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Lewis CM, Hoffmann A, Helmchen F. Linking brain activity across scales with simultaneous opto- and electrophysiology. NEUROPHOTONICS 2024; 11:033403. [PMID: 37662552 PMCID: PMC10472193 DOI: 10.1117/1.nph.11.3.033403] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/12/2023] [Revised: 07/19/2023] [Accepted: 07/24/2023] [Indexed: 09/05/2023]
Abstract
The brain enables adaptive behavior via the dynamic coordination of diverse neuronal signals across spatial and temporal scales: from fast action potential patterns in microcircuits to slower patterns of distributed activity in brain-wide networks. Understanding principles of multiscale dynamics requires simultaneous monitoring of signals in multiple, distributed network nodes. Combining optical and electrical recordings of brain activity is promising for collecting data across multiple scales and can reveal aspects of coordinated dynamics invisible to standard, single-modality approaches. We review recent progress in combining opto- and electrophysiology, focusing on mouse studies that shed new light on the function of single neurons by embedding their activity in the context of brain-wide activity patterns. Optical and electrical readouts can be tailored to desired scales to tackle specific questions. For example, fast dynamics in single cells or local populations recorded with multi-electrode arrays can be related to simultaneously acquired optical signals that report activity in specified subpopulations of neurons, in non-neuronal cells, or in neuromodulatory pathways. Conversely, two-photon imaging can be used to densely monitor activity in local circuits while sampling electrical activity in distant brain areas at the same time. The refinement of combined approaches will continue to reveal previously inaccessible and under-appreciated aspects of coordinated brain activity.
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Affiliation(s)
| | - Adrian Hoffmann
- University of Zurich, Brain Research Institute, Zurich, Switzerland
- University of Zurich, Neuroscience Center Zurich, Zurich, Switzerland
| | - Fritjof Helmchen
- University of Zurich, Brain Research Institute, Zurich, Switzerland
- University of Zurich, Neuroscience Center Zurich, Zurich, Switzerland
- University of Zurich, University Research Priority Program, Adaptive Brain Circuits in Development and Learning, Zurich, Switzerland
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2
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Amitonova LV. Multimode fiber endoscopes for computational brain imaging. NEUROPHOTONICS 2024; 11:S11509. [PMID: 38450327 PMCID: PMC10917391 DOI: 10.1117/1.nph.11.s1.s11509] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/01/2023] [Revised: 01/08/2024] [Accepted: 01/31/2024] [Indexed: 03/08/2024]
Abstract
Advances in imaging tools have always been a pivotal driver for new discoveries in neuroscience. An ability to visualize neurons and subcellular structures deep within the brain of a freely behaving animal is integral to our understanding of the relationship between neural activity and higher cognitive functions. However, fast high-resolution imaging is limited to sub-surface brain regions and generally requires head fixation of the animal under the microscope. Developing new approaches to address these challenges is critical. The last decades have seen rapid progress in minimally invasive endo-microscopy techniques based on bare optical fibers. A single multimode fiber can be used to penetrate deep into the brain without causing significant damage to the overlying structures and provide high-resolution imaging. Here, we discuss how the full potential of high-speed super-resolution fiber endoscopy can be realized by a holistic approach that combines fiber optics, light shaping, and advanced computational algorithms. The recent progress opens up new avenues for minimally invasive deep brain studies in freely behaving mice.
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Affiliation(s)
- Lyubov V. Amitonova
- Vrije Universiteit Amsterdam, Department of Physics and Astronomy, Amsterdam, The Netherlands
- Advanced Research Center for Nanolithography, Amsterdam, The Netherlands
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3
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Lorca-Cámara A, Blot FGC, Accanto N. Recent advances in light patterned optogenetic photostimulation in freely moving mice. NEUROPHOTONICS 2024; 11:S11508. [PMID: 38404422 PMCID: PMC10885521 DOI: 10.1117/1.nph.11.s1.s11508] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/07/2023] [Revised: 01/24/2024] [Accepted: 01/30/2024] [Indexed: 02/27/2024]
Abstract
Optogenetics opened the door to a new era of neuroscience. New optical developments are under way to enable high-resolution neuronal activity imaging and selective photostimulation of neuronal ensembles in freely moving animals. These advancements could allow researchers to interrogate, with cellular precision, functionally relevant neuronal circuits in the framework of naturalistic brain activity. We provide an overview of the current state-of-the-art of imaging and photostimulation in freely moving rodents and present a road map for future optical and engineering developments toward miniaturized microscopes that could reach beyond the currently existing systems.
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Affiliation(s)
| | - François G C Blot
- Sorbonne Université, INSERM, CNRS, Institut de la Vision, Paris, France
| | - Nicolò Accanto
- Sorbonne Université, INSERM, CNRS, Institut de la Vision, Paris, France
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4
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Ding P, Wahn H, Chen FD, Li J, Mu X, Stalmashonak A, Luo X, Lo GQ, Poon JKS, Sacher WD. Photonic neural probe enabled microendoscopes for light-sheet light-field computational fluorescence brain imaging. NEUROPHOTONICS 2024; 11:S11503. [PMID: 38322247 PMCID: PMC10846542 DOI: 10.1117/1.nph.11.s1.s11503] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/08/2023] [Revised: 12/14/2023] [Accepted: 12/20/2023] [Indexed: 02/08/2024]
Abstract
Significance Light-sheet fluorescence microscopy is widely used for high-speed, high-contrast, volumetric imaging. Application of this technique to in vivo brain imaging in non-transparent organisms has been limited by the geometric constraints of conventional light-sheet microscopes, which require orthogonal fluorescence excitation and collection objectives. We have recently demonstrated implantable photonic neural probes that emit addressable light sheets at depth in brain tissue, miniaturizing the excitation optics. Here, we propose a microendoscope consisting of a light-sheet neural probe packaged together with miniaturized fluorescence collection optics based on an image fiber bundle for lensless, light-field, computational fluorescence imaging. Aim Foundry-fabricated, silicon-based, light-sheet neural probes can be packaged together with commercially available image fiber bundles to form microendoscopes for light-sheet light-field fluorescence imaging at depth in brain tissue. Approach Prototype microendoscopes were developed using light-sheet neural probes with five addressable sheets and image fiber bundles. Fluorescence imaging with the microendoscopes was tested with fluorescent beads suspended in agarose and fixed mouse brain tissue. Results Volumetric light-sheet light-field fluorescence imaging was demonstrated using the microendoscopes. Increased imaging depth and enhanced reconstruction accuracy were observed relative to epi-illumination light-field imaging using only a fiber bundle. Conclusions Our work offers a solution toward volumetric fluorescence imaging of brain tissue with a compact size and high contrast. The proof-of-concept demonstrations herein illustrate the operating principles and methods of the imaging approach, providing a foundation for future investigations of photonic neural probe enabled microendoscopes for deep-brain fluorescence imaging in vivo.
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Affiliation(s)
- Peisheng Ding
- Max Planck Institute of Microstructure Physics, Halle, Germany
- University of Toronto, Department of Electrical and Computer Engineering, Toronto, Ontario, Canada
| | - Hannes Wahn
- Max Planck Institute of Microstructure Physics, Halle, Germany
| | - Fu-Der Chen
- Max Planck Institute of Microstructure Physics, Halle, Germany
- University of Toronto, Department of Electrical and Computer Engineering, Toronto, Ontario, Canada
- Max Planck-University of Toronto Centre for Neural Science and Technology, Toronto, Ontario, Canada
| | - Jianfeng Li
- Max Planck Institute of Microstructure Physics, Halle, Germany
- Max Planck-University of Toronto Centre for Neural Science and Technology, Toronto, Ontario, Canada
| | - Xin Mu
- Max Planck Institute of Microstructure Physics, Halle, Germany
- University of Toronto, Department of Electrical and Computer Engineering, Toronto, Ontario, Canada
- Max Planck-University of Toronto Centre for Neural Science and Technology, Toronto, Ontario, Canada
| | | | | | | | - Joyce K. S. Poon
- Max Planck Institute of Microstructure Physics, Halle, Germany
- University of Toronto, Department of Electrical and Computer Engineering, Toronto, Ontario, Canada
- Max Planck-University of Toronto Centre for Neural Science and Technology, Toronto, Ontario, Canada
| | - Wesley D. Sacher
- Max Planck Institute of Microstructure Physics, Halle, Germany
- Max Planck-University of Toronto Centre for Neural Science and Technology, Toronto, Ontario, Canada
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5
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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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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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Hira R. Closed-loop experiments and brain machine interfaces with multiphoton microscopy. NEUROPHOTONICS 2024; 11:033405. [PMID: 38375331 PMCID: PMC10876015 DOI: 10.1117/1.nph.11.3.033405] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/24/2023] [Revised: 01/22/2024] [Accepted: 01/29/2024] [Indexed: 02/21/2024]
Abstract
In the field of neuroscience, the importance of constructing closed-loop experimental systems has increased in conjunction with technological advances in measuring and controlling neural activity in live animals. We provide an overview of recent technological advances in the field, focusing on closed-loop experimental systems where multiphoton microscopy-the only method capable of recording and controlling targeted population activity of neurons at a single-cell resolution in vivo-works through real-time feedback. Specifically, we present some examples of brain machine interfaces (BMIs) using in vivo two-photon calcium imaging and discuss applications of two-photon optogenetic stimulation and adaptive optics to real-time BMIs. We also consider conditions for realizing future optical BMIs at the synaptic level, and their possible roles in understanding the computational principles of the brain.
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Affiliation(s)
- Riichiro Hira
- Tokyo Medical and Dental University, Graduate School of Medical and Dental Sciences, Department of Physiology and Cell Biology, Tokyo, Japan
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8
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Mizuta K, Sato M. Multiphoton imaging of hippocampal neural circuits: techniques and biological insights into region-, cell-type-, and pathway-specific functions. NEUROPHOTONICS 2024; 11:033406. [PMID: 38464393 PMCID: PMC10923542 DOI: 10.1117/1.nph.11.3.033406] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/25/2023] [Revised: 01/31/2024] [Accepted: 02/06/2024] [Indexed: 03/12/2024]
Abstract
Significance The function of the hippocampus in behavior and cognition has long been studied primarily through electrophysiological recordings from freely moving rodents. However, the application of optical recording methods, particularly multiphoton fluorescence microscopy, in the last decade or two has dramatically advanced our understanding of hippocampal function. This article provides a comprehensive overview of techniques and biological findings obtained from multiphoton imaging of hippocampal neural circuits. Aim This review aims to summarize and discuss the recent technical advances in multiphoton imaging of hippocampal neural circuits and the accumulated biological knowledge gained through this technology. Approach First, we provide a brief overview of various techniques of multiphoton imaging of the hippocampus and discuss its advantages, drawbacks, and associated key innovations and practices. Then, we review a large body of findings obtained through multiphoton imaging by region (CA1 and dentate gyrus), cell type (pyramidal neurons, inhibitory interneurons, and glial cells), and cellular compartment (dendrite and axon). Results Multiphoton imaging of the hippocampus is primarily performed under head-fixed conditions and can reveal detailed mechanisms of circuit operation owing to its high spatial resolution and specificity. As the hippocampus lies deep below the cortex, its imaging requires elaborate methods. These include imaging cannula implantation, microendoscopy, and the use of long-wavelength light sources. Although many studies have focused on the dorsal CA1 pyramidal cells, studies of other local and inter-areal circuitry elements have also helped provide a more comprehensive picture of the information processing performed by the hippocampal circuits. Imaging of circuit function in mouse models of Alzheimer's disease and other brain disorders such as autism spectrum disorder has also contributed greatly to our understanding of their pathophysiology. Conclusions Multiphoton imaging has revealed much regarding region-, cell-type-, and pathway-specific mechanisms in hippocampal function and dysfunction in health and disease. Future technological advances will allow further illustration of the operating principle of the hippocampal circuits via the large-scale, high-resolution, multimodal, and minimally invasive imaging.
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Affiliation(s)
- Kotaro Mizuta
- RIKEN BDR, Kobe, Japan
- New York University Abu Dhabi, Department of Biology, Abu Dhabi, United Arab Emirates
| | - Masaaki Sato
- Hokkaido University Graduate School of Medicine, Department of Neuropharmacology, Sapporo, Japan
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Broomer MC, Beacher NJ, Wang MW, Lin DT. Examining a punishment-related brain circuit with miniature fluorescence microscopes and deep learning. ADDICTION NEUROSCIENCE 2024; 11:100154. [PMID: 38680653 PMCID: PMC11044849 DOI: 10.1016/j.addicn.2024.100154] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/01/2024]
Abstract
In humans experiencing substance use disorder (SUD), abstinence from drug use is often motivated by a desire to avoid some undesirable consequence of further use: health effects, legal ramifications, etc. This process can be experimentally modeled in rodents by training and subsequently punishing an operant response in a context-induced reinstatement procedure. Understanding the biobehavioral mechanisms underlying punishment learning is critical to understanding both abstinence and relapse in individuals with SUD. To date, most investigations into the neural mechanisms of context-induced reinstatement following punishment have utilized discrete loss-of-function manipulations that do not capture ongoing changes in neural circuitry related to punishment-induced behavior change. Here, we describe a two-pronged approach to analyzing the biobehavioral mechanisms of punishment learning using miniature fluorescence microscopes and deep learning algorithms. We review recent advancements in both techniques and consider a target neural circuit.
