of the data processing algorithm. Here, we propose a method to reconstruct 3D volume from 2D projections imaged by mirrored Airy beams. We verified that our approach can achieve high accuracy in 3D localization over a large axial range and is applicable to continuous and dense sample. The effective field of view after reconstruction is expanded. It is a promising technique for rapid volumetric 2PM with axial localization at high resolution.
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34
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May MA, Bawart M, Langeslag M, Bernet S, Kress M, Ritsch-Marte M, Jesacher A. High-NA two-photon single cell imaging with remote focusing using a diffractive tunable lens. BIOMEDICAL OPTICS EXPRESS 2020; 11:7183-7191. [PMID: 33408989 PMCID: PMC7747902 DOI: 10.1364/boe.405863] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/20/2020] [Revised: 10/22/2020] [Accepted: 10/25/2020] [Indexed: 06/12/2023]
Abstract
Fast, volumetric structural and functional imaging of cellular and sub-cellular dynamics inside the living brain is one of the most desired capabilities in the neurosciences, but still faces serious challenges. Specifically, while few solutions for rapid 3D scanning exist, it is generally much easier to facilitate fast in-plane scanning than it is to scan axially at high speeds. Remote focusing in which the imaging plane is shifted along the optical axis by a tunable lens while maintaining the position of the sample and objective is a promising approach to increase the axial scan speed, but existing techniques often introduce severe optical aberrations in high-NA imaging systems, eliminating the possibility of diffraction-limited single-cell imaging. Here, we demonstrate near diffraction-limited, volumetric two-photon fluorescence microscopy in which we resolve the deep sub-micron structures of single microglia cells with axial scanning performed using a novel high-NA remote focusing method. Image contrast is maintained to within 7% compared to mechanical sample stepping and the focal volume remains nearly diffraction-limited over an axial range greater than 86 µm.
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Affiliation(s)
- Molly A. May
- Institute of Biomedical Physics, Medical University of Innsbruck, Müllerstraße 44, 6020 Innsbruck, Austria
| | - Martin Bawart
- Institute of Biomedical Physics, Medical University of Innsbruck, Müllerstraße 44, 6020 Innsbruck, Austria
| | - Michiel Langeslag
- Institute of Physiology, Medical University of Innsbruck, Schöpfstraße 41, 6020 Innsbruck, Austria
| | - Stefan Bernet
- Institute of Biomedical Physics, Medical University of Innsbruck, Müllerstraße 44, 6020 Innsbruck, Austria
| | - Michaela Kress
- Institute of Physiology, Medical University of Innsbruck, Schöpfstraße 41, 6020 Innsbruck, Austria
| | - Monika Ritsch-Marte
- Institute of Biomedical Physics, Medical University of Innsbruck, Müllerstraße 44, 6020 Innsbruck, Austria
| | - Alexander Jesacher
- Institute of Biomedical Physics, Medical University of Innsbruck, Müllerstraße 44, 6020 Innsbruck, Austria
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35
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Luo Q. A brief introduction to biophotonic techniques and methods. SCIENCE CHINA LIFE SCIENCES 2020; 63:1771-1775. [PMID: 33355887 PMCID: PMC7756128 DOI: 10.1007/s11427-020-1858-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 11/24/2020] [Indexed: 11/30/2022]
Affiliation(s)
- Qingming Luo
- School of Biomedical Engineering, Hainan University, Haikou, 570228, China.
- Britton Chance Center for Biomedical Photonics, MoE Key Laboratory for Biomedical Photonics, Wuhan National Laboratory for Optoelectronics-Huazhong University of Science and Technology, Wuhan, 430074, China.
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36
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Akondi V, Kowalski B, Burns SA, Dubra A. Dynamic distortion in resonant galvanometric optical scanners. OPTICA 2020; 7:1506-1513. [PMID: 34368405 PMCID: PMC8345821 DOI: 10.1364/optica.405187] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
High-speed optical systems are revolutionizing biomedical imaging in microscopy, DNA sequencing, and flow cytometry, as well as numerous other applications, including data storage, display technologies, printing, and autonomous vehicles. These systems often achieve the necessary imaging or sensing speed through the use of resonant galvanometric optical scanners. Here, we show that the optical performance of these devices suffers due to the dynamic mirror distortion that arises from the variation in torque with angular displacement. In one of two scanners tested, these distortions result in a variation of signal-to-noise (Strehl) ratio by an order of magnitude across the field of view, degrading transverse resolution by more than a factor of 2. This mirror distortion could be mitigated through the use of stiffer materials, such as beryllium or silicon carbide, at the expense of surface roughness, as these cannot be polished to the same degree of smoothness as common optical glasses. The repeatability of the dynamic distortion indicates that computational and optical corrective methods are also possible.
