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Bai L, Cong L, Shi Z, Zhao Y, Zhang Y, Lu B, Zhang J, Xiong ZQ, Xu N, Mu Y, Wang K. Volumetric voltage imaging of neuronal populations in the mouse brain by confocal light-field microscopy. Nat Methods 2024:10.1038/s41592-024-02458-5. [PMID: 39379535 DOI: 10.1038/s41592-024-02458-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2024] [Accepted: 09/06/2024] [Indexed: 10/10/2024]
Abstract
Voltage imaging measures neuronal activity directly and holds promise for understanding information processing within individual neurons and across populations. However, imaging voltage over large neuronal populations has been challenging owing to the simultaneous requirements of high imaging speed and signal-to-noise ratio, large volume coverage and low photobleaching rate. Here, to overcome this challenge, we developed a confocal light-field microscope that surpassed the traditional limits in speed and noise performance by incorporating a speed-enhanced camera, a fast and robust scanning mechanism, laser-speckle-noise elimination and optimized light efficiency. With this method, we achieved simultaneous recording from more than 300 spiking neurons within an 800-µm-diameter and 180-µm-thick volume in the mouse cortex, for more than 20 min. By integrating the spatial and voltage activity profiles, we have mapped three-dimensional neural coordination patterns in awake mouse brains. Our method is robust for routine application in volumetric voltage imaging.
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Affiliation(s)
- Lu Bai
- Institute of Neuroscience, Key Laboratory of Brain Cognition and Brain-Inspired Intelligence Technology, CAS Center for Excellence in Brain Science and Intelligence Technology, Chinese Academy of Sciences, Shanghai, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Lin Cong
- Institute of Neuroscience, Key Laboratory of Brain Cognition and Brain-Inspired Intelligence Technology, CAS Center for Excellence in Brain Science and Intelligence Technology, Chinese Academy of Sciences, Shanghai, China
| | - Ziqi Shi
- Institute of Neuroscience, Key Laboratory of Brain Cognition and Brain-Inspired Intelligence Technology, CAS Center for Excellence in Brain Science and Intelligence Technology, Chinese Academy of Sciences, Shanghai, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Yuchen Zhao
- Institute of Neuroscience, Key Laboratory of Brain Cognition and Brain-Inspired Intelligence Technology, CAS Center for Excellence in Brain Science and Intelligence Technology, Chinese Academy of Sciences, Shanghai, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Yujie Zhang
- Institute of Neuroscience, Key Laboratory of Brain Cognition and Brain-Inspired Intelligence Technology, CAS Center for Excellence in Brain Science and Intelligence Technology, Chinese Academy of Sciences, Shanghai, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Bin Lu
- Institute of Neuroscience, Key Laboratory of Brain Cognition and Brain-Inspired Intelligence Technology, CAS Center for Excellence in Brain Science and Intelligence Technology, Chinese Academy of Sciences, Shanghai, China
| | - Jing Zhang
- Institute of Neuroscience, Key Laboratory of Brain Cognition and Brain-Inspired Intelligence Technology, CAS Center for Excellence in Brain Science and Intelligence Technology, Chinese Academy of Sciences, Shanghai, China
| | - Zhi-Qi Xiong
- Institute of Neuroscience, Key Laboratory of Brain Cognition and Brain-Inspired Intelligence Technology, CAS Center for Excellence in Brain Science and Intelligence Technology, Chinese Academy of Sciences, Shanghai, China
- University of Chinese Academy of Sciences, Beijing, China
- School of Life Science and Technology, ShanghaiTech University, Shanghai, China
- Shanghai Center for Brain Science and Brain-Inspired Intelligence Technology, Shanghai, China
| | - Ninglong Xu
- Institute of Neuroscience, Key Laboratory of Brain Cognition and Brain-Inspired Intelligence Technology, CAS Center for Excellence in Brain Science and Intelligence Technology, Chinese Academy of Sciences, Shanghai, China
- University of Chinese Academy of Sciences, Beijing, China
- Shanghai Center for Brain Science and Brain-Inspired Intelligence Technology, Shanghai, China
| | - Yu Mu
- Institute of Neuroscience, Key Laboratory of Brain Cognition and Brain-Inspired Intelligence Technology, CAS Center for Excellence in Brain Science and Intelligence Technology, Chinese Academy of Sciences, Shanghai, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Kai Wang
- Institute of Neuroscience, Key Laboratory of Brain Cognition and Brain-Inspired Intelligence Technology, CAS Center for Excellence in Brain Science and Intelligence Technology, Chinese Academy of Sciences, Shanghai, China.
- University of Chinese Academy of Sciences, Beijing, China.
- School of Life Science and Technology, ShanghaiTech University, Shanghai, China.
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Xu C, Nedergaard M, Fowell DJ, Friedl P, Ji N. Multiphoton fluorescence microscopy for in vivo imaging. Cell 2024; 187:4458-4487. [PMID: 39178829 PMCID: PMC11373887 DOI: 10.1016/j.cell.2024.07.036] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2024] [Revised: 07/18/2024] [Accepted: 07/22/2024] [Indexed: 08/26/2024]
Abstract
Multiphoton fluorescence microscopy (MPFM) has been a game-changer for optical imaging, particularly for studying biological tissues deep within living organisms. MPFM overcomes the strong scattering of light in heterogeneous tissue by utilizing nonlinear excitation that confines fluorescence emission mostly to the microscope focal volume. This enables high-resolution imaging deep within intact tissue and has opened new avenues for structural and functional studies. MPFM has found widespread applications and has led to numerous scientific discoveries and insights into complex biological processes. Today, MPFM is an indispensable tool in many research communities. Its versatility and effectiveness make it a go-to technique for researchers investigating biological phenomena at the cellular and subcellular levels in their native environments. In this Review, the principles, implementations, capabilities, and limitations of MPFM are presented. Three application areas of MPFM, neuroscience, cancer biology, and immunology, are reviewed in detail and serve as examples for applying MPFM to biological research.
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Affiliation(s)
- Chris Xu
- School of Applied and Engineering Physics, Cornell University, Ithaca, NY 14850, USA
| | - Maiken Nedergaard
- Center for Translational Neuromedicine, Faculty of Health and Medical Sciences, University of Copenhagen, Nørre Alle 3B, 2200 Copenhagen, Denmark; University of Rochester Medical School, 601 Elmwood Avenue, Rochester, NY 14642, USA
| | - Deborah J Fowell
- Department of Microbiology & Immunology, Cornell University, Ithaca, NY 14853, USA
| | - Peter Friedl
- Department of Medical BioSciences, Radboud University Medical Centre, Geert Grooteplein 26-28, Nijmegen HB 6500, the Netherlands
| | - Na Ji
- Department of Neuroscience, Department of Physics, University of California Berkeley, Berkeley, CA 94720, USA.
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Hira R. Closed-loop experiments and brain machine interfaces with multiphoton microscopy. NEUROPHOTONICS 2024; 11:033405. [PMID: 38375331 PMCID: PMC10876015 DOI: 10.1117/1.nph.11.3.033405] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/24/2023] [Revised: 01/22/2024] [Accepted: 01/29/2024] [Indexed: 02/21/2024]
Abstract
In the field of neuroscience, the importance of constructing closed-loop experimental systems has increased in conjunction with technological advances in measuring and controlling neural activity in live animals. We provide an overview of recent technological advances in the field, focusing on closed-loop experimental systems where multiphoton microscopy-the only method capable of recording and controlling targeted population activity of neurons at a single-cell resolution in vivo-works through real-time feedback. Specifically, we present some examples of brain machine interfaces (BMIs) using in vivo two-photon calcium imaging and discuss applications of two-photon optogenetic stimulation and adaptive optics to real-time BMIs. We also consider conditions for realizing future optical BMIs at the synaptic level, and their possible roles in understanding the computational principles of the brain.
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Affiliation(s)
- Riichiro Hira
- Tokyo Medical and Dental University, Graduate School of Medical and Dental Sciences, Department of Physiology and Cell Biology, Tokyo, Japan
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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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Sarafraz H, Nöbauer T, Kim H, Soldevila F, Gigan S, Vaziri A. Speckle-enabled in vivo demixing of neural activity in the mouse brain. BIOMEDICAL OPTICS EXPRESS 2024; 15:3586-3608. [PMID: 38867774 PMCID: PMC11166431 DOI: 10.1364/boe.524521] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/22/2024] [Revised: 04/11/2024] [Accepted: 04/14/2024] [Indexed: 06/14/2024]
Abstract
Functional imaging of neuronal activity in awake animals, using a combination of fluorescent reporters of neuronal activity and various types of microscopy modalities, has become an indispensable tool in neuroscience. While various imaging modalities based on one-photon (1P) excitation and parallel (camera-based) acquisition have been successfully used for imaging more transparent samples, when imaging mammalian brain tissue, due to their scattering properties, two-photon (2P) microscopy systems are necessary. In 2P microscopy, the longer excitation wavelengths reduce the amount of scattering while the diffraction-limited 3D localization of excitation largely eliminates out-of-focus fluorescence. However, this comes at the cost of time-consuming serial scanning of the excitation spot and more complex and expensive instrumentation. Thus, functional 1P imaging modalities that can be used beyond the most transparent specimen are highly desirable. Here, we transform light scattering from an obstacle into a tool. We use speckles with their unique patterns and contrast, formed when fluorescence from individual neurons propagates through rodent cortical tissue, to encode neuronal activity. Spatiotemporal demixing of these patterns then enables functional recording of neuronal activity from a group of discriminable sources. For the first time, we provide an experimental, in vivo characterization of speckle generation, speckle imaging and speckle-assisted demixing of neuronal activity signals in the scattering mammalian brain tissue. We found that despite an initial fast speckle decorrelation, substantial correlation was maintained over minute-long timescales that contributed to our ability to demix temporal activity traces in the mouse brain in vivo. Informed by in vivo quantifications of speckle patterns from single and multiple neurons excited using 2P scanning excitation, we recorded and demixed activity from several sources excited using 1P oblique illumination. In our proof-of-principle experiments, we demonstrate in vivo speckle-assisted demixing of functional signals from groups of sources in a depth range of 220-320 µm in mouse cortex, limited by available speckle contrast. Our results serve as a basis for designing an in vivo functional speckle imaging modality and for maximizing the key resource in any such modality, the speckle contrast. We anticipate that our results will provide critical quantitative guidance to the community for designing techniques that overcome light scattering as a fundamental limitation in bioimaging.
