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Jia S, Yu Z, Onken A, Tian Y, Huang T, Liu JK. Neural System Identification With Spike-Triggered Non-Negative Matrix Factorization. IEEE TRANSACTIONS ON CYBERNETICS 2022; 52:4772-4783. [PMID: 33400673 DOI: 10.1109/tcyb.2020.3042513] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Neuronal circuits formed in the brain are complex with intricate connection patterns. Such complexity is also observed in the retina with a relatively simple neuronal circuit. A retinal ganglion cell (GC) receives excitatory inputs from neurons in previous layers as driving forces to fire spikes. Analytical methods are required to decipher these components in a systematic manner. Recently a method called spike-triggered non-negative matrix factorization (STNMF) has been proposed for this purpose. In this study, we extend the scope of the STNMF method. By using retinal GCs as a model system, we show that STNMF can detect various computational properties of upstream bipolar cells (BCs), including spatial receptive field, temporal filter, and transfer nonlinearity. In addition, we recover synaptic connection strengths from the weight matrix of STNMF. Furthermore, we show that STNMF can separate spikes of a GC into a few subsets of spikes, where each subset is contributed by one presynaptic BC. Taken together, these results corroborate that STNMF is a useful method for deciphering the structure of neuronal circuits.
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Luo L, Xu Y, Pan J, Wang M, Guan J, Liang S, Li Y, Jia H, Chen X, Li X, Zhang C, Liao X. Restoration of Two-Photon Ca 2+ Imaging Data Through Model Blind Spatiotemporal Filtering. Front Neurosci 2021; 15:630250. [PMID: 33935628 PMCID: PMC8085276 DOI: 10.3389/fnins.2021.630250] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2020] [Accepted: 03/12/2021] [Indexed: 11/17/2022] Open
Abstract
Two-photon Ca2+ imaging is a leading technique for recording neuronal activities in vivo with cellular or subcellular resolution. However, during experiments, the images often suffer from corruption due to complex noises. Therefore, the analysis of Ca2+ imaging data requires preprocessing steps, such as denoising, to extract biologically relevant information. We present an approach that facilitates imaging data restoration through image denoising performed by a neural network combining spatiotemporal filtering and model blind learning. Tests with synthetic and real two-photon Ca2+ imaging datasets demonstrate that the proposed approach enables efficient restoration of imaging data. In addition, we demonstrate that the proposed approach outperforms the current state-of-the-art methods by evaluating the qualities of the denoising performance of the models quantitatively. Therefore, our method provides an invaluable tool for denoising two-photon Ca2+ imaging data by model blind spatiotemporal processing.
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Affiliation(s)
- Liyong Luo
- Brain Research Center and State Key Laboratory of Trauma, Burns, and Combined Injury, Third Military Medical University, Chongqing, China
| | - Yuanxu Xu
- Brain Research Center and State Key Laboratory of Trauma, Burns, and Combined Injury, Third Military Medical University, Chongqing, China
| | - Junxia Pan
- Brain Research Center and State Key Laboratory of Trauma, Burns, and Combined Injury, Third Military Medical University, Chongqing, China
| | - Meng Wang
- Brain Research Center and State Key Laboratory of Trauma, Burns, and Combined Injury, Third Military Medical University, Chongqing, China
| | - Jiangheng Guan
- Brain Research Center and State Key Laboratory of Trauma, Burns, and Combined Injury, Third Military Medical University, Chongqing, China
| | - Shanshan Liang
- Brain Research Center and State Key Laboratory of Trauma, Burns, and Combined Injury, Third Military Medical University, Chongqing, China
| | - Yurong Li
- Department of Patient Management, Fifth Medical Center, Chinese PLA General Hospital, Beijing, China
| | - Hongbo Jia
- Brain Research Instrument Innovation Center, Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Sciences, Suzhou, China
| | - Xiaowei Chen
- Brain Research Center and State Key Laboratory of Trauma, Burns, and Combined Injury, Third Military Medical University, Chongqing, China
| | - Xingyi Li
- Center for Neurointelligence, School of Medicine, Chongqing University, Chongqing, China
| | - Chunqing Zhang
- Department of Neurosurgery, Xinqiao Hospital, Third Military Medical University, Chongqing, China
| | - Xiang Liao
- Center for Neurointelligence, School of Medicine, Chongqing University, Chongqing, China
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Involvement of NMDA and GABA(A) receptors in modulation of spontaneous activity in hippocampal culture: Interrelations between burst firing and intracellular calcium signal. Biochem Biophys Res Commun 2021; 553:99-106. [PMID: 33765560 DOI: 10.1016/j.bbrc.2021.02.149] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2021] [Accepted: 02/09/2021] [Indexed: 12/28/2022]
Abstract