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Affiliation(s)
- Vyas Akondi
- Byers Eye Institute, Stanford University, Palo Alto, California 94303, USA
- Corresponding author:
| | | | - Stephen A. Burns
- Indiana University School of Optometry, Bloomington, Indiana 47405, USA
| | - Alfredo Dubra
- Byers Eye Institute, Stanford University, Palo Alto, California 94303, USA
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37
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Moreaux LC, Yatsenko D, Sacher WD, Choi J, Lee C, Kubat NJ, Cotton RJ, Boyden ES, Lin MZ, Tian L, Tolias AS, Poon JKS, Shepard KL, Roukes ML. Integrated Neurophotonics: Toward Dense Volumetric Interrogation of Brain Circuit Activity-at Depth and in Real Time. Neuron 2020; 108:66-92. [PMID: 33058767 PMCID: PMC8061790 DOI: 10.1016/j.neuron.2020.09.043] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2020] [Revised: 08/18/2020] [Accepted: 09/28/2020] [Indexed: 12/17/2022]
Abstract
We propose a new paradigm for dense functional imaging of brain activity to surmount the limitations of present methodologies. We term this approach "integrated neurophotonics"; it combines recent advances in microchip-based integrated photonic and electronic circuitry with those from optogenetics. This approach has the potential to enable lens-less functional imaging from within the brain itself to achieve dense, large-scale stimulation and recording of brain activity with cellular resolution at arbitrary depths. We perform a computational study of several prototype 3D architectures for implantable probe-array modules that are designed to provide fast and dense single-cell resolution (e.g., within a 1-mm3 volume of mouse cortex comprising ∼100,000 neurons). We describe progress toward realizing integrated neurophotonic imaging modules, which can be produced en masse with current semiconductor foundry protocols for chip manufacturing. Implantation of multiple modules can cover extended brain regions.
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Affiliation(s)
- Laurent C Moreaux
- Division of Physics, Mathematics and Astronomy, California Institute of Technology, Pasadena, CA 91125, USA.
| | - Dimitri Yatsenko
- Vathes LLC, Houston, TX 77030, USA; Center for Neuroscience and Artificial Intelligence and Department of Neuroscience, Baylor College of Medicine, Houston, TX 77030, USA
| | - Wesley D Sacher
- Kavli Nanoscience Institute, California Institute of Technology, Pasadena, CA 91125, USA; Division of Engineering and Applied Science, California Institute of Technology, Pasadena, CA 91125, USA; Max Planck Institute for Microstructure Physics, Halle, Germany
| | - Jaebin Choi
- Departments of Electrical Engineering and Biomedical Engineering, Columbia University, New York, NY 10027, USA
| | - Changhyuk Lee
- Departments of Electrical Engineering and Biomedical Engineering, Columbia University, New York, NY 10027, USA; Center for BioMicrosystems, Brain Science Institute, Korea Institute of Science and Technology, Korea
| | - Nicole J Kubat
- Division of Physics, Mathematics and Astronomy, California Institute of Technology, Pasadena, CA 91125, USA
| | - R James Cotton
- Shirley Ryan AbilityLab, Northwestern University, Chicago, IL 60611, USA; Center for Neuroscience and Artificial Intelligence and Department of Neuroscience, Baylor College of Medicine, Houston, TX 77030, USA
| | - Edward S Boyden
- Howard Hughes Medical Institute, Cambridge, MA, USA; McGovern Institute, MIT, Cambridge, USA; Koch Institute, MIT, Cambridge, USA; Departments of Brain and Cognitive Sciences, Media Arts and Sciences, and Biological Engineering, MIT, Cambridge, USA
| | - Michael Z Lin
- Departments of Neurobiology and Bioengineering, Stanford University, Stanford, CA 94305, USA
| | - Lin Tian
- Department of Biochemistry and Molecular Medicine, School of Medicine, University of California, Davis, CA 95616, USA
| | - Andreas S Tolias
- Vathes LLC, Houston, TX 77030, USA; Center for Neuroscience and Artificial Intelligence and Department of Neuroscience, Baylor College of Medicine, Houston, TX 77030, USA; Department of Electrical and Computer Engineering, Rice University, Houston, TX 77005, USA
| | - Joyce K S Poon
- Max Planck Institute for Microstructure Physics, Halle, Germany; Department of Electrical and Computer Engineering, University of Toronto, 10 King's College Rd., Toronto, ON M5S 3G4, Canada
| | - Kenneth L Shepard
- Departments of Electrical Engineering and Biomedical Engineering, Columbia University, New York, NY 10027, USA
| | - Michael L Roukes
- Division of Physics, Mathematics and Astronomy, California Institute of Technology, Pasadena, CA 91125, USA; Kavli Nanoscience Institute, California Institute of Technology, Pasadena, CA 91125, USA; Division of Engineering and Applied Science, California Institute of Technology, Pasadena, CA 91125, USA; Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA.
