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Uhlířová H, Stibůrek M, Pikálek T, Gomes A, Turtaev S, Kolbábková P, Čižmár T. "There's plenty of room at the bottom": deep brain imaging with holographic endo-microscopy. NEUROPHOTONICS 2024; 11:S11504. [PMID: 38250297 PMCID: PMC10798506 DOI: 10.1117/1.nph.11.s1.s11504] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/14/2023] [Revised: 12/09/2023] [Accepted: 12/14/2023] [Indexed: 01/23/2024]
Abstract
Significance Over more than 300 years, microscopic imaging keeps providing fundamental insights into the mechanisms of living organisms. Seeing microscopic structures beyond the reach of free-space light-based microscopy, however, requires dissection of the tissue-an intervention seriously disturbing its physiological functions. The hunt for low-invasiveness tools has led a growing community of physicists and engineers into the realm of complex media photonics. One of its activities represents exploiting multimode optical fibers (MMFs) as ultra-thin endoscopic probes. Employing wavefront shaping, these tools only recently facilitated the first peeks at cells and their sub-cellular compartments at the bottom of the mouse brain with the impact of micro-scale tissue damage. Aim Here, we aim to highlight advances in MMF-based holographic endo-microscopy facilitating microscopic imaging throughout the whole depth of the mouse brain. Approach We summarize the important technical and methodological prerequisites for stabile high-resolution imaging in vivo. Results We showcase images of the microscopic building blocks of brain tissue, including neurons, neuronal processes, vessels, intracellular calcium signaling, and red blood cell velocity in individual vessels. Conclusions This perspective article helps to understand the complexity behind the technology of holographic endo-microscopy, summarizes its recent advances and challenges, and stimulates the mind of the reader for further exploitation of this tool in the neuroscience research.
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Affiliation(s)
- Hana Uhlířová
- Institute of Scientific Instruments of the Czech Academy of Sciences, Brno, Czech Republic
| | - Miroslav Stibůrek
- Institute of Scientific Instruments of the Czech Academy of Sciences, Brno, Czech Republic
| | - Tomáš Pikálek
- Institute of Scientific Instruments of the Czech Academy of Sciences, Brno, Czech Republic
| | - André Gomes
- Leibniz Institute of Photonic Technology, Jena, Germany
| | | | - Petra Kolbábková
- Institute of Scientific Instruments of the Czech Academy of Sciences, Brno, Czech Republic
| | - Tomáš Čižmár
- Institute of Scientific Instruments of the Czech Academy of Sciences, Brno, Czech Republic
- Leibniz Institute of Photonic Technology, Jena, Germany
- Friedrich Schiller University Jena, Institute of Applied Optics, Jena, Germany
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2
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Xia F, Rimoli CV, Akemann W, Ventalon C, Bourdieu L, Gigan S, de Aguiar HB. Neurophotonics beyond the surface: unmasking the brain's complexity exploiting optical scattering. NEUROPHOTONICS 2024; 11:S11510. [PMID: 38617592 PMCID: PMC11014413 DOI: 10.1117/1.nph.11.s1.s11510] [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: 11/08/2023] [Revised: 03/07/2024] [Accepted: 03/14/2024] [Indexed: 04/16/2024]
Abstract
The intricate nature of the brain necessitates the application of advanced probing techniques to comprehensively study and understand its working mechanisms. Neurophotonics offers minimally invasive methods to probe the brain using optics at cellular and even molecular levels. However, multiple challenges persist, especially concerning imaging depth, field of view, speed, and biocompatibility. A major hindrance to solving these challenges in optics is the scattering nature of the brain. This perspective highlights the potential of complex media optics, a specialized area of study focused on light propagation in materials with intricate heterogeneous optical properties, in advancing and improving neuronal readouts for structural imaging and optical recordings of neuronal activity. Key strategies include wavefront shaping techniques and computational imaging and sensing techniques that exploit scattering properties for enhanced performance. We discuss the potential merger of the two fields as well as potential challenges and perspectives toward longer term in vivo applications.
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Affiliation(s)
- Fei Xia
- Sorbonne Université, Collège de France, Laboratoire Kastler Brossel, ENS-Université PSL, CNRS, Paris, France
| | - Caio Vaz Rimoli
- Sorbonne Université, Collège de France, Laboratoire Kastler Brossel, ENS-Université PSL, CNRS, Paris, France
- Université PSL, Institut de Biologie de l’ENS, École Normale Supérieure, CNRS, INSERM, Paris, France
| | - Walther Akemann
- Université PSL, Institut de Biologie de l’ENS, École Normale Supérieure, CNRS, INSERM, Paris, France
| | - Cathie Ventalon
- Université PSL, Institut de Biologie de l’ENS, École Normale Supérieure, CNRS, INSERM, Paris, France
| | - Laurent Bourdieu
- Université PSL, Institut de Biologie de l’ENS, École Normale Supérieure, CNRS, INSERM, Paris, France
| | - Sylvain Gigan
- Sorbonne Université, Collège de France, Laboratoire Kastler Brossel, ENS-Université PSL, CNRS, Paris, France
| | - Hilton B. de Aguiar
- Sorbonne Université, Collège de France, Laboratoire Kastler Brossel, ENS-Université PSL, CNRS, Paris, France
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3
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Rimoli CV, Moretti C, Soldevila F, Brémont E, Ventalon C, Gigan S. Demixing fluorescence time traces transmitted by multimode fibers. Nat Commun 2024; 15:6286. [PMID: 39060262 PMCID: PMC11282286 DOI: 10.1038/s41467-024-50306-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2023] [Accepted: 07/05/2024] [Indexed: 07/28/2024] Open
Abstract
Optical methods based on thin multimode fibers (MMFs) are promising tools for measuring neuronal activity in deep brain regions of freely moving mice thanks to their small diameter. However, current methods are limited: while fiber photometry provides only ensemble activity, imaging techniques using of long multimode fibers are very sensitive to bending and have not been applied to unrestrained rodents yet. Here, we demonstrate the fundamentals of a new approach using a short MMF coupled to a miniscope. In proof-of-principle in vitro experiments, we disentangled spatio-temporal fluorescence signals from multiple fluorescent sources transmitted by a thin (200 µm) and short (8 mm) MMF, using a general unconstrained non-negative matrix factorization algorithm directly on the raw video data. Furthermore, we show that low-cost open-source miniscopes have sufficient sensitivity to image the same fluorescence patterns seen in our proof-of-principle experiment, suggesting a new avenue for novel minimally invasive deep brain studies using multimode fibers in freely behaving mice.
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Affiliation(s)
- Caio Vaz Rimoli
- Laboratoire Kastler Brossel, ENS-Université PSL, CNRS, Sorbonne Université, Collège de France, 24 Rue Lhomond, Paris, F-75005, France
- Institut de Biologie de l'ENS (IBENS), Département de biologie, École normale supérieure, CNRS, INSERM, Université PSL, 75005, Paris, France
| | - Claudio Moretti
- Laboratoire Kastler Brossel, ENS-Université PSL, CNRS, Sorbonne Université, Collège de France, 24 Rue Lhomond, Paris, F-75005, France
| | - Fernando Soldevila
- Laboratoire Kastler Brossel, ENS-Université PSL, CNRS, Sorbonne Université, Collège de France, 24 Rue Lhomond, Paris, F-75005, France
| | - Enora Brémont
- Institut de Biologie de l'ENS (IBENS), Département de biologie, École normale supérieure, CNRS, INSERM, Université PSL, 75005, Paris, France
| | - Cathie Ventalon
- Institut de Biologie de l'ENS (IBENS), Département de biologie, École normale supérieure, CNRS, INSERM, Université PSL, 75005, Paris, France.
| | - Sylvain Gigan
- Laboratoire Kastler Brossel, ENS-Université PSL, CNRS, Sorbonne Université, Collège de France, 24 Rue Lhomond, Paris, F-75005, France.
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4
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Mandracchia B, Zheng C, Rajendran S, Liu W, Forghani P, Xu C, Jia S. High-speed optical imaging with sCMOS pixel reassignment. Nat Commun 2024; 15:4598. [PMID: 38816394 PMCID: PMC11139943 DOI: 10.1038/s41467-024-48987-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2023] [Accepted: 05/13/2024] [Indexed: 06/01/2024] Open
Abstract
Fluorescence microscopy has undergone rapid advancements, offering unprecedented visualization of biological events and shedding light on the intricate mechanisms governing living organisms. However, the exploration of rapid biological dynamics still poses a significant challenge due to the limitations of current digital camera architectures and the inherent compromise between imaging speed and other capabilities. Here, we introduce sHAPR, a high-speed acquisition technique that leverages the operating principles of sCMOS cameras to capture fast cellular and subcellular processes. sHAPR harnesses custom fiber optics to convert microscopy images into one-dimensional recordings, enabling acquisition at the maximum camera readout rate, typically between 25 and 250 kHz. We have demonstrated the utility of sHAPR with a variety of phantom and dynamic systems, including high-throughput flow cytometry, cardiomyocyte contraction, and neuronal calcium waves, using a standard epi-fluorescence microscope. sHAPR is highly adaptable and can be integrated into existing microscopy systems without requiring extensive platform modifications. This method pushes the boundaries of current fluorescence imaging capabilities, opening up new avenues for investigating high-speed biological phenomena.
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Affiliation(s)
- Biagio Mandracchia
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, GA, USA
- E.T.S.I. Telecomunicación, Universidad de Valladolid, Valladolid, Spain
| | - Corey Zheng
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, GA, USA
| | - Suraj Rajendran
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, GA, USA
| | - Wenhao Liu
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, GA, USA
| | - Parvin Forghani
- Department of Pediatrics, School of Medicine, Emory University, Atlanta, GA, USA
| | - Chunhui Xu
- Department of Pediatrics, School of Medicine, Emory University, Atlanta, GA, USA
- Parker H. Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, GA, USA
| | - Shu Jia
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, GA, USA.
- Parker H. Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, GA, USA.
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Gonzalez-Ramos A, Puigsasllosas-Pastor C, Arcas-Marquez A, Tornero D. Updated Toolbox for Assessing Neuronal Network Reconstruction after Cell Therapy. Bioengineering (Basel) 2024; 11:487. [PMID: 38790353 PMCID: PMC11118929 DOI: 10.3390/bioengineering11050487] [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: 03/30/2024] [Revised: 05/02/2024] [Accepted: 05/10/2024] [Indexed: 05/26/2024] Open
Abstract
Cell therapy has proven to be a promising treatment for a range of neurological disorders, including Parkinson Disease, drug-resistant epilepsy, and stroke, by restoring function after brain damage. Nevertheless, evaluating the true effectiveness of these therapeutic interventions requires a deep understanding of the functional integration of grafted cells into existing neural networks. This review explores a powerful arsenal of molecular techniques revolutionizing our ability to unveil functional integration of grafted cells within the host brain. From precise manipulation of neuronal activity to pinpoint the functional contribution of transplanted cells by using opto- and chemo-genetics, to real-time monitoring of neuronal dynamics shedding light on functional connectivity within the reconstructed circuits by using genetically encoded (calcium) indicators in vivo. Finally, structural reconstruction and mapping communication pathways between grafted and host neurons can be achieved by monosynaptic tracing with viral vectors. The cutting-edge toolbox presented here holds immense promise for elucidating the impact of cell therapy on neural circuitry and guiding the development of more effective treatments for neurological disorders.
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Affiliation(s)
- Ana Gonzalez-Ramos
- Stanley Center for Psychiatric Research at Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Claudia Puigsasllosas-Pastor
- Laboratory of Neural Stem Cells and Brain Damage, Department of Biomedical Sciences, Institute of Neurosciences, University of Barcelona, 08036 Barcelona, Spain
- Institut d’Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), 08036 Barcelona, Spain
| | - Ainhoa Arcas-Marquez
- Laboratory of Neural Stem Cells and Brain Damage, Department of Biomedical Sciences, Institute of Neurosciences, University of Barcelona, 08036 Barcelona, Spain
- Institut d’Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), 08036 Barcelona, Spain
| | - Daniel Tornero
- Laboratory of Neural Stem Cells and Brain Damage, Department of Biomedical Sciences, Institute of Neurosciences, University of Barcelona, 08036 Barcelona, Spain
- Institut d’Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), 08036 Barcelona, Spain
- Centro de Investigación Biomédica en Red sobre Enfermedades Neurodegenerativas (CIBERNED), 28029 Madrid, Spain
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6
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Gau YTA, Hsu ET, Cha RJ, Pak RW, Looger LL, Kang JU, Bergles DE. Multicore fiber optic imaging reveals that astrocyte calcium activity in the mouse cerebral cortex is modulated by internal motivational state. Nat Commun 2024; 15:3039. [PMID: 38589390 PMCID: PMC11002016 DOI: 10.1038/s41467-024-47345-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2023] [Accepted: 03/25/2024] [Indexed: 04/10/2024] Open
Abstract
Astrocytes are a direct target of neuromodulators and can influence neuronal activity on broad spatial and temporal scales in response to a rise in cytosolic calcium. However, our knowledge about how astrocytes are recruited during different animal behaviors remains limited. To measure astrocyte activity calcium in vivo during normative behaviors, we utilize a high-resolution, long working distance multicore fiber optic imaging system that allows visualization of individual astrocyte calcium transients in the cerebral cortex of freely moving mice. We define the spatiotemporal dynamics of astrocyte calcium changes during diverse behaviors, ranging from sleep-wake cycles to the exploration of novel objects, showing that their activity is more variable and less synchronous than apparent in head-immobilized imaging conditions. In accordance with their molecular diversity, individual astrocytes often exhibit distinct thresholds and activity patterns during explorative behaviors, allowing temporal encoding across the astrocyte network. Astrocyte calcium events were induced by noradrenergic and cholinergic systems and modulated by internal state. The distinct activity patterns exhibited by astrocytes provides a means to vary their neuromodulatory influence in different behavioral contexts and internal states.