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Affiliation(s)
- Matthew C. Broomer
- Intramural Research Program, National Institute on Drug Abuse, National Institutes of Health, 333 Cassell Drive, Baltimore, MD 21224, USA
| | - Nicholas J. Beacher
- Intramural Research Program, National Institute on Drug Abuse, National Institutes of Health, 333 Cassell Drive, Baltimore, MD 21224, USA
| | - Michael W. Wang
- Intramural Research Program, National Institute on Drug Abuse, National Institutes of Health, 333 Cassell Drive, Baltimore, MD 21224, USA
| | - Da-Ting Lin
- Intramural Research Program, National Institute on Drug Abuse, National Institutes of Health, 333 Cassell Drive, Baltimore, MD 21224, USA
- The Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, 725 N. Wolfe Street, Baltimore, MD 21205, USA
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Fenton AA. Remapping revisited: how the hippocampus represents different spaces. Nat Rev Neurosci 2024; 25:428-448. [PMID: 38714834 DOI: 10.1038/s41583-024-00817-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/04/2024] [Indexed: 05/25/2024]
Abstract
The representation of distinct spaces by hippocampal place cells has been linked to changes in their place fields (the locations in the environment where the place cells discharge strongly), a phenomenon that has been termed 'remapping'. Remapping has been assumed to be accompanied by the reorganization of subsecond cofiring relationships among the place cells, potentially maximizing hippocampal information coding capacity. However, several observations challenge this standard view. For example, place cells exhibit mixed selectivity, encode non-positional variables, can have multiple place fields and exhibit unreliable discharge in fixed environments. Furthermore, recent evidence suggests that, when measured at subsecond timescales, the moment-to-moment cofiring of a pair of cells in one environment is remarkably similar in another environment, despite remapping. Here, I propose that remapping is a misnomer for the changes in place fields across environments and suggest instead that internally organized manifold representations of hippocampal activity are actively registered to different environments to enable navigation, promote memory and organize knowledge.
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Affiliation(s)
- André A Fenton
- Center for Neural Science, New York University, New York, NY, USA.
- Neuroscience Institute at the NYU Langone Medical Center, New York, NY, USA.
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Brooks FP, Davis HC, Wong-Campos JD, Cohen AE. Optical constraints on two-photon voltage imaging. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.11.18.567441. [PMID: 38014011 PMCID: PMC10680948 DOI: 10.1101/2023.11.18.567441] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/29/2023]
Abstract
Significance Genetically encoded voltage indicators (GEVIs) are a valuable tool for studying neural circuits in vivo, but the relative merits and limitations of one-photon (1P) vs. two-photon (2P) voltage imaging are not well characterized. Aim We consider the optical and biophysical constraints particular to 1P and 2P voltage imaging and compare the imaging properties of commonly used GEVIs under 1P and 2P excitation. Approach We measure brightness and voltage sensitivity of voltage indicators from commonly used classes under 1P and 2P illumination. We also measure the decrease in fluorescence as a function of depth in mouse brain. We develop a simple model of the number of measurable cells as a function of reporter properties, imaging parameters, and desired signal-to-noise ratio (SNR). We then discuss how the performance of voltage imaging would be affected by sensor improvements and by recently introduced advanced imaging modalities. Results Compared to 1P excitation, 2P excitation requires ~10 4 -fold more illumination power per cell to produce similar photon count rates. For voltage imaging with JEDI-2P in mouse cortex with a target SNR of 10 (spike height:baseline shot noise), a measurement bandwidth of 1 kHz, a thermally limited laser power of 200 mW, and an imaging depth of > 300 μm, 2P voltage imaging using an 80 MHz source can record from no more 12 cells simultaneously. Conclusions Due to the stringent photon-count requirements of voltage imaging and the modest voltage sensitivity of existing reporters, 2P voltage imaging in vivo faces a stringent tradeoff between shot noise and tissue photodamage. 2P imaging of hundreds of neurons with high SNR at depth > 300 μm will require either major improvements in 2P GEVIs or qualitatively new approaches to imaging.
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Manley J, Lu S, Barber K, Demas J, Kim H, Meyer D, Traub FM, Vaziri A. Simultaneous, cortex-wide dynamics of up to 1 million neurons reveal unbounded scaling of dimensionality with neuron number. Neuron 2024; 112:1694-1709.e5. [PMID: 38452763 PMCID: PMC11098699 DOI: 10.1016/j.neuron.2024.02.011] [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: 11/23/2022] [Revised: 05/18/2023] [Accepted: 02/14/2024] [Indexed: 03/09/2024]
Abstract
The brain's remarkable properties arise from the collective activity of millions of neurons. Widespread application of dimensionality reduction to multi-neuron recordings implies that neural dynamics can be approximated by low-dimensional "latent" signals reflecting neural computations. However, can such low-dimensional representations truly explain the vast range of brain activity, and if not, what is the appropriate resolution and scale of recording to capture them? Imaging neural activity at cellular resolution and near-simultaneously across the mouse cortex, we demonstrate an unbounded scaling of dimensionality with neuron number in populations up to 1 million neurons. Although half of the neural variance is contained within sixteen dimensions correlated with behavior, our discovered scaling of dimensionality corresponds to an ever-increasing number of neuronal ensembles without immediate behavioral or sensory correlates. The activity patterns underlying these higher dimensions are fine grained and cortex wide, highlighting that large-scale, cellular-resolution recording is required to uncover the full substrates of neuronal computations.
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Affiliation(s)
- Jason Manley
- Laboratory of Neurotechnology and Biophysics, The Rockefeller University, New York, NY 10065, USA; The Kavli Neural Systems Institute, The Rockefeller University, New York, NY 10065, USA
| | - Sihao Lu
- Laboratory of Neurotechnology and Biophysics, The Rockefeller University, New York, NY 10065, USA
| | - Kevin Barber
- Laboratory of Neurotechnology and Biophysics, The Rockefeller University, New York, NY 10065, USA
| | - Jeffrey Demas
- Laboratory of Neurotechnology and Biophysics, The Rockefeller University, New York, NY 10065, USA; The Kavli Neural Systems Institute, The Rockefeller University, New York, NY 10065, USA
| | - Hyewon Kim
- Laboratory of Neurotechnology and Biophysics, The Rockefeller University, New York, NY 10065, USA
| | - David Meyer
- Laboratory of Neurotechnology and Biophysics, The Rockefeller University, New York, NY 10065, USA
| | - Francisca Martínez Traub
- Laboratory of Neurotechnology and Biophysics, The Rockefeller University, New York, NY 10065, USA
| | - Alipasha Vaziri
- Laboratory of Neurotechnology and Biophysics, The Rockefeller University, New York, NY 10065, USA; The Kavli Neural Systems Institute, The Rockefeller University, New York, NY 10065, USA.
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Seenivasan P, Basak R, Narayanan R. Cross-strata co-occurrence of ripples with theta-frequency oscillations in the hippocampus of foraging rats. J Physiol 2024; 602:2315-2341. [PMID: 38654581 PMCID: PMC7615956 DOI: 10.1113/jp284629] [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: 03/02/2023] [Accepted: 04/04/2024] [Indexed: 04/26/2024] Open
Abstract
Brain rhythms have been postulated to play central roles in animal cognition. A prominently reported dichotomy of hippocampal rhythms links theta-frequency oscillations (4-12 Hz) and ripples (120-250 Hz) exclusively to preparatory and consummatory behaviours, respectively. However, because of the differential power expression of these two signals across hippocampal strata, such exclusivity requires validation through analyses of simultaneous multi-strata recordings. We assessed co-occurrence of theta-frequency oscillations with ripples in multi-channel recordings of extracellular potentials across hippocampal strata from foraging rats. We detected all ripple events from an identified stratum pyramidale (SP) channel. We then defined theta epochs based on theta oscillations detected from the stratum lacunosum-moleculare (SLM) or the stratum radiatum (SR). We found ∼20% of ripple events (in SP) to co-occur with theta epochs identified from SR/SLM channels, defined here as theta ripples. Strikingly, when theta epochs were instead identified from the SP channel, such co-occurrences were significantly reduced because of a progressive reduction in theta power along the SLM-SR-SP axis. Behaviourally, we found most theta ripples to occur during immobile periods, with comparable theta power during exploratory and immobile theta epochs. Furthermore, the progressive reduction in theta power along the SLM-SR-SP axis was common to exploratory and immobile periods. Finally, we found a strong theta-phase preference of theta ripples within the fourth quadrant [3π/2 - 2π] of the associated theta oscillation. The prevalence of theta ripples expands the potential roles of ripple-frequency oscillations to span the continuum of encoding, retrieval and consolidation, achieved through interactions with theta oscillations. KEY POINTS: The brain manifests oscillations in recorded electrical potentials, with different frequencies of oscillation associated with distinct behavioural states. A prominently reported dichotomy assigns theta-frequency oscillations (4-12 Hz) and ripples (120-250 Hz) recorded in the hippocampus to be exclusively associated with preparatory and consummatory behaviours, respectively. Our multi-strata recordings from the rodent hippocampus coupled with cross-strata analyses provide direct quantitative evidence for the occurrence of ripple events nested within theta oscillations. These results highlight the need for an analysis pipeline that explicitly accounts for the specific strata where individual oscillatory power is high, in analysing simultaneously recorded data from multiple strata. Our observations open avenues for investigations involving cross-strata interactions between theta oscillations and ripples across different behavioural states.
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Affiliation(s)
- Pavithraa Seenivasan
- Cellular Neurophysiology Laboratory, Molecular Biophysics Unit, Indian Institute of Science, Bangalore, India
| | - Reshma Basak
- Cellular Neurophysiology Laboratory, Molecular Biophysics Unit, Indian Institute of Science, Bangalore, India
| | - Rishikesh Narayanan
- Cellular Neurophysiology Laboratory, Molecular Biophysics Unit, Indian Institute of Science, Bangalore, India
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Sprague DY, Rusch K, Dunn RL, Borchardt JM, Bubnis G, Chiu GC, Wen C, Suzuki R, Chaudhary S, Dichter B, Ly R, Onami S, Lu H, Kimura K, Yemini EI, Kato S. Unifying community-wide whole-brain imaging datasets enables robust automated neuron identification and reveals determinants of neuron positioning in C. elegans. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.28.591397. [PMID: 38746302 PMCID: PMC11092512 DOI: 10.1101/2024.04.28.591397] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2024]
Abstract
We develop a data harmonization approach for C. elegans volumetric microscopy data, still or video, consisting of a standardized format, data pre-processing techniques, and a set of human-in-the-loop machine learning based analysis software tools. We unify a diverse collection of 118 whole-brain neural activity imaging datasets from 5 labs, storing these and accompanying tools in an online repository called WormID ( wormid.org ). We use this repository to generate a statistical atlas that, for the first time, enables accurate automated cellular identification that generalizes across labs, approaching human performance in some cases. We mine this repository to identify factors that influence the developmental positioning of neurons. To facilitate communal use of this repository, we created open-source software, code, web-based tools, and tutorials to explore and curate datasets for contribution to the scientific community. This repository provides a growing resource for experimentalists, theorists, and toolmakers to investigate neuroanatomical organization and neural activity across diverse experimental paradigms, develop and benchmark algorithms for automated neuron detection, segmentation, cell identification, tracking, and activity extraction, and inform models of neurobiological development and function.
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15
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Chen FD, Sharma A, Roszko DA, Xue T, Mu X, Luo X, Chua H, Lo PGQ, Sacher WD, Poon JKS. Development of wafer-scale multifunctional nanophotonic neural probes for brain activity mapping. LAB ON A CHIP 2024; 24:2397-2417. [PMID: 38623840 DOI: 10.1039/d3lc00931a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/17/2024]
Abstract
Optical techniques, such as optogenetic stimulation and functional fluorescence imaging, have been revolutionary for neuroscience by enabling neural circuit analysis with cell-type specificity. To probe deep brain regions, implantable light sources are crucial. Silicon photonics, commonly used for data communications, shows great promise in creating implantable devices with complex optical systems in a compact form factor compatible with high volume manufacturing practices. This article reviews recent developments of wafer-scale multifunctional nanophotonic neural probes. The probes can be realized on 200 or 300 mm wafers in commercial foundries and integrate light emitters for photostimulation, microelectrodes for electrophysiological recording, and microfluidic channels for chemical delivery and sampling. By integrating active optical devices to the probes, denser emitter arrays, enhanced on-chip biosensing, and increased ease of use may be realized. Silicon photonics technology makes possible highly versatile implantable neural probes that can transform neuroscience experiments.
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Affiliation(s)
- Fu Der Chen
- Max Planck Institute of Microstructure Physics, Weinberg 2, 06120 Halle, Germany.
- Department of Electrical and Computer Engineering, University of Toronto, 10 King's College Road, Toronto, Ontario M5S 3G4, Canada
| | - Ankita Sharma
- Max Planck Institute of Microstructure Physics, Weinberg 2, 06120 Halle, Germany.
- Department of Electrical and Computer Engineering, University of Toronto, 10 King's College Road, Toronto, Ontario M5S 3G4, Canada
| | - David A Roszko
- Max Planck Institute of Microstructure Physics, Weinberg 2, 06120 Halle, Germany.
- Department of Electrical and Computer Engineering, University of Toronto, 10 King's College Road, Toronto, Ontario M5S 3G4, Canada
| | - Tianyuan Xue
- Max Planck Institute of Microstructure Physics, Weinberg 2, 06120 Halle, Germany.
- Department of Electrical and Computer Engineering, University of Toronto, 10 King's College Road, Toronto, Ontario M5S 3G4, Canada
| | - Xin Mu
- Max Planck Institute of Microstructure Physics, Weinberg 2, 06120 Halle, Germany.