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38
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Chen D, Ren M, Zhang D, Chen J, Gu S, Chen SC. Design of a multi-modality DMD-based two-photon microscope system. OPTICS EXPRESS 2020; 28:30187-30198. [PMID: 33114902 DOI: 10.1364/oe.404652] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/05/2020] [Accepted: 09/14/2020] [Indexed: 06/11/2023]
Abstract
We present the modular design and characterization of a multi-modality video-rate two-photon excitation (TPE) microscope based on integrating a digital micromirror device (DMD), which functions as an ultrafast beam shaper and random-access scanner, with a pair of galvanometric scanners. The TPE microscope system realizes a suite of new imaging functionalities, including (1) multi-layer imaging with 3D programmable imaging planes, (2) DMD-based wavefront correction, and (3) multi-focus optical stimulation (up to 22.7 kHz) with simultaneous TPE imaging, all in real-time. We also report the detailed optomechanical design and software development that achieves high level system automation. To verify the performance of different microscope functions, we have devised and performed imaging experiments on Drosophila brain, mouse kidney and human stem cells. The results not only show improved imaging resolution and depths via the DMD-based adaptive optics, but also demonstrate fast multi-focus stimulation for the first time. With the new imaging capabilities, e.g., tools for optogenetics, the multi-modality TPE microscope may play a critical role in the applications pertinent to neuroscience and biophotonics.
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39
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Terada Y, Obuchi T, Isomura T, Kabashima Y. Inferring Neuronal Couplings From Spiking Data Using a Systematic Procedure With a Statistical Criterion. Neural Comput 2020; 32:2187-2211. [PMID: 32946715 DOI: 10.1162/neco_a_01324] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
Recent remarkable advances in experimental techniques have provided a background for inferring neuronal couplings from point process data that include a great number of neurons. Here, we propose a systematic procedure for pre- and postprocessing generic point process data in an objective manner to handle data in the framework of a binary simple statistical model, the Ising or generalized McCulloch-Pitts model. The procedure has two steps: (1) determining time bin size for transforming the point process data into discrete-time binary data and (2) screening relevant couplings from the estimated couplings. For the first step, we decide the optimal time bin size by introducing the null hypothesis that all neurons would fire independently, then choosing a time bin size so that the null hypothesis is rejected with the strict criteria. The likelihood associated with the null hypothesis is analytically evaluated and used for the rejection process. For the second postprocessing step, after a certain estimator of coupling is obtained based on the preprocessed data set (any estimator can be used with the proposed procedure), the estimate is compared with many other estimates derived from data sets obtained by randomizing the original data set in the time direction. We accept the original estimate as relevant only if its absolute value is sufficiently larger than those of randomized data sets. These manipulations suppress false positive couplings induced by statistical noise. We apply this inference procedure to spiking data from synthetic and in vitro neuronal networks. The results show that the proposed procedure identifies the presence or absence of synaptic couplings fairly well, including their signs, for the synthetic and experimental data. In particular, the results support that we can infer the physical connections of underlying systems in favorable situations, even when using a simple statistical model.
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Affiliation(s)
- Yu Terada
- Laboratory for Neural Computation and Adaptation, RIKEN Center for Brain Science, Wako, Saitama 351-0198, Japan
| | - Tomoyuki Obuchi
- Department of Systems Science, Graduate School of Informatics, Kyoto University, Kyoto 606-8501, Japan
| | - Takuya Isomura
- Laboratory for Neural Computation and Adaptation, RIKEN Center for Brain Science, Wako, Saitama 351-0198, Japan
| | - Yoshiyuki Kabashima
- Institute for Physics of Intelligence, Graduate School of Science, The University of Tokyo, Tokyo 113-0033, Japan
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40
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Zhang Y, Chen J, Bai C, Zhang D, Zhan Q. Dynamical generation of multiple focal spot pairs with controllable position and polarization. OPTICS EXPRESS 2020; 28:26706-26716. [PMID: 32906939 DOI: 10.1364/oe.400735] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/19/2020] [Accepted: 08/16/2020] [Indexed: 06/11/2023]
Abstract
We report a flexible method to dynamically generate multiple sub-wavelength focal spot pairs with adjustable polarization, position and number at the focal plane of a high numerical aperture (NA) objective lens. The desired incident field on the pupil plane can be analytically derived by employing the time-reversed method combined with the dipole antenna radiation theory. The numerical simulations of the corresponding tightly focused field are conducted using the Richards-Wolf vectorial diffraction theory. The validity of the presented method is demonstrated through experimental generation of several designed pupil fields with a versatile vectorial optical field generator and characterization of the produced focused fields with Stokes parameter measurements.