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Affiliation(s)
- Yung-Tian A Gau
- The Solomon H. Snyder Department of Neuroscience, Johns Hopkins University, Baltimore, MD, USA.
| | - Eric T Hsu
- The Solomon H. Snyder Department of Neuroscience, Johns Hopkins University, Baltimore, MD, USA
| | - Richard J Cha
- Department of Electrical and Computer Engineering, Johns Hopkins University, Baltimore, MD, USA
| | - Rebecca W Pak
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, USA
| | - Loren L Looger
- Howard Hughes Medical Institute, Department of Neurosciences, University of California San Diego, La Jolla, CA, USA
| | - Jin U Kang
- Department of Electrical and Computer Engineering, Johns Hopkins University, Baltimore, MD, USA.
- Kavli Neuroscience Discovery Institute, Johns Hopkins University, Baltimore, MD, USA.
| | - Dwight E Bergles
- The Solomon H. Snyder Department of Neuroscience, Johns Hopkins University, Baltimore, MD, USA.
- Kavli Neuroscience Discovery Institute, Johns Hopkins University, Baltimore, MD, USA.
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7
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Xu S, Momin M, Ahmed S, Hossain A, Veeramuthu L, Pandiyan A, Kuo CC, Zhou T. Illuminating the Brain: Advances and Perspectives in Optoelectronics for Neural Activity Monitoring and Modulation. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2023; 35:e2303267. [PMID: 37726261 DOI: 10.1002/adma.202303267] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/07/2023] [Revised: 05/30/2023] [Indexed: 09/21/2023]
Abstract
Optogenetic modulation of brain neural activity that combines optical and electrical modes in a unitary neural system has recently gained robust momentum. Controlling illumination spatial coverage, designing light-activated modulators, and developing wireless light delivery and data transmission are crucial for maximizing the use of optical neuromodulation. To this end, biocompatible electrodes with enhanced optoelectrical performance, device integration for multiplexed addressing, wireless transmission, and multimodal operation in soft systems have been developed. This review provides an outlook for uniformly illuminating large brain areas while spatiotemporally imaging the neural responses upon optoelectrical stimulation with little artifacts. Representative concepts and important breakthroughs, such as head-mounted illumination, multiple implanted optical fibers, and micro-light-delivery devices, are discussed. Examples of techniques that incorporate electrophysiological monitoring and optoelectrical stimulation are presented. Challenges and perspectives are posed for further research efforts toward high-density optoelectrical neural interface modulation, with the potential for nonpharmacological neurological disease treatments and wireless optoelectrical stimulation.
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Affiliation(s)
- Shumao Xu
- Department of Engineering Science and Mechanics, Center for Neural Engineering, The Pennsylvania State University, Pennsylvania, 16802, USA
| | - Marzia Momin
- Department of Engineering Science and Mechanics, Center for Neural Engineering, The Pennsylvania State University, Pennsylvania, 16802, USA
| | - Salahuddin Ahmed
- Department of Engineering Science and Mechanics, Center for Neural Engineering, The Pennsylvania State University, Pennsylvania, 16802, USA
| | - Arafat Hossain
- Department of Electrical Engineering, The Pennsylvania State University, Pennsylvania, 16802, USA
| | - Loganathan Veeramuthu
- Department of Molecular Science and Engineering, National Taipei University of Technology, Taipei, 10608, Republic of China
| | - Archana Pandiyan
- Department of Molecular Science and Engineering, National Taipei University of Technology, Taipei, 10608, Republic of China
| | - Chi-Ching Kuo
- Department of Molecular Science and Engineering, National Taipei University of Technology, Taipei, 10608, Republic of China
| | - Tao Zhou
- Department of Engineering Science and Mechanics, Center for Neural Engineering, The Pennsylvania State University, Pennsylvania, 16802, USA
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8
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Kim S, Moon HS, Vo TT, Kim CH, Im GH, Lee S, Choi M, Kim SG. Whole-brain mapping of effective connectivity by fMRI with cortex-wide patterned optogenetics. Neuron 2023; 111:1732-1747.e6. [PMID: 37001524 DOI: 10.1016/j.neuron.2023.03.002] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2022] [Revised: 11/23/2022] [Accepted: 03/02/2023] [Indexed: 04/03/2023]
Abstract
Functional magnetic resonance imaging (fMRI) with optogenetic neural manipulation is a powerful tool that enables brain-wide mapping of effective functional networks. To achieve flexible manipulation of neural excitation throughout the mouse cortex, we incorporated spatiotemporal programmable optogenetic stimuli generated by a digital micromirror device into an MRI scanner via an optical fiber bundle. This approach offered versatility in space and time in planning the photostimulation pattern, combined with in situ optical imaging and cell-type-specific or circuit-specific genetic targeting in individual mice. Brain-wide effective connectivity obtained by fMRI with optogenetic stimulation of atlas-based cortical regions is generally congruent with anatomically defined axonal tracing data but is affected by the types of anesthetics that act selectively on specific connections. fMRI combined with flexible optogenetics opens a new path to investigate dynamic changes in functional brain states in the same animal through high-throughput brain-wide effective connectivity mapping.
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Affiliation(s)
- Seonghoon Kim
- Center for Neuroscience Imaging Research, Institute for Basic Science, Suwon, Republic of Korea; School of Biological Sciences, Seoul National University, Seoul, Republic of Korea
| | - Hyun Seok Moon
- Center for Neuroscience Imaging Research, Institute for Basic Science, Suwon, Republic of Korea; Department of Biomedical Engineering, Sungkyunkwan University, Suwon, Republic of Korea; Department of Intelligent Precision Healthcare Convergence, Sungkyunkwan University, Suwon, Republic of Korea
| | - Thanh Tan Vo
- Center for Neuroscience Imaging Research, Institute for Basic Science, Suwon, Republic of Korea; Department of Biomedical Engineering, Sungkyunkwan University, Suwon, Republic of Korea; Department of Intelligent Precision Healthcare Convergence, Sungkyunkwan University, Suwon, Republic of Korea
| | - Chang-Ho Kim
- School of Biological Sciences, Seoul National University, Seoul, Republic of Korea; Institute of Molecular Biology and Genetics, Seoul National University, Seoul, Republic of Korea
| | - Geun Ho Im
- Center for Neuroscience Imaging Research, Institute for Basic Science, Suwon, Republic of Korea
| | - Sungho Lee
- School of Biological Sciences, Seoul National University, Seoul, Republic of Korea
| | - Myunghwan Choi
- Center for Neuroscience Imaging Research, Institute for Basic Science, Suwon, Republic of Korea; School of Biological Sciences, Seoul National University, Seoul, Republic of Korea; Institute of Molecular Biology and Genetics, Seoul National University, Seoul, Republic of Korea.
| | - Seong-Gi Kim
- Center for Neuroscience Imaging Research, Institute for Basic Science, Suwon, Republic of Korea; Department of Biomedical Engineering, Sungkyunkwan University, Suwon, Republic of Korea; Department of Intelligent Precision Healthcare Convergence, Sungkyunkwan University, Suwon, Republic of Korea.
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9
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Hu X, Zhao J, Antonio-Lopez JE, Correa RA, Schülzgen A. Unsupervised full-color cellular image reconstruction through disordered optical fiber. LIGHT, SCIENCE & APPLICATIONS 2023; 12:125. [PMID: 37221183 DOI: 10.1038/s41377-023-01183-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Revised: 05/11/2023] [Accepted: 05/12/2023] [Indexed: 05/25/2023]
Abstract
Recent years have witnessed the tremendous development of fusing fiber-optic imaging with supervised deep learning to enable high-quality imaging of hard-to-reach areas. Nevertheless, the supervised deep learning method imposes strict constraints on fiber-optic imaging systems, where the input objects and the fiber outputs have to be collected in pairs. To unleash the full potential of fiber-optic imaging, unsupervised image reconstruction is in demand. Unfortunately, neither optical fiber bundles nor multimode fibers can achieve a point-to-point transmission of the object with a high sampling density, as is a prerequisite for unsupervised image reconstruction. The recently proposed disordered fibers offer a new solution based on the transverse Anderson localization. Here, we demonstrate unsupervised full-color imaging with a cellular resolution through a meter-long disordered fiber in both transmission and reflection modes. The unsupervised image reconstruction consists of two stages. In the first stage, we perform a pixel-wise standardization on the fiber outputs using the statistics of the objects. In the second stage, we recover the fine details of the reconstructions through a generative adversarial network. Unsupervised image reconstruction does not need paired images, enabling a much more flexible calibration under various conditions. Our new solution achieves full-color high-fidelity cell imaging within a working distance of at least 4 mm by only collecting the fiber outputs after an initial calibration. High imaging robustness is also demonstrated when the disordered fiber is bent with a central angle of 60°. Moreover, the cross-domain generality on unseen objects is shown to be enhanced with a diversified object set.
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Affiliation(s)
- Xiaowen Hu
- CREOL, The College of Optics and Photonics, University of Central Florida, Orlando, FL, 32816, USA
| | - Jian Zhao
- The Picower Institute for Learning and Memory, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA.
| | | | - Rodrigo Amezcua Correa
- CREOL, The College of Optics and Photonics, University of Central Florida, Orlando, FL, 32816, USA
| | - Axel Schülzgen
- CREOL, The College of Optics and Photonics, University of Central Florida, Orlando, FL, 32816, USA
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10
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Gau YTA, Hsu E, Cha J, Pak RW, Looger LL, Kang JU, Bergles DE. Multicore fiber optic imaging reveals that astrocyte calcium activity in the cerebral cortex is modulated by internal motivational state. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.18.541390. [PMID: 37292710 PMCID: PMC10245653 DOI: 10.1101/2023.05.18.541390] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Astrocytes are a direct target of neuromodulators and can influence neuronal activity on broad spatial and temporal scales through their close proximity to synapses. However, our knowledge about how astrocytes are functionally recruited during different animal behaviors and their diverse effects on the CNS remains limited. To enable measurement of astrocyte activity patterns in vivo during normative behaviors, we developed a high-resolution, long working distance, multi-core fiber optic imaging platform that allows visualization of cortical astrocyte calcium transients through a cranial window in freely moving mice. Using this platform, we defined the spatiotemporal dynamics of astrocytes during diverse behaviors, ranging from circadian fluctuations to novelty exploration, showing that astrocyte activity patterns are more variable and less synchronous than apparent in head-immobilized imaging conditions. Although the activity of astrocytes in visual cortex was highly synchronized during quiescence to arousal transitions, individual astrocytes often exhibited distinct thresholds and activity patterns during explorative behaviors, in accordance with their molecular diversity, allowing temporal sequencing across the astrocyte network. Imaging astrocyte activity during self-initiated behaviors revealed that noradrenergic and cholinergic systems act synergistically to recruit astrocytes during state transitions associated with arousal and attention, which was profoundly modulated by internal state. The distinct activity patterns exhibited by astrocytes in the cerebral cortex may provide a means to vary their neuromodulatory influence in response to different behaviors and internal states.
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Affiliation(s)
- Yung-Tian A. Gau
- The Solomon H. Snyder Department of Neuroscience, Johns Hopkins University, Baltimore, MD 21205, United States
| | - Eric Hsu
- The Solomon H. Snyder Department of Neuroscience, Johns Hopkins University, Baltimore, MD 21205, United States
| | - Jaepyeong Cha
- Department of Electrical and Computer Engineering, Johns Hopkins University, Baltimore, MD 21218, United States
| | - Rebecca W. Pak
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD 21205, United States
| | - Loren L. Looger
- Howard Hughes Medical Institute, Department of Neurosciences, University of California San Diego, La Jolla, CA 92093, United States
| | - Jin U. Kang
- Department of Electrical and Computer Engineering, Johns Hopkins University, Baltimore, MD 21218, United States
- Kavli Neuroscience Discovery Institute, Johns Hopkins University, Baltimore, MD 21205, United States
| | - Dwight E. Bergles
- The Solomon H. Snyder Department of Neuroscience, Johns Hopkins University, Baltimore, MD 21205, United States
- Kavli Neuroscience Discovery Institute, Johns Hopkins University, Baltimore, MD 21205, United States
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11
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Kumar V, Behrman K, Speed F, Saladrigas CA, Supekar O, Huang Z, Bright VM, Welle CG, Restrepo D, Gopinath JT, Gibson EA, Kymissis I. MicroLED light source for optical sectioning structured illumination microscopy. OPTICS EXPRESS 2023; 31:16709-16718. [PMID: 37157744 PMCID: PMC10316754 DOI: 10.1364/oe.486754] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/01/2023] [Revised: 04/14/2023] [Accepted: 04/19/2023] [Indexed: 05/10/2023]
Abstract
Optical sectioning structured illumination microscopy (OS-SIM) provides optical sectioning capability in wide-field microscopy. The required illumination patterns have traditionally been generated using spatial light modulators (SLM), laser interference patterns, or digital micromirror devices (DMDs) which are too complex to implement in miniscope systems. MicroLEDs have emerged as an alternative light source for patterned illumination due to their extreme brightness capability and small emitter sizes. This paper presents a directly addressable striped microLED microdisplay with 100 rows on a flexible cable (70 cm long) for use as an OS-SIM light source in a benchtop setup. The overall design of the microdisplay is described in detail with luminance-current-voltage characterization. OS-SIM implementation with a benchtop setup shows the optical sectioning capability of the system by imaging within a 500 µm thick fixed brain slice from a transgenic mouse where oligodendrocytes are labeled with a green fluorescent protein (GFP). Results show improved contrast in reconstructed optically sectioned images of 86.92% (OS-SIM) compared with 44.31% (pseudo-widefield). MicroLED based OS-SIM therefore offers a new capability for deep tissue widefield imaging.