- Department of Electrical and Computer Engineering, University of Toronto, 10 King's College Road, Toronto, Ontario M5S 3G4, Canada
| | - Xianshu Luo
- Advanced Micro Foundry Pte Ltd, 11 Science Park Road, Singapore Science Park II, 117685, Singapore
| | - Hongyao Chua
- Advanced Micro Foundry Pte Ltd, 11 Science Park Road, Singapore Science Park II, 117685, Singapore
| | - Patrick Guo-Qiang Lo
- Advanced Micro Foundry Pte Ltd, 11 Science Park Road, Singapore Science Park II, 117685, Singapore
| | - Wesley D Sacher
- Max Planck Institute of Microstructure Physics, Weinberg 2, 06120 Halle, Germany.
| | - Joyce K S Poon
- Max Planck Institute of Microstructure Physics, Weinberg 2, 06120 Halle, Germany.
- Department of Electrical and Computer Engineering, University of Toronto, 10 King's College Road, Toronto, Ontario M5S 3G4, Canada
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16
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Beshkov K, Fyhn M, Hafting T, Einevoll GT. Topological structure of population activity in mouse visual cortex encodes densely sampled stimulus rotations. iScience 2024; 27:109370. [PMID: 38523791 PMCID: PMC10959658 DOI: 10.1016/j.isci.2024.109370] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2023] [Revised: 10/06/2023] [Accepted: 02/26/2024] [Indexed: 03/26/2024] Open
Abstract
The primary visual cortex is one of the most well understood regions supporting the processing involved in sensory computation. Following the popularization of high-density neural recordings, it has been observed that the activity of large neural populations is often constrained to low dimensional manifolds. In this work, we quantify the structure of such neural manifolds in the visual cortex. We do this by analyzing publicly available two-photon optical recordings of mouse primary visual cortex in response to visual stimuli with a densely sampled rotation angle. Using a geodesic metric along with persistent homology, we discover that population activity in response to such stimuli generates a circular manifold, encoding the angle of rotation. Furthermore, we observe that this circular manifold is expressed differently in subpopulations of neurons with differing orientation and direction selectivity. Finally, we discuss some of the obstacles to reliably retrieving the truthful topology generated by a neural population.
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Affiliation(s)
- Kosio Beshkov
- Center for Integrative Neuroplasticity, Department of Bioscience, University of Oslo, Oslo, Norway
| | - Marianne Fyhn
- Center for Integrative Neuroplasticity, Department of Bioscience, University of Oslo, Oslo, Norway
| | - Torkel Hafting
- Center for Integrative Neuroplasticity, Department of Bioscience, University of Oslo, Oslo, Norway
- Institute of Basic Medical Sciences, University of Oslo, Oslo, Norway
| | - Gaute T. Einevoll
- Center for Integrative Neuroplasticity, Department of Bioscience, University of Oslo, Oslo, Norway
- Department of Physics, Norwegian University of Life Sciences, As, Norway
- Department of Physics, University of Oslo, Oslo, Norway
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17
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Wang Z, Yu J, Zhai M, Wang Z, Sheng K, Zhu Y, Wang T, Liu M, Wang L, Yan M, Zhang J, Xu Y, Wang X, Ma L, Hu W, Cheng H. System-level time computation and representation in the suprachiasmatic nucleus revealed by large-scale calcium imaging and machine learning. Cell Res 2024:10.1038/s41422-024-00956-x. [PMID: 38605178 DOI: 10.1038/s41422-024-00956-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Accepted: 03/28/2024] [Indexed: 04/13/2024] Open
Abstract
The suprachiasmatic nucleus (SCN) is the mammalian central circadian pacemaker with heterogeneous neurons acting in concert while each neuron harbors a self-sustained molecular clockwork. Nevertheless, how system-level SCN signals encode time of the day remains enigmatic. Here we show that population-level Ca2+ signals predict hourly time, via a group decision-making mechanism coupled with a spatially modular time feature representation in the SCN. Specifically, we developed a high-speed dual-view two-photon microscope for volumetric Ca2+ imaging of up to 9000 GABAergic neurons in adult SCN slices, and leveraged machine learning methods to capture emergent properties from multiscale Ca2+ signals as a whole. We achieved hourly time prediction by polling random cohorts of SCN neurons, reaching 99.0% accuracy at a cohort size of 900. Further, we revealed that functional neuron subtypes identified by contrastive learning tend to aggregate separately in the SCN space, giving rise to bilaterally symmetrical ripple-like modular patterns. Individual modules represent distinctive time features, such that a module-specifically learned time predictor can also accurately decode hourly time from random polling of the same module. These findings open a new paradigm in deciphering the design principle of the biological clock at the system level.
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Affiliation(s)
- Zichen Wang
- National Biomedical Imaging Center, State Key Laboratory of Membrane Biology, Institute of Molecular Medicine, Peking-Tsinghua Center for Life Sciences, College of Future Technology, Peking University, Beijing, China
- Research Unit of Mitochondria in Brain Diseases, Chinese Academy of Medical Sciences, PKU-Nanjing Institute of Translational Medicine, Nanjing, Jiangsu, China
| | - Jing Yu
- National Biomedical Imaging Center, State Key Laboratory of Membrane Biology, Institute of Molecular Medicine, Peking-Tsinghua Center for Life Sciences, College of Future Technology, Peking University, Beijing, China
- Research Unit of Mitochondria in Brain Diseases, Chinese Academy of Medical Sciences, PKU-Nanjing Institute of Translational Medicine, Nanjing, Jiangsu, China
| | - Muyue Zhai
- National Biomedical Imaging Center, State Key Laboratory of Membrane Biology, Institute of Molecular Medicine, Peking-Tsinghua Center for Life Sciences, College of Future Technology, Peking University, Beijing, China
| | - Zehua Wang
- Wangxuan Institute of Computer Technology, Peking University, Beijing, China
- Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, China
| | - Kaiwen Sheng
- Beijing Academy of Artificial Intelligence, Beijing, China
- Department of Bioengineering, Stanford University, Stanford, CA, USA
| | - Yu Zhu
- Beijing Academy of Artificial Intelligence, Beijing, China
| | - Tianyu Wang
- National Biomedical Imaging Center, State Key Laboratory of Membrane Biology, Institute of Molecular Medicine, Peking-Tsinghua Center for Life Sciences, College of Future Technology, Peking University, Beijing, China
| | - Mianzhi Liu
- National Biomedical Imaging Center, State Key Laboratory of Membrane Biology, Institute of Molecular Medicine, Peking-Tsinghua Center for Life Sciences, College of Future Technology, Peking University, Beijing, China
| | - Lu Wang
- National Biomedical Imaging Center, State Key Laboratory of Membrane Biology, Institute of Molecular Medicine, Peking-Tsinghua Center for Life Sciences, College of Future Technology, Peking University, Beijing, China
| | - Miao Yan
- National Biomedical Imaging Center, State Key Laboratory of Membrane Biology, Institute of Molecular Medicine, Peking-Tsinghua Center for Life Sciences, College of Future Technology, Peking University, Beijing, China
| | - Jue Zhang
- Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, China
- College of Engineering, Peking University, Beijing, China
| | - Ying Xu
- Jiangsu Key Laboratory of Neuropsychiatric Diseases and Cambridge-Su Genomic Resource Center, Medical School of Soochow University, Suzhou, Jiangsu, China
| | - Xianhua Wang
- National Biomedical Imaging Center, State Key Laboratory of Membrane Biology, Institute of Molecular Medicine, Peking-Tsinghua Center for Life Sciences, College of Future Technology, Peking University, Beijing, China
- Research Unit of Mitochondria in Brain Diseases, Chinese Academy of Medical Sciences, PKU-Nanjing Institute of Translational Medicine, Nanjing, Jiangsu, China
| | - Lei Ma
- National Biomedical Imaging Center, State Key Laboratory of Membrane Biology, Institute of Molecular Medicine, Peking-Tsinghua Center for Life Sciences, College of Future Technology, Peking University, Beijing, China.
- Beijing Academy of Artificial Intelligence, Beijing, China.
| | - Wei Hu
- Wangxuan Institute of Computer Technology, Peking University, Beijing, China.
| | - Heping Cheng
- National Biomedical Imaging Center, State Key Laboratory of Membrane Biology, Institute of Molecular Medicine, Peking-Tsinghua Center for Life Sciences, College of Future Technology, Peking University, Beijing, China.
- Research Unit of Mitochondria in Brain Diseases, Chinese Academy of Medical Sciences, PKU-Nanjing Institute of Translational Medicine, Nanjing, Jiangsu, China.
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18
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Celinskis D, Black CJ, Murphy J, Barrios-Anderson A, Friedman NG, Shaner NC, Saab CY, Gomez-Ramirez M, Borton DA, Moore CI. Toward a brighter constellation: multiorgan neuroimaging of neural and vascular dynamics in the spinal cord and brain. NEUROPHOTONICS 2024; 11:024209. [PMID: 38725801 PMCID: PMC11079446 DOI: 10.1117/1.nph.11.2.024209] [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: 12/05/2023] [Revised: 03/18/2024] [Accepted: 03/19/2024] [Indexed: 05/12/2024]
Abstract
Significance Pain comprises a complex interaction between motor action and somatosensation that is dependent on dynamic interactions between the brain and spinal cord. This makes understanding pain particularly challenging as it involves rich interactions between many circuits (e.g., neural and vascular) and signaling cascades throughout the body. As such, experimentation on a single region may lead to an incomplete and potentially incorrect understanding of crucial underlying mechanisms. Aim We aimed to develop and validate tools to enable detailed and extended observation of neural and vascular activity in the brain and spinal cord. The first key set of innovations was targeted to developing novel imaging hardware that addresses the many challenges of multisite imaging. The second key set of innovations was targeted to enabling bioluminescent (BL) imaging, as this approach can address limitations of fluorescent microscopy including photobleaching, phototoxicity, and decreased resolution due to scattering of excitation signals. Approach We designed 3D-printed brain and spinal cord implants to enable effective surgical implantations and optical access with wearable miniscopes or an open window (e.g., for one- or two-photon microscopy or optogenetic stimulation). We also tested the viability for BL imaging and developed a novel modified miniscope optimized for these signals (BLmini). Results We describe "universal" implants for acute and chronic simultaneous brain-spinal cord imaging and optical stimulation. We further describe successful imaging of BL signals in both foci and a new miniscope, the "BLmini," which has reduced weight, cost, and form-factor relative to standard wearable miniscopes. Conclusions The combination of 3D-printed implants, advanced imaging tools, and bioluminescence imaging techniques offers a coalition of methods for understanding spinal cord-brain interactions. Our work has the potential for use in future research into neuropathic pain and other sensory disorders and motor behavior.
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Affiliation(s)
- Dmitrijs Celinskis
- Carney Institute for Brain Science, Providence, Rhode Island, United States
| | | | - Jeremy Murphy
- Carney Institute for Brain Science, Providence, Rhode Island, United States
| | | | - Nina G. Friedman
- Carney Institute for Brain Science, Providence, Rhode Island, United States
| | - Nathan C. Shaner
- University of California San Diego, School of Medicine, La Jolla, California, United States
| | - Carl Y. Saab
- Cleveland Clinic Lerner Research Institute, Neurological Institute, Department of Biomedical Engineering, Cleveland, Ohio, United States
| | - Manuel Gomez-Ramirez
- University of Rochester, School of Arts and Sciences, Rochester, New York, United States
| | - David A. Borton
- Carney Institute for Brain Science, Providence, Rhode Island, United States
- Brown University, School of Engineering, Providence, Rhode Island, United States
- Center for Neurorestoration and Neurotechnology, Providence VA Medical Center, Providence, Rhode Island, United States
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19
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Kopsick JD, Kilgore JA, Adam GC, Ascoli GA. Formation and Retrieval of Cell Assemblies in a Biologically Realistic Spiking Neural Network Model of Area CA3 in the Mouse Hippocampus. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.27.586909. [PMID: 38585941 PMCID: PMC10996657 DOI: 10.1101/2024.03.27.586909] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/09/2024]
Abstract
The hippocampal formation is critical for episodic memory, with area Cornu Ammonis 3 (CA3) a necessary substrate for auto-associative pattern completion. Recent theoretical and experimental evidence suggests that the formation and retrieval of cell assemblies enable these functions. Yet, how cell assemblies are formed and retrieved in a full-scale spiking neural network (SNN) of CA3 that incorporates the observed diversity of neurons and connections within this circuit is not well understood. Here, we demonstrate that a data-driven SNN model quantitatively reflecting the neuron type-specific population sizes, intrinsic electrophysiology, connectivity statistics, synaptic signaling, and long-term plasticity of the mouse CA3 is capable of robust auto-association and pattern completion via cell assemblies. Our results show that a broad range of assembly sizes could successfully and systematically retrieve patterns from heavily incomplete or corrupted cues after a limited number of presentations. Furthermore, performance was robust with respect to partial overlap of assemblies through shared cells, substantially enhancing memory capacity. These novel findings provide computational evidence that the specific biological properties of the CA3 circuit produce an effective neural substrate for associative learning in the mammalian brain.