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41
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Two-Photon Voltage Imaging of Spontaneous Activity from Multiple Neurons Reveals Network Activity in Brain Tissue. iScience 2020; 23:101363. [PMID: 32717641 PMCID: PMC7393527 DOI: 10.1016/j.isci.2020.101363] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2020] [Revised: 04/07/2020] [Accepted: 07/09/2020] [Indexed: 11/23/2022] Open
Abstract
Recording the electrical activity of multiple neurons simultaneously would greatly facilitate studies on the function of neuronal circuits. The combination of the fast scanning by random-access multiphoton microscopy (RAMP) and the latest two-photon-compatible high-performance fluorescent genetically encoded voltage indicators (GEVIs) has enabled action potential detection in deep layers in in vivo brain. However, neuron connectivity analysis on optically recorded action potentials from multiple neurons in brain tissue has yet to be achieved. With high expression of a two-photon-compatible GEVI, ASAP3, via in utero electroporation and RAMP, we achieved voltage recording of spontaneous activities from multiple neurons in brain slice. We provide evidence for the developmental changes in intralaminar horizontal connections in somatosensory cortex layer 2/3 with a greater sensitivity than calcium imaging. This method thus enables investigation of neuronal network connectivity at the cellular resolution in brain tissue.
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42
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Imaging volumetric dynamics at high speed in mouse and zebrafish brain with confocal light field microscopy. Nat Biotechnol 2020; 39:74-83. [PMID: 32778840 DOI: 10.1038/s41587-020-0628-7] [Citation(s) in RCA: 63] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2020] [Accepted: 07/08/2020] [Indexed: 12/12/2022]
Abstract
A detailed understanding of the function of neural networks and how they are supported by a dynamic vascular system requires fast three-dimensional imaging in thick tissues. Here we present confocal light field microscopy, a method that enables fast volumetric imaging in the brain at depths of hundreds of micrometers. It uses a generalized confocal detection scheme that selectively collects fluorescent signals from the in-focus volume and provides optical sectioning capability to improve imaging resolution and sensitivity in thick tissues. We demonstrate recording of whole-brain calcium transients in freely swimming zebrafish larvae and observe behaviorally correlated activities in single neurons during prey capture. Furthermore, in the mouse brain, we detect neural activities at depths of up to 370 μm and track blood cells at 70 Hz over a volume of diameter 800 μm × thickness 150 μm and depth of up to 600 μm.
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Song P, Jadan HV, Howe CL, Quicke P, Foust AJ, Dragotti PL. 3D Localization for Light-Field Microscopy via Convolutional Sparse Coding on Epipolar Images. IEEE TRANSACTIONS ON COMPUTATIONAL IMAGING 2020; 6:1017-1032. [PMID: 32851121 PMCID: PMC7442043 DOI: 10.1109/tci.2020.2997301] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/09/2020] [Revised: 04/16/2020] [Accepted: 05/18/2020] [Indexed: 05/27/2023]
Abstract
Light-field microscopy (LFM) is a type of all-optical imaging system that is able to capture 4D geometric information of light rays and can reconstruct a 3D model from a single snapshot. In this paper, we propose a new 3D localization approach to effectively detect 3D positions of neuronal cells from a single light-field image with high accuracy and outstanding robustness to light scattering. This is achieved by constructing a depth-aware dictionary and by combining it with convolutional sparse coding. Specifically, our approach includes 3 key parts: light-field calibration, depth-aware dictionary construction, and localization based on convolutional sparse coding (CSC). In the first part, an observed raw light-field image is calibrated and then decoded into a two-plane parameterized 4D format which leads to the epi-polar plane image (EPI). The second part involves simulating a set of light-fields using a wave-optics forward model for a ball-shaped volume that is located at different depths. Then, a depth-aware dictionary is constructed where each element is a synthetic EPI associated to a specific depth. Finally, by taking full advantage of the sparsity prior and shift-invariance property of EPI, 3D localization is achieved via convolutional sparse coding on an observed EPI with respect to the depth-aware EPI dictionary. We evaluate our approach on both non-scattering specimen (fluorescent beads suspended in agarose gel) and scattering media (brain tissues of genetically encoded mice). Extensive experiments demonstrate that our approach can reliably detect the 3D positions of granular targets with small Root Mean Square Error (RMSE), high robustness to optical aberration and light scattering in mammalian brain tissues.