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Affiliation(s)
| | | | - Forest Speed
- University of Colorado Anschutz, Aurora, CO 80045, USA
| | | | - Omkar Supekar
- University of Colorado Boulder, Boulder, CO 80309, USA
| | - Zicong Huang
- Columbia University, New York City, NY 10027, USA
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12
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Fişek M, Herrmann D, Egea-Weiss A, Cloves M, Bauer L, Lee TY, Russell LE, Häusser M. Cortico-cortical feedback engages active dendrites in visual cortex. Nature 2023; 617:769-776. [PMID: 37138089 DOI: 10.1038/s41586-023-06007-6] [Citation(s) in RCA: 16] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2020] [Accepted: 03/23/2023] [Indexed: 05/05/2023]
Abstract
Sensory processing in the neocortex requires both feedforward and feedback information flow between cortical areas1. In feedback processing, higher-level representations provide contextual information to lower levels, and facilitate perceptual functions such as contour integration and figure-ground segmentation2,3. However, we have limited understanding of the circuit and cellular mechanisms that mediate feedback influence. Here we use long-range all-optical connectivity mapping in mice to show that feedback influence from the lateromedial higher visual area (LM) to the primary visual cortex (V1) is spatially organized. When the source and target of feedback represent the same area of visual space, feedback is relatively suppressive. By contrast, when the source is offset from the target in visual space, feedback is relatively facilitating. Two-photon calcium imaging data show that this facilitating feedback is nonlinearly integrated in the apical tuft dendrites of V1 pyramidal neurons: retinotopically offset (surround) visual stimuli drive local dendritic calcium signals indicative of regenerative events, and two-photon optogenetic activation of LM neurons projecting to identified feedback-recipient spines in V1 can drive similar branch-specific local calcium signals. Our results show how neocortical feedback connectivity and nonlinear dendritic integration can together form a substrate to support both predictive and cooperative contextual interactions.
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Affiliation(s)
- Mehmet Fişek
- Wolfson Institute for Biomedical Research and Department of Neuroscience, Physiology and Pharmacology, University College London, London, UK.
| | - Dustin Herrmann
- Wolfson Institute for Biomedical Research and Department of Neuroscience, Physiology and Pharmacology, University College London, London, UK
| | - Alexander Egea-Weiss
- Wolfson Institute for Biomedical Research and Department of Neuroscience, Physiology and Pharmacology, University College London, London, UK
| | - Matilda Cloves
- Wolfson Institute for Biomedical Research and Department of Neuroscience, Physiology and Pharmacology, University College London, London, UK
| | - Lisa Bauer
- Wolfson Institute for Biomedical Research and Department of Neuroscience, Physiology and Pharmacology, University College London, London, UK
| | - Tai-Ying Lee
- Wolfson Institute for Biomedical Research and Department of Neuroscience, Physiology and Pharmacology, University College London, London, UK
| | - Lloyd E Russell
- Wolfson Institute for Biomedical Research and Department of Neuroscience, Physiology and Pharmacology, University College London, London, UK
| | - Michael Häusser
- Wolfson Institute for Biomedical Research and Department of Neuroscience, Physiology and Pharmacology, University College London, London, UK.
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13
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Accanto N, Blot FGC, Lorca-Cámara A, Zampini V, Bui F, Tourain C, Badt N, Katz O, Emiliani V. A flexible two-photon fiberscope for fast activity imaging and precise optogenetic photostimulation of neurons in freely moving mice. Neuron 2023; 111:176-189.e6. [PMID: 36395773 DOI: 10.1016/j.neuron.2022.10.030] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2021] [Revised: 07/28/2022] [Accepted: 10/19/2022] [Indexed: 11/17/2022]
Abstract
We developed a flexible two-photon microendoscope (2P-FENDO) capable of all-optical brain investigation at near cellular resolution in freely moving mice. The system performs fast two-photon (2P) functional imaging and 2P holographic photostimulation of single and multiple cells using axially confined extended spots. Proof-of-principle experiments were performed in freely moving mice co-expressing jGCaMP7s and the opsin ChRmine in the visual or barrel cortex. On a field of view of 250 μm in diameter, we demonstrated functional imaging at a frame rate of up to 50 Hz and precise photostimulation of selected groups of cells. With the capability to simultaneously image and control defined neuronal networks in freely moving animals, 2P-FENDO will enable a precise investigation of neuronal functions in the brain during naturalistic behaviors.
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Affiliation(s)
- Nicolò Accanto
- Sorbonne Université, INSERM, CNRS, Institut de la Vision, F-75012 Paris, France.
| | - François G C Blot
- Sorbonne Université, INSERM, CNRS, Institut de la Vision, F-75012 Paris, France
| | | | - Valeria Zampini
- Sorbonne Université, INSERM, CNRS, Institut de la Vision, F-75012 Paris, France
| | - Florence Bui
- Sorbonne Université, INSERM, CNRS, Institut de la Vision, F-75012 Paris, France
| | - Christophe Tourain
- Sorbonne Université, INSERM, CNRS, Institut de la Vision, F-75012 Paris, France
| | - Noam Badt
- Department of Applied Physics, Hebrew University of Jerusalem, Jerusalem 9190401, Israel
| | - Ori Katz
- Department of Applied Physics, Hebrew University of Jerusalem, Jerusalem 9190401, Israel
| | - Valentina Emiliani
- Sorbonne Université, INSERM, CNRS, Institut de la Vision, F-75012 Paris, France.
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14
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Jost-Mousseau T, Chalabi M, Shulz DE, Férézou I. Imaging the brain in action: a motorized optical rotary joint for wide field fibroscopy in freely moving animals. NEUROPHOTONICS 2023; 10:015009. [PMID: 36970016 PMCID: PMC10037343 DOI: 10.1117/1.nph.10.1.015009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/27/2022] [Accepted: 02/28/2023] [Indexed: 06/18/2023]
Abstract
SIGNIFICANCE The study of neuronal processes governing behavior in awake behaving mice is constantly boosted by the development of technological strategies, such as miniaturized microscopes and closed-loop virtual reality systems. However, the former limits the quality of recorded signals due to constrains in size and weight and the latter suffers from the restriction of the movement repertoire of the animal, therefore, hardly reproducing the complexity of natural multisensory scenes. AIM Another strategy that takes advantage of both approaches consists of the use of a fiber-bundle interface to carry optical signals from a moving animal to a conventional imaging system. However, as the bundle is usually fixed below the optics, its torsion resulting from rotations of the animal inevitably constrains the behavior over long recordings. Our aim was to overcome this major limitation of fibroscopic imaging. APPROACH We developed a motorized optical rotary joint controlled by an inertial measurement unit at the animal's head. RESULTS We show its principle of operation, demonstrate its efficacy in a locomotion task, and propose several modes of operation for a wide range of experimental designs. CONCLUSIONS Combined with an optical rotary joint, fibroscopic approaches represent an outstanding tool to link neuronal activity with behavior in mice at the millisecond timescale.
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Affiliation(s)
- Timothé Jost-Mousseau
- Université Paris-Saclay, Centre National de la Recherche Scientifique, Institut des Neurosciences Paris-Saclay (NeuroPSI), Saclay, France
| | - Max Chalabi
- Université Paris-Saclay, Centre National de la Recherche Scientifique, Institut des Neurosciences Paris-Saclay (NeuroPSI), Saclay, France
| | - Daniel E. Shulz
- Université Paris-Saclay, Centre National de la Recherche Scientifique, Institut des Neurosciences Paris-Saclay (NeuroPSI), Saclay, France
| | - Isabelle Férézou
- Université Paris-Saclay, Centre National de la Recherche Scientifique, Institut des Neurosciences Paris-Saclay (NeuroPSI), Saclay, France
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15
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Li S, Feng X, Bian H. Optogenetics: Emerging strategies for neuropathic pain treatment. Front Neurol 2022; 13:982223. [PMID: 36536805 PMCID: PMC9758006 DOI: 10.3389/fneur.2022.982223] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Accepted: 11/10/2022] [Indexed: 10/13/2023] Open
Abstract
Neuropathic pain (NP) is a chronic health condition that presents a significant burden on patients, society, and even healthcare systems. However, in recent years, an emerging field in the treatment of neuropathic pain - optogenetic technology has dawned, heralding a new era in the field of medicine, and which has brought with it unlimited possibilities for studying the mechanism of NP and the treatment of research. Optogenetics is a new and growing field that uses the combination of light and molecular genetics for the first time ever. This rare combination is used to control the activity of living cells by expressing photosensitive proteins to visualize signaling events and manipulate cell activity. The treatments for NP are limited and have hardly achieved the desirable efficacy. NP differs from other types of pain, such as nociceptive pain, in that the treatments for NP are far more complex and highly challenging for clinical practice. This review presents the background of optogenetics, current applications in various fields, and the findings of optogenetics in NP. It also elaborates on the basic concepts of neuropathy, therapeutic applications, and the potential of optogenetics from the bench to the bedside in the near future.
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Affiliation(s)
- Siyu Li
- Department of Physiology, Faculty of Basic Medical Science, Kunming Medical University, Kunming, Yunnan, China
| | - Xiaoli Feng
- Department of Physiology, Faculty of Basic Medical Science, Kunming Medical University, Kunming, Yunnan, China
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences and Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, China
| | - Hui Bian
- Department of Physiology, Faculty of Basic Medical Science, Kunming Medical University, Kunming, Yunnan, China
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16
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Wu Q, Wang C, Zhu L, Wang S, Zhao L, Xing Z, Zhang B, Jia W, Ma Y, Wang Y. Effects of glutamine on growth performance and immune function of high-concentrate fattening Hu lambs. Small Rumin Res 2022. [DOI: 10.1016/j.smallrumres.2022.106808] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2022]
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17
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Wei Z, Liu X, Yan R, Sun G, Yu W, Liu Q, Guo Q. Pixel-level multimodal fusion deep networks for predicting subcellular organelle localization from label-free live-cell imaging. Front Genet 2022; 13:1002327. [PMID: 36386823 PMCID: PMC9644055 DOI: 10.3389/fgene.2022.1002327] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2022] [Accepted: 09/26/2022] [Indexed: 01/25/2023] Open
Abstract
Complex intracellular organizations are commonly represented by dividing the metabolic process of cells into different organelles. Therefore, identifying sub-cellular organelle architecture is significant for understanding intracellular structural properties, specific functions, and biological processes in cells. However, the discrimination of these structures in the natural organizational environment and their functional consequences are not clear. In this article, we propose a new pixel-level multimodal fusion (PLMF) deep network which can be used to predict the location of cellular organelle using label-free cell optical microscopy images followed by deep-learning-based automated image denoising. It provides valuable insights that can be of tremendous help in improving the specificity of label-free cell optical microscopy by using the Transformer-Unet network to predict the ground truth imaging which corresponds to different sub-cellular organelle architectures. The new prediction method proposed in this article combines the advantages of a transformer's global prediction and CNN's local detail analytic ability of background features for label-free cell optical microscopy images, so as to improve the prediction accuracy. Our experimental results showed that the PLMF network can achieve over 0.91 Pearson's correlation coefficient (PCC) correlation between estimated and true fractions on lung cancer cell-imaging datasets. In addition, we applied the PLMF network method on the cell images for label-free prediction of several different subcellular components simultaneously, rather than using several fluorescent labels. These results open up a new way for the time-resolved study of subcellular components in different cells, especially for cancer cells.