Spontaneous burst firing is a hallmark attributed to the neuronal network activity. It is known to be accompanied by intracellular calcium [Са2+]i oscillations within the bursting neurons. Studying mechanisms underlying regulation of burst firing is highly relevant, since impairment in neuronal bursting accompanies different neurological disorders. In the present study, the contribution of NMDA and GABA(A) receptors to the shape formation of spontaneous burst -was studied in cultured hippocampal neurons. A combination of inhibitory analysis with simultaneous registration of neuronal bursting by whole-cell patch clamp and calcium imaging was used to assess spontaneous burst firing and [Са2+]i level. Using bicuculline and D-AP5 we showed that GABA(A) and NMDA receptors effectively modulate burst plateau phase and [Са2+]i transient spike which can further affect action potential (AP) amplitudes and firing frequency within a burst. Bicuculline significantly elevated the amplitude and reduced the duration of both burst plateau phase and [Са2+]i spike resulting in an increase of AP firing frequency and shortening of AP amplitudes within a burst. D-AP5 significantly decreases the amplitude of both plateau phase and [Са2+]i spike along with a burst duration that correlated with an increase in AP amplitudes and reduced firing frequency within a burst. The effect of bicuculline was occluded by co-addition of D-AP5 revealing modulatory role of GABA(A) receptors to the NMDA receptor-mediated formation of the burst. Our results provide new evidence on importance of NMDA and GABA(A) receptors in shaping burst firing and Ca2+transient spikes in cultured hippocampal neurons.
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Noguchi A, Ikegaya Y, Matsumoto N. In Vivo Whole-Cell Patch-Clamp Methods: Recent Technical Progress and Future Perspectives. SENSORS (BASEL, SWITZERLAND) 2021; 21:1448. [PMID: 33669656 PMCID: PMC7922023 DOI: 10.3390/s21041448] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/23/2020] [Revised: 02/12/2021] [Accepted: 02/16/2021] [Indexed: 02/01/2023]
Abstract
Brain functions are fundamental for the survival of organisms, and they are supported by neural circuits consisting of a variety of neurons. To investigate the function of neurons at the single-cell level, researchers often use whole-cell patch-clamp recording techniques. These techniques enable us to record membrane potentials (including action potentials) of individual neurons of not only anesthetized but also actively behaving animals. This whole-cell recording method enables us to reveal how neuronal activities support brain function at the single-cell level. In this review, we introduce previous studies using in vivo patch-clamp recording techniques and recent findings primarily regarding neuronal activities in the hippocampus for behavioral function. We further discuss how we can bridge the gap between electrophysiology and biochemistry.
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Affiliation(s)
- Asako Noguchi
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, Tokyo 113-0033, Japan; (A.N.); (Y.I.)
| | - Yuji Ikegaya
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, Tokyo 113-0033, Japan; (A.N.); (Y.I.)
- Institute for AI and Beyond, The University of Tokyo, Tokyo 113-0033, Japan
- Center for Information and Neural Networks, National Institute of Information and Communications Technology, Suita City, Osaka 565-0871, Japan
| | - Nobuyoshi Matsumoto
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, Tokyo 113-0033, Japan; (A.N.); (Y.I.)
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Moreaux LC, Yatsenko D, Sacher WD, Choi J, Lee C, Kubat NJ, Cotton RJ, Boyden ES, Lin MZ, Tian L, Tolias AS, Poon JKS, Shepard KL, Roukes ML. Integrated Neurophotonics: Toward Dense Volumetric Interrogation of Brain Circuit Activity-at Depth and in Real Time. Neuron 2020; 108:66-92. [PMID: 33058767 PMCID: PMC8061790 DOI: 10.1016/j.neuron.2020.09.043] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2020] [Revised: 08/18/2020] [Accepted: 09/28/2020] [Indexed: 12/17/2022]
Abstract
We propose a new paradigm for dense functional imaging of brain activity to surmount the limitations of present methodologies. We term this approach "integrated neurophotonics"; it combines recent advances in microchip-based integrated photonic and electronic circuitry with those from optogenetics. This approach has the potential to enable lens-less functional imaging from within the brain itself to achieve dense, large-scale stimulation and recording of brain activity with cellular resolution at arbitrary depths. We perform a computational study of several prototype 3D architectures for implantable probe-array modules that are designed to provide fast and dense single-cell resolution (e.g., within a 1-mm3 volume of mouse cortex comprising ∼100,000 neurons). We describe progress toward realizing integrated neurophotonic imaging modules, which can be produced en masse with current semiconductor foundry protocols for chip manufacturing. Implantation of multiple modules can cover extended brain regions.