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Affiliation(s)
- Jeffrey D. Kopsick
- Center for Neural Informatics, Structures, & Plasticity, College of Engineering and Computing, George Mason University, Fairfax, VA, United States
- Interdisciplinary Program in Neuroscience, College of Science, George Mason University, Fairfax, VA, United States
| | - Joseph A. Kilgore
- Department of Electrical and Computer Engineering, George Washington University, Washington, D.C., United States
| | - Gina C. Adam
- Department of Electrical and Computer Engineering, George Washington University, Washington, D.C., United States
| | - Giorgio A. Ascoli
- Center for Neural Informatics, Structures, & Plasticity, College of Engineering and Computing, George Mason University, Fairfax, VA, United States
- Interdisciplinary Program in Neuroscience, College of Science, George Mason University, Fairfax, VA, United States
- Bioengineering Department, College of Engineering and Computing, George Mason University, Fairfax, VA, United States
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20
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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. ARXIV 2024:arXiv:2403.14809v1. [PMID: 38562443 PMCID: PMC10984001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Subscribe] [Scholar Register] [Indexed: 04/04/2024]
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
- Laboratoire Kastler Brossel, ENS-Université PSL, CNRS, Sorbonne Université, Collège de France, 24 rue Lhomond, 75005 Paris, France
| | - Caio Vaz Rimoli
- Laboratoire Kastler Brossel, ENS-Université PSL, CNRS, Sorbonne Université, Collège de France, 24 rue Lhomond, 75005 Paris, France
- Institut de Biologie de l'ENS (IBENS), École Normale Supérieure, CNRS, INSERM, Université PSL, Paris, France
| | - Walther Akemann
- Institut de Biologie de l'ENS (IBENS), École Normale Supérieure, CNRS, INSERM, Université PSL, Paris, France
| | - Cathie Ventalon
- Institut de Biologie de l'ENS (IBENS), École Normale Supérieure, CNRS, INSERM, Université PSL, Paris, France
| | - Laurent Bourdieu
- Institut de Biologie de l'ENS (IBENS), École Normale Supérieure, CNRS, INSERM, Université PSL, Paris, France
| | - Sylvain Gigan
- Laboratoire Kastler Brossel, ENS-Université PSL, CNRS, Sorbonne Université, Collège de France, 24 rue Lhomond, 75005 Paris, France
| | - Hilton B de Aguiar
- Laboratoire Kastler Brossel, ENS-Université PSL, CNRS, Sorbonne Université, Collège de France, 24 rue Lhomond, 75005 Paris, France
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21
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Beetz MJ. A perspective on neuroethology: what the past teaches us about the future of neuroethology. J Comp Physiol A Neuroethol Sens Neural Behav Physiol 2024; 210:325-346. [PMID: 38411712 PMCID: PMC10995053 DOI: 10.1007/s00359-024-01695-5] [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: 12/13/2023] [Revised: 02/12/2024] [Accepted: 02/13/2024] [Indexed: 02/28/2024]
Abstract
For 100 years, the Journal of Comparative Physiology-A has significantly supported research in the field of neuroethology. The celebration of the journal's centennial is a great time point to appreciate the recent progress in neuroethology and to discuss possible avenues of the field. Animal behavior is the main source of inspiration for neuroethologists. This is illustrated by the huge diversity of investigated behaviors and species. To explain behavior at a mechanistic level, neuroethologists combine neuroscientific approaches with sophisticated behavioral analysis. The rapid technological progress in neuroscience makes neuroethology a highly dynamic and exciting field of research. To summarize the recent scientific progress in neuroethology, I went through all abstracts of the last six International Congresses for Neuroethology (ICNs 2010-2022) and categorized them based on the sensory modalities, experimental model species, and research topics. This highlights the diversity of neuroethology and gives us a perspective on the field's scientific future. At the end, I highlight three research topics that may, among others, influence the future of neuroethology. I hope that sharing my roots may inspire other scientists to follow neuroethological approaches.
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Affiliation(s)
- M Jerome Beetz
- Zoology II, Biocenter, University of Würzburg, 97074, Würzburg, Germany.
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22
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Lai AT, Espinosa G, Wink GE, Angeloni CF, Dombeck DA, MacIver MA. A robot-rodent interaction arena with adjustable spatial complexity for ethologically relevant behavioral studies. Cell Rep 2024; 43:113671. [PMID: 38280195 DOI: 10.1016/j.celrep.2023.113671] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2023] [Revised: 10/19/2023] [Accepted: 12/26/2023] [Indexed: 01/29/2024] Open
Abstract
Outside of the laboratory, animals behave in spaces where they can transition between open areas and coverage as they interact with others. Replicating these conditions in the laboratory can be difficult to control and record. This has led to a dominance of relatively simple, static behavioral paradigms that reduce the ethological relevance of behaviors and may alter the engagement of cognitive processes such as planning and decision-making. Therefore, we developed a method for controllable, repeatable interactions with others in a reconfigurable space. Mice navigate a large honeycomb lattice of adjustable obstacles as they interact with an autonomous robot coupled to their actions. We illustrate the system using the robot as a pseudo-predator, delivering airpuffs to the mice. The combination of obstacles and a mobile threat elicits a diverse set of behaviors, such as increased path diversity, peeking, and baiting, providing a method to explore ethologically relevant behaviors in the laboratory.
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Affiliation(s)
- Alexander T Lai
- Department of Biomedical Engineering, Technological Institute E311, Northwestern University, 2145 Sheridan Road, Evanston, IL 60208, USA
| | - German Espinosa
- Department of Computer Science, Northwestern University, Seeley Mudd 3219, 2233 Tech Drive, Evanston, IL 60208, USA
| | - Gabrielle E Wink
- Department of Mechanical Engineering, Technological Institute B224, Northwestern University, 2145 Sheridan Road, Evanston, IL 60208, USA
| | - Christopher F Angeloni
- Department of Neurobiology, Northwestern University, Hogan 2-160, 2205 Tech Drive, Evanston, IL 60208, USA
| | - Daniel A Dombeck
- Department of Neurobiology, Northwestern University, Hogan 2-160, 2205 Tech Drive, Evanston, IL 60208, USA.
| | - Malcolm A MacIver
- Department of Biomedical Engineering, Technological Institute E311, Northwestern University, 2145 Sheridan Road, Evanston, IL 60208, USA; Department of Computer Science, Northwestern University, Seeley Mudd 3219, 2233 Tech Drive, Evanston, IL 60208, USA; Department of Mechanical Engineering, Technological Institute B224, Northwestern University, 2145 Sheridan Road, Evanston, IL 60208, USA; Department of Neurobiology, Northwestern University, Hogan 2-160, 2205 Tech Drive, Evanston, IL 60208, USA.
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23
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Li Y, Cheng Z, Wang C, Lin J, Jiang H, Cui M. Geometric transformation adaptive optics (GTAO) for volumetric deep brain imaging through gradient-index lenses. Nat Commun 2024; 15:1031. [PMID: 38310087 PMCID: PMC10838304 DOI: 10.1038/s41467-024-45434-5] [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: 07/27/2023] [Accepted: 01/22/2024] [Indexed: 02/05/2024] Open
Abstract
The advance of genetic function indicators has enabled the observation of neuronal activities at single-cell resolutions. A major challenge for the applications on mammalian brains is the limited optical access depth. Currently, the method of choice to access deep brain structures is to insert miniature optical components. Among these validated miniature optics, the gradient-index (GRIN) lens has been widely employed for its compactness and simplicity. However, due to strong fourth-order astigmatism, GRIN lenses suffer from a small imaging field of view, which severely limits the measurement throughput and success rate. To overcome these challenges, we developed geometric transformation adaptive optics (GTAO), which enables adaptable achromatic large-volume correction through GRIN lenses. We demonstrate its major advances through in vivo structural and functional imaging of mouse brains. The results suggest that GTAO can serve as a versatile solution to enable large-volume recording of deep brain structures and activities through GRIN lenses.
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Affiliation(s)
- Yuting Li
- School of Electrical and Computer Engineering, Purdue University, West Lafayette, IN, 47907, USA
- Bindley Bioscience Center, Purdue University, West Lafayette, IN, 47907, USA
| | - Zongyue Cheng
- School of Electrical and Computer Engineering, Purdue University, West Lafayette, IN, 47907, USA
- Bindley Bioscience Center, Purdue University, West Lafayette, IN, 47907, USA
| | - Chenmao Wang
- School of Electrical and Computer Engineering, Purdue University, West Lafayette, IN, 47907, USA
- Bindley Bioscience Center, Purdue University, West Lafayette, IN, 47907, USA
| | - Jianian Lin
- School of Electrical and Computer Engineering, Purdue University, West Lafayette, IN, 47907, USA
- Bindley Bioscience Center, Purdue University, West Lafayette, IN, 47907, USA
| | - Hehai Jiang
- School of Electrical and Computer Engineering, Purdue University, West Lafayette, IN, 47907, USA
- Bindley Bioscience Center, Purdue University, West Lafayette, IN, 47907, USA
| | - Meng Cui
- School of Electrical and Computer Engineering, Purdue University, West Lafayette, IN, 47907, USA.
- Bindley Bioscience Center, Purdue University, West Lafayette, IN, 47907, USA.
- Department of Biology, Purdue University, West Lafayette, IN, 47907, USA.
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24
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Masala N, Mittag M, Giovannetti EA, O'Neil DA, Distler F, Rupprecht P, Helmchen F, Yuste R, Fuhrmann M, Beck H, Wenzel M, Kelly T. Aberrant hippocampal Ca 2+ micro-waves following synapsin-dependent adeno-associated viral expression of Ca 2+ indicators. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.11.08.566169. [PMID: 37986838 PMCID: PMC10659308 DOI: 10.1101/2023.11.08.566169] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2023]
Abstract
Genetically encoded calcium indicators (GECIs) such as GCaMP are invaluable tools in neuroscience to monitor neuronal activity using optical imaging. The viral transduction of GECIs is commonly used to target expression to specific brain regions, can be conveniently used with any mouse strain of interest without the need for prior crossing with a GECI mouse line and avoids potential hazards due to the chronic expression of GECIs during development. A key requirement for monitoring neuronal activity with an indicator is that the indicator itself minimally affects activity. Here, using common adeno-associated viral (AAV) transduction procedures, we describe spatially confined aberrant Ca2+ micro-waves slowly travelling through the hippocampus following expression of GCaMP6, GCaMP7 or R-CaMP1.07 driven by the synapsin promoter with AAV-dependent gene transfer, in a titre-dependent fashion. Ca2+ micro-waves developed in hippocampal CA1 and CA3, but not dentate gyrus (DG) nor neocortex, were typically first observed at 4 weeks after viral transduction, and persisted up to at least 8 weeks. The phenomenon was robust, observed across laboratories with various experimenters and setups. Our results indicate that aberrant hippocampal Ca2+ micro-waves depend on the promoter and viral titre of the GECI, density of expression as well as the targeted brain region. We used an alternative viral transduction method of GCaMP which avoids this artifact. The results show that commonly used Ca2+-indicator AAV transduction procedures can produce artefactual Ca2+ responses. Our aim is to raise awareness in the field of these artefactual transduction-induced Ca2+ micro-waves and we provide a potential solution.
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Affiliation(s)
- Nicola Masala
- University of Bonn, Faculty of Medicine, Institute for Experimental Epileptology and Cognition Research (IEECR), Bonn, Germany
- University Hospital Bonn
- Department of Epileptology, University Hospital Bonn, Bonn, Germany
| | - Manuel Mittag
- Neuroimmunology and Imaging Group, German Center for Neurodegenerative Diseases (DZNE), Bonn, Germany
| | | | - Darik A O'Neil
- NeuroTechnology Center, Columbia University, New York, NY, USA
| | - Fabian Distler
- University of Bonn, Faculty of Medicine, Institute for Experimental Epileptology and Cognition Research (IEECR), Bonn, Germany
- University Hospital Bonn
| | - Peter Rupprecht
- Brain Research Institute, University of Zurich, Zurich, Switzerland
- Neuroscience Center Zurich, University of Zurich, Zurich, Switzerland
| | - Fritjof Helmchen
- Brain Research Institute, University of Zurich, Zurich, Switzerland
- Neuroscience Center Zurich, University of Zurich, Zurich, Switzerland
| | - Rafael Yuste
- NeuroTechnology Center, Columbia University, New York, NY, USA
| | - Martin Fuhrmann
- Neuroimmunology and Imaging Group, German Center for Neurodegenerative Diseases (DZNE), Bonn, Germany
| | - Heinz Beck
- University of Bonn, Faculty of Medicine, Institute for Experimental Epileptology and Cognition Research (IEECR), Bonn, Germany
- University Hospital Bonn
- German Center for Neurodegenerative Diseases (DZNE), Bonn, Germany
| | - Michael Wenzel
- University of Bonn, Faculty of Medicine, Institute for Experimental Epileptology and Cognition Research (IEECR), Bonn, Germany
- University Hospital Bonn
- Department of Epileptology, University Hospital Bonn, Bonn, Germany
| | - Tony Kelly
- University of Bonn, Faculty of Medicine, Institute for Experimental Epileptology and Cognition Research (IEECR), Bonn, Germany
- University Hospital Bonn
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25
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Diehl GW, Redish AD. Measuring excitation-inhibition balance through spectral components of local field potentials. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.24.577086. [PMID: 38328057 PMCID: PMC10849740 DOI: 10.1101/2024.01.24.577086] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/09/2024]
Abstract
The balance between excitation and inhibition is critical to brain functioning, and dysregulation of this balance is a hallmark of numerous psychiatric conditions. Measuring this excitation-inhibition (E:I) balance in vivo has remained difficult, but theoretical models have proposed that characteristics of local field potentials (LFP) may provide an accurate proxy. To establish a conclusive link between LFP and E:I balance, we recorded single units and LFP from the prefrontal cortex (mPFC) of rats during decision making. Dynamic measures of synaptic coupling strength facilitated direct quantification of E:I balance and revealed a strong inverse relationship to broadband spectral power of LFP. These results provide a critical link between LFP and underlying network properties, opening the door for non-invasive recordings to measure E:I balance in clinical settings.