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Affiliation(s)
- Zhihao Wei
- Academy of Artificial Intelligence, Beijing Institute of Petrochemical Technology, Beijing, China
| | - Xi Liu
- Academy of Artificial Intelligence, Beijing Institute of Petrochemical Technology, Beijing, China
| | - Ruiqing Yan
- Academy of Artificial Intelligence, Beijing Institute of Petrochemical Technology, Beijing, China
| | - Guocheng Sun
- Academy of Artificial Intelligence, Beijing Institute of Petrochemical Technology, Beijing, China,School of Mechanical Engineering & Hydrogen Energy Research Centre, Beijing Institute of Petrochemical Technology, Beijing, China
| | - Weiyong Yu
- Academy of Artificial Intelligence, Beijing Institute of Petrochemical Technology, Beijing, China
| | - Qiang Liu
- Academy of Artificial Intelligence, Beijing Institute of Petrochemical Technology, Beijing, China
| | - Qianjin Guo
- Academy of Artificial Intelligence, Beijing Institute of Petrochemical Technology, Beijing, China,School of Mechanical Engineering & Hydrogen Energy Research Centre, Beijing Institute of Petrochemical Technology, Beijing, China,*Correspondence: Qianjin Guo,
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18
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Xue Y. Computational optics for high-throughput imaging of neural activity. NEUROPHOTONICS 2022; 9:041408. [PMID: 35607516 PMCID: PMC9122092 DOI: 10.1117/1.nph.9.4.041408] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/01/2022] [Accepted: 04/19/2022] [Indexed: 06/15/2023]
Abstract
Optical microscopy offers a noninvasive way to image neural activity in the mouse brain. To simultaneously record neural activity across a large population of neurons, optical systems that have high spatiotemporal resolution and can access a large volume are necessary. The throughput of a system, that is, the number of resolvable spots acquired by the system at a given time, is usually limited by optical hardware. To overcome this limitation, computation optics that designs optical hardware and computer software jointly becomes a new approach that achieves micronscale resolution, millimeter-scale field-of-view, and hundreds of hertz imaging speed at the same time. This review article summarizes recent advances in computational optics for high-throughput imaging of neural activity, highlighting technologies for three-dimensional parallelized excitation and detection. Computational optics can substantially accelerate the study of neural circuits with previously unattainable precision and speed.
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Affiliation(s)
- Yi Xue
- University of California, Davis, Department of Biomedical Engineering, Davis, California, United States
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19
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Multiple Parallel Fusion Network for Predicting Protein Subcellular Localization from Stimulated Raman Scattering (SRS) Microscopy Images in Living Cells. Int J Mol Sci 2022; 23:ijms231810827. [PMID: 36142736 PMCID: PMC9504098 DOI: 10.3390/ijms231810827] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2022] [Revised: 09/10/2022] [Accepted: 09/13/2022] [Indexed: 11/23/2022] Open
Abstract
Stimulated Raman Scattering Microscopy (SRS) is a powerful tool for label-free detailed recognition and investigation of the cellular and subcellular structures of living cells. Determining subcellular protein localization from the cell level of SRS images is one of the basic goals of cell biology, which can not only provide useful clues for their functions and biological processes but also help to determine the priority and select the appropriate target for drug development. However, the bottleneck in predicting subcellular protein locations of SRS cell imaging lies in modeling complicated relationships concealed beneath the original cell imaging data owing to the spectral overlap information from different protein molecules. In this work, a multiple parallel fusion network, MPFnetwork, is proposed to study the subcellular locations from SRS images. This model used a multiple parallel fusion model to construct feature representations and combined multiple nonlinear decomposing algorithms as the automated subcellular detection method. Our experimental results showed that the MPFnetwork could achieve over 0.93 dice correlation between estimated and true fractions on SRS lung cancer cell datasets. In addition, we applied the MPFnetwork method to cell images for label-free prediction of several different subcellular components simultaneously, rather than using several fluorescent labels. These results open up a new method for the time-resolved study of subcellular components in different cells, especially cancer cells.
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20
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Chen K, Tian Z, Kong L. Advances of optical miniscopes for in vivo imaging of neural activity in freely moving animals. Front Neurosci 2022; 16:994079. [PMID: 36161177 PMCID: PMC9490007 DOI: 10.3389/fnins.2022.994079] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2022] [Accepted: 08/17/2022] [Indexed: 01/09/2023] Open
Abstract
To study neural mechanisms of ethologically relevant behaviors including many social behaviors and navigations, optical miniscopes, which can be carried by the model animals, are indispensable. Recently, a variety of optical miniscopes have been developed to meet this urgent requirement, and successfully applied in the study of neural network activity in free-moving mice, rats, and bats, etc. Generally, miniature fluorescence microscopes can be classified into single-photon and multi-photon fluorescence miniscopes, considering their differences in imaging mechanisms and hardware setups. In this review, we introduce their fundamental principles and system structures, summarize technical advances, and discuss limitations and future trends, for in vivo imaging of neural activity in freely moving animals.
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Affiliation(s)
- Kunpeng Chen
- State Key Laboratory of Precision Measurement Technology and Instrument, Department of Precision Instrument, Tsinghua University, Beijing, China,Weiyang College, Tsinghua University, Beijing, China
| | - Zhaoshi Tian
- State Key Laboratory of Precision Measurement Technology and Instrument, Department of Precision Instrument, Tsinghua University, Beijing, China,Weiyang College, Tsinghua University, Beijing, China
| | - Lingjie Kong
- State Key Laboratory of Precision Measurement Technology and Instrument, Department of Precision Instrument, Tsinghua University, Beijing, China,Tsinghua-IDG/McGovern Institute for Brain Research, Tsinghua University, Beijing, China,*Correspondence: Lingjie Kong,
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21
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A one-photon endoscope for simultaneous patterned optogenetic stimulation and calcium imaging in freely behaving mice. Nat Biomed Eng 2022; 7:499-510. [PMID: 35970930 DOI: 10.1038/s41551-022-00920-3] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2021] [Accepted: 07/04/2022] [Indexed: 11/08/2022]
Abstract
Optogenetics and calcium imaging can be combined to simultaneously stimulate and record neural activity in vivo. However, this usually requires two-photon microscopes, which are not portable nor affordable. Here we report the design and implementation of a miniaturized one-photon endoscope for performing simultaneous optogenetic stimulation and calcium imaging. By integrating digital micromirrors, the endoscope makes it possible to activate any neuron of choice within the field of view, and to apply arbitrary spatiotemporal patterns of photostimulation while imaging calcium activity. We used the endoscope to image striatal neurons from either the direct pathway or the indirect pathway in freely moving mice while activating any chosen neuron in the field of view. The endoscope also allows for the selection of neurons based on their relationship with specific animal behaviour, and to recreate the behaviour by mimicking the natural neural activity with photostimulation. The miniaturized endoscope may facilitate the study of how neural activity gives rise to behaviour in freely moving animals.
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22
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Yu Z, Li H, Zhong T, Park JH, Cheng S, Woo CM, Zhao Q, Yao J, Zhou Y, Huang X, Pang W, Yoon H, Shen Y, Liu H, Zheng Y, Park Y, Wang LV, Lai P. Wavefront shaping: A versatile tool to conquer multiple scattering in multidisciplinary fields. Innovation (N Y) 2022; 3:100292. [PMID: 36032195 PMCID: PMC9405113 DOI: 10.1016/j.xinn.2022.100292] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Accepted: 07/23/2022] [Indexed: 10/26/2022] Open
Abstract
Optical techniques offer a wide variety of applications as light-matter interactions provide extremely sensitive mechanisms to probe or treat target media. Most of these implementations rely on the usage of ballistic or quasi-ballistic photons to achieve high spatial resolution. However, the inherent scattering nature of light in biological tissues or tissue-like scattering media constitutes a critical obstacle that has restricted the penetration depth of non-scattered photons and hence limited the implementation of most optical techniques for wider applications. In addition, the components of an optical system are usually designed and manufactured for a fixed function or performance. Recent advances in wavefront shaping have demonstrated that scattering- or component-induced phase distortions can be compensated by optimizing the wavefront of the input light pattern through iteration or by conjugating the transmission matrix of the scattering medium. This offers unprecedented opportunities in many applications to achieve controllable optical delivery or detection at depths or dynamically configurable functionalities by using scattering media to substitute conventional optical components. In this article, the recent progress of wavefront shaping in multidisciplinary fields is reviewed, from optical focusing and imaging with scattering media, functionalized devices, modulation of mode coupling, and nonlinearity in multimode fiber to multimode fiber-based applications. Apart from insights into the underlying principles and recent advances in wavefront shaping implementations, practical limitations and roadmap for future development are discussed in depth. Looking back and looking forward, it is believed that wavefront shaping holds a bright future that will open new avenues for noninvasive or minimally invasive optical interactions and arbitrary control inside deep tissues. The high degree of freedom with multiple scattering will also provide unprecedented opportunities to develop novel optical devices based on a single scattering medium (generic or customized) that can outperform traditional optical components.
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23
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Sun J, Wu J, Wu S, Goswami R, Girardo S, Cao L, Guck J, Koukourakis N, Czarske JW. Quantitative phase imaging through an ultra-thin lensless fiber endoscope. LIGHT, SCIENCE & APPLICATIONS 2022; 11:204. [PMID: 35790748 PMCID: PMC9255502 DOI: 10.1038/s41377-022-00898-2] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/08/2022] [Revised: 06/10/2022] [Accepted: 06/16/2022] [Indexed: 05/29/2023]
Abstract
Quantitative phase imaging (QPI) is a label-free technique providing both morphology and quantitative biophysical information in biomedicine. However, applying such a powerful technique to in vivo pathological diagnosis remains challenging. Multi-core fiber bundles (MCFs) enable ultra-thin probes for in vivo imaging, but current MCF imaging techniques are limited to amplitude imaging modalities. We demonstrate a computational lensless microendoscope that uses an ultra-thin bare MCF to perform quantitative phase imaging with microscale lateral resolution and nanoscale axial sensitivity of the optical path length. The incident complex light field at the measurement side is precisely reconstructed from the far-field speckle pattern at the detection side, enabling digital refocusing in a multi-layer sample without any mechanical movement. The accuracy of the quantitative phase reconstruction is validated by imaging the phase target and hydrogel beads through the MCF. With the proposed imaging modality, three-dimensional imaging of human cancer cells is achieved through the ultra-thin fiber endoscope, promising widespread clinical applications.
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Affiliation(s)
- Jiawei Sun
- Laboratory of Measurement and Sensor System Technique (MST), TU Dresden, Helmholtzstrasse 18, 01069, Dresden, Germany.
- Competence Center for Biomedical Computational Laser Systems (BIOLAS), TU Dresden, Dresden, Germany.
| | - Jiachen Wu
- Laboratory of Measurement and Sensor System Technique (MST), TU Dresden, Helmholtzstrasse 18, 01069, Dresden, Germany
- State Key Laboratory of Precision Measurement Technology and Instruments, Department of Precision Instruments, Tsinghua University, 100084, Beijing, China
| | - Song Wu
- Institute for Integrative Nanosciences, IFW Dresden, Helmholtzstraße 20, 01069, Dresden, Germany
| | - Ruchi Goswami
- Max Planck Institute for the Science of Light & Max-Planck-Zentrum für Physik und Medizin, 91058, Erlangen, Germany
| | - Salvatore Girardo
- Max Planck Institute for the Science of Light & Max-Planck-Zentrum für Physik und Medizin, 91058, Erlangen, Germany
| | - Liangcai Cao
- State Key Laboratory of Precision Measurement Technology and Instruments, Department of Precision Instruments, Tsinghua University, 100084, Beijing, China
| | - Jochen Guck
- Max Planck Institute for the Science of Light & Max-Planck-Zentrum für Physik und Medizin, 91058, Erlangen, Germany
- Cluster of Excellence Physics of Life, TU Dresden, Dresden, Germany
| | - Nektarios Koukourakis
- Laboratory of Measurement and Sensor System Technique (MST), TU Dresden, Helmholtzstrasse 18, 01069, Dresden, Germany.
- Competence Center for Biomedical Computational Laser Systems (BIOLAS), TU Dresden, Dresden, Germany.
| | - Juergen W Czarske
- Laboratory of Measurement and Sensor System Technique (MST), TU Dresden, Helmholtzstrasse 18, 01069, Dresden, Germany.
- Competence Center for Biomedical Computational Laser Systems (BIOLAS), TU Dresden, Dresden, Germany.
- Cluster of Excellence Physics of Life, TU Dresden, Dresden, Germany.
- Institute of Applied Physics, TU Dresden, Dresden, Germany.
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24
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Russell LE, Dalgleish HWP, Nutbrown R, Gauld OM, Herrmann D, Fişek M, Packer AM, Häusser M. All-optical interrogation of neural circuits in behaving mice. Nat Protoc 2022; 17:1579-1620. [PMID: 35478249 PMCID: PMC7616378 DOI: 10.1038/s41596-022-00691-w] [Citation(s) in RCA: 26] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2021] [Accepted: 02/09/2022] [Indexed: 12/22/2022]
Abstract
Recent advances combining two-photon calcium imaging and two-photon optogenetics with computer-generated holography now allow us to read and write the activity of large populations of neurons in vivo at cellular resolution and with high temporal resolution. Such 'all-optical' techniques enable experimenters to probe the effects of functionally defined neurons on neural circuit function and behavioral output with new levels of precision. This greatly increases flexibility, resolution, targeting specificity and throughput compared with alternative approaches based on electrophysiology and/or one-photon optogenetics and can interrogate larger and more densely labeled populations of neurons than current voltage imaging-based implementations. This protocol describes the experimental workflow for all-optical interrogation experiments in awake, behaving head-fixed mice. We describe modular procedures for the setup and calibration of an all-optical system (~3 h), the preparation of an indicator and opsin-expressing and task-performing animal (~3-6 weeks), the characterization of functional and photostimulation responses (~2 h per field of view) and the design and implementation of an all-optical experiment (achievable within the timescale of a normal behavioral experiment; ~3-5 h per field of view). We discuss optimizations for efficiently selecting and targeting neuronal ensembles for photostimulation sequences, as well as generating photostimulation response maps from the imaging data that can be used to examine the impact of photostimulation on the local circuit. We demonstrate the utility of this strategy in three brain areas by using different experimental setups. This approach can in principle be adapted to any brain area to probe functional connectivity in neural circuits and investigate the relationship between neural circuit activity and behavior.