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Affiliation(s)
- Laurent C Moreaux
- Division of Physics, Mathematics and Astronomy, California Institute of Technology, Pasadena, CA 91125, USA.
| | - Dimitri Yatsenko
- Vathes LLC, Houston, TX 77030, USA; Center for Neuroscience and Artificial Intelligence and Department of Neuroscience, Baylor College of Medicine, Houston, TX 77030, USA
| | - Wesley D Sacher
- Kavli Nanoscience Institute, California Institute of Technology, Pasadena, CA 91125, USA; Division of Engineering and Applied Science, California Institute of Technology, Pasadena, CA 91125, USA; Max Planck Institute for Microstructure Physics, Halle, Germany
| | - Jaebin Choi
- Departments of Electrical Engineering and Biomedical Engineering, Columbia University, New York, NY 10027, USA
| | - Changhyuk Lee
- Departments of Electrical Engineering and Biomedical Engineering, Columbia University, New York, NY 10027, USA; Center for BioMicrosystems, Brain Science Institute, Korea Institute of Science and Technology, Korea
| | - Nicole J Kubat
- Division of Physics, Mathematics and Astronomy, California Institute of Technology, Pasadena, CA 91125, USA
| | - R James Cotton
- Shirley Ryan AbilityLab, Northwestern University, Chicago, IL 60611, USA; Center for Neuroscience and Artificial Intelligence and Department of Neuroscience, Baylor College of Medicine, Houston, TX 77030, USA
| | - Edward S Boyden
- Howard Hughes Medical Institute, Cambridge, MA, USA; McGovern Institute, MIT, Cambridge, USA; Koch Institute, MIT, Cambridge, USA; Departments of Brain and Cognitive Sciences, Media Arts and Sciences, and Biological Engineering, MIT, Cambridge, USA
| | - Michael Z Lin
- Departments of Neurobiology and Bioengineering, Stanford University, Stanford, CA 94305, USA
| | - Lin Tian
- Department of Biochemistry and Molecular Medicine, School of Medicine, University of California, Davis, CA 95616, USA
| | - Andreas S Tolias
- Vathes LLC, Houston, TX 77030, USA; Center for Neuroscience and Artificial Intelligence and Department of Neuroscience, Baylor College of Medicine, Houston, TX 77030, USA; Department of Electrical and Computer Engineering, Rice University, Houston, TX 77005, USA
| | - Joyce K S Poon
- Max Planck Institute for Microstructure Physics, Halle, Germany; Department of Electrical and Computer Engineering, University of Toronto, 10 King's College Rd., Toronto, ON M5S 3G4, Canada
| | - Kenneth L Shepard
- Departments of Electrical Engineering and Biomedical Engineering, Columbia University, New York, NY 10027, USA
| | - Michael L Roukes
- Division of Physics, Mathematics and Astronomy, California Institute of Technology, Pasadena, CA 91125, USA; Kavli Nanoscience Institute, California Institute of Technology, Pasadena, CA 91125, USA; Division of Engineering and Applied Science, California Institute of Technology, Pasadena, CA 91125, USA; Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA.
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6
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Li Y, Ding R, Wang F, Guo C, Liu A, Wei L, Yuan S, Chen F, Hou S, Ma Z, Zhang Y, Cudmore RH, Wang X, Shen H. Transient ischemia-reperfusion induces cortical hyperactivity and AMPAR trafficking in the somatosensory cortex. Aging (Albany NY) 2020; 12:4299-4321. [PMID: 32155129 PMCID: PMC7093173 DOI: 10.18632/aging.102881] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2019] [Accepted: 02/05/2020] [Indexed: 01/20/2023]
Abstract
Brain ischemia results from cardiac arrest, stroke or head trauma. The structural basis of rescuing the synaptic impairment and cortical dysfunctions induced in the stage of ischemic-reperfusion can occur if therapeutic interventions are applied in time, but the functional basis for this resilience remains elusive. Here, we explore the changes in cortical activity and a-amino-3-hydroxy-5-methyl-4-isoxazole propionic acid receptor (AMPAR) GluA1 subunit in spine (sGluA1) after transient ischemia-reperfusion in vivo for 28 days. Using in vivo two-photon microscopy in the mouse somatosensory cortex, we found that the average frequency of Ca2+ transients in the spine (there was an unusual synchrony) was higher after 15 min of ischemia-reperfusion. In addition, the transient ischemia-reperfusion caused a reflective enhancement of AMPARs, which eventually restored to normal. The cortical hyperactivity (Ca2+ transients) and the increase in AMPARs were successfully blocked by an NMDA receptor antagonist. Thus, the increase of AMPARs, cortical hyperactivity and the unusual synchrony might be the reason for reperfusion injury after short-term transient ischemia.