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Affiliation(s)
- Pingfan Song
- Department of Electronic & Electrical
EngineeringImperial College LondonLondonSW7 2AZU.K.
| | - Herman Verinaz Jadan
- Department of Electronic & Electrical
EngineeringImperial College LondonLondonSW7 2AZU.K.
| | - Carmel L. Howe
- Department of Bioengineering, and Center
for NeurotechnologyImperial College LondonLondonSW7 2AZU.K.
| | - Peter Quicke
- Department of Bioengineering, and Center
for NeurotechnologyImperial College LondonLondonSW7 2AZU.K.
| | - Amanda J. Foust
- Department of Bioengineering, and Center
for NeurotechnologyImperial College LondonLondonSW7 2AZU.K.
| | - Pier Luigi Dragotti
- Department of Electronic & Electrical
EngineeringImperial College LondonLondonSW7 2AZU.K.
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44
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Karpf S, Riche CT, Di Carlo D, Goel A, Zeiger WA, Suresh A, Portera-Cailliau C, Jalali B. Spectro-temporal encoded multiphoton microscopy and fluorescence lifetime imaging at kilohertz frame-rates. Nat Commun 2020; 11:2062. [PMID: 32346060 PMCID: PMC7188897 DOI: 10.1038/s41467-020-15618-w] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2019] [Accepted: 03/18/2020] [Indexed: 12/21/2022] Open
Abstract
Two-Photon Microscopy has become an invaluable tool for biological and medical research, providing high sensitivity, molecular specificity, inherent three-dimensional sub-cellular resolution and deep tissue penetration. In terms of imaging speeds, however, mechanical scanners still limit the acquisition rates to typically 10-100 frames per second. Here we present a high-speed non-linear microscope achieving kilohertz frame rates by employing pulse-modulated, rapidly wavelength-swept lasers and inertia-free beam steering through angular dispersion. In combination with a high bandwidth, single-photon sensitive detector, this enables recording of fluorescent lifetimes at speeds of 88 million pixels per second. We show high resolution, multi-modal - two-photon fluorescence and fluorescence lifetime (FLIM) - microscopy and imaging flow cytometry with a digitally reconfigurable laser, imaging system and data acquisition system. These high speeds should enable high-speed and high-throughput image-assisted cell sorting.
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Affiliation(s)
- Sebastian Karpf
- Department of Electrical Engineering and Computational Science, University of California, Los Angeles (UCLA), Los Angeles, CA-90095, USA.
- Institute of Biomedical Optics (BMO), University of Luebeck, 23562, Luebeck, Germany.
| | - Carson T Riche
- Department of Bioengineering, University of California, Los Angeles (UCLA), Los Angeles, CA-90095, USA
| | - Dino Di Carlo
- Department of Bioengineering, University of California, Los Angeles (UCLA), Los Angeles, CA-90095, USA
| | - Anubhuti Goel
- Department of Neurology, University of California, Los Angeles (UCLA), Los Angeles, CA-90095, USA
| | - William A Zeiger
- Department of Neurology, University of California, Los Angeles (UCLA), Los Angeles, CA-90095, USA
| | - Anand Suresh
- Department of Neurology, University of California, Los Angeles (UCLA), Los Angeles, CA-90095, USA
| | - Carlos Portera-Cailliau
- Department of Neurology, University of California, Los Angeles (UCLA), Los Angeles, CA-90095, USA
| | - Bahram Jalali
- Department of Electrical Engineering and Computational Science, University of California, Los Angeles (UCLA), Los Angeles, CA-90095, USA
- Department of Bioengineering, University of California, Los Angeles (UCLA), Los Angeles, CA-90095, USA
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45
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Papagiakoumou E, Ronzitti E, Emiliani V. Scanless two-photon excitation with temporal focusing. Nat Methods 2020; 17:571-581. [PMID: 32284609 DOI: 10.1038/s41592-020-0795-y] [Citation(s) in RCA: 60] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2019] [Accepted: 02/28/2020] [Indexed: 11/09/2022]
Abstract
Temporal focusing, with its ability to focus light in time, enables scanless illumination of large surface areas at the sample with micrometer axial confinement and robust propagation through scattering tissue. In conventional two-photon microscopy, widely used for the investigation of intact tissue in live animals, images are formed by point scanning of a spatially focused pulsed laser beam, resulting in limited temporal resolution of the excitation. Replacing point scanning with temporally focused widefield illumination removes this limitation and represents an important milestone in two-photon microscopy. Temporal focusing uses a diffusive or dispersive optical element placed in a plane conjugate to the objective focal plane to generate position-dependent temporal pulse broadening that enables axially confined multiphoton absorption, without the need for tight spatial focusing. Many techniques have benefitted from temporal focusing, including scanless imaging, super-resolution imaging, photolithography, uncaging of caged neurotransmitters and control of neuronal activity via optogenetics.