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Affiliation(s)
- Hossein Sarafraz
- Laboratory of Neurotechnology and Biophysics, The Rockefeller University, New York, NY, USA
| | - Tobias Nöbauer
- Laboratory of Neurotechnology and Biophysics, The Rockefeller University, New York, NY, USA
- The Kavli Neural Systems Institute, The Rockefeller University, New York, NY, USA
| | - Hyewon Kim
- Laboratory of Neurotechnology and Biophysics, The Rockefeller University, New York, NY, USA
| | - Fernando Soldevila
- Laboratoire Kastler Brossel, ENS–Université PSL, CNRS, Sorbonne Université, College de France, 24 Rue Lhomond, F-75005 Paris, France
| | - Sylvain Gigan
- Laboratoire Kastler Brossel, ENS–Université PSL, CNRS, Sorbonne Université, College de France, 24 Rue Lhomond, F-75005 Paris, France
| | - Alipasha Vaziri
- Laboratory of Neurotechnology and Biophysics, The Rockefeller University, New York, NY, USA
- The Kavli Neural Systems Institute, The Rockefeller University, New York, NY, USA
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Ching-Roa VD, Huang CZ, Giacomelli MG. Suppression of Subpixel Jitter in Resonant Scanning Systems With Phase-locked Sampling. IEEE TRANSACTIONS ON MEDICAL IMAGING 2024; 43:2159-2168. [PMID: 38265914 PMCID: PMC11147734 DOI: 10.1109/tmi.2024.3358191] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/26/2024]
Abstract
Resonant scanning is critical to high speed and in vivo imaging in many applications of laser scanning microscopy. However, resonant scanning suffers from well-known image artifacts due to scanner jitter, limiting adoption of high-speed imaging technologies. Here, we introduce a real-time, inexpensive and all electrical method to suppress jitter more than an order of magnitude below the diffraction limit that can be applied to most existing microscope systems with no software changes. By phase-locking imaging to the resonant scanner period, we demonstrate an 86% reduction in pixel jitter, a 15% improvement in point spread function with resonant scanning and show that this approach enables two widely used models of resonant scanners to achieve comparable accuracy to galvanometer scanners running two orders of magnitude slower. Finally, we demonstrate the versatility of this method by retrofitting a commercial two photon microscope and show that this approach enables significant quantitative and qualitative improvements in biological imaging.
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Liu G, Chen B, Tian Z, Zhong Q, Chen SC. Compressive sensing-based multi-focus line-scanning two-photon microscopy for fast 3D imaging. OPTICS EXPRESS 2024; 32:17143-17151. [PMID: 38858904 DOI: 10.1364/oe.522671] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/28/2024] [Accepted: 04/03/2024] [Indexed: 06/12/2024]
Abstract
Fast 3D volume imaging methods have been playing increasingly important roles in biological studies. In this article, we present the design and characterization of a multi-focus line-scanning two-photon microscope. Specifically, a digital micromirror device (DMD) is employed to generate a randomly distributed focus array on a plane (i.e., x-z) via binary holography. Next, a galvanometric mirror scans the focus array in a direction normal to the plane (i.e., y-axis) over the imaging volume. For sparse samples, e.g., neural networks in a brain, 1-3 foci are used together with compressive sensing algorithm to achieve a volume imaging rate of 15.5 volumes/sec over 77 × 120 × 40 µm3. High-resolution optical cross-sectional images on selected planes and regions can be generated by sequentially scanning the laser focus generated on the x-z plane with good imaging speeds (e.g., 107 frames/sec over 80 × 120 × 40 µm3). In the experiments, microbeads, pollens, and mouse brain slices have been imaged to characterize the point spread function and volume image rate and quality at different sampling ratios. The results show that the multi-focus line-scanning microscope presents a fast and versatile 3D imaging platform for deep tissue imaging and dynamic live animal studies.
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8
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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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Farinella DM, Stanek S, Jayakumar H, Newman ZL, Gable J, Leger J, Kerlin A. Two-dimensional electro-optical multiphoton microscopy. NEUROPHOTONICS 2024; 11:025005. [PMID: 38841422 PMCID: PMC11151658 DOI: 10.1117/1.nph.11.2.025005] [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: 02/10/2024] [Revised: 05/08/2024] [Accepted: 05/15/2024] [Indexed: 06/07/2024]
Abstract
Significance The development of genetically encoded fluorescent indicators of neural activity with millisecond dynamics has generated demand for ever faster two-photon (2P) imaging systems, but acoustic and mechanical beam scanning technologies are approaching fundamental limits. We demonstrate that potassium tantalate niobate (KTN) electro-optical deflectors (EODs), which are not subject to the same fundamental limits, are capable of ultrafast two-dimensional (2D) 2P imaging in vivo. Aim To determine if KTN-EODs are suitable for 2P imaging, compatible with 2D scanning, and capable of ultrafast in vivo imaging of genetically encoded indicators with millisecond dynamics. Approach The performance of a commercially available KTN-EOD was characterized across a range of drive frequencies and laser parameters relevant to in vivo 2P microscopy. A second KTN-EOD was incorporated into a dual-axis scan module, and the system was validated by imaging signals in vivo from ASAP3, a genetically encoded voltage indicator. Results Optimal KTN-EOD deflection of laser light with a central wavelength of 960 nm was obtained up to the highest average powers and pulse intensities tested (power: 350 mW; pulse duration: 118 fs). Up to 32 resolvable spots per line at a 560 kHz line scan rate could be obtained with single-axis deflection. The complete dual-axis EO 2P microscope was capable of imaging a 13 μ m by 13 μ m field-of-view at over 10 kHz frame rate with ∼ 0.5 μ m lateral resolution. We demonstrate in vivo imaging of neurons expressing ASAP3 with high temporal resolution. Conclusions We demonstrate the suitability of KTN-EODs for ultrafast 2P cellular imaging in vivo, providing a foundation for future high-performance microscopes to incorporate emerging advances in KTN-based scanning technology.
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Affiliation(s)
- Deano M. Farinella
- University of Minnesota, Department of Neuroscience, Minneapolis, Minnesota, United States
| | - Samuel Stanek
- University of Minnesota, Department of Electrical and Computer Engineering, Minneapolis, Minnesota, United States
| | - Harishankar Jayakumar
- University of Minnesota, Department of Neuroscience, Minneapolis, Minnesota, United States
| | - Zachary L. Newman
- University of Minnesota, Department of Neuroscience, Minneapolis, Minnesota, United States
| | - Jacob Gable
- University of Minnesota, Department of Neuroscience, Minneapolis, Minnesota, United States
| | - James Leger
- University of Minnesota, Department of Electrical and Computer Engineering, Minneapolis, Minnesota, United States
| | - Aaron Kerlin
- University of Minnesota, Department of Neuroscience, Minneapolis, Minnesota, United States
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10
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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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11
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Zhou A, Mihelic SA, Engelmann SA, Tomar A, Dunn AK, Narasimhan VM. A Deep Learning Approach for Improving Two-Photon Vascular Imaging Speeds. Bioengineering (Basel) 2024; 11:111. [PMID: 38391597 PMCID: PMC10886311 DOI: 10.3390/bioengineering11020111] [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: 11/07/2023] [Revised: 01/09/2024] [Accepted: 01/10/2024] [Indexed: 02/24/2024] Open
Abstract
A potential method for tracking neurovascular disease progression over time in preclinical models is multiphoton fluorescence microscopy (MPM), which can image cerebral vasculature with capillary-level resolution. However, obtaining high-quality, three-dimensional images with traditional point scanning MPM is time-consuming and limits sample sizes for chronic studies. Here, we present a convolutional neural network-based (PSSR Res-U-Net architecture) algorithm for fast upscaling of low-resolution or sparsely sampled images and combine it with a segmentation-less vectorization process for 3D reconstruction and statistical analysis of vascular network structure. In doing so, we also demonstrate that the use of semi-synthetic training data can replace the expensive and arduous process of acquiring low- and high-resolution training pairs without compromising vectorization outcomes, and thus open the possibility of utilizing such approaches for other MPM tasks where collecting training data is challenging. We applied our approach to images with large fields of view from a mouse model and show that our method generalizes across imaging depths, disease states and other differences in neurovasculature. Our pretrained models and lightweight architecture can be used to reduce MPM imaging time by up to fourfold without any changes in underlying hardware, thereby enabling deployability across a range of settings.
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Affiliation(s)
- Annie Zhou
- Department of Biomedical Engineering, The University of Texas at Austin, 107 W. Dean Keeton C0800, Austin, TX 78712, USA
| | - Samuel A Mihelic
- Department of Biomedical Engineering, The University of Texas at Austin, 107 W. Dean Keeton C0800, Austin, TX 78712, USA
| | - Shaun A Engelmann
- Department of Biomedical Engineering, The University of Texas at Austin, 107 W. Dean Keeton C0800, Austin, TX 78712, USA
| | - Alankrit Tomar
- Department of Biomedical Engineering, The University of Texas at Austin, 107 W. Dean Keeton C0800, Austin, TX 78712, USA
| | - Andrew K Dunn
- Department of Biomedical Engineering, The University of Texas at Austin, 107 W. Dean Keeton C0800, Austin, TX 78712, USA
| | - Vagheesh M Narasimhan
- Department of Integrative Biology, The University of Texas at Austin, 2415 Speedway C0930, Austin, TX 78712, USA
- Department of Statistics and Data Sciences, The University of Texas at Austin, 105 E. 24th St D9800, Austin, TX 78712, USA
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Lee CH, Park YK, Lee K. Recent strategies for neural dynamics observation at a larger scale and wider scope. Biosens Bioelectron 2023; 240:115638. [PMID: 37647685 DOI: 10.1016/j.bios.2023.115638] [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: 04/14/2023] [Revised: 08/15/2023] [Accepted: 08/24/2023] [Indexed: 09/01/2023]
Abstract
The tremendous technical progress in neuroscience offers opportunities to observe a more minor or/and broader dynamic picture of the brain. Moreover, the large-scale neural activity of individual neurons enables the dissection of detailed mechanistic links between neural populations and behaviors. To measure neural activity in-vivo, multi-neuron recording, and neuroimaging techniques are employed and developed to acquire more neurons. The tools introduced concurrently recorded dozens to hundreds of neurons in the coordinated brain regions and elucidated the neuronal ensembles from a massive population perspective of diverse neurons at cellular resolution. In particular, the increasing spatiotemporal resolution of neuronal monitoring across the whole brain dramatically facilitates our understanding of additional nervous system functions in health and disease. Here, we will introduce state-of-the-art neuroscience tools involving large-scale neural population recording and the long-range connections spanning multiple brain regions. Their synergic effects provide to clarify the controversial circuitry underlying neuroscience. These challenging neural tools present a promising outlook for the fundamental dynamic interplay across levels of synaptic cellular, circuit organization, and brain-wide. Hence, more observations of neural dynamics will provide more clues to elucidate brain functions and push forward innovative technology at the intersection of neural engineering disciplines. We hope this review will provide insight into the use or development of recent neural techniques considering spatiotemporal scales of brain observation.