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Affiliation(s)
- Geoffrey W Diehl
- Department of Neuroscience, University of Minnesota, Minneapolis, MN, United States
| | - A David Redish
- Department of Neuroscience, University of Minnesota, Minneapolis, MN, United States
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26
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Tolooshams B, Matias S, Wu H, Temereanca S, Uchida N, Murthy VN, Masset P, Ba D. Interpretable deep learning for deconvolutional analysis of neural signals. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.05.574379. [PMID: 38260512 PMCID: PMC10802267 DOI: 10.1101/2024.01.05.574379] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/24/2024]
Abstract
The widespread adoption of deep learning to build models that capture the dynamics of neural populations is typically based on "black-box" approaches that lack an interpretable link between neural activity and function. Here, we propose to apply algorithm unrolling, a method for interpretable deep learning, to design the architecture of sparse deconvolutional neural networks and obtain a direct interpretation of network weights in relation to stimulus-driven single-neuron activity through a generative model. We characterize our method, referred to as deconvolutional unrolled neural learning (DUNL), and show its versatility by applying it to deconvolve single-trial local signals across multiple brain areas and recording modalities. To exemplify use cases of our decomposition method, we uncover multiplexed salience and reward prediction error signals from midbrain dopamine neurons in an unbiased manner, perform simultaneous event detection and characterization in somatosensory thalamus recordings, and characterize the responses of neurons in the piriform cortex. Our work leverages the advances in interpretable deep learning to gain a mechanistic understanding of neural dynamics.
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Affiliation(s)
- Bahareh Tolooshams
- Center for Brain Science, Harvard University, Cambridge MA, 02138
- John A. Paulson School of Engineering and Applied Sciences, Harvard University, Cambridge MA, 02138
- Computing + Mathematical Sciences, California Institute of Technology, Pasadena, CA, 91125
| | - Sara Matias
- Center for Brain Science, Harvard University, Cambridge MA, 02138
- Department of Molecular and Cellular Biology, Harvard University, Cambridge MA, 02138
| | - Hao Wu
- Center for Brain Science, Harvard University, Cambridge MA, 02138
- Department of Molecular and Cellular Biology, Harvard University, Cambridge MA, 02138
| | - Simona Temereanca
- Carney Institute for Brain Science, Brown University, Providence, RI, 02906
| | - Naoshige Uchida
- Center for Brain Science, Harvard University, Cambridge MA, 02138
- Department of Molecular and Cellular Biology, Harvard University, Cambridge MA, 02138
| | - Venkatesh N. Murthy
- Center for Brain Science, Harvard University, Cambridge MA, 02138
- Department of Molecular and Cellular Biology, Harvard University, Cambridge MA, 02138
| | - Paul Masset
- Center for Brain Science, Harvard University, Cambridge MA, 02138
- Department of Molecular and Cellular Biology, Harvard University, Cambridge MA, 02138
- Department of Psychology, McGill University, Montréal QC, H3A 1G1
| | - Demba Ba
- Center for Brain Science, Harvard University, Cambridge MA, 02138
- John A. Paulson School of Engineering and Applied Sciences, Harvard University, Cambridge MA, 02138
- Kempner Institute for the Study of Natural & Artificial Intelligence, Harvard University, Cambridge MA, 02138
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27
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Manley J, Demas J, Kim H, Traub FM, Vaziri A. Simultaneous, cortex-wide and cellular-resolution neuronal population dynamics reveal an unbounded scaling of dimensionality with neuron number. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.15.575721. [PMID: 38293036 PMCID: PMC10827059 DOI: 10.1101/2024.01.15.575721] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/01/2024]
Abstract
The brain's remarkable properties arise from collective activity of millions of neurons. Widespread application of dimensionality reduction to multi-neuron recordings implies that neural dynamics can be approximated by low-dimensional "latent" signals reflecting neural computations. However, what would be the biological utility of such a redundant and metabolically costly encoding scheme and what is the appropriate resolution and scale of neural recording to understand brain function? Imaging the activity of one million neurons at cellular resolution and near-simultaneously across mouse cortex, we demonstrate an unbounded scaling of dimensionality with neuron number. While half of the neural variance lies within sixteen behavior-related dimensions, we find this unbounded scaling of dimensionality to correspond to an ever-increasing number of internal variables without immediate behavioral correlates. The activity patterns underlying these higher dimensions are fine-grained and cortex-wide, highlighting that large-scale recording is required to uncover the full neural substrates of internal and potentially cognitive processes.
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Affiliation(s)
- Jason Manley
- Laboratory of Neurotechnology and Biophysics, The Rockefeller University, New York, NY 10065, USA
- The Kavli Neural Systems Institute, The Rockefeller University, New York, NY 10065, USA
| | - Jeffrey Demas
- Laboratory of Neurotechnology and Biophysics, The Rockefeller University, New York, NY 10065, USA
- The Kavli Neural Systems Institute, The Rockefeller University, New York, NY 10065, USA
| | - Hyewon Kim
- Laboratory of Neurotechnology and Biophysics, The Rockefeller University, New York, NY 10065, USA
| | - Francisca Martínez Traub
- Laboratory of Neurotechnology and Biophysics, The Rockefeller University, New York, NY 10065, USA
| | - Alipasha Vaziri
- Laboratory of Neurotechnology and Biophysics, The Rockefeller University, New York, NY 10065, USA
- The Kavli Neural Systems Institute, The Rockefeller University, New York, NY 10065, USA
- Lead Contact
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28
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Li S, Liu Y, Zhang N, Li W, Xu WJ, Xu YQ, Chen YY, Cui X, Zhu B, Gao XY. Perspective of Calcium Imaging Technology Applied to Acupuncture Research. Chin J Integr Med 2024; 30:3-9. [PMID: 36795265 DOI: 10.1007/s11655-023-3692-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/18/2022] [Indexed: 02/17/2023]
Abstract
Acupuncture, a therapeutic treatment defined as the insertion of needles into the body at specific points (ie, acupoints), has growing in popularity world-wide to treat various diseases effectively, especially acute and chronic pain. In parallel, interest in the physiological mechanisms underlying acupuncture analgesia, particularly the neural mechanisms have been increasing. Over the past decades, our understanding of how the central nervous system and peripheral nervous system process signals induced by acupuncture has developed rapidly by using electrophysiological methods. However, with the development of neuroscience, electrophysiology is being challenged by calcium imaging in view field, neuron population and visualization in vivo. Owing to the outstanding spatial resolution, the novel imaging approaches provide opportunities to enrich our knowledge about the neurophysiological mechanisms of acupuncture analgesia at subcellular, cellular, and circuit levels in combination with new labeling, genetic and circuit tracing techniques. Therefore, this review will introduce the principle and the method of calcium imaging applied to acupuncture research. We will also review the current findings in pain research using calcium imaging from in vitro to in vivo experiments and discuss the potential methodological considerations in studying acupuncture analgesia.
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Affiliation(s)
- Sha Li
- Institute of Acupuncture and Moxibustion, China Academy of Chinese Medical Sciences, Beijing, 100700, China
| | - Yun Liu
- Institute of Acupuncture and Moxibustion, China Academy of Chinese Medical Sciences, Beijing, 100700, China
| | - Nan Zhang
- Institute of Acupuncture and Moxibustion, China Academy of Chinese Medical Sciences, Beijing, 100700, China
| | - Wang Li
- Institute of Acupuncture and Moxibustion, China Academy of Chinese Medical Sciences, Beijing, 100700, China
| | - Wen-Jie Xu
- Institute of Acupuncture and Moxibustion, China Academy of Chinese Medical Sciences, Beijing, 100700, China
| | - Yi-Qian Xu
- Institute of Acupuncture and Moxibustion, China Academy of Chinese Medical Sciences, Beijing, 100700, China
| | - Yi-Yuan Chen
- Institute of Acupuncture and Moxibustion, China Academy of Chinese Medical Sciences, Beijing, 100700, China
| | - Xiang Cui
- Institute of Acupuncture and Moxibustion, China Academy of Chinese Medical Sciences, Beijing, 100700, China
| | - Bing Zhu
- Institute of Acupuncture and Moxibustion, China Academy of Chinese Medical Sciences, Beijing, 100700, China
| | - Xin-Yan Gao
- Institute of Acupuncture and Moxibustion, China Academy of Chinese Medical Sciences, Beijing, 100700, China.
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29
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Xue F, Li F, Zhang KM, Ding L, Wang Y, Zhao X, Xu F, Zhang D, Sun M, Lau PM, Zhu Q, Zhou P, Bi GQ. Multi-region calcium imaging in freely behaving mice with ultra-compact head-mounted fluorescence microscopes. Natl Sci Rev 2024; 11:nwad294. [PMID: 38288367 PMCID: PMC10824555 DOI: 10.1093/nsr/nwad294] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2023] [Revised: 09/26/2023] [Accepted: 11/23/2023] [Indexed: 01/31/2024] Open
Abstract
To investigate the circuit-level neural mechanisms of behavior, simultaneous imaging of neuronal activity in multiple cortical and subcortical regions is highly desired. Miniature head-mounted microscopes offer the capability of calcium imaging in freely behaving animals. However, implanting multiple microscopes on a mouse brain remains challenging due to space constraints and the cumbersome weight of the equipment. Here, we present TINIscope, a Tightly Integrated Neuronal Imaging microscope optimized for electronic and opto-mechanical design. With its compact and lightweight design of 0.43 g, TINIscope enables unprecedented simultaneous imaging of behavior-relevant activity in up to four brain regions in mice. Proof-of-concept experiments with TINIscope recorded over 1000 neurons in four hippocampal subregions and revealed concurrent activity patterns spanning across these regions. Moreover, we explored potential multi-modal experimental designs by integrating additional modules for optogenetics, electrical stimulation or local field potential recordings. Overall, TINIscope represents a timely and indispensable tool for studying the brain-wide interregional coordination that underlies unrestrained behaviors.
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Affiliation(s)
- Feng Xue
- Department of Precision Machinery and Precision Instruments, University of Science and Technology of China, Hefei 230026, China
- Hefei National Laboratory for Physical Sciences at the Microscale, University of Science and Technology of China, Hefei 230026, China
| | - Fei Li
- Interdisciplinary Center for Brain Information, the Brain Cognition and Brain Disease Institute, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
- Faculty of Life and Health Sciences, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
| | - Ke-ming Zhang
- Hefei National Laboratory for Physical Sciences at the Microscale, University of Science and Technology of China, Hefei 230026, China
- School of Life Sciences, University of Science and Technology of China, Hefei 230026, China
| | - Lufeng Ding
- Interdisciplinary Center for Brain Information, the Brain Cognition and Brain Disease Institute, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
- School of Life Sciences, University of Science and Technology of China, Hefei 230026, China
| | - Yang Wang
- Institute of Semiconductors, Chinese Academy of Sciences, Beijing 100083, China
| | - Xingtao Zhao
- Department of Modern Life Sciences and Biotecnology, Xiongan Institute of Innovation, Xiongan New Area, Xiongan 071899, China
| | - Fang Xu
- Interdisciplinary Center for Brain Information, the Brain Cognition and Brain Disease Institute, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
- Faculty of Life and Health Sciences, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
- Shenzhen-Hong Kong Institute of Brain Science-Shenzhen Fundamental Research Institutions, Shenzhen 518055, China
| | - Danke Zhang
- Interdisciplinary Center for Brain Information, the Brain Cognition and Brain Disease Institute, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
| | - Mingzhai Sun
- Suzhou Institute for Advanced Research, University of Science and Technology of China, Suzhou 215123, China
| | - Pak-Ming Lau
- Hefei National Laboratory for Physical Sciences at the Microscale, University of Science and Technology of China, Hefei 230026, China
- Interdisciplinary Center for Brain Information, the Brain Cognition and Brain Disease Institute, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
- School of Life Sciences, University of Science and Technology of China, Hefei 230026, China
- Shenzhen-Hong Kong Institute of Brain Science-Shenzhen Fundamental Research Institutions, Shenzhen 518055, China
- Institute of Artificial Intelligence, Hefei Comprehensive National Science Center, Hefei 230088, China
| | - Qingyuan Zhu
- Hefei National Laboratory for Physical Sciences at the Microscale, University of Science and Technology of China, Hefei 230026, China
| | - Pengcheng Zhou
- Interdisciplinary Center for Brain Information, the Brain Cognition and Brain Disease Institute, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
- Faculty of Life and Health Sciences, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
| | - Guo-Qiang Bi
- Hefei National Laboratory for Physical Sciences at the Microscale, University of Science and Technology of China, Hefei 230026, China
- Interdisciplinary Center for Brain Information, the Brain Cognition and Brain Disease Institute, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
- School of Life Sciences, University of Science and Technology of China, Hefei 230026, China
- Shenzhen-Hong Kong Institute of Brain Science-Shenzhen Fundamental Research Institutions, Shenzhen 518055, China
- Institute of Artificial Intelligence, Hefei Comprehensive National Science Center, Hefei 230088, China
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30
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Blanco-Hernández E, Balsamo G, Preston-Ferrer P, Burgalossi A. Sensory and behavioral modulation of thalamic head-direction cells. Nat Neurosci 2024; 27:28-33. [PMID: 38177338 DOI: 10.1038/s41593-023-01506-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2022] [Accepted: 10/24/2023] [Indexed: 01/06/2024]
Abstract
Head-direction (HD) neurons are thought to exclusively encode directional heading. In awake mice, we found that sensory stimuli evoked robust short-latency responses in thalamic HD cells, but not in non-HD neurons. The activity of HD cells, but not that of non-HD neurons, was tightly correlated to brain-state fluctuations and dynamically modulated during social interactions. These data point to a new role for the thalamic compass in relaying sensory and behavioral-state information.