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Affiliation(s)
- Lloyd E Russell
- Wolfson Institute for Biomedical Research, University College London, London, UK
| | - Henry W P Dalgleish
- Wolfson Institute for Biomedical Research, University College London, London, UK
- Sainsbury Wellcome Centre, University College London, London, UK
| | - Rebecca Nutbrown
- Wolfson Institute for Biomedical Research, University College London, London, UK
| | - Oliver M Gauld
- Wolfson Institute for Biomedical Research, University College London, London, UK
| | - Dustin Herrmann
- Wolfson Institute for Biomedical Research, University College London, London, UK
| | - Mehmet Fişek
- Wolfson Institute for Biomedical Research, University College London, London, UK
| | - Adam M Packer
- Wolfson Institute for Biomedical Research, University College London, London, UK.
- Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford, UK.
| | - Michael Häusser
- Wolfson Institute for Biomedical Research, University College London, London, UK.
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25
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Zanon M, Zanini D, Haase A. All-optical manipulation of the Drosophila olfactory system. Sci Rep 2022; 12:8506. [PMID: 35595846 PMCID: PMC9123005 DOI: 10.1038/s41598-022-12237-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2022] [Accepted: 05/09/2022] [Indexed: 11/09/2022] Open
Abstract
Thanks to its well-known neuroanatomy, limited brain size, complex behaviour, and the extensive genetic methods, Drosophila has become an indispensable model in neuroscience. A vast number of studies have focused on its olfactory system and the processing of odour information. Optogenetics is one of the recently developed genetic tools that significantly advance this field of research, allowing to replace odour stimuli by direct neuronal activation with light. This becomes a universal all-optical toolkit when spatially selective optogenetic activation is combined with calcium imaging to read out neuronal responses. Initial experiments showed a successful implementation to study the olfactory system in fish and mice, but the olfactory system of Drosophila has been so far precluded from an application. To fill this gap, we present here optogenetic tools to selectively stimulate functional units in the Drosophila olfactory system, combined with two-photon calcium imaging to read out the activity patterns elicited by these stimuli at different levels of the brain. This method allows to study the spatial and temporal features of the information flow and reveals the functional connectivity in the olfactory network.
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Affiliation(s)
- Mirko Zanon
- Center for Mind/Brain Sciences, University of Trento, Rovereto, Italy.
- Department of Physics, University of Trento, Trento, Italy.
| | - Damiano Zanini
- Center for Mind/Brain Sciences, University of Trento, Rovereto, Italy
- Neurobiology and Genetics, Biocenter, University of Würzburg, Würzburg, Germany
| | - Albrecht Haase
- Center for Mind/Brain Sciences, University of Trento, Rovereto, Italy.
- Department of Physics, University of Trento, Trento, Italy.
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26
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Sun J, Wu J, Koukourakis N, Cao L, Kuschmierz R, Czarske J. Real-time complex light field generation through a multi-core fiber with deep learning. Sci Rep 2022; 12:7732. [PMID: 35546604 PMCID: PMC9095618 DOI: 10.1038/s41598-022-11803-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2022] [Accepted: 04/28/2022] [Indexed: 12/26/2022] Open
Abstract
The generation of tailored complex light fields with multi-core fiber (MCF) lensless microendoscopes is widely used in biomedicine. However, the computer-generated holograms (CGHs) used for such applications are typically generated by iterative algorithms, which demand high computation effort, limiting advanced applications like fiber-optic cell manipulation. The random and discrete distribution of the fiber cores in an MCF induces strong spatial aliasing to the CGHs, hence, an approach that can rapidly generate tailored CGHs for MCFs is highly demanded. We demonstrate a novel deep neural network-CoreNet, providing accurate tailored CGHs generation for MCFs at a near video rate. The CoreNet is trained by unsupervised learning and speeds up the computation time by two magnitudes with high fidelity light field generation compared to the previously reported CGH algorithms for MCFs. Real-time generated tailored CGHs are on-the-fly loaded to the phase-only spatial light modulator (SLM) for near video-rate complex light fields generation through the MCF microendoscope. This paves the avenue for real-time cell rotation and several further applications that require real-time high-fidelity light delivery in biomedicine.
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Affiliation(s)
- Jiawei Sun
- Laboratory of Measurement and Sensor System Technique (MST), TU Dresden, Helmholtzstrasse 18, 01069, Dresden, Germany. .,Competence Center for Biomedical Computational Laser Systems (BIOLAS), TU Dresden, Dresden, Germany.
| | - Jiachen Wu
- Laboratory of Measurement and Sensor System Technique (MST), TU Dresden, Helmholtzstrasse 18, 01069, Dresden, Germany. .,State Key Laboratory of Precision Measurement Technology and Instruments, Department of Precision Instruments, Tsinghua University, Beijing, 100084, China.
| | - Nektarios Koukourakis
- Laboratory of Measurement and Sensor System Technique (MST), TU Dresden, Helmholtzstrasse 18, 01069, Dresden, Germany.,Competence Center for Biomedical Computational Laser Systems (BIOLAS), TU Dresden, Dresden, Germany
| | - Liangcai Cao
- State Key Laboratory of Precision Measurement Technology and Instruments, Department of Precision Instruments, Tsinghua University, Beijing, 100084, China
| | - Robert Kuschmierz
- Laboratory of Measurement and Sensor System Technique (MST), TU Dresden, Helmholtzstrasse 18, 01069, Dresden, Germany.,Competence Center for Biomedical Computational Laser Systems (BIOLAS), TU Dresden, Dresden, Germany
| | - Juergen Czarske
- Laboratory of Measurement and Sensor System Technique (MST), TU Dresden, Helmholtzstrasse 18, 01069, Dresden, Germany. .,Competence Center for Biomedical Computational Laser Systems (BIOLAS), TU Dresden, Dresden, Germany. .,Cluster of Excellence Physics of Life, TU Dresden, Dresden, Germany. .,Institute of Applied Physics, TU Dresden, Dresden, Germany.
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27
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Supekar OD, Sias A, Hansen SR, Martinez G, Peet GC, Peng X, Bright VM, Hughes EG, Restrepo D, Shepherd DP, Welle CG, Gopinath JT, Gibson EA. Miniature structured illumination microscope for in vivo 3D imaging of brain structures with optical sectioning. BIOMEDICAL OPTICS EXPRESS 2022; 13:2530-2541. [PMID: 35519247 PMCID: PMC9045919 DOI: 10.1364/boe.449533] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/24/2021] [Revised: 02/26/2022] [Accepted: 03/05/2022] [Indexed: 05/25/2023]
Abstract
We present a high-resolution miniature, light-weight fluorescence microscope with electrowetting lens and onboard CMOS for high resolution volumetric imaging and structured illumination for rejection of out-of-focus and scattered light. The miniature microscope (SIMscope3D) delivers structured light using a coherent fiber bundle to obtain optical sectioning with an axial resolution of 18 µm. Volumetric imaging of eGFP labeled cells in fixed mouse brain tissue at depths up to 260 µm is demonstrated. The functionality of SIMscope3D to provide background free 3D imaging is shown by recording time series of microglia dynamics in awake mice at depths up to 120 µm in the brain.
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Affiliation(s)
- Omkar D Supekar
- Department of Electrical, Energy and Computer Engineering, University of Colorado Boulder, CO 80309, USA
- Department of Mechanical Engineering, University of Colorado Boulder, CO 80309, USA
| | - Andrew Sias
- Department of Bioengineering, University of Colorado Anschutz Medical Campus, CO 80045, USA
| | - Sean R Hansen
- Department of Bioengineering, University of Colorado Anschutz Medical Campus, CO 80045, USA
| | - Gabriel Martinez
- Department of Bioengineering, University of Colorado Anschutz Medical Campus, CO 80045, USA
| | - Graham C Peet
- Department of Cell and Developmental Biology, University of Colorado Anschutz Medical Campus, CO 80045, USA
| | - Xiaoyu Peng
- Department of Physiology and Biophysics, University of Colorado Anschutz Medical Campus, CO 80045, USA
| | - Victor M Bright
- Department of Mechanical Engineering, University of Colorado Boulder, CO 80309, USA
| | - Ethan G Hughes
- Department of Cell and Developmental Biology, University of Colorado Anschutz Medical Campus, CO 80045, USA
| | - Diego Restrepo
- Department of Cell and Developmental Biology, University of Colorado Anschutz Medical Campus, CO 80045, USA
| | | | - Cristin G Welle
- Department of Physiology and Biophysics, University of Colorado Anschutz Medical Campus, CO 80045, USA
- Department of Neurosurgery, University of Colorado Anschutz Medical Campus, CO 80045, USA
| | - Juliet T Gopinath
- Department of Electrical, Energy and Computer Engineering, University of Colorado Boulder, CO 80309, USA
- Department of Physics, University of Colorado Boulder, CO 80309, USA
| | - Emily A Gibson
- Department of Bioengineering, University of Colorado Anschutz Medical Campus, CO 80045, USA
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28
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Xue Y, Waller L, Adesnik H, Pégard N. Three-dimensional multi-site random access photostimulation (3D-MAP). eLife 2022; 11:73266. [PMID: 35156923 PMCID: PMC8843094 DOI: 10.7554/elife.73266] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2021] [Accepted: 01/19/2022] [Indexed: 11/22/2022] Open
Abstract
Optical control of neural ensemble activity is crucial for understanding brain function and disease, yet no technology can achieve optogenetic control of very large numbers of neurons at an extremely fast rate over a large volume. State-of-the-art multiphoton holographic optogenetics requires high-power illumination that only addresses relatively small populations of neurons in parallel. Conversely, one-photon holographic techniques can stimulate more neurons with two to three orders lower power, but with limited resolution or addressable volume. Perhaps most problematically, two-photon holographic optogenetic systems are extremely expensive and sophisticated which has precluded their broader adoption in the neuroscience community. To address this technical gap, we introduce a new one-photon light sculpting technique, three-dimensional multi-site random access photostimulation (3D-MAP), that overcomes these limitations by modulating light dynamically, both in the spatial and in the angular domain at multi-kHz rates. We use 3D-MAP to interrogate neural circuits in 3D and demonstrate simultaneous photostimulation and imaging of dozens of user-selected neurons in the intact mouse brain in vivo with high spatio-temporal resolution. 3D-MAP can be broadly adopted for high-throughput all-optical interrogation of brain circuits owing to its powerful combination of scale, speed, simplicity, and cost.
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Affiliation(s)
- Yi Xue
- Department of Electrical Engineering & Computer Sciences, University of California, Berkeley
| | - Laura Waller
- Department of Electrical Engineering & Computer Sciences, University of California, Berkeley
| | - Hillel Adesnik
- Department of Molecular & Cell Biology, University of California, Berkeley
- Helen Wills Neuroscience Institute, University of California, Berkeley
| | - Nicolas Pégard
- Department of Applied Physical Sciences, University of North Carolina at Chapel Hill
- Department of Biomedical Engineering, University of North Carolina at Chapel Hill
- UNC Neuroscience Center, University of North Carolina at Chapel Hill
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29
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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: 68] [Impact Index Per Article: 34.0] [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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30
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Piñeiro M, Mena W, Ewer J, Orio P. Extracting temporal relationships between weakly coupled peptidergic and motoneuronal signaling: Application to Drosophila ecdysis behavior. PLoS Comput Biol 2021; 17:e1008933. [PMID: 34910730 PMCID: PMC8716061 DOI: 10.1371/journal.pcbi.1008933] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2021] [Revised: 12/29/2021] [Accepted: 11/14/2021] [Indexed: 11/18/2022] Open
Abstract
Neuromodulators, such as neuropeptides, can regulate and reconfigure neural circuits to alter their output, affecting in this way animal physiology and behavior. The interplay between the activity of neuronal circuits, their modulation by neuropeptides, and the resulting behavior, is still poorly understood. Here, we present a quantitative framework to study the relationships between the temporal pattern of activity of peptidergic neurons and of motoneurons during Drosophila ecdysis behavior, a highly stereotyped motor sequence that is critical for insect growth. We analyzed, in the time and frequency domains, simultaneous intracellular calcium recordings of peptidergic CCAP (crustacean cardioactive peptide) neurons and motoneurons obtained from isolated central nervous systems throughout fictive ecdysis behavior induced ex vivo by Ecdysis triggering hormone. We found that the activity of both neuronal populations is tightly coupled in a cross-frequency manner, suggesting that CCAP neurons modulate the frequency of motoneuron firing. To explore this idea further, we used a probabilistic logistic model to show that calcium dynamics in CCAP neurons can predict the oscillation of motoneurons, both in a simple model and in a conductance-based model capable of simulating many features of the observed neural dynamics. Finally, we developed an algorithm to quantify the motor behavior observed in videos of pupal ecdysis, and compared their features to the patterns of neuronal calcium activity recorded ex vivo. We found that the motor activity of the intact animal is more regular than the motoneuronal activity recorded from ex vivo preparations during fictive ecdysis behavior; the analysis of the patterns of movement also allowed us to identify a new post-ecdysis phase.