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Affiliation(s)
- Chang Hak Lee
- Department of Brain Sciences, Daegu Gyeongbuk Institute of Science & Technology (DGIST), Daegu, South Korea
| | - Young Kwon Park
- Department of Brain Sciences, Daegu Gyeongbuk Institute of Science & Technology (DGIST), Daegu, South Korea
| | - Kwang Lee
- Department of Brain Sciences, Daegu Gyeongbuk Institute of Science & Technology (DGIST), Daegu, South Korea.
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13
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Klioutchnikov A, Kerr JND. Chasing cortical behavior: designing multiphoton microscopes for imaging neuronal populations in freely moving rodents. NEUROPHOTONICS 2023; 10:044411. [PMID: 37886044 PMCID: PMC10599648 DOI: 10.1117/1.nph.10.4.044411] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/12/2023] [Revised: 09/22/2023] [Accepted: 10/03/2023] [Indexed: 10/28/2023]
Abstract
Imaging in the freely moving animal gives unparalleled access to circuit activity as the animal interacts with its environment in a self-guided way. Over the past few years, new imaging technologies have enabled the interrogation of neuronal populations located at any depth of the cortex in freely moving mice while preserving the animal's behavioral repertoire. This commentary gives an updated overview of the recent advances that have enabled the link between behavior and the underlying neuronal activity to be explored.
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Affiliation(s)
- Alexandr Klioutchnikov
- Max Planck Institute for Neurobiology of Behavior, Department of Behavior and Brain Organization, Bonn, Germany
| | - Jason N. D. Kerr
- Max Planck Institute for Neurobiology of Behavior, Department of Behavior and Brain Organization, Bonn, Germany
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14
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Song J, Kang J, Kang U, Nam HS, Kim HJ, Kim RH, Kim JW, Yoo H. SNR enhanced high-speed two-photon microscopy using a pulse picker and time gating detection. Sci Rep 2023; 13:14244. [PMID: 37648768 PMCID: PMC10468500 DOI: 10.1038/s41598-023-41270-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2023] [Accepted: 08/24/2023] [Indexed: 09/01/2023] Open
Abstract
Two-photon microscopy (TPM) is an attractive biomedical imaging method due to its large penetration depth and optical sectioning capability. In particular, label-free autofluorescence imaging offers various advantages for imaging biological samples. However, relatively low intensity of autofluorescence leads to low signal-to-noise ratio (SNR), causing practical challenges for imaging biological samples. In this study, we present TPM using a pulse picker to utilize low pulse repetition rate of femtosecond pulsed laser to increase the pulse peak power of the excitation source leading to higher emission of two-photon fluorescence with the same average illumination power. Stronger autofluorescence emission allowed us to obtain higher SNR images of arterial and liver tissues. In addition, by applying the time gating detection method to the pulse signals obtained by TPM, we were able to significantly reduce the background noise of two-photon images. As a result, our TPM system using the pulsed light source with a 19 times lower repetition rate allowed us to obtain the same SNR image more than 19 times faster with the same average power. Although high pulse energy can increase the photobleaching, we also observed that high-speed imaging with low total illumination energy can mitigate the photobleaching effect to a level similar to that of conventional illumination with a high repetition rate. We anticipate that this simple approach will provide guidance for SNR enhancement with high-speed imaging in TPM as well as other nonlinear microscopy.
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Affiliation(s)
- Jeonggeun Song
- Department of Mechanical Engineering, Korea Advanced Institute of Science and Technology, 291 Daehak-Ro, Daejeon, 34141, South Korea
| | - Juehyung Kang
- Department of Biomedical Engineering, Hanyang University, 222 Wangsimni-Ro, Seoul, 04763, Republic of Korea
| | - Ungyo Kang
- Department of Mechanical Engineering, Korea Advanced Institute of Science and Technology, 291 Daehak-Ro, Daejeon, 34141, South Korea
| | - Hyeong Soo Nam
- Department of Mechanical Engineering, Korea Advanced Institute of Science and Technology, 291 Daehak-Ro, Daejeon, 34141, South Korea
| | - Hyun Jung Kim
- Cardiovascular Center, Korea University Guro Hospital, 148 Gurodong-Ro, Seoul, 08308, South Korea
| | - Ryeong Hyeon Kim
- Cardiovascular Center, Korea University Guro Hospital, 148 Gurodong-Ro, Seoul, 08308, South Korea
| | - Jin Won Kim
- Cardiovascular Center, Korea University Guro Hospital, 148 Gurodong-Ro, Seoul, 08308, South Korea
| | - Hongki Yoo
- Department of Mechanical Engineering, Korea Advanced Institute of Science and Technology, 291 Daehak-Ro, Daejeon, 34141, South Korea.
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15
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Zhao B, Koyama M, Mertz J. High-resolution multi-z confocal microscopy with a diffractive optical element. BIOMEDICAL OPTICS EXPRESS 2023; 14:3057-3071. [PMID: 37342696 PMCID: PMC10278611 DOI: 10.1364/boe.491538] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/23/2023] [Revised: 05/16/2023] [Accepted: 05/18/2023] [Indexed: 06/23/2023]
Abstract
There has been recent interest in the development of fluorescence microscopes that provide high-speed volumetric imaging for life-science applications. For example, multi-z confocal microscopy enables simultaneous optically-sectioned imaging at multiple depths over relatively large fields of view. However, to date, multi-z microscopy has been hampered by limited spatial resolution owing to its initial design. Here we present a variant of multi-z microscopy that recovers the full spatial resolution of a conventional confocal microscope while retaining the simplicity and ease of use of our initial design. By introducing a diffractive optical element in the illumination path of our microscope, we engineer the excitation beam into multiple tightly focused spots that are conjugated to axially distributed confocal pinholes. We discuss the performance of this multi-z microscope in terms of resolution and detectability and demonstrate its versatility by performing in-vivo imaging of beating cardiomyocytes in engineered heart tissues and neuronal activity in c. elegans and zebrafish brains.
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Affiliation(s)
- Bingying Zhao
- Department of Electrical and Computer Engineering, Boston University, 44 Cummington Mall, Boston, MA 02215, USA
| | - Minoru Koyama
- Department of Cell and Systems Biology, University of Toronto, 1265 Military Trail, Scarborough, ON M1C1A4, Canada
| | - Jerome Mertz
- Department of Biomedical Engineering, Boston University, 44 Cummington Mall, Boston, MA 02215, USA
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16
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Zhao Z, Zhou Y, Liu B, He J, Zhao J, Cai Y, Fan J, Li X, Wang Z, Lu Z, Wu J, Qi H, Dai Q. Two-photon synthetic aperture microscopy for minimally invasive fast 3D imaging of native subcellular behaviors in deep tissue. Cell 2023; 186:2475-2491.e22. [PMID: 37178688 DOI: 10.1016/j.cell.2023.04.016] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2022] [Revised: 02/21/2023] [Accepted: 04/10/2023] [Indexed: 05/15/2023]
Abstract
Holistic understanding of physio-pathological processes requires noninvasive 3D imaging in deep tissue across multiple spatial and temporal scales to link diverse transient subcellular behaviors with long-term physiogenesis. Despite broad applications of two-photon microscopy (TPM), there remains an inevitable tradeoff among spatiotemporal resolution, imaging volumes, and durations due to the point-scanning scheme, accumulated phototoxicity, and optical aberrations. Here, we harnessed the concept of synthetic aperture radar in TPM to achieve aberration-corrected 3D imaging of subcellular dynamics at a millisecond scale for over 100,000 large volumes in deep tissue, with three orders of magnitude reduction in photobleaching. With its advantages, we identified direct intercellular communications through migrasome generation following traumatic brain injury, visualized the formation process of germinal center in the mouse lymph node, and characterized heterogeneous cellular states in the mouse visual cortex, opening up a horizon for intravital imaging to understand the organizations and functions of biological systems at a holistic level.