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Affiliation(s)
- Yuanyuan Li
- School of Biomedical Engineering, Tianjin Medical University, Tianjin, China
| | - Ran Ding
- Chinese Institute for Brain Research, Beijing (CIBR), Beijing, China
| | - Feifei Wang
- School of Biomedical Engineering, Tianjin Medical University, Tianjin, China
| | - Cuiping Guo
- Department of Pathophysiology, School of Basic Medicine, Key Laboratory of Ministry of Education of China for Neurological Disorders, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Aili Liu
- School of Biomedical Engineering, Tianjin Medical University, Tianjin, China
| | - Liangpeng Wei
- School of Biomedical Engineering, Tianjin Medical University, Tianjin, China
| | - Shiyang Yuan
- School of Biomedical Engineering, Tianjin Medical University, Tianjin, China
| | - Feng Chen
- School of Biomedical Engineering, Tianjin Medical University, Tianjin, China
| | - Shaowei Hou
- School of Biomedical Engineering, Tianjin Medical University, Tianjin, China
| | - Zengguang Ma
- School of Biomedical Engineering, Tianjin Medical University, Tianjin, China
| | - Yan Zhang
- Tianjin Key Laboratory of Retinal Function and Diseases, Tianjin Medical University Eye Hospital, Eye Institute and School of Optometry and Ophthalmology, Tianjin Medical University, Tianjin, China
| | - Robert H Cudmore
- Department of Physiology and Membrane Biology, University of California Davis School of Medicine, Sacramento, CA 95817, USA
| | - Xiaochuan Wang
- Department of Pathophysiology, School of Basic Medicine, Key Laboratory of Ministry of Education of China for Neurological Disorders, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China.,Division of Neurodegenerative Disorders, Co-innovation Center of Neuroregeneration, Nantong University, Nantong, China
| | - Hui Shen
- School of Biomedical Engineering, Tianjin Medical University, Tianjin, China.,Research Institute of Neurology, General Hospital, Tianjin Medical University, Tianjin, China
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Two-photon imaging of neuronal activity in motor cortex of marmosets during upper-limb movement tasks. Nat Commun 2018; 9:1879. [PMID: 29760466 PMCID: PMC5951821 DOI: 10.1038/s41467-018-04286-6] [Citation(s) in RCA: 54] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2017] [Accepted: 04/18/2018] [Indexed: 12/23/2022] Open
Abstract
Two-photon imaging in behaving animals has revealed neuronal activities related to behavioral and cognitive function at single-cell resolution. However, marmosets have posed a challenge due to limited success in training on motor tasks. Here we report the development of protocols to train head-fixed common marmosets to perform upper-limb movement tasks and simultaneously perform two-photon imaging. After 2–5 months of training sessions, head-fixed marmosets can control a manipulandum to move a cursor to a target on a screen. We conduct two-photon calcium imaging of layer 2/3 neurons in the motor cortex during this motor task performance, and detect task-relevant activity from multiple neurons at cellular and subcellular resolutions. In a two-target reaching task, some neurons show direction-selective activity over the training days. In a short-term force-field adaptation task, some neurons change their activity when the force field is on. Two-photon calcium imaging in behaving marmosets may become a fundamental technique for determining the spatial organization of the cortical dynamics underlying action and cognition. Marmosets are an important model organism in neuroscience but there has only been limited success in training them on behavioral tasks. Here the authors report their ability to train marmosets in various motor tasks and simultaneously image neural dynamics in motor cortex with 2-photon imaging.