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Affiliation(s)
- Eirini Papagiakoumou
- Wavefront-Engineering Microscopy Group, Photonics Department, Institut de la Vision, Sorbonne University, Inserm S968, CNRS UMR7210, Fondation Voir et Entendre, Paris, France
| | - Emiliano Ronzitti
- Wavefront-Engineering Microscopy Group, Photonics Department, Institut de la Vision, Sorbonne University, Inserm S968, CNRS UMR7210, Fondation Voir et Entendre, Paris, France
| | - Valentina Emiliani
- Wavefront-Engineering Microscopy Group, Photonics Department, Institut de la Vision, Sorbonne University, Inserm S968, CNRS UMR7210, Fondation Voir et Entendre, Paris, France.
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46
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Simultaneous multiplane imaging with reverberation two-photon microscopy. Nat Methods 2020; 17:283-286. [PMID: 32042186 DOI: 10.1038/s41592-019-0728-9] [Citation(s) in RCA: 50] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2019] [Accepted: 12/19/2019] [Indexed: 11/08/2022]
Abstract
Multiphoton microscopy has gained enormous popularity because of its unique capacity to provide high-resolution images from deep within scattering tissue. Here, we demonstrate video-rate multiplane imaging with two-photon microscopy by performing near-instantaneous axial scanning while maintaining three-dimensional micrometer-scale resolution. Our technique, termed reverberation microscopy, enables the monitoring of neuronal populations over large depth ranges and can be implemented as a simple add-on to a conventional design.
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47
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Ren YX, Wu J, Lai QTK, Lai HM, Siu DMD, Wu W, Wong KKY, Tsia KK. Parallelized volumetric fluorescence microscopy with a reconfigurable coded incoherent light-sheet array. LIGHT, SCIENCE & APPLICATIONS 2020; 9:8. [PMID: 31993126 PMCID: PMC6971027 DOI: 10.1038/s41377-020-0245-8] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/31/2019] [Revised: 12/23/2019] [Accepted: 01/06/2020] [Indexed: 05/12/2023]
Abstract
Parallelized fluorescence imaging has been a long-standing pursuit that can address the unmet need for a comprehensive three-dimensional (3D) visualization of dynamical biological processes with minimal photodamage. However, the available approaches are limited to incomplete parallelization in only two dimensions or sparse sampling in three dimensions. We hereby develop a novel fluorescence imaging approach, called coded light-sheet array microscopy (CLAM), which allows complete parallelized 3D imaging without mechanical scanning. Harnessing the concept of an "infinity mirror", CLAM generates a light-sheet array with controllable sheet density and degree of coherence. Thus, CLAM circumvents the common complications of multiple coherent light-sheet generation in terms of dedicated wavefront engineering and mechanical dithering/scanning. Moreover, the encoding of multiplexed optical sections in CLAM allows the synchronous capture of all sectioned images within the imaged volume. We demonstrate the utility of CLAM in different imaging scenarios, including a light-scattering medium, an optically cleared tissue, and microparticles in fluidic flow. CLAM can maximize the signal-to-noise ratio and the spatial duty cycle, and also provides a further reduction in photobleaching compared to the major scanning-based 3D imaging systems. The flexible implementation of CLAM regarding both hardware and software ensures compatibility with any light-sheet imaging modality and could thus be instrumental in a multitude of areas in biological research.
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Affiliation(s)
- Yu-Xuan Ren
- Department of Electrical and Electronic Engineering, The University of Hong Kong, Pokfulam Road, Hong Kong, SAR 999077 China
| | - Jianglai Wu
- Department of Electrical and Electronic Engineering, The University of Hong Kong, Pokfulam Road, Hong Kong, SAR 999077 China
- Department of Physics, University of California, Berkeley, CA 94720 USA
| | - Queenie T. K. Lai
- Department of Electrical and Electronic Engineering, The University of Hong Kong, Pokfulam Road, Hong Kong, SAR 999077 China
| | - Hei Ming Lai
- School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, SAR 999077 China
- Department of Psychiatry, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong, SAR 999077 China
| | - Dickson M. D. Siu
- Department of Electrical and Electronic Engineering, The University of Hong Kong, Pokfulam Road, Hong Kong, SAR 999077 China