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Affiliation(s)
- Zhifeng Zhao
- Department of Automation, Tsinghua University, Beijing 100084, China; Institute for Brain and Cognitive Sciences, Tsinghua University, Beijing 100084, China; Beijing Key Laboratory of Multi-dimension & Multi-scale Computational Photography (MMCP), Tsinghua University, Beijing 100084, China; IDG/McGovern Institute for Brain Research, Tsinghua University, Beijing 100084, China; Hangzhou Zhuoxi Institute of Brain and Intelligence, Hangzhou 311100, China
| | - Yiliang Zhou
- Department of Automation, Tsinghua University, Beijing 100084, China; Institute for Brain and Cognitive Sciences, Tsinghua University, Beijing 100084, China; Beijing Key Laboratory of Multi-dimension & Multi-scale Computational Photography (MMCP), Tsinghua University, Beijing 100084, China; IDG/McGovern Institute for Brain Research, Tsinghua University, Beijing 100084, China; Hangzhou Zhuoxi Institute of Brain and Intelligence, Hangzhou 311100, China
| | - Bo Liu
- Tsinghua-Peking Center for Life Sciences, Beijing 100084, China; Laboratory of Dynamic Immunobiology, Institute for Immunology, Tsinghua University, Beijing 100084, China; Department of Basic Medical Sciences, School of Medicine, Tsinghua University, Beijing 100084, China
| | - Jing He
- Department of Automation, Tsinghua University, Beijing 100084, China; Institute for Brain and Cognitive Sciences, Tsinghua University, Beijing 100084, China; Beijing Key Laboratory of Multi-dimension & Multi-scale Computational Photography (MMCP), Tsinghua University, Beijing 100084, China; IDG/McGovern Institute for Brain Research, Tsinghua University, Beijing 100084, China
| | - Jiayin Zhao
- Department of Automation, Tsinghua University, Beijing 100084, China; Institute for Brain and Cognitive Sciences, Tsinghua University, Beijing 100084, China; Beijing Key Laboratory of Multi-dimension & Multi-scale Computational Photography (MMCP), Tsinghua University, Beijing 100084, China; Tsinghua Shenzhen International Graduate School, Tsinghua University, Shenzhen 518071, China
| | - Yeyi Cai
- Department of Automation, Tsinghua University, Beijing 100084, China; Institute for Brain and Cognitive Sciences, Tsinghua University, Beijing 100084, China; Beijing Key Laboratory of Multi-dimension & Multi-scale Computational Photography (MMCP), Tsinghua University, Beijing 100084, China; IDG/McGovern Institute for Brain Research, Tsinghua University, Beijing 100084, China
| | - Jingtao Fan
- Department of Automation, Tsinghua University, Beijing 100084, China; Institute for Brain and Cognitive Sciences, Tsinghua University, Beijing 100084, China; Beijing Key Laboratory of Multi-dimension & Multi-scale Computational Photography (MMCP), Tsinghua University, Beijing 100084, China
| | - Xinyang Li
- Department of Automation, Tsinghua University, Beijing 100084, China; Institute for Brain and Cognitive Sciences, Tsinghua University, Beijing 100084, China; Beijing Key Laboratory of Multi-dimension & Multi-scale Computational Photography (MMCP), Tsinghua University, Beijing 100084, China; Hangzhou Zhuoxi Institute of Brain and Intelligence, Hangzhou 311100, China; Tsinghua Shenzhen International Graduate School, Tsinghua University, Shenzhen 518071, China
| | - Zilin Wang
- Institute for Brain and Cognitive Sciences, Tsinghua University, Beijing 100084, China; Department of Anesthesiology, the First Medical Center, Chinese PLA General Hospital, Beijing 100853, China
| | - Zhi Lu
- Department of Automation, Tsinghua University, Beijing 100084, China; Institute for Brain and Cognitive Sciences, Tsinghua University, Beijing 100084, China; Beijing Key Laboratory of Multi-dimension & Multi-scale Computational Photography (MMCP), Tsinghua University, Beijing 100084, China; IDG/McGovern Institute for Brain Research, Tsinghua University, Beijing 100084, China; Hangzhou Zhuoxi Institute of Brain and Intelligence, Hangzhou 311100, China
| | - Jiamin Wu
- Department of Automation, Tsinghua University, Beijing 100084, China; Institute for Brain and Cognitive Sciences, Tsinghua University, Beijing 100084, China; Beijing Key Laboratory of Multi-dimension & Multi-scale Computational Photography (MMCP), Tsinghua University, Beijing 100084, China; IDG/McGovern Institute for Brain Research, Tsinghua University, Beijing 100084, China.
| | - Hai Qi
- Tsinghua-Peking Center for Life Sciences, Beijing 100084, China; Laboratory of Dynamic Immunobiology, Institute for Immunology, Tsinghua University, Beijing 100084, China; Department of Basic Medical Sciences, School of Medicine, Tsinghua University, Beijing 100084, China; Beijing Key Laboratory for Immunological Research on Chronic Diseases, Tsinghua University, Beijing 100084, China; Beijing Frontier Research Center for Biological Structure, Tsinghua University, Beijing 100084, China.
| | - Qionghai Dai
- Department of Automation, Tsinghua University, Beijing 100084, China; Institute for Brain and Cognitive Sciences, Tsinghua University, Beijing 100084, China; Beijing Key Laboratory of Multi-dimension & Multi-scale Computational Photography (MMCP), Tsinghua University, Beijing 100084, China; IDG/McGovern Institute for Brain Research, Tsinghua University, Beijing 100084, China.
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17
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Hsu CW, Lin CY, Hu YY, Chen SJ. Dual-resonant scanning multiphoton microscope with ultrasound lens and resonant mirror for rapid volumetric imaging. Sci Rep 2023; 13:161. [PMID: 36599927 DOI: 10.1038/s41598-022-27370-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2022] [Accepted: 12/30/2022] [Indexed: 01/06/2023] Open
Abstract
A dual-resonant scanning multiphoton (DRSM) microscope incorporating a tunable acoustic gradient index of refraction lens with a resonant mirror is developed for high-speed volumetric imaging. In the proposed microscope, the pulse train signal of a femtosecond laser is used to trigger an embedded field programmable gate array to sample the multiphoton excited fluorescence signal at the rate of one pixel per laser pulse. It is shown that a frame rate of around 8000 Hz can be obtained in the x-z plane for an image region with a size of 256 × 80 pixels. Moreover, a volumetric imaging rate of over 30 Hz can be obtained for a large image volume of 343 × 343 × 120 μm3 with an image size of 256 × 256 × 80 voxels. Moreover, a volumetric imaging rate of over 30 Hz can be obtained for a large image volume of 256 × 256 × 80 voxels, which represents 343 × 343 × 120 μm3 in field-of-view. The rapid volumetric imaging rate eliminates the aliasing effect for observed temporal frequencies lower than 15 Hz. The practical feasibility of the DRSM microscope is demonstrated by observing the mushroom bodies of a drosophila brain and performing 3D dynamic observations of moving 10-μm fluorescent beads.
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Affiliation(s)
- Chia-Wei Hsu
- College of Photonics, National Yang Ming Chiao Tung University, Tainan, 71150, Taiwan
| | - Chun-Yu Lin
- College of Photonics, National Yang Ming Chiao Tung University, Tainan, 71150, Taiwan
| | - Yvonne Yuling Hu
- Department of Photonics, National Cheng Kung University, Tainan, 70101, Taiwan
| | - Shean-Jen Chen
- College of Photonics, National Yang Ming Chiao Tung University, Tainan, 71150, Taiwan.
- Taiwan Instrument Research Institute, National Applied Research Laboratories, Hsinchu, 300, Taiwan.
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18
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Hsu CW, Lin CY, Hu YY, Wang CY, Chang ST, Chiang AS, Chen SJ. Three-dimensional-generator U-net for dual-resonant scanning multiphoton microscopy image inpainting and denoising. BIOMEDICAL OPTICS EXPRESS 2022; 13:6273-6283. [PMID: 36589554 PMCID: PMC9774857 DOI: 10.1364/boe.474082] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/24/2022] [Revised: 10/24/2022] [Accepted: 11/01/2022] [Indexed: 06/17/2023]
Abstract
A dual-resonant scanning multiphoton (DRSM) microscope incorporating a tunable acoustic gradient index of refraction lens and a resonant mirror is developed for rapid volumetric bioimaging. It is shown that the microscope achieves a volumetric imaging rate up to 31.25 volumes per second (vps) for a scanning volume of up to 200 × 200 × 100 µm3 with 256 × 256 × 128 voxels. However, the volumetric images have a severe negative signal-to-noise ratio (SNR) as a result of a large number of missing voxels for a large scanning volume and the presence of Lissajous patterning residuals. Thus, a modified three-dimensional (3D)-generator U-Net model trained using simulated microbead images is proposed and used to inpaint and denoise the images. The performance of the 3D U-Net model for bioimaging applications is enhanced by training the model with high-SNR in-vitro drosophila brain images captured using a conventional point scanning multiphoton microscope. The trained model shows the ability to produce clear in-vitro drosophila brain images at a rate of 31.25 vps with a SNR improvement of approximately 20 dB over the original images obtained by the DRSM microscope. The training convergence time of the modified U-Net model is just half that of a general 3D U-Net model. The model thus has significant potential for 3D in-vivo bioimaging transfer learning. Through the assistance of transfer learning, the model can be extended to the restoration of in-vivo drosophila brain images with a high image quality and a rapid training time.
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Affiliation(s)
- Chia-Wei Hsu
- College of Photonics, National Yang Ming Chiao Tung University, Tainan 711, Taiwan
| | - Chun-Yu Lin
- College of Photonics, National Yang Ming Chiao Tung University, Tainan 711, Taiwan
| | - Yvonne Yuling Hu
- Department of Photonics, National Cheng Kung University, Tainan, 701, Taiwan
| | - Chi-Yu Wang
- College of Photonics, National Yang Ming Chiao Tung University, Tainan 711, Taiwan
| | - Shin-Tsu Chang
- Department of Physical Medicine and Rehabilitation, Kaohsiung Veterans General Hospital, Kaohsiung 813, Taiwan
| | - Ann-Shyn Chiang
- Brain Research Center, National Tsing Hua University, Hsinchu 300, Taiwan
| | - Shean-Jen Chen
- College of Photonics, National Yang Ming Chiao Tung University, Tainan 711, Taiwan
- Taiwan Instrument Research Institute, National Applied Research Laboratories, Hsinchu 300, Taiwan
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19
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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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20
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Zhou Q, Nozdriukhin D, Chen Z, Glandorf L, Hofmann UAT, Reiss M, Tang L, Deán‐Ben XL, Razansky D. Depth-Resolved Localization Microangiography in the NIR-II Window. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2022; 10:e2204782. [PMID: 36403231 PMCID: PMC9811471 DOI: 10.1002/advs.202204782] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/19/2022] [Revised: 10/17/2022] [Indexed: 06/16/2023]
Abstract
Detailed characterization of microvascular alterations requires high-resolution 3D imaging methods capable of providing both morphological and functional information. Existing optical microscopy tools are routinely used for microangiography, yet offer suboptimal trade-offs between the achievable field of view and spatial resolution with the intense light scattering in biological tissues further limiting the achievable penetration depth. Herein, a new approach for volumetric deep-tissue microangiography based on stereovision combined with super-resolution localization imaging is introduced that overcomes the spatial resolution limits imposed by light diffusion and optical diffraction in wide-field imaging configurations. The method capitalizes on localization and tracking of flowing fluorescent particles in the second near-infrared window (NIR-II, ≈1000-1700 nm), with the third (depth) dimension added by triangulation and stereo-matching of images acquired with two short-wave infrared cameras operating in a dual-view mode. The 3D imaging capability enabled with the proposed method facilitates a detailed visualization of microvascular networks and an accurate blood flow quantification. Experiments performed in tissue-mimicking phantoms demonstrate that high resolution is preserved up to a depth of 4 mm in a turbid medium. Transcranial microangiography of the entire murine cortex and penetrating vessels is further demonstrated at capillary level resolution.
