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Aggarwal A, Negrean A, Chen Y, Iyer R, Reep D, Liu A, Palutla A, Xie ME, MacLennan BJ, Hagihara KM, Kinsey LW, Sun JL, Yao P, Zheng J, Tsang A, Tsegaye G, Zhang Y, Patel RH, Arthur BJ, Hiblot J, Leippe P, Tarnawski M, Marvin JS, Vevea JD, Turaga SC, Tebo AG, Carandini M, Federico Rossi L, Kleinfeld D, Konnerth A, Svoboda K, Turner GC, Hasseman J, Podgorski K. Glutamate indicators with increased sensitivity and tailored deactivation rates. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2025:2025.03.20.643984. [PMID: 40196590 PMCID: PMC11974752 DOI: 10.1101/2025.03.20.643984] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 04/09/2025]
Abstract
Identifying the input-output operations of neurons requires measurements of synaptic transmission simultaneously at many of a neuron's thousands of inputs in the intact brain. To facilitate this goal, we engineered and screened 3365 variants of the fluorescent protein glutamate indicator iGluSnFR3 in neuron culture, and selected variants in the mouse visual cortex. Two variants have high sensitivity, fast activation (< 2 ms) and deactivation times tailored for recording large populations of synapses (iGluSnFR4s, 153 ms) or rapid dynamics (iGluSnFR4f, 26 ms). By imaging action-potential evoked signals on axons and visually-evoked signals on dendritic spines, we show that iGluSnFR4s/4f primarily detect local synaptic glutamate with single-vesicle sensitivity. The indicators detect a wide range of naturalistic synaptic transmission, including in the vibrissal cortex layer 4 and in hippocampal CA1 dendrites. iGluSnFR4 increases the sensitivity and scale (4s) or speed (4f) of tracking information flow in neural networks in vivo.
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Affiliation(s)
- Abhi Aggarwal
- Allen Institute for Neural Dynamics, Seattle, Washington, USA
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, Virginia, USA
- University of Calgary Cumming School of Medicine and Hotchkiss Brain Institute, Calgary, Alberta, Canada
| | - Adrian Negrean
- Allen Institute for Neural Dynamics, Seattle, Washington, USA
| | - Yang Chen
- Institute of Neuroscience and Munich Cluster for Systems Neurology, Technical University of Munich, Munich, Germany
| | - Rishyashring Iyer
- Department of Physics, University of California, San Diego, La Jolla, California, USA
| | - Daniel Reep
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, Virginia, USA
- The GENIE Project Team
| | - Anyi Liu
- University College London, Gower St, London, United Kingdom
| | - Anirudh Palutla
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, Virginia, USA
| | - Michael E. Xie
- Allen Institute for Neural Dynamics, Seattle, Washington, USA
- Johns Hopkins University, Baltimore, MD, USA
| | | | | | - Lucas W. Kinsey
- Allen Institute for Neural Dynamics, Seattle, Washington, USA
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, Virginia, USA
| | - Julianna L. Sun
- Neuronal Cell Biology Division, Department of Developmental Neurobiology, St. Jude Children’s Research Hospital, Memphis, TN, USA
| | - Pantong Yao
- Department of Neurosciences, University of California, San Diego, La Jolla, California, USA
| | - Jihong Zheng
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, Virginia, USA
- The GENIE Project Team
| | - Arthur Tsang
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, Virginia, USA
- The GENIE Project Team
| | - Getahun Tsegaye
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, Virginia, USA
- The GENIE Project Team
| | - Yonghai Zhang
- Institute of Neuroscience and Munich Cluster for Systems Neurology, Technical University of Munich, Munich, Germany
| | - Ronak H. Patel
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, Virginia, USA
| | - Benjamin J. Arthur
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, Virginia, USA
| | - Julien Hiblot
- Max Planck Institute for Medical Research, Heidelberg, Germany
| | - Philipp Leippe
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Wien, Austria
| | | | - Jonathan S. Marvin
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, Virginia, USA
| | - Jason D. Vevea
- Neuronal Cell Biology Division, Department of Developmental Neurobiology, St. Jude Children’s Research Hospital, Memphis, TN, USA
| | - Srinivas C. Turaga
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, Virginia, USA