| | - Wutian Wu
- School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, SAR 999077 China
- GHM Institute of CNS Regeneration, Jinan University, 601 Huangpu Avenue West, Guangzhou, 510632 China
- Re-Stem Biotechnology, Suzhou, 215007 China
| | - Kenneth K. Y. Wong
- Department of Electrical and Electronic Engineering, The University of Hong Kong, Pokfulam Road, Hong Kong, SAR 999077 China
| | - Kevin K. Tsia
- Department of Electrical and Electronic Engineering, The University of Hong Kong, Pokfulam Road, Hong Kong, SAR 999077 China
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48
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Chakraborty T, Chen B, Daetwyler S, Chang BJ, Vanderpoorten O, Sapoznik E, Kaminski CF, Knowles TPJ, Dean KM, Fiolka R. Converting lateral scanning into axial focusing to speed up three-dimensional microscopy. LIGHT, SCIENCE & APPLICATIONS 2020; 9:165. [PMID: 33024553 PMCID: PMC7501866 DOI: 10.1038/s41377-020-00401-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/18/2020] [Revised: 08/25/2020] [Accepted: 09/02/2020] [Indexed: 05/04/2023]
Abstract
In optical microscopy, the slow axial scanning rate of the objective or the sample has traditionally limited the speed of volumetric imaging. Recently, by conjugating either a movable mirror to the image plane in a remote-focusing geometry or an electrically tuneable lens (ETL) to the back focal plane, rapid axial scanning has been achieved. However, mechanical actuation of a mirror limits the axial scanning rate (usually only 10-100 Hz for piezoelectric or voice coil-based actuators), while ETLs introduce spherical and higher-order aberrations that prevent high-resolution imaging. In an effort to overcome these limitations, we introduce a novel optical design that transforms a lateral-scan motion into a spherical aberration-free axial scan that can be used for high-resolution imaging. Using a galvanometric mirror, we scan a laser beam laterally in a remote-focusing arm, which is then back-reflected from different heights of a mirror in the image space. We characterize the optical performance of this remote-focusing technique and use it to accelerate axially swept light-sheet microscopy by an order of magnitude, allowing the quantification of rapid vesicular dynamics in three dimensions. We also demonstrate resonant remote focusing at 12 kHz with a two-photon raster-scanning microscope, which allows rapid imaging of brain tissues and zebrafish cardiac dynamics with diffraction-limited resolution.
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Affiliation(s)
- Tonmoy Chakraborty
- Department of Cell Biology, UT Southwestern Medical Center, Dallas, TX USA
- Department of Physics and Astronomy, University of New Mexico, Albuquerque, NM USA
| | - Bingying Chen
- Department of Cell Biology, UT Southwestern Medical Center, Dallas, TX USA
| | - Stephan Daetwyler
- Department of Cell Biology, UT Southwestern Medical Center, Dallas, TX USA
| | - Bo-Jui Chang
- Department of Cell Biology, UT Southwestern Medical Center, Dallas, TX USA
| | - Oliver Vanderpoorten
- Department of Chemical Engineering and Biotechnology, University of Cambridge, Cambridge, CB3 0AS UK
| | - Etai Sapoznik
- Department of Cell Biology, UT Southwestern Medical Center, Dallas, TX USA
| | - Clemens F. Kaminski
- Department of Chemical Engineering and Biotechnology, University of Cambridge, Cambridge, CB3 0AS UK
| | - Tuomas P. J. Knowles
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW UK
| | - Kevin M. Dean
- Department of Cell Biology, UT Southwestern Medical Center, Dallas, TX USA
| | - Reto Fiolka
- Department of Cell Biology, UT Southwestern Medical Center, Dallas, TX USA
- Lyda Hill Department of Bioinformatics, UT Southwestern Medical Center, Dallas, TX USA
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49
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Abstract
Fluorescence microscopy has long been a valuable tool for biological and medical imaging. Control of optical parameters such as the amplitude, phase, polarization and propagation angle of light gives fluorescence imaging great capabilities ranging from super-resolution imaging to long-term real-time observation of living organisms. In this review, we discuss current fluorescence imaging techniques in terms of the use of tailored or structured light for the sample illumination and fluorescence detection, providing a clear overview of their working principles and capabilities.