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Affiliation(s)
- Quanyu Zhou
- Institute of Pharmacology and Toxicology and Institute for Biomedical EngineeringFaculty of MedicineUniversity of ZurichZurich8057Switzerland
- Institute for Biomedical EngineeringDepartment of Information Technology and Electrical EngineeringETH ZurichZurich8093Switzerland
| | - Daniil Nozdriukhin
- Institute of Pharmacology and Toxicology and Institute for Biomedical EngineeringFaculty of MedicineUniversity of ZurichZurich8057Switzerland
- Institute for Biomedical EngineeringDepartment of Information Technology and Electrical EngineeringETH ZurichZurich8093Switzerland
| | - Zhenyue Chen
- Institute of Pharmacology and Toxicology and Institute for Biomedical EngineeringFaculty of MedicineUniversity of ZurichZurich8057Switzerland
- Institute for Biomedical EngineeringDepartment of Information Technology and Electrical EngineeringETH ZurichZurich8093Switzerland
| | - Lukas Glandorf
- Institute of Pharmacology and Toxicology and Institute for Biomedical EngineeringFaculty of MedicineUniversity of ZurichZurich8057Switzerland
- Institute for Biomedical EngineeringDepartment of Information Technology and Electrical EngineeringETH ZurichZurich8093Switzerland
| | - Urs A. T. Hofmann
- Institute of Pharmacology and Toxicology and Institute for Biomedical EngineeringFaculty of MedicineUniversity of ZurichZurich8057Switzerland
- Institute for Biomedical EngineeringDepartment of Information Technology and Electrical EngineeringETH ZurichZurich8093Switzerland
| | - Michael Reiss
- Institute of Pharmacology and Toxicology and Institute for Biomedical EngineeringFaculty of MedicineUniversity of ZurichZurich8057Switzerland
- Institute for Biomedical EngineeringDepartment of Information Technology and Electrical EngineeringETH ZurichZurich8093Switzerland
| | - Lin Tang
- Institute of Pharmacology and Toxicology and Institute for Biomedical EngineeringFaculty of MedicineUniversity of ZurichZurich8057Switzerland
- Institute for Biomedical EngineeringDepartment of Information Technology and Electrical EngineeringETH ZurichZurich8093Switzerland
| | - Xosé Luís Deán‐Ben
- Institute of Pharmacology and Toxicology and Institute for Biomedical EngineeringFaculty of MedicineUniversity of ZurichZurich8057Switzerland
- Institute for Biomedical EngineeringDepartment of Information Technology and Electrical EngineeringETH ZurichZurich8093Switzerland
| | - Daniel Razansky
- Institute of Pharmacology and Toxicology and Institute for Biomedical EngineeringFaculty of MedicineUniversity of ZurichZurich8057Switzerland
- Institute for Biomedical EngineeringDepartment of Information Technology and Electrical EngineeringETH ZurichZurich8093Switzerland
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21
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Cai Y, Wu J, Dai Q. Review on data analysis methods for mesoscale neural imaging in vivo. NEUROPHOTONICS 2022; 9:041407. [PMID: 35450225 PMCID: PMC9010663 DOI: 10.1117/1.nph.9.4.041407] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/30/2021] [Accepted: 03/23/2022] [Indexed: 06/14/2023]
Abstract
Significance: Mesoscale neural imaging in vivo has gained extreme popularity in neuroscience for its capacity of recording large-scale neurons in action. Optical imaging with single-cell resolution and millimeter-level field of view in vivo has been providing an accumulated database of neuron-behavior correspondence. Meanwhile, optical detection of neuron signals is easily contaminated by noises, background, crosstalk, and motion artifacts, while neural-level signal processing and network-level coordinate are extremely complicated, leading to laborious and challenging signal processing demands. The existing data analysis procedure remains unstandardized, which could be daunting to neophytes or neuroscientists without computational background. Aim: We hope to provide a general data analysis pipeline of mesoscale neural imaging shared between imaging modalities and systems. Approach: We divide the pipeline into two main stages. The first stage focuses on extracting high-fidelity neural responses at single-cell level from raw images, including motion registration, image denoising, neuron segmentation, and signal extraction. The second stage focuses on data mining, including neural functional mapping, clustering, and brain-wide network deduction. Results: Here, we introduce the general pipeline of processing the mesoscale neural images. We explain the principles of these procedures and compare different approaches and their application scopes with detailed discussions about the shortcomings and remaining challenges. Conclusions: There are great challenges and opportunities brought by the large-scale mesoscale data, such as the balance between fidelity and efficiency, increasing computational load, and neural network interpretability. We believe that global circuits on single-neuron level will be more extensively explored in the future.
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Affiliation(s)
- Yeyi Cai
- Tsinghua University, Department of Automation, Beijing, China
| | - Jiamin Wu
- Tsinghua University, Department of Automation, Beijing, China
| | - Qionghai Dai
- Tsinghua University, Department of Automation, Beijing, China
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22
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Benisty H, Song A, Mishne G, Charles AS. Review of data processing of functional optical microscopy for neuroscience. NEUROPHOTONICS 2022; 9:041402. [PMID: 35937186 PMCID: PMC9351186 DOI: 10.1117/1.nph.9.4.041402] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/04/2022] [Accepted: 07/15/2022] [Indexed: 05/04/2023]
Abstract
Functional optical imaging in neuroscience is rapidly growing with the development of optical systems and fluorescence indicators. To realize the potential of these massive spatiotemporal datasets for relating neuronal activity to behavior and stimuli and uncovering local circuits in the brain, accurate automated processing is increasingly essential. We cover recent computational developments in the full data processing pipeline of functional optical microscopy for neuroscience data and discuss ongoing and emerging challenges.
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Affiliation(s)
- Hadas Benisty
- Yale Neuroscience, New Haven, Connecticut, United States
| | - Alexander Song
- Max Planck Institute for Intelligent Systems, Stuttgart, Germany
| | - Gal Mishne
- UC San Diego, Halıcığlu Data Science Institute, Department of Electrical and Computer Engineering and the Neurosciences Graduate Program, La Jolla, California, United States
| | - Adam S. Charles
- Johns Hopkins University, Kavli Neuroscience Discovery Institute, Center for Imaging Science, Department of Biomedical Engineering, Department of Neuroscience, and Mathematical Institute for Data Science, Baltimore, Maryland, United States
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23
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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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24
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Charles AS, Cermak N, Affan RO, Scott BB, Schiller J, Mishne G. GraFT: Graph Filtered Temporal Dictionary Learning for Functional Neural Imaging. IEEE TRANSACTIONS ON IMAGE PROCESSING : A PUBLICATION OF THE IEEE SIGNAL PROCESSING SOCIETY 2022; 31:3509-3524. [PMID: 35533160 PMCID: PMC9278524 DOI: 10.1109/tip.2022.3171414] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Optical imaging of calcium signals in the brain has enabled researchers to observe the activity of hundreds-to-thousands of individual neurons simultaneously. Current methods predominantly use morphological information, typically focusing on expected shapes of cell bodies, to better identify neurons in the field-of-view. The explicit shape constraints limit the applicability of automated cell identification to other important imaging scales with more complex morphologies, e.g., dendritic or widefield imaging. Specifically, fluorescing components may be broken up, incompletely found, or merged in ways that do not accurately describe the underlying neural activity. Here we present Graph Filtered Temporal Dictionary (GraFT), a new approach that frames the problem of isolating independent fluorescing components as a dictionary learning problem. Specifically, we focus on the time-traces-the main quantity used in scientific discovery-and learn a time trace dictionary with the spatial maps acting as the presence coefficients encoding which pixels the time-traces are active in. Furthermore, we present a novel graph filtering model which redefines connectivity between pixels in terms of their shared temporal activity, rather than spatial proximity. This model greatly eases the ability of our method to handle data with complex non-local spatial structure. We demonstrate important properties of our method, such as robustness to morphology, simultaneously detecting different neuronal types, and implicitly inferring number of neurons, on both synthetic data and real data examples. Specifically, we demonstrate applications of our method to calcium imaging both at the dendritic, somatic, and widefield scales.
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25
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Moore JJ, Robert V, Rashid SK, Basu J. Assessing Local and Branch-specific Activity in Dendrites. Neuroscience 2022; 489:143-164. [PMID: 34756987 PMCID: PMC9125998 DOI: 10.1016/j.neuroscience.2021.10.022] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2021] [Revised: 10/09/2021] [Accepted: 10/21/2021] [Indexed: 01/12/2023]
Abstract
Dendrites are elaborate neural processes which integrate inputs from various sources in space and time. While decades of work have suggested an independent role for dendrites in driving nonlinear computations for the cell, only recently have technological advances enabled us to capture the variety of activity in dendrites and their coupling dynamics with the soma. Under certain circumstances, activity generated in a given dendritic branch remains isolated, such that the soma or even sister dendrites are not privy to these localized signals. Such branch-specific activity could radically increase the capacity and flexibility of coding for the cell as a whole. Here, we discuss these forms of localized and branch-specific activity, their functional relevance in plasticity and behavior, and their supporting biophysical and circuit-level mechanisms. We conclude by showcasing electrical and optical approaches in hippocampal area CA3, using original experimental data to discuss experimental and analytical methodology and key considerations to take when investigating the functional relevance of independent dendritic activity.