| | - Alison G. Tebo
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, Virginia, USA
| | | | - L. Federico Rossi
- University College London, Gower St, London, United Kingdom
- Center for Neuroscience and Cognitive Systems, Italian Institute of Technology, Rovereto, Italy
| | - David Kleinfeld
- Department of Physics, University of California, San Diego, La Jolla, California, USA
- Department of Neurobiology, University of California, San Diego, La Jolla, California, USA
| | - Arthur Konnerth
- Institute of Neuroscience and Munich Cluster for Systems Neurology, Technical University of Munich, Munich, Germany
| | - Karel Svoboda
- Allen Institute for Neural Dynamics, Seattle, Washington, USA
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, Virginia, USA
| | - Glenn C. Turner
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, Virginia, USA
- The GENIE Project Team
| | - Jeremy Hasseman
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, Virginia, USA
- The GENIE Project Team
| | - Kaspar Podgorski
- Allen Institute for Neural Dynamics, Seattle, Washington, USA
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, Virginia, USA
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3
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Kim J, McHugh TJ, Kim CH, Lau H, Nam MH. The future of neurotechnology: From big data to translation. Neuron 2025; 113:814-816. [PMID: 40068678 DOI: 10.1016/j.neuron.2025.02.019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2025] [Revised: 02/14/2025] [Accepted: 02/18/2025] [Indexed: 03/22/2025]
Abstract
Advances in neurotechnologies, including molecular tools, neural sensors, and large-scale recording, are transforming neuroscience and generating vast datasets. A recent meeting highlighted the resulting challenges in global collaboration, data management, and effective translation, emphasizing the need for innovative strategies to harness big data for diagnosing and treating brain disorders.
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Affiliation(s)
- Jinhyun Kim
- Brain Science Institute, Korea Institute of Science and Technology (KIST), Seoul, South Korea.
| | - Thomas J McHugh
- Brain Science Institute, Korea Institute of Science and Technology (KIST), Seoul, South Korea; Laboratory for Circuit and Behavioral Physiology, RIKEN Center for Brain Science, Wako-shi, Saitama, Japan.
| | - Chul Hoon Kim
- Yonsei University College of Medicine, Seoul, South Korea
| | - Hakwan Lau
- Center for Neuroscience Imaging Research, Institute for Basic Science, Suwon, South Korea; Department of Biomedical Engineering, Sungkyunkwan University, Suwon, South Korea; RIKEN Center for Brain Science, Wako, Japan
| | - Min-Ho Nam
- Brain Science Institute, Korea Institute of Science and Technology (KIST), Seoul, South Korea
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4
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O'Neill PS, Baccino-Calace M, Rupprecht P, Lee S, Hao YA, Lin MZ, Friedrich RW, Mueller M, Delvendahl I. A deep learning framework for automated and generalized synaptic event analysis. eLife 2025; 13:RP98485. [PMID: 40042890 PMCID: PMC11882139 DOI: 10.7554/elife.98485] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/13/2025] Open
Abstract
Quantitative information about synaptic transmission is key to our understanding of neural function. Spontaneously occurring synaptic events carry fundamental information about synaptic function and plasticity. However, their stochastic nature and low signal-to-noise ratio present major challenges for the reliable and consistent analysis. Here, we introduce miniML, a supervised deep learning-based method for accurate classification and automated detection of spontaneous synaptic events. Comparative analysis using simulated ground-truth data shows that miniML outperforms existing event analysis methods in terms of both precision and recall. miniML enables precise detection and quantification of synaptic events in electrophysiological recordings. We demonstrate that the deep learning approach generalizes easily to diverse synaptic preparations, different electrophysiological and optical recording techniques, and across animal species. miniML provides not only a comprehensive and robust framework for automated, reliable, and standardized analysis of synaptic events, but also opens new avenues for high-throughput investigations of neural function and dysfunction.