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Agnati LF, Marcoli M, Maura G, Woods A, Guidolin D. The brain as a "hyper-network": the key role of neural networks as main producers of the integrated brain actions especially via the "broadcasted" neuroconnectomics. J Neural Transm (Vienna) 2018; 125:883-897. [PMID: 29427068 DOI: 10.1007/s00702-018-1855-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2017] [Accepted: 02/04/2018] [Indexed: 02/07/2023]
Abstract
Investigations of brain complex integrative actions should consider beside neural networks, glial, extracellular molecular, and fluid channels networks. The present paper proposes that all these networks are assembled into the brain hyper-network that has as fundamental components, the tetra-partite synapses, formed by neural, glial, and extracellular molecular networks. Furthermore, peri-synaptic astrocytic processes by modulating the perviousness of extracellular fluid channels control the signals impinging on the tetra-partite synapses. It has also been surmised that global signalling via astrocytes networks and highly pervasive signals, such as electromagnetic fields (EMFs), allow the appropriate integration of the various networks especially at crucial nodes level, the tetra-partite synapses. As a matter of fact, it has been shown that astrocytes can form gap-junction-coupled syncytia allowing intercellular communication characterised by a rapid and possibly long-distance transfer of signals. As far as the EMFs are concerned, the concept of broadcasted neuroconnectomics (BNC) has been introduced to describe highly pervasive signals involved in resetting the information handling of brain networks at various miniaturisation levels. In other words, BNC creates, thanks to the EMFs, generated especially by neurons, different assemblages among the various networks forming the brain hyper-network. Thus, it is surmised that neuronal networks are the "core components" of the brain hyper-network that has as special "nodes" the multi-facet tetra-partite synapses. Furthermore, it is suggested that investigations on the functional plasticity of multi-partite synapses in response to BNC can be the background for a new understanding and perhaps a new modelling of brain morpho-functional organisation and integrative actions.
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Affiliation(s)
- Luigi F Agnati
- Department of Diagnostic, Clinical Medicine and Public Health, University of Modena and Reggio Emilia, Modena, Italy. .,Department of Neuroscience, Karolinska Institutet, Stockholm, Sweden.
| | - Manuela Marcoli
- Section of Pharmacology and Toxicology, Department of Pharmacy, University of Genova, Viale Cembrano 4, 16148, Genoa, Italy. .,Centre of Excellence for Biomedical Research CEBR, University of Genova, Genoa, Italy.
| | - Guido Maura
- Section of Pharmacology and Toxicology, Department of Pharmacy, University of Genova, Viale Cembrano 4, 16148, Genoa, Italy
| | - Amina Woods
- Structural Biology Unit, National Institutes of Health, National Institute of Drug Abuse-Intramural Research Program, Baltimore, MD, 21224, USA
| | - Diego Guidolin
- Department of Molecular Medicine, University of Padova, Padua, Italy
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Rasmussen R, Yonehara K. Circuit Mechanisms Governing Local vs. Global Motion Processing in Mouse Visual Cortex. Front Neural Circuits 2017; 11:109. [PMID: 29311845 PMCID: PMC5743699 DOI: 10.3389/fncir.2017.00109] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2017] [Accepted: 12/14/2017] [Indexed: 11/21/2022] Open
Abstract
A withstanding question in neuroscience is how neural circuits encode representations and perceptions of the external world. A particularly well-defined visual computation is the representation of global object motion by pattern direction-selective (PDS) cells from convergence of motion of local components represented by component direction-selective (CDS) cells. However, how PDS and CDS cells develop their distinct response properties is still unresolved. The visual cortex of the mouse is an attractive model for experimentally solving this issue due to the large molecular and genetic toolbox available. Although mouse visual cortex lacks the highly ordered orientation columns of primates, it is organized in functional sub-networks and contains striate- and extrastriate areas like its primate counterparts. In this Perspective article, we provide an overview of the experimental and theoretical literature on global motion processing based on works in primates and mice. Lastly, we propose what types of experiments could illuminate what circuit mechanisms are governing cortical global visual motion processing. We propose that PDS cells in mouse visual cortex appear as the perfect arena for delineating and solving how individual sensory features extracted by neural circuits in peripheral brain areas are integrated to build our rich cohesive sensory experiences.
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Affiliation(s)
- Rune Rasmussen
- The Danish Research Institute of Translational Neuroscience-DANDRITE, Nordic EMBL Partnership for Molecular Medicine, Department of Biomedicine, Aarhus University, Aarhus, Denmark
| | - Keisuke Yonehara
- The Danish Research Institute of Translational Neuroscience-DANDRITE, Nordic EMBL Partnership for Molecular Medicine, Department of Biomedicine, Aarhus University, Aarhus, Denmark
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