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Affiliation(s)
- Miguel Piñeiro
- Centro Interdisciplinario de Neurociencia de Valparaíso, Universidad de Valparaíso, Valparaíso, Chile
| | - Wilson Mena
- Centro Interdisciplinario de Neurociencia de Valparaíso, Universidad de Valparaíso, Valparaíso, Chile
- Department of Neuroscience, Institut Pasteur, Paris, France
| | - John Ewer
- Centro Interdisciplinario de Neurociencia de Valparaíso, Universidad de Valparaíso, Valparaíso, Chile
- Instituto de Neurociencias, Facultad de Ciencias, Universidad de Valparaíso, Valparaíso, Chile
- * E-mail: (JE); (PO)
| | - Patricio Orio
- Centro Interdisciplinario de Neurociencia de Valparaíso, Universidad de Valparaíso, Valparaíso, Chile
- Instituto de Neurociencias, Facultad de Ciencias, Universidad de Valparaíso, Valparaíso, Chile
- * E-mail: (JE); (PO)
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31
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Adesnik H, Abdeladim L. Probing neural codes with two-photon holographic optogenetics. Nat Neurosci 2021; 24:1356-1366. [PMID: 34400843 PMCID: PMC9793863 DOI: 10.1038/s41593-021-00902-9] [Citation(s) in RCA: 60] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2020] [Accepted: 06/30/2021] [Indexed: 02/07/2023]
Abstract
Optogenetics ushered in a revolution in how neuroscientists interrogate brain function. Because of technical limitations, the majority of optogenetic studies have used low spatial resolution activation schemes that limit the types of perturbations that can be made. However, neural activity manipulations at finer spatial scales are likely to be important to more fully understand neural computation. Spatially precise multiphoton holographic optogenetics promises to address this challenge and opens up many new classes of experiments that were not previously possible. More specifically, by offering the ability to recreate extremely specific neural activity patterns in both space and time in functionally defined ensembles of neurons, multiphoton holographic optogenetics could allow neuroscientists to reveal fundamental aspects of the neural codes for sensation, cognition and behavior that have been beyond reach. This Review summarizes recent advances in multiphoton holographic optogenetics that substantially expand its capabilities, highlights outstanding technical challenges and provides an overview of the classes of experiments it can execute to test and validate key theoretical models of brain function. Multiphoton holographic optogenetics could substantially accelerate the pace of neuroscience discovery by helping to close the loop between experimental and theoretical neuroscience, leading to fundamental new insights into nervous system function and disorder.
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Affiliation(s)
- Hillel Adesnik
- Department of Molecular and Cell Biology and the Helen Wills Neuroscience Institute, University of California, Berkeley, Berkeley, CA, USA.
| | - Lamiae Abdeladim
- Department of Molecular and Cell Biology and the Helen Wills Neuroscience Institute, University of California, Berkeley, Berkeley, CA, USA
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32
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Lafferty CK, Christinck TD, Britt JP. All-optical approaches to studying psychiatric disease. Methods 2021; 203:46-55. [PMID: 34314828 DOI: 10.1016/j.ymeth.2021.07.007] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2021] [Revised: 07/20/2021] [Accepted: 07/22/2021] [Indexed: 11/17/2022] Open
Abstract
Improvements in all-optical means of monitoring and manipulating neural activity have generated new ways of studying psychiatric disease. The combination of calcium imaging techniques with optogenetics to concurrently record and manipulate neural activity has been used to create new disease models that link distinct circuit abnormalities to specific disease dimensions. These approaches represent a new path towards the development of more effective treatments, as they allow researchers to identify circuit manipulations that normalize pathological network activity. In this review we highlight the utility of all-optical approaches to generate new psychiatric disease models where the specific circuit abnormalities associated with disease symptomology can be assessed in vivo and in response to manipulations designed to normalize disease states. We then outline the principles underlying all-optical interrogations of neural circuits and discuss practical considerations for experimental design.
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Affiliation(s)
- Christopher K Lafferty
- Department of Psychology, McGill University, Montreal, QC, Canada; Center for Studies in Behavioral Neurobiology, Concordia University, Montreal, QC, Canada
| | - Thomas D Christinck
- Center for Studies in Behavioral Neurobiology, Concordia University, Montreal, QC, Canada; Integrated Program in Neuroscience, McGill University, Montreal, QC, Canada
| | - Jonathan P Britt
- Department of Psychology, McGill University, Montreal, QC, Canada; Center for Studies in Behavioral Neurobiology, Concordia University, Montreal, QC, Canada; Integrated Program in Neuroscience, McGill University, Montreal, QC, Canada.
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33
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Schweihoff JF, Loshakov M, Pavlova I, Kück L, Ewell LA, Schwarz MK. DeepLabStream enables closed-loop behavioral experiments using deep learning-based markerless, real-time posture detection. Commun Biol 2021; 4:130. [PMID: 33514883 PMCID: PMC7846585 DOI: 10.1038/s42003-021-01654-9] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2020] [Accepted: 12/31/2020] [Indexed: 12/30/2022] Open
Abstract
In general, animal behavior can be described as the neuronal-driven sequence of reoccurring postures through time. Most of the available current technologies focus on offline pose estimation with high spatiotemporal resolution. However, to correlate behavior with neuronal activity it is often necessary to detect and react online to behavioral expressions. Here we present DeepLabStream, a versatile closed-loop tool providing real-time pose estimation to deliver posture dependent stimulations. DeepLabStream has a temporal resolution in the millisecond range, can utilize different input, as well as output devices and can be tailored to multiple experimental designs. We employ DeepLabStream to semi-autonomously run a second-order olfactory conditioning task with freely moving mice and optogenetically label neuronal ensembles active during specific head directions.
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Affiliation(s)
- Jens F Schweihoff
- Functional Neuroconnectomics Group, Institute of Experimental Epileptology and Cognition Research, Medical Faculty, University of Bonn, Bonn, Germany
| | - Matvey Loshakov
- Functional Neuroconnectomics Group, Institute of Experimental Epileptology and Cognition Research, Medical Faculty, University of Bonn, Bonn, Germany
| | - Irina Pavlova
- Functional Neuroconnectomics Group, Institute of Experimental Epileptology and Cognition Research, Medical Faculty, University of Bonn, Bonn, Germany
| | - Laura Kück
- Institute of Experimental Epileptology and Cognition Research, Medical Faculty, University of Bonn, Bonn, Germany
| | - Laura A Ewell
- Institute of Experimental Epileptology and Cognition Research, Medical Faculty, University of Bonn, Bonn, Germany
| | - Martin K Schwarz
- Functional Neuroconnectomics Group, Institute of Experimental Epileptology and Cognition Research, Medical Faculty, University of Bonn, Bonn, Germany.
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34
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Kim CK, Sanchez MI, Hoerbelt P, Fenno LE, Malenka RC, Deisseroth K, Ting AY. A Molecular Calcium Integrator Reveals a Striatal Cell Type Driving Aversion. Cell 2020; 183:2003-2019.e16. [PMID: 33308478 PMCID: PMC9839359 DOI: 10.1016/j.cell.2020.11.015] [Citation(s) in RCA: 40] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2020] [Revised: 09/18/2020] [Accepted: 11/06/2020] [Indexed: 01/17/2023]
Abstract
The ability to record transient cellular events in the DNA or RNA of cells would enable precise, large-scale analysis, selection, and reprogramming of heterogeneous cell populations. Here, we report a molecular technology for stable genetic tagging of cells that exhibit activity-related increases in intracellular calcium concentration (FLiCRE). We used FLiCRE to transcriptionally label activated neural ensembles in the nucleus accumbens of the mouse brain during brief stimulation of aversive inputs. Using single-cell RNA sequencing, we detected FLiCRE transcripts among the endogenous transcriptome, providing simultaneous readout of both cell-type and calcium activation history. We identified a cell type in the nucleus accumbens activated downstream of long-range excitatory projections. Taking advantage of FLiCRE's modular design, we expressed an optogenetic channel selectively in this cell type and showed that direct recruitment of this otherwise genetically inaccessible population elicits behavioral aversion. The specificity and minute resolution of FLiCRE enables molecularly informed characterization, manipulation, and reprogramming of activated cellular ensembles.
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Affiliation(s)
- Christina K. Kim
- Department of Genetics, Stanford University, Stanford, CA 94305, USA.,These authors contributed equally to this work
| | - Mateo I. Sanchez
- Department of Genetics, Stanford University, Stanford, CA 94305, USA.,Chan Zuckerberg Biohub, San Francisco, CA 94158, USA.,These authors contributed equally to this work
| | - Paul Hoerbelt
- Department of Psychiatry and Behavioral Sciences, Stanford University, Stanford, CA 94305, USA
| | - Lief E. Fenno
- Department of Psychiatry and Behavioral Sciences, Stanford University, Stanford, CA 94305, USA.,Department of Bioengineering, Stanford University, Stanford, CA 94035, USA.,Howard Hughes Medical Institute, Stanford University, Stanford, CA 94305, USA
| | - Robert C. Malenka
- Department of Psychiatry and Behavioral Sciences, Stanford University, Stanford, CA 94305, USA
| | - Karl Deisseroth
- Department of Psychiatry and Behavioral Sciences, Stanford University, Stanford, CA 94305, USA.,Department of Bioengineering, Stanford University, Stanford, CA 94035, USA.,Howard Hughes Medical Institute, Stanford University, Stanford, CA 94305, USA.,Correspondence to: or
| | - Alice Y. Ting
- Department of Genetics, Stanford University, Stanford, CA 94305, USA.,Chan Zuckerberg Biohub, San Francisco, CA 94158, USA.,Department of Biology, Stanford University, Stanford, CA 94305, USA.,Lead contact:
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35
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Kostyuk AI, Panova AS, Kokova AD, Kotova DA, Maltsev DI, Podgorny OV, Belousov VV, Bilan DS. In Vivo Imaging with Genetically Encoded Redox Biosensors. Int J Mol Sci 2020; 21:E8164. [PMID: 33142884 PMCID: PMC7662651 DOI: 10.3390/ijms21218164] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2020] [Revised: 10/28/2020] [Accepted: 10/29/2020] [Indexed: 12/13/2022] Open
Abstract
Redox reactions are of high fundamental and practical interest since they are involved in both normal physiology and the pathogenesis of various diseases. However, this area of research has always been a relatively problematic field in the context of analytical approaches, mostly because of the unstable nature of the compounds that are measured. Genetically encoded sensors allow for the registration of highly reactive molecules in real-time mode and, therefore, they began a new era in redox biology. Their strongest points manifest most brightly in in vivo experiments and pave the way for the non-invasive investigation of biochemical pathways that proceed in organisms from different systematic groups. In the first part of the review, we briefly describe the redox sensors that were used in vivo as well as summarize the model systems to which they were applied. Next, we thoroughly discuss the biological results obtained in these studies in regard to animals, plants, as well as unicellular eukaryotes and prokaryotes. We hope that this work reflects the amazing power of this technology and can serve as a useful guide for biologists and chemists who work in the field of redox processes.
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Affiliation(s)
- Alexander I. Kostyuk
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, 117997 Moscow, Russia; (A.I.K.); (A.S.P.); (A.D.K.); (D.A.K.); (D.I.M.); (O.V.P.); (V.V.B.)
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Pirogov Russian National Research Medical University, 117997 Moscow, Russia
| | - Anastasiya S. Panova
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, 117997 Moscow, Russia; (A.I.K.); (A.S.P.); (A.D.K.); (D.A.K.); (D.I.M.); (O.V.P.); (V.V.B.)
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Pirogov Russian National Research Medical University, 117997 Moscow, Russia
| | - Aleksandra D. Kokova
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, 117997 Moscow, Russia; (A.I.K.); (A.S.P.); (A.D.K.); (D.A.K.); (D.I.M.); (O.V.P.); (V.V.B.)
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Pirogov Russian National Research Medical University, 117997 Moscow, Russia
| | - Daria A. Kotova
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, 117997 Moscow, Russia; (A.I.K.); (A.S.P.); (A.D.K.); (D.A.K.); (D.I.M.); (O.V.P.); (V.V.B.)
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Pirogov Russian National Research Medical University, 117997 Moscow, Russia
| | - Dmitry I. Maltsev
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, 117997 Moscow, Russia; (A.I.K.); (A.S.P.); (A.D.K.); (D.A.K.); (D.I.M.); (O.V.P.); (V.V.B.)
- Federal Center for Cerebrovascular Pathology and Stroke, 117997 Moscow, Russia
| | - Oleg V. Podgorny
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, 117997 Moscow, Russia; (A.I.K.); (A.S.P.); (A.D.K.); (D.A.K.); (D.I.M.); (O.V.P.); (V.V.B.)
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Pirogov Russian National Research Medical University, 117997 Moscow, Russia
| | - Vsevolod V. Belousov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, 117997 Moscow, Russia; (A.I.K.); (A.S.P.); (A.D.K.); (D.A.K.); (D.I.M.); (O.V.P.); (V.V.B.)
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Pirogov Russian National Research Medical University, 117997 Moscow, Russia
- Federal Center for Cerebrovascular Pathology and Stroke, 117997 Moscow, Russia
- Institute for Cardiovascular Physiology, Georg August University Göttingen, D-37073 Göttingen, Germany
| | - Dmitry S. Bilan
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, 117997 Moscow, Russia; (A.I.K.); (A.S.P.); (A.D.K.); (D.A.K.); (D.I.M.); (O.V.P.); (V.V.B.)