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Affiliation(s)
- Philipp S O'Neill
- Department of Molecular Life Sciences, University of Zurich (UZH)ZurichSwitzerland
- Neuroscience Center ZurichZurichSwitzerland
- Institute of Physiology, Faculty of Medicine, University of FreiburgFreiburgGermany
| | | | - Peter Rupprecht
- Neuroscience Center ZurichZurichSwitzerland
- Brain Research Institute, University of ZurichZurichSwitzerland
| | - Sungmoo Lee
- Department of Neurobiology, Stanford UniversityStanfordUnited States
| | - Yukun A Hao
- Department of Neurobiology, Stanford UniversityStanfordUnited States
| | - Michael Z Lin
- Department of Neurobiology, Stanford UniversityStanfordUnited States
- Department of Bioengineering, Stanford UniversityStanfordUnited States
| | - Rainer W Friedrich
- Friedrich Miescher Institute for Biomedical ResearchBaselSwitzerland
- Faculty of Natural Sciences, University of BaselBaselSwitzerland
| | - Martin Mueller
- Department of Molecular Life Sciences, University of Zurich (UZH)ZurichSwitzerland
- Neuroscience Center ZurichZurichSwitzerland
- University Research Priority Program (URPP), Adaptive Brain Circuits in Development and Learning (AdaBD), University of ZurichZurichSwitzerland
| | - Igor Delvendahl
- Department of Molecular Life Sciences, University of Zurich (UZH)ZurichSwitzerland
- Neuroscience Center ZurichZurichSwitzerland
- Institute of Physiology, Faculty of Medicine, University of FreiburgFreiburgGermany
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5
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Pjanovic V, Zavatone-Veth J, Masset P, Keemink S, Nardin M. Combining Sampling Methods with Attractor Dynamics in Spiking Models of Head-Direction Systems. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2025:2025.02.25.640158. [PMID: 40060526 PMCID: PMC11888369 DOI: 10.1101/2025.02.25.640158] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 03/15/2025]
Abstract
Uncertainty is a fundamental aspect of the natural environment, requiring the brain to infer and integrate noisy signals to guide behavior effectively. Sampling-based inference has been proposed as a mechanism for dealing with uncertainty, particularly in early sensory processing. However, it is unclear how to reconcile sampling-based methods with operational principles of higher-order brain areas, such as attractor dynamics of persistent neural representations. In this study, we present a spiking neural network model for the head-direction (HD) system that combines sampling-based inference with attractor dynamics. To achieve this, we derive the required spiking neural network dynamics and interactions to perform sampling from a large family of probability distributions-including variables encoded with Poisson noise. We then propose a method that allows the network to update its estimate of the current head direction by integrating angular velocity samples-derived from noisy inputs-with a pull towards a circular manifold, thereby maintaining consistent attractor dynamics. This model makes specific, testable predictions about the HD system that can be examined in future neurophysiological experiments: it predicts correlated subthreshold voltage fluctuations; distinctive short- and long-term firing correlations among neurons; and characteristic statistics of the movement of the neural activity "bump" representing the head direction. Overall, our approach extends previous theories on probabilistic sampling with spiking neurons, offers a novel perspective on the computations responsible for orientation and navigation, and supports the hypothesis that sampling-based methods can be combined with attractor dynamics to provide a viable framework for studying neural dynamics across the brain.
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Affiliation(s)
- Vojko Pjanovic
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA
- Department of Machine Learning and Neural Computing, Donders Institute for Brain, Cognition and Behaviour, Radboud University, Netherlands
| | - Jacob Zavatone-Veth
- Society of Fellows and Center for Brain Science, Harvard University, Cambridge, MA, USA
| | - Paul Masset
- Department of Psychology, McGill University, Montréal QC, Canada
| | - Sander Keemink
- Department of Machine Learning and Neural Computing, Donders Institute for Brain, Cognition and Behaviour, Radboud University, Netherlands
| | - Michele Nardin
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA
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