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Affiliation(s)
- Eduardo Blanco-Hernández
- Institute of Neurobiology, University of Tübingen, Tübingen, Germany
- Werner-Reichardt Centre for Integrative Neuroscience, Tübingen, Germany
| | - Giuseppe Balsamo
- Institute of Neurobiology, University of Tübingen, Tübingen, Germany
- Werner-Reichardt Centre for Integrative Neuroscience, Tübingen, Germany
- Graduate Training Centre of Neuroscience, IMPRS, Tübingen, Germany
| | - Patricia Preston-Ferrer
- Institute of Neurobiology, University of Tübingen, Tübingen, Germany.
- Werner-Reichardt Centre for Integrative Neuroscience, Tübingen, Germany.
| | - Andrea Burgalossi
- Institute of Neurobiology, University of Tübingen, Tübingen, Germany.
- Werner-Reichardt Centre for Integrative Neuroscience, Tübingen, Germany.
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31
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Celinskis D, Black CJ, Murphy J, Barrios-Anderson A, Friedman N, Shaner NC, Saab C, Gomez-Ramirez M, Lipscombe D, Borton DA, Moore CI. Towards a Brighter Constellation: Multi-Organ Neuroimaging of Neural and Vascular Dynamics in the Spinal Cord and Brain. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.12.25.573323. [PMID: 38234789 PMCID: PMC10793404 DOI: 10.1101/2023.12.25.573323] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/19/2024]
Abstract
Significance Pain is comprised of a complex interaction between motor action and somatosensation that is dependent on dynamic interactions between the brain and spinal cord. This makes understanding pain particularly challenging as it involves rich interactions between many circuits (e.g., neural and vascular) and signaling cascades throughout the body. As such, experimentation on a single region may lead to an incomplete and potentially incorrect understanding of crucial underlying mechanisms. Aim Here, we aimed to develop and validate new tools to enable detailed and extended observation of neural and vascular activity in the brain and spinal cord. The first key set of innovations were targeted to developing novel imaging hardware that addresses the many challenges of multi-site imaging. The second key set of innovations were targeted to enabling bioluminescent imaging, as this approach can address limitations of fluorescent microscopy including photobleaching, phototoxicity and decreased resolution due to scattering of excitation signals. Approach We designed 3D-printed brain and spinal cord implants to enable effective surgical implantations and optical access with wearable miniscopes or an open window (e.g., for one- or two-photon microscopy or optogenetic stimulation). We also tested the viability for bioluminescent imaging, and developed a novel modified miniscope optimized for these signals (BLmini). Results Here, we describe novel 'universal' implants for acute and chronic simultaneous brain-spinal cord imaging and optical stimulation. We further describe successful imaging of bioluminescent signals in both foci, and a new miniscope, the 'BLmini,' which has reduced weight, cost and form-factor relative to standard wearable miniscopes. Conclusions The combination of 3D printed implants, advanced imaging tools, and bioluminescence imaging techniques offers a new coalition of methods for understanding spinal cord-brain interactions. This work has the potential for use in future research into neuropathic pain and other sensory disorders and motor behavior.
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Affiliation(s)
| | | | - Jeremy Murphy
- Carney Institute for Brain Science, Providence, RI, USA
| | | | - Nina Friedman
- Carney Institute for Brain Science, Providence, RI, USA
| | - Nathan C. Shaner
- University of California San Diego School of Medicine, La Jolla, CA, USA
| | - Carl Saab
- Cleveland Clinic Lerner Research Institute, Department of Biomedical Engineering and Neurological Institute, Cleveland, OH, USA
| | | | | | - David A. Borton
- Carney Institute for Brain Science, Providence, RI, USA
- School of Engineering, Brown University, RI, USA
- Center for Neurorestoration and Neurotechnology, Providence VA Medical Center, RI, USA
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32
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Pinke D, Issa JB, Dara GA, Dobos G, Dombeck DA. Full field-of-view virtual reality goggles for mice. Neuron 2023; 111:3941-3952.e6. [PMID: 38070501 PMCID: PMC10841834 DOI: 10.1016/j.neuron.2023.11.019] [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: 06/07/2023] [Revised: 10/03/2023] [Accepted: 11/15/2023] [Indexed: 12/23/2023]
Abstract
Visual virtual reality (VR) systems for head-fixed mice offer advantages over real-world studies for investigating the neural circuitry underlying behavior. However, current VR approaches do not fully cover the visual field of view of mice, do not stereoscopically illuminate the binocular zone, and leave the lab frame visible. To overcome these limitations, we developed iMRSIV (Miniature Rodent Stereo Illumination VR)-VR goggles for mice. Our system is compact, separately illuminates each eye for stereo vision, and provides each eye with an ∼180° field of view, thus excluding the lab frame while accommodating saccades. Mice using iMRSIV while navigating engaged in virtual behaviors more quickly than in a current monitor-based system and displayed freezing and fleeing reactions to overhead looming stimulation. Using iMRSIV with two-photon functional imaging, we found large populations of hippocampal place cells during virtual navigation, global remapping during environment changes, and unique responses of place cell ensembles to overhead looming stimulation.
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Affiliation(s)
- Domonkos Pinke
- Department of Neurobiology, Northwestern University, Evanston, IL 60208, USA
| | - John B Issa
- Department of Neurobiology, Northwestern University, Evanston, IL 60208, USA
| | - Gabriel A Dara
- Department of Neurobiology, Northwestern University, Evanston, IL 60208, USA
| | - Gergely Dobos
- 360world Ltd, Sümegvár köz 9, 1118 Budapest, Hungary
| | - Daniel A Dombeck
- Department of Neurobiology, Northwestern University, Evanston, IL 60208, USA.
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33
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Phillips ML, Urban NT, Salemi T, Dong Z, Yasuda R. Functional imaging of nine distinct neuronal populations under a miniscope in freely behaving animals. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.12.13.571122. [PMID: 38168225 PMCID: PMC10760119 DOI: 10.1101/2023.12.13.571122] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/05/2024]
Abstract
Head-mounted miniscopes have allowed for functional fluorescence imaging in freely moving animals. However, current capabilities of state-of-the-art technology can record only up to two, spectrally distinct fluorophores. This severely limits the number of cell types identifiable in a functional imaging experiment. Here we present a pipeline that enables the distinction of nine neuronal subtypes from regions defined by behaviorally relevant cells during in vivo GCaMP imaging. These subtypes are identified utilizing unique fluorophores that are co-expressed with GCaMP, unmixed by spectral imaging on a confocal microscope and co-registering these spectral fingerprints with functional data obtained on miniaturized microscopes. This method facilitates detailed analyses of circuit-level encoding of behavior.
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Affiliation(s)
- Mary L. Phillips
- Max Planck Florida Institute for Neuroscience, Jupiter, FL
- ZEISS Research Microscopy Solutions, White Plains, NY
| | | | - Taddeo Salemi
- Max Planck Florida Institute for Neuroscience, Jupiter, FL
| | | | - Ryohei Yasuda
- Max Planck Florida Institute for Neuroscience, Jupiter, FL
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34
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Zhou ZC, Gordon-Fennell A, Piantadosi SC, Ji N, Smith SL, Bruchas MR, Stuber GD. Deep-brain optical recording of neural dynamics during behavior. Neuron 2023; 111:3716-3738. [PMID: 37804833 PMCID: PMC10843303 DOI: 10.1016/j.neuron.2023.09.006] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2023] [Revised: 08/24/2023] [Accepted: 09/06/2023] [Indexed: 10/09/2023]
Abstract
In vivo fluorescence recording techniques have produced landmark discoveries in neuroscience, providing insight into how single cell and circuit-level computations mediate sensory processing and generate complex behaviors. While much attention has been given to recording from cortical brain regions, deep-brain fluorescence recording is more complex because it requires additional measures to gain optical access to harder to reach brain nuclei. Here we discuss detailed considerations and tradeoffs regarding deep-brain fluorescence recording techniques and provide a comprehensive guide for all major steps involved, from project planning to data analysis. The goal is to impart guidance for new and experienced investigators seeking to use in vivo deep fluorescence optical recordings in awake, behaving rodent models.
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Affiliation(s)
- Zhe Charles Zhou
- Department of Anesthesiology and Pain Medicine, University of Washington, Seattle, WA 98195, USA; Center for Neurobiology of Addiction, Pain, and Emotion, University of Washington, Seattle, WA 98195, USA
| | - Adam Gordon-Fennell
- Department of Anesthesiology and Pain Medicine, University of Washington, Seattle, WA 98195, USA; Center for Neurobiology of Addiction, Pain, and Emotion, University of Washington, Seattle, WA 98195, USA
| | - Sean C Piantadosi
- Department of Anesthesiology and Pain Medicine, University of Washington, Seattle, WA 98195, USA; Center for Neurobiology of Addiction, Pain, and Emotion, University of Washington, Seattle, WA 98195, USA
| | - Na Ji
- Department of Physics, University of California, Berkeley, Berkeley, CA 94720, USA; Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA; Helen Wills Neuroscience Institute, University of California, Berkeley, Berkeley, CA 94720, USA; Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Spencer LaVere Smith
- Department of Electrical and Computer Engineering, University of California Santa Barbara, Santa Barbara, CA 93106, USA
| | - Michael R Bruchas
- Department of Anesthesiology and Pain Medicine, University of Washington, Seattle, WA 98195, USA; Center for Neurobiology of Addiction, Pain, and Emotion, University of Washington, Seattle, WA 98195, USA; Department of Pharmacology, University of Washington, Seattle, WA 98195, USA; Department of Bioengineering, University of Washington, Seattle, WA 98195, USA.
| | - Garret D Stuber
- Department of Anesthesiology and Pain Medicine, University of Washington, Seattle, WA 98195, USA; Center for Neurobiology of Addiction, Pain, and Emotion, University of Washington, Seattle, WA 98195, USA; Department of Pharmacology, University of Washington, Seattle, WA 98195, USA.
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Liu Y, Zhang H, Li X. Technologies for depth scanning in miniature optical imaging systems [Invited]. BIOMEDICAL OPTICS EXPRESS 2023; 14:6542-6562. [PMID: 38420321 PMCID: PMC10898578 DOI: 10.1364/boe.507078] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/27/2023] [Revised: 11/16/2023] [Accepted: 11/17/2023] [Indexed: 03/02/2024]
Abstract
Biomedical optical imaging has found numerous clinical and research applications. For achieving 3D imaging, depth scanning presents the most significant challenge, particularly in miniature imaging devices. This paper reviews the state-of-art technologies for depth scanning in miniature optical imaging systems, which include two general approaches: 1) physically shifting part of or the entire imaging device to allow imaging at different depths and 2) optically changing the focus of the imaging optics. We mainly focus on the second group of methods, introducing a wide variety of tunable microlenses, covering the underlying physics, actuation mechanisms, and imaging performance. Representative applications in clinical and neuroscience research are briefly presented. Major challenges and future perspectives of depth/focus scanning technologies for biomedical optical imaging are also discussed.
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Affiliation(s)
- Yuehan Liu
- Department of Electrical and Computer Engineering, Johns Hopkins University, Baltimore, Maryland 21218, USA
| | - Haolin Zhang
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, Maryland 21205, USA
| | - Xingde Li
- Department of Electrical and Computer Engineering, Johns Hopkins University, Baltimore, Maryland 21218, USA
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, Maryland 21205, USA
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36
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Ghosh S, Dahiya M, Kumar A, Bheri M, Pandey GK. Calcium imaging: a technique to monitor calcium dynamics in biological systems. PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS : AN INTERNATIONAL JOURNAL OF FUNCTIONAL PLANT BIOLOGY 2023; 29:1777-1811. [PMID: 38222278 PMCID: PMC10784449 DOI: 10.1007/s12298-023-01405-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/01/2023] [Revised: 12/07/2023] [Accepted: 12/11/2023] [Indexed: 01/16/2024]
Abstract
Calcium ion (Ca2+) is a multifaceted signaling molecule that acts as an important second messenger. During the course of evolution, plants and animals have developed Ca2+ signaling in order to respond against diverse stimuli, to regulate a large number of physiological and developmental pathways. Our understanding of Ca2+ signaling and its components in physiological phenomena ranging from lower to higher organisms, and from single cell to multiple tissues has grown exponentially. The generation of Ca2+ transients or signatures for various stress factor is a well-known mechanism adopted in plant and animal systems. However, the decoding of such remarkable signatures is an uphill task and is always an interesting goal for the scientific community. In the past few decades, studies on the concentration and dynamics of intracellular Ca2+ are significantly increasing and have become a trend in modern biology. The advancement in approaches from Ca2+ binding dyes to in vivo Ca2+ imaging through the use of Ca2+ biosensors to achieve spatio-temporal resolution in micro and milliseconds range, provide us phenomenal opportunities to study live cell Ca2+ imaging or dynamics. Here, we describe the usage, improvement and advancement of Ca2+ based dyes, genetically encoded probes and sensors to achieve extraordinary Ca2+ imaging in plants and animals. Graphical abstract
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Affiliation(s)
- Soma Ghosh
- Department of Plant Molecular Biology, University of Delhi South Campus, Benito Juarez Road, Dhaula Kuan, New Delhi, 110021 India
| | - Monika Dahiya
- Department of Plant Molecular Biology, University of Delhi South Campus, Benito Juarez Road, Dhaula Kuan, New Delhi, 110021 India
| | - Amit Kumar
- Department of Plant Molecular Biology, University of Delhi South Campus, Benito Juarez Road, Dhaula Kuan, New Delhi, 110021 India
| | - Malathi Bheri
- Department of Plant Molecular Biology, University of Delhi South Campus, Benito Juarez Road, Dhaula Kuan, New Delhi, 110021 India
| | - Girdhar K. Pandey
- Department of Plant Molecular Biology, University of Delhi South Campus, Benito Juarez Road, Dhaula Kuan, New Delhi, 110021 India
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Lee CH, Park YK, Lee K. Recent strategies for neural dynamics observation at a larger scale and wider scope. Biosens Bioelectron 2023; 240:115638. [PMID: 37647685 DOI: 10.1016/j.bios.2023.115638] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2023] [Revised: 08/15/2023] [Accepted: 08/24/2023] [Indexed: 09/01/2023]
Abstract
The tremendous technical progress in neuroscience offers opportunities to observe a more minor or/and broader dynamic picture of the brain. Moreover, the large-scale neural activity of individual neurons enables the dissection of detailed mechanistic links between neural populations and behaviors. To measure neural activity in-vivo, multi-neuron recording, and neuroimaging techniques are employed and developed to acquire more neurons. The tools introduced concurrently recorded dozens to hundreds of neurons in the coordinated brain regions and elucidated the neuronal ensembles from a massive population perspective of diverse neurons at cellular resolution. In particular, the increasing spatiotemporal resolution of neuronal monitoring across the whole brain dramatically facilitates our understanding of additional nervous system functions in health and disease. Here, we will introduce state-of-the-art neuroscience tools involving large-scale neural population recording and the long-range connections spanning multiple brain regions. Their synergic effects provide to clarify the controversial circuitry underlying neuroscience. These challenging neural tools present a promising outlook for the fundamental dynamic interplay across levels of synaptic cellular, circuit organization, and brain-wide. Hence, more observations of neural dynamics will provide more clues to elucidate brain functions and push forward innovative technology at the intersection of neural engineering disciplines. We hope this review will provide insight into the use or development of recent neural techniques considering spatiotemporal scales of brain observation.