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Affiliation(s)
- Jason J Moore
- Neuroscience Institute, New York University Langone Health, New York, NY 10016, USA
| | - Vincent Robert
- Neuroscience Institute, New York University Langone Health, New York, NY 10016, USA
| | - Shannon K Rashid
- Neuroscience Institute, New York University Langone Health, New York, NY 10016, USA
| | - Jayeeta Basu
- Neuroscience Institute, New York University Langone Health, New York, NY 10016, USA; Department of Neuroscience and Physiology, New York University Grossman School of Medicine, New York, NY 10016, USA; Department of Psychiatry, New York University Grossman School of Medicine, New York, NY 10016, USA.
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26
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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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27
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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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28
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Pahlevaninezhad M, Huang YW, Pahlevani M, Bouma B, Suter MJ, Capasso F, Pahlevaninezhad H. Metasurface-based bijective illumination collection imaging provides high-resolution tomography in three dimensions. NATURE PHOTONICS 2022; 16:203-211. [PMID: 35937091 PMCID: PMC9355264 DOI: 10.1038/s41566-022-00956-6] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/01/2021] [Accepted: 01/10/2022] [Indexed: 06/08/2023]
Abstract
Microscopic imaging in three dimensions enables numerous biological and clinical applications. However, high-resolution optical imaging preserved in a relatively large depth range is hampered by the rapid spread of tightly confined light due to diffraction. Here, we show that a particular disposition of light illumination and collection paths liberates optical imaging from the restrictions imposed by diffraction. This arrangement, realized by metasurfaces, decouples lateral resolution from depth-of-focus by establishing a one-to-one correspondence (bijection) along a focal line between the incident and collected light. Implementing this approach in optical coherence tomography, we demonstrate tissue imaging at 1.3 μm wavelength with ~ 3.2 μm lateral resolution, maintained nearly intact over 1.25 mm depth-of-focus, with no additional acquisition or computation burden. This method, termed bijective illumination collection imaging, is general and might be adapted across various existing imaging modalities.
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Affiliation(s)
- Masoud Pahlevaninezhad
- Harvard Medical School and Massachusetts General Hospital, Boston, MA, USA
- Department of Electrical and Computer Engineering, Queen’s University, Kingston, Ontario, Canada
- Department of Mechanical and Materials Engineering, Queen’s University, Kingston, Ontario, Canada
| | - Yao-Wei Huang
- Harvard John A. Paulson School of Engineering and Applied Sciences, Harvard University, Cambridge, MA, USA
| | - Majid Pahlevani
- Department of Electrical and Computer Engineering, Queen’s University, Kingston, Ontario, Canada
| | - Brett Bouma
- Harvard Medical School and Massachusetts General Hospital, Boston, MA, USA
- Harvard-MIT Health Science and Technology, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Melissa J. Suter
- Harvard Medical School and Massachusetts General Hospital, Boston, MA, USA
| | - Federico Capasso
- Harvard John A. Paulson School of Engineering and Applied Sciences, Harvard University, Cambridge, MA, USA
| | - Hamid Pahlevaninezhad
- Harvard Medical School and Massachusetts General Hospital, Boston, MA, USA
- Harvard John A. Paulson School of Engineering and Applied Sciences, Harvard University, Cambridge, MA, USA
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29
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Zhou A, Engelmann SA, Mihelic SA, Tomar A, Hassan AM, Dunn AK. Evaluation of resonant scanning as a high-speed imaging technique for two-photon imaging of cortical vasculature. BIOMEDICAL OPTICS EXPRESS 2022; 13:1374-1385. [PMID: 35414984 PMCID: PMC8973172 DOI: 10.1364/boe.448473] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/19/2021] [Revised: 01/19/2022] [Accepted: 01/23/2022] [Indexed: 05/12/2023]
Abstract
We demonstrate a simple, low-cost two-photon microscope design with both galvo-galvo and resonant-galvo scanning capabilities. We quantify and compare the signal-to-noise ratios and imaging speeds of the galvo-galvo and resonant-galvo scanning modes when used for murine neurovascular imaging. The two scanning modes perform as expected under shot-noise limited detection and are found to achieve comparable signal-to-noise ratios. Resonant-galvo scanning is capable of reaching desired signal-to-noise ratios using less acquisition time when higher excitation power can be used. Given equal excitation power and total pixel dwell time between the two methods, galvo-galvo scanning outperforms resonant-galvo scanning in image quality when detection deviates from being shot-noise limited.
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Affiliation(s)
- Annie Zhou
- Department of Biomedical Engineering, The University of Texas at Austin, 107 W. Dean Keeton C0800, Austin, TX 78712, USA
| | - Shaun A. Engelmann
- Department of Biomedical Engineering, The University of Texas at Austin, 107 W. Dean Keeton C0800, Austin, TX 78712, USA
| | - Samuel A. Mihelic
- Department of Biomedical Engineering, The University of Texas at Austin, 107 W. Dean Keeton C0800, Austin, TX 78712, USA
| | - Alankrit Tomar
- Department of Biomedical Engineering, The University of Texas at Austin, 107 W. Dean Keeton C0800, Austin, TX 78712, USA
| | - Ahmed M. Hassan
- Department of Biomedical Engineering, The University of Texas at Austin, 107 W. Dean Keeton C0800, Austin, TX 78712, USA
| | - Andrew K. Dunn
- Department of Biomedical Engineering, The University of Texas at Austin, 107 W. Dean Keeton C0800, Austin, TX 78712, USA
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30
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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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31
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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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Sherlock B, Chen J, Mansfield J, Green E, Winlove C. Biophotonic tools for probing extracellular matrix mechanics. Matrix Biol Plus 2021; 12:100093. [PMID: 34934939 PMCID: PMC8661043 DOI: 10.1016/j.mbplus.2021.100093] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Revised: 11/07/2021] [Accepted: 11/11/2021] [Indexed: 12/11/2022] Open
Abstract
The complex, hierarchical and heterogeneous biomechanics of the extracellular matrix (ECM) are central to the health of multicellular organisms. Characterising the distribution, dynamics and above all else origins of ECM biomechanics are challenges that have captivated researchers for decades. Recently, a suite of biophotonics techniques have emerged as powerful new tools to investigate ECM biomechanics. In this mini-review, we discuss how the non-destructive, sub-micron resolution imaging capabilities of Raman spectroscopy and nonlinear microscopy are being used to interrogate the biomechanics of thick, living tissues. These high speed, label-free techniques are implemented during mechanical testing, providing unprecedented insight into the compositional and structural response of the ECM to changes in the mechanical environment.
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Affiliation(s)
- B.E. Sherlock
- College of Medicine and Health, University of Exeter, Exeter EX1 2LU, United Kingdom
| | - J. Chen
- College of Engineering, Mathematical and Physical Sciences, University of Exeter, Exeter EX4 4QF, United Kingdom
| | - J.C. Mansfield
- College of Engineering, Mathematical and Physical Sciences, University of Exeter, Exeter EX4 4QF, United Kingdom
| | - E. Green
- College of Engineering, Mathematical and Physical Sciences, University of Exeter, Exeter EX4 4QF, United Kingdom
| | - C.P. Winlove
- College of Engineering, Mathematical and Physical Sciences, University of Exeter, Exeter EX4 4QF, United Kingdom
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33
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Edrei E, Weiss A, Engelberg J, Zektzer R, Mazurski N, Levy U. Spectrally Gated Microscopy (SGM) with Meta Optics for Parallel Three-Dimensional Imaging. ACS NANO 2021; 15:17375-17383. [PMID: 34633801 DOI: 10.1021/acsnano.1c06646] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Volumetric imaging with high spatiotemporal resolution is of utmost importance for various applications ranging from aerospace and defense to real-time imaging of dynamic biological processes. To facilitate three-dimensional sectioning, current technology relies on mechanisms to reject light from adjacent out-of-focus planes either spatially or by other means. Yet, the combination of rapid acquisition time and high axial resolution is still elusive, motivating a persistent pursuit for emerging imaging approaches. Here we introduce and experimentally demonstrate a concept named spectrally gated microscopy (SGM), which enables a single-shot interrogation over the full axial dimension while maintaining a submicron sectioning resolution. SGM utilizes two important features enabled by flat optics (i.e., metalenses or diffractive lenses), namely, a short focal length and strong chromatic aberrations. Using SGM we demonstrate three-dimensional imaging of millimeter-scale samples while scanning only the lateral dimension, presenting a significant advantage over state-of-the-art technology.
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Affiliation(s)
- Eitan Edrei
- Department of Applied Physics, The Center for Nanoscience and Nanotechnology, The Hebrew University, Jerusalem 91904, Israel
| | - Aharon Weiss
- Department of Applied Physics, The Center for Nanoscience and Nanotechnology, The Hebrew University, Jerusalem 91904, Israel
| | - Jacob Engelberg
- Department of Applied Physics, The Center for Nanoscience and Nanotechnology, The Hebrew University, Jerusalem 91904, Israel
| | - Roy Zektzer
- Department of Applied Physics, The Center for Nanoscience and Nanotechnology, The Hebrew University, Jerusalem 91904, Israel
| | - Noa Mazurski
- Department of Applied Physics, The Center for Nanoscience and Nanotechnology, The Hebrew University, Jerusalem 91904, Israel
| | - Uriel Levy
- Department of Applied Physics, The Center for Nanoscience and Nanotechnology, The Hebrew University, Jerusalem 91904, Israel
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34
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Xiao S, Davison I, Mertz J. Scan multiplier unit for ultrafast laser scanning beyond the inertia limit. OPTICA 2021; 8:1403-1404. [PMID: 37275678 PMCID: PMC10237152 DOI: 10.1364/optica.445254] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/06/2021] [Accepted: 10/09/2021] [Indexed: 06/07/2023]
Abstract
A passive add-on greatly multiplies the sweep rate of any mechanical scanner while also enhancing throughput, enabling a single linear scanner to produce ultrafast 1D or 2D laser scans for general applications.