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Pirogov Russian National Research Medical University, 117997 Moscow, Russia
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36
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Functional interrogation of neural circuits with virally transmitted optogenetic tools. J Neurosci Methods 2020; 345:108905. [PMID: 32795553 DOI: 10.1016/j.jneumeth.2020.108905] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2020] [Revised: 08/03/2020] [Accepted: 08/06/2020] [Indexed: 12/12/2022]
Abstract
The vertebrate brain comprises a plethora of cell types connected by intertwined pathways. Optogenetics enriches the neuroscientific tool set for disentangling these neuronal circuits in a manner which exceeds the spatio-temporal precision of previously existing techniques. Technically, optogenetics can be divided in three types of optical and genetic combinations: (1) it is primarily understood as the manipulation of the activity of genetically modified cells (typically neurons) with light, i.e. optical actuators. (2) A second combination refers to visualizing the activity of genetically modified cells (again typically neurons), i.e. optical sensors. (3) A completely different interpretation of optogenetics refers to the light activated expression of a genetically induced construct. Here, we focus on the first two types of optogenetics, i.e. the optical actuators and sensors in an attempt to give an overview into the topic. We first cover methods to express opsins into neurons and introduce strategies of targeting specific neuronal populations in different animal species. We then summarize combinations of optogenetics with behavioral read out and neuronal imaging. Finally, we give an overview of the current state-of-the-art and an outlook on future perspectives.
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Hoffman CE, Parker WE, Rapoport BI, Zhao M, Ma H, Schwartz TH. Innovations in the Neurosurgical Management of Epilepsy. World Neurosurg 2020; 139:775-788. [PMID: 32689698 DOI: 10.1016/j.wneu.2020.03.031] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2019] [Accepted: 03/02/2020] [Indexed: 10/23/2022]
Abstract
Technical limitations and clinical challenges have historically limited the diagnostic tools and treatment methods available for surgical approaches to the management of epilepsy. By contrast, recent technological innovations in several areas hold significant promise in improving outcomes and decreasing morbidity. We review innovations in the neurosurgical management of epilepsy in several areas, including wireless recording and stimulation systems (particularly responsive neurostimulation [NeuroPace]), conformal electrodes for high-resolution electrocorticography, robot-assisted stereotactic surgery, optogenetics and optical imaging methods, novel positron emission tomography ligands, and new applications of focused ultrasonography. Investigation into genetic causes of and susceptibilities to epilepsy has introduced a new era of precision medicine, enabling the understanding of cell signaling mechanisms underlying epileptic activity as well as patient-specific molecularly targeted treatment options. We discuss the emerging path to individualized treatment plans, predicted outcomes, and improved selection of effective interventions, on the basis of these developments.
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Affiliation(s)
- Caitlin E Hoffman
- Department of Neurological Surgery, Weill Cornell Medical College, NewYork-Presbyterian Hospital, New York, New York, USA.
| | - Whitney E Parker
- Department of Neurological Surgery, Weill Cornell Medical College, NewYork-Presbyterian Hospital, New York, New York, USA
| | - Benjamin I Rapoport
- Department of Neurological Surgery, Weill Cornell Medical College, NewYork-Presbyterian Hospital, New York, New York, USA
| | - Mingrui Zhao
- Department of Neurological Surgery, Weill Cornell Medical College, NewYork-Presbyterian Hospital, New York, New York, USA
| | - Hongtao Ma
- Department of Neurological Surgery, Weill Cornell Medical College, NewYork-Presbyterian Hospital, New York, New York, USA
| | - Theodore H Schwartz
- Department of Neurological Surgery, Weill Cornell Medical College, NewYork-Presbyterian Hospital, New York, New York, USA
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Kuner R, Kuner T. Cellular Circuits in the Brain and Their Modulation in Acute and Chronic Pain. Physiol Rev 2020; 101:213-258. [PMID: 32525759 DOI: 10.1152/physrev.00040.2019] [Citation(s) in RCA: 143] [Impact Index Per Article: 35.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Chronic, pathological pain remains a global health problem and a challenge to basic and clinical sciences. A major obstacle to preventing, treating, or reverting chronic pain has been that the nature of neural circuits underlying the diverse components of the complex, multidimensional experience of pain is not well understood. Moreover, chronic pain involves diverse maladaptive plasticity processes, which have not been decoded mechanistically in terms of involvement of specific circuits and cause-effect relationships. This review aims to discuss recent advances in our understanding of circuit connectivity in the mammalian brain at the level of regional contributions and specific cell types in acute and chronic pain. A major focus is placed on functional dissection of sub-neocortical brain circuits using optogenetics, chemogenetics, and imaging technological tools in rodent models with a view towards decoding sensory, affective, and motivational-cognitive dimensions of pain. The review summarizes recent breakthroughs and insights on structure-function properties in nociceptive circuits and higher order sub-neocortical modulatory circuits involved in aversion, learning, reward, and mood and their modulation by endogenous GABAergic inhibition, noradrenergic, cholinergic, dopaminergic, serotonergic, and peptidergic pathways. The knowledge of neural circuits and their dynamic regulation via functional and structural plasticity will be beneficial towards designing and improving targeted therapies.
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Affiliation(s)
- Rohini Kuner
- Institute of Pharmacology, Heidelberg University, Heidelberg, Germany; and Department of Functional Neuroanatomy, Institute for Anatomy and Cell Biology, Heidelberg University, Heidelberg, Germany
| | - Thomas Kuner
- Institute of Pharmacology, Heidelberg University, Heidelberg, Germany; and Department of Functional Neuroanatomy, Institute for Anatomy and Cell Biology, Heidelberg University, Heidelberg, Germany
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39
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Harel A, Ryan TJ. The memory toolbox: how genetic manipulations and cellular imaging are transforming our understanding of learned information. Curr Opin Behav Sci 2020. [DOI: 10.1016/j.cobeha.2020.02.016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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40
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Yuan W, Chen D, Sarabia-Estrada R, Guerrero-Cázares H, Li D, Quiñones-Hinojosa A, Li X. Theranostic OCT microneedle for fast ultrahigh-resolution deep-brain imaging and efficient laser ablation in vivo. SCIENCE ADVANCES 2020; 6:eaaz9664. [PMID: 32300661 PMCID: PMC7148106 DOI: 10.1126/sciadv.aaz9664] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/24/2019] [Accepted: 01/15/2020] [Indexed: 05/21/2023]
Abstract
Current minimally invasive optical techniques for in vivo deep-brain imaging provide a limited resolution, field of view, and speed. These limitations prohibit direct assessment of detailed histomorphology of various deep-seated brain diseases at their native state and therefore hinder the potential clinical utilities of those techniques. Here, we report an ultracompact (580 μm in outer diameter) theranostic deep-brain microneedle combining 800-nm optical coherence tomography imaging with laser ablation. Its performance was demonstrated by in vivo ultrahigh-resolution (1.7 μm axial and 5.7 μm transverse), high-speed (20 frames per second) volumetric imaging of mouse brain microstructures and optical attenuation coefficients. Its translational potential was further demonstrated by in vivo cancer visualization (with an imaging depth of 1.23 mm) and efficient tissue ablation (with a 1448-nm continuous-wave laser at a 350-mW power) in a deep mouse brain (with an ablation depth of about 600 μm).
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Affiliation(s)
- Wu Yuan
- Department of Biomedical Engineering, School of Medicine, Johns Hopkins University, Baltimore, MD 21205, USA
| | - Defu Chen
- Department of Biomedical Engineering, School of Medicine, Johns Hopkins University, Baltimore, MD 21205, USA
| | | | | | - Dawei Li
- Department of Biomedical Engineering, School of Medicine, Johns Hopkins University, Baltimore, MD 21205, USA
| | | | - Xingde Li
- Department of Biomedical Engineering, School of Medicine, Johns Hopkins University, Baltimore, MD 21205, USA
- Corresponding author.
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Brondi M, Moroni M, Vecchia D, Molano-Mazón M, Panzeri S, Fellin T. High-Accuracy Detection of Neuronal Ensemble Activity in Two-Photon Functional Microscopy Using Smart Line Scanning. Cell Rep 2020; 30:2567-2580.e6. [PMID: 32101736 PMCID: PMC7043026 DOI: 10.1016/j.celrep.2020.01.105] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2019] [Revised: 01/10/2020] [Accepted: 01/29/2020] [Indexed: 11/07/2022] Open
Abstract
Two-photon functional imaging using genetically encoded calcium indicators (GECIs) is one prominent tool to map neural activity. Under optimized experimental conditions, GECIs detect single action potentials in individual cells with high accuracy. However, using current approaches, these optimized conditions are never met when imaging large ensembles of neurons. Here, we developed a method that substantially increases the signal-to-noise ratio (SNR) of population imaging of GECIs by using galvanometric mirrors and fast smart line scan (SLS) trajectories. We validated our approach in anesthetized and awake mice on deep and dense GCaMP6 staining in the mouse barrel cortex during spontaneous and sensory-evoked activity. Compared to raster population imaging, SLS led to increased SNR, higher probability of detecting calcium events, and more precise identification of functional neuronal ensembles. SLS provides a cheap and easily implementable tool for high-accuracy population imaging of neural GCaMP6 signals by using galvanometric-based two-photon microscopes.
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Affiliation(s)
- Marco Brondi
- Optical Approaches to Brain Function Laboratory, Istituto Italiano di Tecnologia, Genova, Italy; Neural Coding Laboratory, Istituto Italiano di Tecnologia, Genova and Rovereto, Italy
| | - Monica Moroni
- Neural Coding Laboratory, Istituto Italiano di Tecnologia, Genova and Rovereto, Italy; Neural Computation Laboratory, Center for Neuroscience and Cognitive Systems @UniTn, Istituto Italiano di Tecnologia, Rovereto, Italy; Center for Mind and Brain Sciences (CIMeC), University of Trento, Trento, Italy
| | - Dania Vecchia
- Optical Approaches to Brain Function Laboratory, Istituto Italiano di Tecnologia, Genova, Italy; Neural Coding Laboratory, Istituto Italiano di Tecnologia, Genova and Rovereto, Italy
| | - Manuel Molano-Mazón
- Neural Coding Laboratory, Istituto Italiano di Tecnologia, Genova and Rovereto, Italy; Neural Computation Laboratory, Center for Neuroscience and Cognitive Systems @UniTn, Istituto Italiano di Tecnologia, Rovereto, Italy
| | - Stefano Panzeri
- Neural Coding Laboratory, Istituto Italiano di Tecnologia, Genova and Rovereto, Italy; Neural Computation Laboratory, Center for Neuroscience and Cognitive Systems @UniTn, Istituto Italiano di Tecnologia, Rovereto, Italy
| | - Tommaso Fellin
- Optical Approaches to Brain Function Laboratory, Istituto Italiano di Tecnologia, Genova, Italy; Neural Coding Laboratory, Istituto Italiano di Tecnologia, Genova and Rovereto, Italy.
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Renteria C, Liu YZ, Chaney EJ, Barkalifa R, Sengupta P, Boppart SA. Dynamic Tracking Algorithm for Time-Varying Neuronal Network Connectivity using Wide-Field Optical Image Video Sequences. Sci Rep 2020; 10:2540. [PMID: 32054882 PMCID: PMC7018813 DOI: 10.1038/s41598-020-59227-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2019] [Accepted: 01/27/2020] [Indexed: 12/18/2022] Open
Abstract
Propagation of signals between neurons and brain regions provides information about the functional properties of neural networks, and thus information transfer. Advances in optical imaging and statistical analyses of acquired optical signals have yielded various metrics for inferring neural connectivity, and hence for mapping signal intercorrelation. However, a single coefficient is traditionally derived to classify the connection strength between two cells, ignoring the fact that neural systems are inherently time-variant systems. To overcome these limitations, we utilized a time-varying Pearson's correlation coefficient, spike-sorting, wavelet transform, and wavelet coherence of calcium transients from DIV 12-15 hippocampal neurons from GCaMP6s mice after applying various concentrations of glutamate. Results provide a comprehensive overview of resulting firing patterns, network connectivity, signal directionality, and network properties. Together, these metrics provide a more comprehensive and robust method of analyzing transient neural signals, and enable future investigations for tracking the effects of different stimuli on network properties.
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Affiliation(s)
- Carlos Renteria
- Beckman Institute for Advanced Science and Technology, Urbana, USA
- Department of Bioengineering, Urbana, USA
| | - Yuan-Zhi Liu
- Beckman Institute for Advanced Science and Technology, Urbana, USA
| | - Eric J Chaney
- Beckman Institute for Advanced Science and Technology, Urbana, USA
| | - Ronit Barkalifa
- Beckman Institute for Advanced Science and Technology, Urbana, USA
| | - Parijat Sengupta
- Beckman Institute for Advanced Science and Technology, Urbana, USA
| | - Stephen A Boppart
- Beckman Institute for Advanced Science and Technology, Urbana, USA.
- Department of Bioengineering, Urbana, USA.
- Department of Electrical and Computer Engineering, Urbana, USA.
- Neuroscience Program, Urbana, USA.
- Carle Illinois College of Medicine, University of Illinois at Urbana-Champaign, Champaign, USA.