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Affiliation(s)
- Chang Hak Lee
- Department of Brain Sciences, Daegu Gyeongbuk Institute of Science & Technology (DGIST), Daegu, South Korea
| | - Young Kwon Park
- Department of Brain Sciences, Daegu Gyeongbuk Institute of Science & Technology (DGIST), Daegu, South Korea
| | - Kwang Lee
- Department of Brain Sciences, Daegu Gyeongbuk Institute of Science & Technology (DGIST), Daegu, South Korea.
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38
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Pardasani M, Ramakrishnan AM, Mahajan S, Kantroo M, McGowan E, Das S, Srikanth P, Pandey S, Abraham NM. Perceptual learning deficits mediated by somatostatin releasing inhibitory interneurons of olfactory bulb in an early life stress mouse model. Mol Psychiatry 2023; 28:4693-4706. [PMID: 37726451 PMCID: PMC10914616 DOI: 10.1038/s41380-023-02244-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/07/2023] [Revised: 08/21/2023] [Accepted: 08/25/2023] [Indexed: 09/21/2023]
Abstract
Early life adversity (ELA) causes aberrant functioning of neural circuits affecting the health of an individual. While ELA-induced behavioural disorders resulting from sensory and cognitive disabilities can be assessed clinically, the neural mechanisms need to be probed using animal models by employing multi-pronged experimental approaches. As ELA can alter sensory perception, we investigated the effect of early weaning on murine olfaction. By implementing go/no-go odour discrimination paradigm, we observed olfactory learning and memory impairments in early life stressed (ELS) male mice. As olfactory bulb (OB) circuitry plays a critical role in odour learning, we studied the plausible changes in the OB of ELS mice. Lowered c-Fos activity in the external plexiform layer and a reduction in the number of dendritic processes of somatostatin-releasing, GABAergic interneurons (SOM-INs) in the ELS mice led us to hypothesise the underlying circuit. We recorded reduced synaptic inhibitory feedback on mitral/tufted (M/T) cells, in the OB slices from ELS mice, explaining the learning deficiency caused by compromised refinement of OB output. The reduction in synaptic inhibition was nullified by the photo-activation of ChR2-expressing SOM-INs in ELS mice. The role of SOM-INs was revealed by learning-dependent refinement of Ca2+dynamics quantified by GCaMP6f signals, which was absent in ELS mice. Further, the causal role of SOM-INs involving circuitry was investigated by optogenetic modulation during the odour discrimination learning. Photo-activating these neurons rescued the ELA-induced learning deficits. Conversely, photo-inhibition caused learning deficiency in control animals, while it completely abolished the learning in ELS mice, confirming the adverse effects mediated by SOM-INs. Our results thus establish the role of specific inhibitory circuit in pre-cortical sensory area in orchestrating ELA-dependent changes.
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Affiliation(s)
- Meenakshi Pardasani
- Laboratory of Neural Circuits and Behaviour (LNCB), Department of Biology, Indian Institute of Science Education and Research (IISER), Pune, Maharashtra, 411008, India
| | - Anantha Maharasi Ramakrishnan
- Laboratory of Neural Circuits and Behaviour (LNCB), Department of Biology, Indian Institute of Science Education and Research (IISER), Pune, Maharashtra, 411008, India
| | - Sarang Mahajan
- Laboratory of Neural Circuits and Behaviour (LNCB), Department of Biology, Indian Institute of Science Education and Research (IISER), Pune, Maharashtra, 411008, India
| | - Meher Kantroo
- Laboratory of Neural Circuits and Behaviour (LNCB), Department of Biology, Indian Institute of Science Education and Research (IISER), Pune, Maharashtra, 411008, India
| | - Eleanor McGowan
- Laboratory of Neural Circuits and Behaviour (LNCB), Department of Biology, Indian Institute of Science Education and Research (IISER), Pune, Maharashtra, 411008, India
| | - Susobhan Das
- Laboratory of Neural Circuits and Behaviour (LNCB), Department of Biology, Indian Institute of Science Education and Research (IISER), Pune, Maharashtra, 411008, India
| | - Priyadharshini Srikanth
- Laboratory of Neural Circuits and Behaviour (LNCB), Department of Biology, Indian Institute of Science Education and Research (IISER), Pune, Maharashtra, 411008, India
| | - Sanyukta Pandey
- Laboratory of Neural Circuits and Behaviour (LNCB), Department of Biology, Indian Institute of Science Education and Research (IISER), Pune, Maharashtra, 411008, India
| | - Nixon M Abraham
- Laboratory of Neural Circuits and Behaviour (LNCB), Department of Biology, Indian Institute of Science Education and Research (IISER), Pune, Maharashtra, 411008, India.
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Balasubramanian H, Hobson CM, Chew TL, Aaron JS. Imagining the future of optical microscopy: everything, everywhere, all at once. Commun Biol 2023; 6:1096. [PMID: 37898673 PMCID: PMC10613274 DOI: 10.1038/s42003-023-05468-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2023] [Accepted: 10/16/2023] [Indexed: 10/30/2023] Open
Abstract
The optical microscope has revolutionized biology since at least the 17th Century. Since then, it has progressed from a largely observational tool to a powerful bioanalytical platform. However, realizing its full potential to study live specimens is hindered by a daunting array of technical challenges. Here, we delve into the current state of live imaging to explore the barriers that must be overcome and the possibilities that lie ahead. We venture to envision a future where we can visualize and study everything, everywhere, all at once - from the intricate inner workings of a single cell to the dynamic interplay across entire organisms, and a world where scientists could access the necessary microscopy technologies anywhere.
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Affiliation(s)
| | - Chad M Hobson
- Advanced Imaging Center; Howard Hughes Medical Institute Janelia Research Campus, Ashburn, VA, 20147, USA
| | - Teng-Leong Chew
- Advanced Imaging Center; Howard Hughes Medical Institute Janelia Research Campus, Ashburn, VA, 20147, USA
| | - Jesse S Aaron
- Advanced Imaging Center; Howard Hughes Medical Institute Janelia Research Campus, Ashburn, VA, 20147, USA.
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40
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Eichenberger BT, Griesbach E, Mitchell J, Chao JA. Following the Birth, Life, and Death of mRNAs in Single Cells. Annu Rev Cell Dev Biol 2023; 39:253-275. [PMID: 37843928 DOI: 10.1146/annurev-cellbio-022723-024045] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2023]
Abstract
Recent advances in single-molecule imaging of mRNAs in fixed and living cells have enabled the lives of mRNAs to be studied with unprecedented spatial and temporal detail. These approaches have moved beyond simply being able to observe specific events and have begun to allow an understanding of how regulation is coupled between steps in the mRNA life cycle. Additionally, these methodologies are now being applied in multicellular systems and animals to provide more nuanced insights into the physiological regulation of RNA metabolism.
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Affiliation(s)
- Bastian T Eichenberger
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland;
- University of Basel, Basel, Switzerland
| | - Esther Griesbach
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland;
| | - Jessica Mitchell
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland;
| | - Jeffrey A Chao
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland;
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41
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Das A, Holden S, Borovicka J, Icardi J, O'Niel A, Chaklai A, Patel D, Patel R, Kaech Petrie S, Raber J, Dana H. Large-scale recording of neuronal activity in freely-moving mice at cellular resolution. Nat Commun 2023; 14:6399. [PMID: 37828016 PMCID: PMC10570384 DOI: 10.1038/s41467-023-42083-y] [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: 09/12/2022] [Accepted: 09/28/2023] [Indexed: 10/14/2023] Open
Abstract
Current methods for recording large-scale neuronal activity from behaving mice at single-cell resolution require either fixing the mouse head under a microscope or attachment of a recording device to the animal's skull. Both of these options significantly affect the animal behavior and hence also the recorded brain activity patterns. Here, we introduce a different method to acquire snapshots of single-cell cortical activity maps from freely-moving mice using a calcium sensor called CaMPARI. CaMPARI has a unique property of irreversibly changing its color from green to red inside active neurons when illuminated with 400 nm light. We capitalize on this property to demonstrate cortex-wide activity recording without any head fixation, tethering, or attachment of a miniaturized device to the mouse's head. Multiple cortical regions were recorded while the mouse was performing a battery of behavioral and cognitive tests. We identified task-dependent activity patterns across motor and somatosensory cortices, with significant differences across sub-regions of the motor cortex and correlations across several activity patterns and task parameters. This CaMPARI-based recording method expands the capabilities of recording neuronal activity from freely-moving and behaving mice under minimally-restrictive experimental conditions and provides large-scale volumetric data that are currently not accessible otherwise.
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Affiliation(s)
- Aniruddha Das
- Department of Neurosciences, Lerner Research Institute, Cleveland Clinic Foundation, Cleveland, OH, USA
| | - Sarah Holden
- Department of Behavioral Neuroscience, Oregon Health and Science University, Portland, OR, USA
| | - Julie Borovicka
- Department of Neurosciences, Lerner Research Institute, Cleveland Clinic Foundation, Cleveland, OH, USA
| | - Jacob Icardi
- Department of Neurosciences, Lerner Research Institute, Cleveland Clinic Foundation, Cleveland, OH, USA
| | - Abigail O'Niel
- Department of Behavioral Neuroscience, Oregon Health and Science University, Portland, OR, USA
| | - Ariel Chaklai
- Department of Behavioral Neuroscience, Oregon Health and Science University, Portland, OR, USA
| | - Davina Patel
- Department of Neurosciences, Lerner Research Institute, Cleveland Clinic Foundation, Cleveland, OH, USA
| | - Rushik Patel
- Department of Neurosciences, Lerner Research Institute, Cleveland Clinic Foundation, Cleveland, OH, USA
| | | | - Jacob Raber
- Department of Behavioral Neuroscience, Oregon Health and Science University, Portland, OR, USA
- Departments of Neurology and Radiation Medicine, Division of Neuroscience, ONPRC, Oregon Health and Science University, Portland, OR, USA
| | - Hod Dana
- Department of Neurosciences, Lerner Research Institute, Cleveland Clinic Foundation, Cleveland, OH, USA.
- Department of Molecular Medicine, Cleveland Clinic Lerner College of Medicine, School of Medicine, Case Western Reserve University, Cleveland, OH, USA.
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42
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Kim SJ, Affan RO, Frostig H, Scott BB, Alexander AS. Advances in cellular resolution microscopy for brain imaging in rats. NEUROPHOTONICS 2023; 10:044304. [PMID: 38076724 PMCID: PMC10704261 DOI: 10.1117/1.nph.10.4.044304] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/05/2023] [Revised: 09/23/2023] [Accepted: 11/07/2023] [Indexed: 02/12/2024]
Abstract
Rats are used in neuroscience research because of their physiological similarities with humans and accessibility as model organisms, trainability, and behavioral repertoire. In particular, rats perform a wide range of sophisticated social, cognitive, motor, and learning behaviors within the contexts of both naturalistic and laboratory environments. Further progress in neuroscience can be facilitated by using advanced imaging methods to measure the complex neural and physiological processes during behavior in rats. However, compared with the mouse, the rat nervous system offers a set of challenges, such as larger brain size, decreased neuron density, and difficulty with head restraint. Here, we review recent advances in in vivo imaging techniques in rats with a special focus on open-source solutions for calcium imaging. Finally, we provide suggestions for both users and developers of in vivo imaging systems for rats.