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Affiliation(s)
- Sheng Xiao
- Department of Biomedical Engineering, Boston University, 44 Cummington Mall, Boston MA 02215, USA
| | - Ian Davison
- Department of Biology, Boston University, 24 Cummington Mall, Boston MA 02215, USA
| | - Jerome Mertz
- Department of Biomedical Engineering, Boston University, 44 Cummington Mall, Boston MA 02215, USA
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35
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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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36
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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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37
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Schienstock D, Mueller SN. Moving beyond velocity: Opportunities and challenges to quantify immune cell behavior. Immunol Rev 2021; 306:123-136. [PMID: 34786722 DOI: 10.1111/imr.13038] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2021] [Revised: 10/20/2021] [Accepted: 11/02/2021] [Indexed: 12/22/2022]
Abstract
The analysis of cellular behavior using intravital multi-photon microscopy has contributed substantially to our understanding of the priming and effector phases of immune responses. Yet, many questions remain unanswered and unexplored. Though advancements in intravital imaging techniques and animal models continue to drive new discoveries, continued improvements in analysis methods are needed to extract detailed information about cellular behavior. Focusing on dendritic cell (DC) and T cell interactions as an exemplar, here we discuss key limitations for intravital imaging studies and review and explore alternative approaches to quantify immune cell behavior. We touch upon current developments in deep learning models, as well as established methods from unrelated fields such as ecology to detect and track objects over time. As developments in open-source software make it possible to process and interactively view larger datasets, the challenge for the field will be to determine how best to combine intravital imaging with multi-parameter imaging of larger tissue regions to discover new facets of leukocyte dynamics and how these contribute to immune responses.
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Affiliation(s)
- Dominik Schienstock
- Department of Microbiology and Immunology, The Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Melbourne, Vic, Australia
| | - Scott N Mueller
- Department of Microbiology and Immunology, The Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Melbourne, Vic, Australia
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38
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Zhang Y, Lu Z, Wu J, Lin X, Jiang D, Cai Y, Xie J, Wang Y, Zhu T, Ji X, Dai Q. Computational optical sectioning with an incoherent multiscale scattering model for light-field microscopy. Nat Commun 2021; 12:6391. [PMID: 34737278 PMCID: PMC8568979 DOI: 10.1038/s41467-021-26730-w] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2020] [Accepted: 10/14/2021] [Indexed: 11/09/2022] Open
Abstract
Quantitative volumetric fluorescence imaging at high speed across a long term is vital to understand various cellular and subcellular behaviors in living organisms. Light-field microscopy provides a compact computational solution by imaging the entire volume in a tomographic way, while facing severe degradation in scattering tissue or densely-labelled samples. To address this problem, we propose an incoherent multiscale scattering model in a complete space for quantitative 3D reconstruction in complicated environments, which is called computational optical sectioning. Without the requirement of any hardware modifications, our method can be generally applied to different light-field schemes with reduction in background fluorescence, reconstruction artifacts, and computational costs, facilitating more practical applications of LFM in a broad community. We validate the superior performance by imaging various biological dynamics in Drosophila embryos, zebrafish larvae, and mice.
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Affiliation(s)
- Yi Zhang
- Department of Automation, Tsinghua University, 100084, Beijing, China
- Institute for Brain and Cognitive Sciences, Tsinghua University, 100084, Beijing, China
| | - Zhi Lu
- Department of Automation, Tsinghua University, 100084, Beijing, China
- Institute for Brain and Cognitive Sciences, Tsinghua University, 100084, Beijing, China
| | - Jiamin Wu
- Department of Automation, Tsinghua University, 100084, Beijing, China.
- Institute for Brain and Cognitive Sciences, Tsinghua University, 100084, Beijing, China.
| | - Xing Lin
- Department of Automation, Tsinghua University, 100084, Beijing, China
- Institute for Brain and Cognitive Sciences, Tsinghua University, 100084, Beijing, China
- Beijing National Research Center for Information Science and Technology, Tsinghua University, 100084, Beijing, China
| | - Dong Jiang
- State Key Laboratory of Membrane Biology, Tsinghua University-Peking University Joint Centre for Life Sciences, Beijing Frontier Research Centre for Biological Structure, School of Life Sciences, Tsinghua University, 100084, Beijing, China
| | - Yeyi Cai
- Department of Automation, Tsinghua University, 100084, Beijing, China
| | - Jiachen Xie
- Department of Automation, Tsinghua University, 100084, Beijing, China
- Institute for Brain and Cognitive Sciences, Tsinghua University, 100084, Beijing, China
| | - Yuling Wang
- Department of Automation, Tsinghua University, 100084, Beijing, China
| | - Tianyi Zhu
- Department of Automation, Tsinghua University, 100084, Beijing, China
- Institute for Brain and Cognitive Sciences, Tsinghua University, 100084, Beijing, China
| | - Xiangyang Ji
- Department of Automation, Tsinghua University, 100084, Beijing, China.
- Institute for Brain and Cognitive Sciences, Tsinghua University, 100084, Beijing, China.
- Beijing National Research Center for Information Science and Technology, Tsinghua University, 100084, Beijing, China.
| | - Qionghai Dai
- Department of Automation, Tsinghua University, 100084, Beijing, China.
- Institute for Brain and Cognitive Sciences, Tsinghua University, 100084, Beijing, China.
- Beijing National Research Center for Information Science and Technology, Tsinghua University, 100084, Beijing, China.
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39
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Quan X, Kato D, Daria V, Matoba O, Wake H. Holographic microscope and its biological application. Neurosci Res 2021; 179:57-64. [PMID: 34740727 DOI: 10.1016/j.neures.2021.10.012] [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: 10/29/2021] [Accepted: 10/29/2021] [Indexed: 10/19/2022]
Abstract
Holographic structured illumination combined with optogenetics enables patterned stimulation of neurons and glial cells in an intact living brain. Moreover, in vivo functional imaging of cellular activity with recent advanced microscope technologies allows for visualization of the cellular responses during learning, emotion and cognition. Integrating these techniques can be used to verify the link between cell function and behavior output. However, there are technical limitations to stimulate multiple cells with high spatial and temporal resolution with available techniques of optogenetic stimulation. Here, we summarized a two-photon microscope combined with holographic system to stimulate multiple cells with high spatial and temporal resolution for living mice and their biological application.
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Affiliation(s)
- Xiangyu Quan
- Department of System Science, Kobe University Graduate School of System Informatics, Kobe, Japan
| | - Daisuke Kato
- Department of Anatomy and Molecular Cell Biology, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Vincent Daria
- Research School of Physics, The Australian National University, Canberra, Australia
| | - Osamu Matoba
- Department of System Science, Kobe University Graduate School of System Informatics, Kobe, Japan
| | - Hiroaki Wake
- Department of Anatomy and Molecular Cell Biology, Nagoya University Graduate School of Medicine, Nagoya, Japan; Division of Multicellular Circuit Dynamics, National Institute for Physiological Sciences, National Institute of Natural Sciences, Okazaki, Japan; Core Research for Evolutional Science and Technology, Japan Science and Technology Agency, Saitama, Japan.
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40
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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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41
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Luo Y, Chu CH, Vyas S, Kuo HY, Chia YH, Chen MK, Shi X, Tanaka T, Misawa H, Huang YY, Tsai DP. Varifocal Metalens for Optical Sectioning Fluorescence Microscopy. NANO LETTERS 2021; 21:5133-5142. [PMID: 34097419 DOI: 10.1021/acs.nanolett.1c01114] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Fluorescence microscopy with optical sectioning capabilities is extensively utilized in biological research to obtain three-dimensional structural images of volumetric samples. Tunable lenses have been applied in microscopy for axial scanning to acquire multiplane images. However, images acquired by conventional tunable lenses suffer from spherical aberration and distortions. Here, we design, fabricate, and implement a dielectric Moiré metalens for fluorescence imaging. The Moiré metalens consists of two complementary phase metasurfaces, with variable focal length, ranging from ∼10 to ∼125 mm at 532 nm by tuning mutual angles. In addition, a telecentric configuration using the Moiré metalens is designed for high-contrast multiplane fluorescence imaging. The performance of our system is evaluated by optically sectioned images obtained from HiLo illumination of fluorescently labeled beads, as well as ex vivo mice intestine tissue samples. The compact design of the varifocal metalens may find important applications in fluorescence microscopy and endoscopy for clinical purposes.
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Affiliation(s)
- Yuan Luo
- Institute of Medical Device and Imaging, National Taiwan University, Taipei 10051, Taiwan
- YongLin Institute of Health, National Taiwan University, Taipei 10672, Taiwan
- Institute of Biomedical Engineering, National Taiwan University, Taipei 10051, Taiwan
| | - Cheng Hung Chu
- Institute of Medical Device and Imaging, National Taiwan University, Taipei 10051, Taiwan
- Research Center for Applied Sciences, Academia Sinica, Taipei 11529, Taiwan
- Innovative Photon Manipulation Research Team, RIKEN Center for Advanced Photonics, Saitama 351-0198, Japan
| | - Sunil Vyas
- Institute of Medical Device and Imaging, National Taiwan University, Taipei 10051, Taiwan
| | - Hsin Yu Kuo
- Institute of Medical Device and Imaging, National Taiwan University, Taipei 10051, Taiwan
- Research Center for Applied Sciences, Academia Sinica, Taipei 11529, Taiwan
- Department of Physics, National Taiwan University, Taipei 10617, Taiwan
| | - Yu Hsin Chia
- Institute of Medical Device and Imaging, National Taiwan University, Taipei 10051, Taiwan
- Institute of Biomedical Engineering, National Taiwan University, Taipei 10051, Taiwan
| | - Mu Ku Chen
- Department of Electronic and Information Engineering, The Hong Kong Polytechnic University, Kowloon 999077, Hong Kong
| | - Xu Shi
- Research Institute for Electronic Science Hokkaido University, Sapporo 001-0021, Japan
| | - Takuo Tanaka
- Innovative Photon Manipulation Research Team, RIKEN Center for Advanced Photonics, Saitama 351-0198, Japan
- Metamaterial Laboratory, RIKEN Cluster for Pioneering Research, Saitama 351-0198, Japan
- Institute of Post-LED Photonics, Tokushima University, Tokushima 770-8506, Japan
| | - Hiroaki Misawa
- Research Institute for Electronic Science Hokkaido University, Sapporo 001-0021, Japan
| | - Yi-You Huang
- Institute of Biomedical Engineering, National Taiwan University, Taipei 10051, Taiwan
- Department of Biomedical Engineering, National Taiwan University Hospital, Taipei 100225, Taiwan
| | - Din Ping Tsai
- Research Center for Applied Sciences, Academia Sinica, Taipei 11529, Taiwan
- Department of Physics, National Taiwan University, Taipei 10617, Taiwan
- Department of Electronic and Information Engineering, The Hong Kong Polytechnic University, Kowloon 999077, Hong Kong
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42
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Wang Y, Xi L. Chronic cranial window for photoacoustic imaging: a mini review. Vis Comput Ind Biomed Art 2021; 4:15. [PMID: 34037873 PMCID: PMC8155166 DOI: 10.1186/s42492-021-00081-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2020] [Accepted: 04/27/2021] [Indexed: 12/31/2022] Open
Abstract
Photoacoustic (PA) microscopy is being increasingly used to visualize the microcirculation of the brain cortex at the micron level in living rodents. By combining it with long-term cranial window techniques, vasculature can be monitored over a period of days extending to months through a field of view. To fulfill the requirements of long-term in vivo PA imaging, the cranial window must involve a simple and rapid surgical procedure, biological compatibility, and sufficient optical-acoustic transparency, which are major challenges. Recently, several cranial window techniques have been reported for longitudinal PA imaging. Here, the development of chronic cranial windows for PA imaging is reviewed and its technical details are discussed, including window installation, imaging quality, and longitudinal stability.