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RENTERIA CARLOS, SUáREZ JAVIER, LICUDINE ALYSSA, BOPPART STEPHENA. Depixelation and enhancement of fiber bundle images by bundle rotation. APPLIED OPTICS 2020; 59:536-544. [PMID: 32225338 PMCID: PMC7286003 DOI: 10.1364/ao.59.000536] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Fiber bundles have become widely adopted for use in endoscopy, live-organism imaging, and other imaging applications. An inherent consequence of imaging with these bundles is the introduction of a honeycomb-like artifact that arises from the inter-fiber spacing, which obscures features of objects in the image. This artifact subsequently limits applicability and can make interpretation of the image-based data difficult. This work presents a method to reduce this artifact by on-axis rotation of the fiber bundle. Fiber bundle images were first low-pass and median filtered to improve image quality. Consecutive filtered images with rotated samples were then co-registered and averaged to generate a final, reconstructed image. The results demonstrate removal of the artifacts, in addition to increased signal contrast and signal-to-noise ratio. This approach combines digital filtering and spatial resampling to reconstruct higher-quality images, enhancing the utility of images acquired using fiber bundles.
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Affiliation(s)
- CARLOS RENTERIA
- Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
- Department of Bioengineering, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
| | - JAVIER SUáREZ
- Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
- Department of Electrical and Computer Engineering, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
| | - ALYSSA LICUDINE
- Department of Electrical and Computer Engineering, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
| | - STEPHEN A. BOPPART
- Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
- Department of Bioengineering, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
- Department of Electrical and Computer Engineering, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
- Carle Illinois College of Medicine, University of Illinois at Urbana-Champaign, Champaign, Illinois 61820, USA
- Corresponding author:
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Picot A, Dominguez S, Liu C, Chen IW, Tanese D, Ronzitti E, Berto P, Papagiakoumou E, Oron D, Tessier G, Forget BC, Emiliani V. Temperature Rise under Two-Photon Optogenetic Brain Stimulation. Cell Rep 2019; 24:1243-1253.e5. [PMID: 30067979 DOI: 10.1016/j.celrep.2018.06.119] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2017] [Revised: 03/26/2018] [Accepted: 06/28/2018] [Indexed: 10/28/2022] Open
Abstract
In recent decades, optogenetics has been transforming neuroscience research, enabling neuroscientists to drive and read neural circuits. The recent development in illumination approaches combined with two-photon (2P) excitation, either sequential or parallel, has opened the route for brain circuit manipulation with single-cell resolution and millisecond temporal precision. Yet, the high excitation power required for multi-target photostimulation, especially under 2P illumination, raises questions about the induced local heating inside samples. Here, we present and experimentally validate a theoretical model that makes it possible to simulate 3D light propagation and heat diffusion in optically scattering samples at high spatial and temporal resolution under the illumination configurations most commonly used to perform 2P optogenetics: single- and multi-spot holographic illumination and spiral laser scanning. By investigating the effects of photostimulation repetition rate, spot spacing, and illumination dependence of heat diffusion, we found conditions that make it possible to design a multi-target 2P optogenetics experiment with minimal sample heating.
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Affiliation(s)
- Alexis Picot
- Wavefront-Engineering Microscopy Group, Neurophotonics Laboratory, UMR 8250 CNRS, University Paris Descartes, 45 rue des Saints-Pères, 75006 Paris, France
| | - Soledad Dominguez
- Wavefront-Engineering Microscopy Group, Neurophotonics Laboratory, UMR 8250 CNRS, University Paris Descartes, 45 rue des Saints-Pères, 75006 Paris, France
| | - Chang Liu
- Holographic Microscopy Group, Neurophotonics Laboratory, UMR 8250 CNRS, University Paris Descartes, 45 rue des Saints-Pères, 75006 Paris, France; Sorbonne Université, CNRS, INSERM, Institut de la Vision, 17 Rue Moreau, 75011 Paris, France
| | - I-Wen Chen
- Wavefront-Engineering Microscopy Group, Neurophotonics Laboratory, UMR 8250 CNRS, University Paris Descartes, 45 rue des Saints-Pères, 75006 Paris, France
| | - Dimitrii Tanese
- Wavefront-Engineering Microscopy Group, Neurophotonics Laboratory, UMR 8250 CNRS, University Paris Descartes, 45 rue des Saints-Pères, 75006 Paris, France
| | - Emiliano Ronzitti
- Wavefront-Engineering Microscopy Group, Neurophotonics Laboratory, UMR 8250 CNRS, University Paris Descartes, 45 rue des Saints-Pères, 75006 Paris, France; Sorbonne Université, CNRS, INSERM, Institut de la Vision, 17 Rue Moreau, 75011 Paris, France
| | - Pascal Berto
- Holographic Microscopy Group, Neurophotonics Laboratory, UMR 8250 CNRS, University Paris Descartes, 45 rue des Saints-Pères, 75006 Paris, France
| | - Eirini Papagiakoumou
- Wavefront-Engineering Microscopy Group, Neurophotonics Laboratory, UMR 8250 CNRS, University Paris Descartes, 45 rue des Saints-Pères, 75006 Paris, France; Institut National de la Santé et de la Recherche Médicale (Inserm), Paris, France
| | - Dan Oron
- Department of Physics of Complex Systems, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Gilles Tessier
- Holographic Microscopy Group, Neurophotonics Laboratory, UMR 8250 CNRS, University Paris Descartes, 45 rue des Saints-Pères, 75006 Paris, France; Sorbonne Université, CNRS, INSERM, Institut de la Vision, 17 Rue Moreau, 75011 Paris, France
| | - Benoît C Forget
- Wavefront-Engineering Microscopy Group, Neurophotonics Laboratory, UMR 8250 CNRS, University Paris Descartes, 45 rue des Saints-Pères, 75006 Paris, France
| | - Valentina Emiliani
- Wavefront-Engineering Microscopy Group, Neurophotonics Laboratory, UMR 8250 CNRS, University Paris Descartes, 45 rue des Saints-Pères, 75006 Paris, France.
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Liu K, Wang L. Optogenetics: Therapeutic spark in neuropathic pain. Bosn J Basic Med Sci 2019; 19:321-327. [PMID: 30995901 DOI: 10.17305/bjbms.2019.4114] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2019] [Accepted: 03/11/2019] [Indexed: 01/14/2023] Open
Abstract
Optogenetics is an emerging field, which uses light and molecular genetics to manipulate the activity of live cells by expressing light-sensitive proteins. With the discovery of bacteriorhodopsin, a light-sensitive bacterial protein, in 1971 Oesterhelt and Stoeckenius laid the pavement of optogenetics. However, the cross-integration of different disciplines is a little more than a decade old. The toolbox contains fluorescent sensors and optogenetic actuators that enable visualization of signaling events and manipulation of cellular activities, respectively. Neuropathic pain is pain caused either by damage or disease that affects the somatosensory system. The exact mechanism for neuropathic pain is not known, however proposed mechanisms include immune reactions, ion channel expressions, and inflammation. Current regimen for the disease provides about 50% relief for only 40-60% of patients. Recent in vivo and in vitro studies demonstrate the potential therapeutic applications of optogenetics by manipulating the activity of neurons. This review summarizes the basic concept, therapeutic applications for neuropathy, and potential of optogenetics to reach from bench to bedside in the near future.
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Affiliation(s)
- Kang Liu
- Department of Anesthesiology, Renmin Hospital of Wuhan University, Wuhan, Hubei Province, China.
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46
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Lamprecht R. Regulation of signaling proteins in the brain by light. Prog Neurobiol 2019; 180:101638. [DOI: 10.1016/j.pneurobio.2019.101638] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2019] [Revised: 05/29/2019] [Accepted: 06/06/2019] [Indexed: 12/20/2022]
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47
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Tadayon MA, Chaitanya S, Martyniuk KM, McGowan JC, Roberts SP, Denny CA, Lipson M. 3D microphotonic probe for high resolution deep tissue imaging. OPTICS EXPRESS 2019; 27:22352-22362. [PMID: 31510530 DOI: 10.1364/oe.27.022352] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
Ultra-compact miniaturized optical components for microendoscopic tools and miniaturized microscopes are required for minimally invasive imaging. Current microendoscopic technologies used for deep tissue imaging procedures are limited to a large diameter and/or low resolution due to manufacturing restrictions. We demonstrate a platform for miniaturization of an optical imaging system for microendoscopic applications with a resolution of 1 µm. We designed our probe using cascaded micro-lenses and waveguides (lensguide) to achieve a probe as small as 100 µm x 100 µm with a field of view of 60 µm in diameter. We demonstrate wide-field microscopy based on our polymeric probe fabricated using photolithography and a two-photon polymerization process.
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48
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Nelson NA, Wang X, Cook D, Carey EM, Nimmerjahn A. Imaging spinal cord activity in behaving animals. Exp Neurol 2019; 320:112974. [PMID: 31175843 DOI: 10.1016/j.expneurol.2019.112974] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2019] [Revised: 06/02/2019] [Accepted: 06/04/2019] [Indexed: 01/06/2023]
Abstract
The spinal cord is the primary neurological link between the brain and peripheral organs. How important it is in everyday life is apparent in patients with spinal cord injury or motoneuron disease, who have dramatically reduced musculoskeletal control or capacity to sense their environment. Despite its crucial role in sensory and motor processing little is known about the cellular and molecular signaling events that underlie spinal cord function under naturalistic conditions. While genetic, electrophysiological, pharmacological, and circuit tracing studies have revealed important roles for different molecularly defined neurons, these approaches insufficiently describe the moment-to-moment neuronal and non-neuronal activity patterns that underlie sensory-guided motor behaviors in health and disease. The recent development of imaging methods for real-time interrogation of cellular activity in the spinal cord of behaving mice has removed longstanding technical obstacles to spinal cord research and allowed new insight into how different cell types encode sensory information from mechanoreceptors and nociceptors in the skin. Here, we review the current state-of-the-art in interrogating cellular and microcircuit function in the spinal cord of behaving mammals and discuss current opportunities and technological challenges.
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Affiliation(s)
- Nicholas A Nelson
- Waitt Advanced Biophotonics Center, Salk Institute for Biological Studies, 10010 North Torrey Pines Road, La Jolla, CA 92037, USA; Biologial Sciences Graduate Program, University of California, San Diego, La Jolla, CA 92037, USA
| | - Xiang Wang
- Waitt Advanced Biophotonics Center, Salk Institute for Biological Studies, 10010 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Daniela Cook
- Waitt Advanced Biophotonics Center, Salk Institute for Biological Studies, 10010 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Erin M Carey
- Waitt Advanced Biophotonics Center, Salk Institute for Biological Studies, 10010 North Torrey Pines Road, La Jolla, CA 92037, USA
| | - Axel Nimmerjahn
- Waitt Advanced Biophotonics Center, Salk Institute for Biological Studies, 10010 North Torrey Pines Road, La Jolla, CA 92037, USA.
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Multiplexed temporally focused light shaping through a gradient index lens for precise in-depth optogenetic photostimulation. Sci Rep 2019; 9:7603. [PMID: 31110187 PMCID: PMC6527563 DOI: 10.1038/s41598-019-43933-w] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2018] [Accepted: 04/25/2019] [Indexed: 11/08/2022] Open
Abstract
In the past 10 years, the use of light has become irreplaceable for the optogenetic study and control of neurons and neural circuits. Optical techniques are however limited by scattering and can only see through a depth of few hundreds µm in living tissues. GRIN lens based micro-endoscopes represent a powerful solution to reach deeper regions. In this work we demonstrate that cutting edge optical methods for the precise photostimulation of multiple neurons in three dimensions can be performed through a GRIN lens. By spatio-temporally shaping a laser beam in the two-photon regime we project several tens of spatially confined targets in a volume of at least 100 × 150 × 300 µm3. We then apply such approach to the optogenetic stimulation of multiple neurons simultaneously in vivo in mice. Our work paves the way for an all-optical investigation of neural circuits in previously inaccessible brain areas.
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50
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Zhao J, Peysokhan M, Antonio-Lopez JE, Sun Y, Abaie B, Mafi A, Amezcua Correa R, Pang S, Schülzgen A. A path to high-quality imaging through disordered optical fibers: a review. APPLIED OPTICS 2019; 58:D50-D60. [PMID: 31044820 DOI: 10.1364/ao.58.000d50] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/03/2018] [Accepted: 03/07/2019] [Indexed: 06/09/2023]
Abstract
In this paper, we review recent progress in disordered optical fiber featuring transverse Anderson localization and its applications for imaging. Anderson localizing optical fiber has a transversely random but longitudinally uniform refractive index profile. The strong scattering from the transversely disordered refractive index profiles generates thousands of guiding modes that are spatially isolated and mainly demonstrate single-mode properties. By making use of these beam transmission channels, robust and high-fidelity imaging transport can be realized. The first disordered optical fiber of this type, the polymer Anderson localizing optical fiber, has been utilized to demonstrate better imaging performance than some of the commercial multicore fibers within a few centimeters transmission distance. To obtain longer transmission lengths and better imaging qualities, glass-air disordered optical fibers are desirable due to their lower loss and larger refractive index contrast. Recently developed high air-filling fraction glass-air disordered fiber can provide bending-independent and high-quality image transport through a meter-long transmission distance. By integrating a deep-learning algorithm with glass-air disordered fiber, a fully flexible, artifact-free, and lensless fiber imaging system is demonstrated, with potential benefits for biomedical and clinical applications. Future research will focus on optimizing structural parameters of disordered optical fiber as well as developing more efficient deep-learning algorithms to further improve the imaging performance.
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