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Affiliation(s)
- Su Jin Kim
- Johns Hopkins University, Department of Psychological and Brain Sciences, Baltimore, Maryland, United States
| | - Rifqi O. Affan
- Boston University, Center for Systems Neuroscience, Department of Psychological and Brain Sciences, Boston, Massachusetts, United States
- Boston University, Graduate Program in Neuroscience, Boston, Massachusetts, United States
| | - Hadas Frostig
- Boston University, Center for Systems Neuroscience, Department of Psychological and Brain Sciences, Boston, Massachusetts, United States
| | - Benjamin B. Scott
- Boston University, Center for Systems Neuroscience, Department of Psychological and Brain Sciences, Boston, Massachusetts, United States
- Boston University, Neurophotonics Center and Photonics Center, Boston, Massachusetts, United States
| | - Andrew S. Alexander
- University of California Santa Barbara, Department of Psychological and Brain Sciences, Santa Barbara, California, United States
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43
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Grieco SF, Holmes TC, Xu X. Probing neural circuit mechanisms in Alzheimer's disease using novel technologies. Mol Psychiatry 2023; 28:4407-4420. [PMID: 36959497 PMCID: PMC10827671 DOI: 10.1038/s41380-023-02018-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/02/2022] [Revised: 02/20/2023] [Accepted: 02/24/2023] [Indexed: 03/25/2023]
Abstract
The study of Alzheimer's Disease (AD) has traditionally focused on neuropathological mechanisms that has guided therapies that attenuate neuropathological features. A new direction is emerging in AD research that focuses on the progressive loss of cognitive function due to disrupted neural circuit mechanisms. Evidence from humans and animal models of AD show that dysregulated circuits initiate a cascade of pathological events that culminate in functional loss of learning, memory, and other aspects of cognition. Recent progress in single-cell, spatial, and circuit omics informs this circuit-focused approach by determining the identities, locations, and circuitry of the specific cells affected by AD. Recently developed neuroscience tools allow for precise access to cell type-specific circuitry so that their functional roles in AD-related cognitive deficits and disease progression can be tested. An integrated systems-level understanding of AD-associated neural circuit mechanisms requires new multimodal and multi-scale interrogations that longitudinally measure and/or manipulate the ensemble properties of specific molecularly-defined neuron populations first susceptible to AD. These newly developed technological and conceptual advances present new opportunities for studying and treating circuits vulnerable in AD and represent the beginning of a new era for circuit-based AD research.
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Affiliation(s)
- Steven F Grieco
- Department of Anatomy and Neurobiology, School of Medicine, University of California, Irvine, CA, 92697, USA
- Center for Neural Circuit Mapping (CNCM), University of California, Irvine, CA, 92697, USA
| | - Todd C Holmes
- Center for Neural Circuit Mapping (CNCM), University of California, Irvine, CA, 92697, USA
- Department of Physiology and Biophysics, School of Medicine, University of California, Irvine, CA, 92697, USA
| | - Xiangmin Xu
- Department of Anatomy and Neurobiology, School of Medicine, University of California, Irvine, CA, 92697, USA.
- Center for Neural Circuit Mapping (CNCM), University of California, Irvine, CA, 92697, USA.
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44
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Klioutchnikov A, Kerr JND. Chasing cortical behavior: designing multiphoton microscopes for imaging neuronal populations in freely moving rodents. NEUROPHOTONICS 2023; 10:044411. [PMID: 37886044 PMCID: PMC10599648 DOI: 10.1117/1.nph.10.4.044411] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/12/2023] [Revised: 09/22/2023] [Accepted: 10/03/2023] [Indexed: 10/28/2023]
Abstract
Imaging in the freely moving animal gives unparalleled access to circuit activity as the animal interacts with its environment in a self-guided way. Over the past few years, new imaging technologies have enabled the interrogation of neuronal populations located at any depth of the cortex in freely moving mice while preserving the animal's behavioral repertoire. This commentary gives an updated overview of the recent advances that have enabled the link between behavior and the underlying neuronal activity to be explored.
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Affiliation(s)
- Alexandr Klioutchnikov
- Max Planck Institute for Neurobiology of Behavior, Department of Behavior and Brain Organization, Bonn, Germany
| | - Jason N. D. Kerr
- Max Planck Institute for Neurobiology of Behavior, Department of Behavior and Brain Organization, Bonn, Germany
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45
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Ding J, Peng L, Moon S, Lee HJ, Patel DS, Lu H. An expanded GCaMP reporter toolkit for functional imaging in Caenorhabditis elegans. G3 (BETHESDA, MD.) 2023; 13:jkad183. [PMID: 37565483 PMCID: PMC10542313 DOI: 10.1093/g3journal/jkad183] [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: 06/10/2023] [Accepted: 07/16/2023] [Indexed: 08/12/2023]
Abstract
In living organisms, changes in calcium flux are integral to many different cellular functions and are especially critical for the activity of neurons and myocytes. Genetically encoded calcium indicators (GECIs) have been popular tools for reporting changes in calcium levels in vivo. In particular, GCaMPs, derived from GFP, are the most widely used GECIs and have become an invaluable toolkit for neurophysiological studies. Recently, new variants of GCaMP, which offer a greater variety of temporal dynamics and improved brightness, have been developed. However, these variants are not readily available to the Caenorhabditis elegans research community. This work reports a set of GCaMP6 and jGCaMP7 reporters optimized for C. elegans studies. Our toolkit provides reporters with improved dynamic range, varied kinetics, and targeted subcellular localizations. Besides optimized routine uses, this set of reporters is also well suited for studies requiring fast imaging speeds and low magnification or low-cost platforms.
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Affiliation(s)
- Jimmy Ding
- Interdisciplinary Bioengineering Graduate Program, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - Lucinda Peng
- Interdisciplinary Bioengineering Graduate Program, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - Sihoon Moon
- School of Chemical & Biomolecular Engineering, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - Hyun Jee Lee
- School of Chemical & Biomolecular Engineering, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - Dhaval S Patel
- School of Chemical & Biomolecular Engineering, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - Hang Lu
- Interdisciplinary Bioengineering Graduate Program, Georgia Institute of Technology, Atlanta, GA 30332, USA
- School of Chemical & Biomolecular Engineering, Georgia Institute of Technology, Atlanta, GA 30332, USA
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46
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Zhao C, Zhu Y, Zhang D, Fu Q, Pan M, Wu R, Wang A, Cheng H. Millimeter field-of-view miniature two-photon microscopy for brain imaging in freely moving mice. OPTICS EXPRESS 2023; 31:32925-32934. [PMID: 37859084 DOI: 10.1364/oe.492674] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/07/2023] [Accepted: 09/07/2023] [Indexed: 10/21/2023]
Abstract
Development of miniature two-photon microscopy (m2PM) has made it possible to observe fine structure and activity of neurons in the brain of freely moving animals. However, the imaging field-of-view of existing m2PM is still significantly smaller than that of miniature single-photon microscopy. Here we report that, through the design of low-magnification objective, large field-of-view scan lens and small tilt angle microscanner, a 2.5-g m2PM achieved a field-of-view of 1000 × 788 µm2, comparable to that of a typical single-photon miniscope. We demonstrated its capability by imaging neurons, dendrites and spines in the millimeter field-of-view, and simultaneous recording calcium activities, through a gradient-index lens, of approximately 400 neurons in the dorsal hippocampal CA1 in a freely moving mouse. Integrated with a detachable 1.2-g fast z-scanning module, it enables a 1000 × 788 × 500 µm3 volumetric neuronal imaging in the cerebral cortex. Thus, millimeter FOV m2PM provides a powerful tool for deciphering neuronal population dynamics in experimental paradigms allowing for animal's free movement.
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47
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Peering into bats' brains as the animals fly and feed together. Nature 2023:10.1038/d41586-023-02451-6. [PMID: 37648823 DOI: 10.1038/d41586-023-02451-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/01/2023]
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48
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Case SL, Lin R, Thibault O. Age- and sex-dependent alterations in primary somatosensory cortex neuronal calcium network dynamics during locomotion. Aging Cell 2023; 22:e13898. [PMID: 37269157 PMCID: PMC10410056 DOI: 10.1111/acel.13898] [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: 03/16/2023] [Revised: 05/12/2023] [Accepted: 05/22/2023] [Indexed: 06/04/2023] Open
Abstract
Over the past 30 years, the calcium (Ca2+ ) hypothesis of brain aging has provided clear evidence that hippocampal neuronal Ca2+ dysregulation is a key biomarker of aging. Age-dependent Ca2+ -mediated changes in intrinsic excitability, synaptic plasticity, and activity have helped identify some of the mechanisms engaged in memory and cognitive decline based on work done mostly at the single-cell level and in the slice preparation. Recently, our lab identified age- and Ca2+ -related neuronal network dysregulation in the cortex of the anesthetized animal. Still, investigations in the awake animal are needed to test the generalizability of the Ca2+ hypothesis of brain aging. Here, we used in vigilo two-photon imaging in ambulating mice, to image GCaMP8f in the primary somatosensory cortex (S1), during ambulation and at rest. We investigated aging- and sex-related changes in neuronal networks in the C56BL/6J mouse. Following imaging, gait behavior was characterized to test for changes in locomotor stability. During ambulation, in both young adult and aged mice, an increase in network connectivity and synchronicity was noted. An age-dependent increase in synchronicity was seen in ambulating aged males only. Additionally, females displayed increases in the number of active neurons, Ca2+ transients, and neuronal activity compared to males, particularly during ambulation. These results suggest S1 Ca2+ dynamics and network synchronicity are likely contributors of locomotor stability. We believe this work raises awareness of age- and sex-dependent alterations in S1 neuronal networks, perhaps underlying the increase in falls with age.
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Affiliation(s)
- Sami L. Case
- Department of Pharmacology & Nutritional SciencesUniversity of Kentucky College of MedicineLexingtonKentuckyUSA
| | - Ruei‐Lung Lin
- Department of Pharmacology & Nutritional SciencesUniversity of Kentucky College of MedicineLexingtonKentuckyUSA
| | - Olivier Thibault
- Department of Pharmacology & Nutritional SciencesUniversity of Kentucky College of MedicineLexingtonKentuckyUSA
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García MJ, Kamaid A, Malacrida L. Label-free fluorescence microscopy: revisiting the opportunities with autofluorescent molecules and harmonic generations as biosensors and biomarkers for quantitative biology. Biophys Rev 2023; 15:709-719. [PMID: 37681086 PMCID: PMC10480099 DOI: 10.1007/s12551-023-01083-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2023] [Accepted: 06/19/2023] [Indexed: 09/09/2023] Open
Abstract
Over the past decade, the utilization of advanced fluorescence microscopy technologies has presented numerous opportunities to study or re-investigate autofluorescent molecules and harmonic generation signals as molecular biomarkers and biosensors for in vivo cell and tissue studies. The label-free approaches benefit from the endogenous fluorescent molecules within the cell and take advantage of their spectroscopy properties to address biological questions. Harmonic generation can be used as a tool to identify the occurrence of fibrillar or lipid deposits in tissues, by using second and third-harmonic generation microscopy. Combining autofluorescence with novel techniques and tools such as fluorescence lifetime imaging microscopy (FLIM) and hyperspectral imaging (HSI) with model-free analysis of phasor plots has revolutionized the understanding of molecular processes such as cellular metabolism. These tools provide quantitative information that is often hidden under classical intensity-based microscopy. In this short review, we aim to illustrate how some of these technologies and techniques may enable investigation without the need to add a foreign fluorescence molecule that can modify or affect the results. We address some of the most important autofluorescence molecules and their spectroscopic properties to illustrate the potential of these combined tools. We discuss using them as biomarkers and biosensors and, under the lens of this new technology, identify some of the challenges and potentials for future advances in the field.
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Affiliation(s)
- María José García
- Departamento de Fisiopatología, Hospital de Clínicas, Facultad de Medicina, Universidad de La República, Montevideo, Uruguay
- Advanced Bioimaging Unit, Institut Pasteur de Montevideo & Universidad de la República, Montevideo, Uruguay
| | - Andrés Kamaid
- Advanced Bioimaging Unit, Institut Pasteur de Montevideo & Universidad de la República, Montevideo, Uruguay
| | - Leonel Malacrida
- Departamento de Fisiopatología, Hospital de Clínicas, Facultad de Medicina, Universidad de La República, Montevideo, Uruguay
- Advanced Bioimaging Unit, Institut Pasteur de Montevideo & Universidad de la República, Montevideo, Uruguay
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Keshavarzi S, Velez-Fort M, Margrie TW. Cortical Integration of Vestibular and Visual Cues for Navigation, Visual Processing, and Perception. Annu Rev Neurosci 2023; 46:301-320. [PMID: 37428601 DOI: 10.1146/annurev-neuro-120722-100503] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/12/2023]
Abstract
Despite increasing evidence of its involvement in several key functions of the cerebral cortex, the vestibular sense rarely enters our consciousness. Indeed, the extent to which these internal signals are incorporated within cortical sensory representation and how they might be relied upon for sensory-driven decision-making, during, for example, spatial navigation, is yet to be understood. Recent novel experimental approaches in rodents have probed both the physiological and behavioral significance of vestibular signals and indicate that their widespread integration with vision improves both the cortical representation and perceptual accuracy of self-motion and orientation. Here, we summarize these recent findings with a focus on cortical circuits involved in visual perception and spatial navigation and highlight the major remaining knowledge gaps. We suggest that vestibulo-visual integration reflects a process of constant updating regarding the status of self-motion, and access to such information by the cortex is used for sensory perception and predictions that may be implemented for rapid, navigation-related decision-making.
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Affiliation(s)
- Sepiedeh Keshavarzi
- The Sainsbury Wellcome Centre for Neural Circuits and Behavior, University College London, London, United Kingdom;
| | - Mateo Velez-Fort
- The Sainsbury Wellcome Centre for Neural Circuits and Behavior, University College London, London, United Kingdom;
| | - Troy W Margrie
- The Sainsbury Wellcome Centre for Neural Circuits and Behavior, University College London, London, United Kingdom;
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