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Affiliation(s)
- Jialei Tang
- CREOL, The College of Optics and Photonics, University of Central Florida, Orlando, Florida, USA
- These authors contributed equally to this work
| | - Jinhan Ren
- CREOL, The College of Optics and Photonics, University of Central Florida, Orlando, Florida, USA
- These authors contributed equally to this work
| | - Kyu Young Han
- CREOL, The College of Optics and Photonics, University of Central Florida, Orlando, Florida, USA
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50
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Yang M, Zhou Z, Zhang J, Jia S, Li T, Guan J, Liao X, Leng B, Lyu J, Zhang K, Li M, Gong Y, Zhu Z, Yan J, Zhou Y, Liu JK, Varga Z, Konnerth A, Tang Y, Gao J, Chen X, Jia H. MATRIEX imaging: multiarea two-photon real-time in vivo explorer. LIGHT, SCIENCE & APPLICATIONS 2019; 8:109. [PMID: 31798848 PMCID: PMC6881438 DOI: 10.1038/s41377-019-0219-x] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/16/2019] [Revised: 10/31/2019] [Accepted: 11/05/2019] [Indexed: 06/01/2023]
Abstract
Two-photon laser scanning microscopy has been extensively applied to study in vivo neuronal activity at cellular and subcellular resolutions in mammalian brains. However, the extent of such studies is typically confined to a single functional region of the brain. Here, we demonstrate a novel technique, termed the multiarea two-photon real-time in vivo explorer (MATRIEX), that allows the user to target multiple functional brain regions distributed within a zone of up to 12 mm in diameter, each with a field of view (FOV) of ~200 μm in diameter, thus performing two-photon Ca2+ imaging with single-cell resolution in all of the regions simultaneously. For example, we demonstrate real-time functional imaging of single-neuron activities in the primary visual cortex, primary motor cortex and hippocampal CA1 region of mice in both anesthetized and awake states. A unique advantage of the MATRIEX technique is the configuration of multiple microscopic FOVs that are distributed in three-dimensional space over macroscopic distances (>1 mm) both laterally and axially but that are imaged by a single conventional laser scanning device. In particular, the MATRIEX technique can be effectively implemented as an add-on optical module for an existing conventional single-beam-scanning two-photon microscope without requiring any modification to the microscope itself. Thus, the MATRIEX technique can be readily applied to substantially facilitate the exploration of multiarea neuronal activity in vivo for studies of brain-wide neural circuit function with single-cell resolution.
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Affiliation(s)
- Mengke Yang
- Key Laboratory of Optical System Advanced Manufacturing Technology, Changchun Institute of Optics, Fine Mechanics and Physics, Chinese Academy of Sciences, Changchun, 130033 China
- Graduate School, University of the Chinese Academy of Sciences, Beijing, 100039 China
- Brain Research Instrument Innovation Center, Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Sciences, Suzhou, 215163 China
| | - Zhenqiao Zhou
- Brain Research Instrument Innovation Center, Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Sciences, Suzhou, 215163 China
| | - Jianxiong Zhang
- Brain Research Center and State Key Laboratory of Trauma, Burns, and Combined Injury, Third Military Medical University, Chongqing, 400038 China
| | - Shanshan Jia
- Brain Research Center and State Key Laboratory of Trauma, Burns, and Combined Injury, Third Military Medical University, Chongqing, 400038 China
| | - Tong Li
- Brain Research Center and State Key Laboratory of Trauma, Burns, and Combined Injury, Third Military Medical University, Chongqing, 400038 China
| | - Jiangheng Guan
- Brain Research Center and State Key Laboratory of Trauma, Burns, and Combined Injury, Third Military Medical University, Chongqing, 400038 China
| | - Xiang Liao
- Center for Neurointelligence, Chongqing University, Chongqing, 401331 China
| | - Bing Leng
- Brain Research Instrument Innovation Center, Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Sciences, Suzhou, 215163 China
| | - Jing Lyu
- Brain Research Instrument Innovation Center, Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Sciences, Suzhou, 215163 China
| | - Kuan Zhang
- Brain Research Center and State Key Laboratory of Trauma, Burns, and Combined Injury, Third Military Medical University, Chongqing, 400038 China
| | - Min Li
- Brain Research Instrument Innovation Center, Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Sciences, Suzhou, 215163 China
| | - Yan Gong
- Brain Research Instrument Innovation Center, Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Sciences, Suzhou, 215163 China
| | - Zhiming Zhu
- Center for Hypertension and Metabolic Diseases, Daping Hospital, Chongqing, 400042 China
| | - Junan Yan
- Advanced Institute of Brain and Intelligence, Guangxi University, Nanning, 530005 China
| | - Yi Zhou
- Advanced Institute of Brain and Intelligence, Guangxi University, Nanning, 530005 China
| | - Jian K Liu
- Centre for Systems Neuroscience, Department of Neuroscience, Psychology and Behaviour, University of Leicester, Leicester, UK
| | - Zsuzsanna Varga
- Institute of Neuroscience, Technical University Munich, 80802 Munich, Germany
| | - Arthur Konnerth
- Institute of Neuroscience, Technical University Munich, 80802 Munich, Germany
| | - Yuguo Tang
- Brain Research Instrument Innovation Center, Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Sciences, Suzhou, 215163 China
| | - Jinsong Gao
- Key Laboratory of Optical System Advanced Manufacturing Technology, Changchun Institute of Optics, Fine Mechanics and Physics, Chinese Academy of Sciences, Changchun, 130033 China
| | - Xiaowei Chen
- Brain Research Center and State Key Laboratory of Trauma, Burns, and Combined Injury, Third Military Medical University, Chongqing, 400038 China
| | - Hongbo Jia
- Brain Research Instrument Innovation Center, Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Sciences, Suzhou, 215163 China
- Institute of Neuroscience, Technical University Munich, 80802 Munich, Germany
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