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Affiliation(s)
- Yongchao Wang
- School of Physics, University of Electronic Science and Technology of China, Chengdu, 610054, Sichuan, China.,Department of Biomedical Engineering, Southern University of Science and Technology, Shenzhen, 518055, Guangdong, China
| | - Lei Xi
- Department of Biomedical Engineering, Southern University of Science and Technology, Shenzhen, 518055, Guangdong, China.
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43
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Zhuang C, Cao J, Zhang R, Xiao G, Hu J, Xie H, Dai Q. Real-time brain-wide multi-planar microscopy for simultaneous cortex and hippocampus imaging at the cellular resolution in mice. BIOMEDICAL OPTICS EXPRESS 2021; 12:1858-1868. [PMID: 33996203 PMCID: PMC8086472 DOI: 10.1364/boe.418229] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Revised: 02/19/2021] [Accepted: 02/25/2021] [Indexed: 06/12/2023]
Abstract
Interactions between the cerebral cortex and the deep cerebellar nuclei play important roles in cognitive processes. However, conventional microscopes fail to dynamically record cellular structures in distinct brain regions and at different depths, which requires high resolution, large field of view (FOV), and depth of field (DOF). Here we propose a single-photon excited fluorescence microscopy technique that performs simultaneous cortex and hippocampus imaging, enabled by a customized microscope and a chronic optical window. After we implant a glass microwindow above the hippocampus, the surface of the hippocampus is shifted to the superficial plane. We demonstrate that the proposed technique is able to image cellular structures and blood vessel dynamics in the cortex and the hippocampus in in vivo experiments, and is compatible with various mesoscopic systems.
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Affiliation(s)
- Chaowei Zhuang
- Department of Automation, Tsinghua University, Beijing 100084, China
- These authors contributed equally to this work
| | - Jiangbei Cao
- Department of Anesthesiology, the First Medical Center, Chinese PLA General Hospital, Beijing 100853, China
- These authors contributed equally to this work
| | - Rujin Zhang
- Department of Anesthesiology, the First Medical Center, Chinese PLA General Hospital, Beijing 100853, China
- Medical Company, CPLA Unit No. 32139, Beijing 101200, China
- These authors contributed equally to this work
| | - Guihua Xiao
- Department of Automation, Tsinghua University, Beijing 100084, China
- Institute of Brain and Cognitive Science, Tsinghua University, Beijing 100084, China
| | - Jing Hu
- State Key Laboratory of Modern Optical Instrumentation, Zhejiang University, Hangzhou 310027, China
| | - Hao Xie
- Department of Automation, Tsinghua University, Beijing 100084, China
- Institute of Brain and Cognitive Science, Tsinghua University, Beijing 100084, China
| | - Qionghai Dai
- Department of Automation, Tsinghua University, Beijing 100084, China
- Institute of Brain and Cognitive Science, Tsinghua University, Beijing 100084, China
- IDG/McGovern Institute for Brain Research, Tsinghua University, Beijing 100084, China
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44
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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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45
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Moon J, Lim YS, Yoon S, Choi W. Single-shot multi-depth full-field optical coherence tomography using spatial frequency division multiplexing. OPTICS EXPRESS 2021; 29:7060-7069. [PMID: 33726214 DOI: 10.1364/oe.417950] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Accepted: 02/11/2021] [Indexed: 06/12/2023]
Abstract
Fast 3D volumetric imaging has been essential for biology, medicine and industrial inspections, and various optical coherence tomography (OCT) methods have been developed to meet such needs. Point-scanning based approaches, such as swept-source OCT and spectral domain OCT, can obtain a depth information at once, but they require lateral scan for full 3D imaging. On the contrary, full-field OCT needs the scanning of imaging depth while it records a full lateral information at once. Here, we present a full-field OCT system that can obtain multi-depth information at once by a single-shot recording. We combine a 2D diffraction grating and a custom-made echelon to prepare multiple reference beams having different pathlengths and propagating angles. By recording a single interference image between the reflected wave from a sample and these multiple reference beams, we reconstruct full-field images at multiple depths associated with the pathlengths of the individual reference beams. We demonstrated the single-shot recording of 7 different depth images at 10 µm for biological tissues. Our method can potentially be useful for applications where high-speed recording of multiple en-face images is crucial.
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46
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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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47
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Zong W. New solution for fast axial scanning in fluorescence microscopy. LIGHT, SCIENCE & APPLICATIONS 2020; 9:199. [PMID: 33318466 PMCID: PMC7736891 DOI: 10.1038/s41377-020-00442-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
A novel technique based on the remote-focusing concept, using a galvanometer scanner combined with a self-fabricated "step mirror" or "tilted mirror" to transform fast lateral scanning into axial scanning, was reported as a new solution for fast, subcellular, 3D fluorescence imaging.
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Affiliation(s)
- Weijian Zong
- Kavli Institute for Systems Neuroscience and Centre for Neural Computation, Norwegian University of Science and Technology, Trondheim, Norway.
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48
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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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49
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Quémener M, Guénette J, Borne J, Thibault S. Toric lens analysis as a focal ring and Bessel beam generator. JOURNAL OF THE OPTICAL SOCIETY OF AMERICA. A, OPTICS, IMAGE SCIENCE, AND VISION 2020; 37:1657-1661. [PMID: 33104613 DOI: 10.1364/josaa.402378] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/09/2020] [Accepted: 09/07/2020] [Indexed: 06/11/2023]
Abstract
We propose an analytical solution of the focal ring generated at the focus of a toric lens. The analytical field of the focal ring is used with a Fourier transform lens to generate a Bessel beam. A comparative analysis between the use of an illuminated annular aperture, an axicon, and a toric lens to generate a Bessel beam is performed, and the benefits and drawbacks of each are discussed. This highlights the advantages of using a toric lens with a Gaussian beam to produce a focal line of increasing intensity, which is advantageous for applications such as high depth-of-field microscopy.
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50
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Maioli V, Boniface A, Mahou P, Ortas JF, Abdeladim L, Beaurepaire E, Supatto W. Fast in vivo multiphoton light-sheet microscopy with optimal pulse frequency. BIOMEDICAL OPTICS EXPRESS 2020; 11:6012-6026. [PMID: 33150002 PMCID: PMC7587280 DOI: 10.1364/boe.400113] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/15/2020] [Revised: 09/09/2020] [Accepted: 09/17/2020] [Indexed: 05/05/2023]
Abstract
Improving the imaging speed of multiphoton microscopy is an active research field. Among recent strategies, light-sheet illumination holds distinctive advantages for achieving fast imaging in vivo. However, photoperturbation in multiphoton light-sheet microscopy remains poorly investigated. We show here that the heart beat rate of zebrafish embryos is a sensitive probe of linear and nonlinear photoperturbations. By analyzing its behavior with respect to laser power, pulse frequency and wavelength, we derive guidelines to find the best balance between signal and photoperturbation. We then demonstrate one order-of-magnitude signal enhancement over previous implementations by optimizing the laser pulse frequency. These results open new opportunities for fast live tissue imaging.
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Affiliation(s)
- Vincent Maioli
- Laboratory for Optics and Biosciences, Ecole Polytechnique, CNRS, INSERM, Institut Polytechnique de Paris, 91128 Palaiseau, France
| | - Antoine Boniface
- Laboratory for Optics and Biosciences, Ecole Polytechnique, CNRS, INSERM, Institut Polytechnique de Paris, 91128 Palaiseau, France
| | - Pierre Mahou
- Laboratory for Optics and Biosciences, Ecole Polytechnique, CNRS, INSERM, Institut Polytechnique de Paris, 91128 Palaiseau, France
| | - Júlia Ferrer Ortas
- Laboratory for Optics and Biosciences, Ecole Polytechnique, CNRS, INSERM, Institut Polytechnique de Paris, 91128 Palaiseau, France
| | - Lamiae Abdeladim
- Laboratory for Optics and Biosciences, Ecole Polytechnique, CNRS, INSERM, Institut Polytechnique de Paris, 91128 Palaiseau, France
| | - Emmanuel Beaurepaire
- Laboratory for Optics and Biosciences, Ecole Polytechnique, CNRS, INSERM, Institut Polytechnique de Paris, 91128 Palaiseau, France
| | - Willy Supatto
- Laboratory for Optics and Biosciences, Ecole Polytechnique, CNRS, INSERM, Institut Polytechnique de Paris, 91128 Palaiseau, France
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