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Agyeman KA, Lee DJ, Russin J, Kreydin EI, Choi W, Abedi A, Lo YT, Cavaleri J, Wu K, Edgerton VR, Liu C, Christopoulos VN. Functional ultrasound imaging of the human spinal cord. Neuron 2024; 112:1710-1722.e3. [PMID: 38458198 DOI: 10.1016/j.neuron.2024.02.012] [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: 06/08/2023] [Revised: 11/03/2023] [Accepted: 02/15/2024] [Indexed: 03/10/2024]
Abstract
Utilizing the first in-human functional ultrasound imaging (fUSI) of the spinal cord, we demonstrate the integration of spinal functional responses to electrical stimulation. We record and characterize the hemodynamic responses of the spinal cord to a neuromodulatory intervention commonly used for treating pain and increasingly used for the restoration of sensorimotor and autonomic function. We found that the hemodynamic response to stimulation reflects a spatiotemporal modulation of the spinal cord circuitry not previously recognized. Our analytical capability offers a mechanism to assess blood flow changes with a new level of spatial and temporal precision in vivo and demonstrates that fUSI can decode the functional state of spinal networks in a single trial, which is of fundamental importance for developing real-time closed-loop neuromodulation systems. This work is a critical step toward developing a vital technique to study spinal cord function and effects of clinical neuromodulation.
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Affiliation(s)
- K A Agyeman
- Department of Bioengineering, University of California Riverside, Riverside, CA, USA
| | - D J Lee
- Department of Neurological Surgery, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA; Neurorestoration Center, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA; Rancho Los Amigos National Rehabilitation Center, Downey, CA, USA; Department of Biomedical Engineering, Viterbi School of Engineering, University of Southern California, Los Angeles, CA, USA
| | - J Russin
- Department of Neurological Surgery, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA; Neurorestoration Center, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA; Rancho Los Amigos National Rehabilitation Center, Downey, CA, USA; Department of Biomedical Engineering, Viterbi School of Engineering, University of Southern California, Los Angeles, CA, USA
| | - E I Kreydin
- Department of Neurological Surgery, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA; Neurorestoration Center, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA; Rancho Los Amigos National Rehabilitation Center, Downey, CA, USA; Institute of Urology, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - W Choi
- Department of Neurological Surgery, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA; Neurorestoration Center, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - A Abedi
- Department of Neurological Surgery, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA; Neurorestoration Center, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Y T Lo
- Department of Neurological Surgery, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA; Neurorestoration Center, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA; Department of Neurosurgery, National Neuroscience Institute, Singapore, Singapore
| | - J Cavaleri
- Department of Neurological Surgery, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - K Wu
- Department of Neurological Surgery, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA; Neurorestoration Center, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - V R Edgerton
- Neurorestoration Center, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA; Rancho Los Amigos National Rehabilitation Center, Downey, CA, USA.
| | - C Liu
- Department of Neurological Surgery, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA; Neurorestoration Center, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA; Rancho Los Amigos National Rehabilitation Center, Downey, CA, USA; Institute of Urology, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA; Department of Biomedical Engineering, Viterbi School of Engineering, University of Southern California, Los Angeles, CA, USA.
| | - V N Christopoulos
- Department of Bioengineering, University of California Riverside, Riverside, CA, USA; Department of Neurological Surgery, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA; Neurorestoration Center, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA; Neuroscience Graduate Program, University of California Riverside, Riverside, CA, USA.
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2
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Kogan JF, Fontanini A. Learning enhances representations of taste-guided decisions in the mouse gustatory insular cortex. Curr Biol 2024; 34:1880-1892.e5. [PMID: 38631343 DOI: 10.1016/j.cub.2024.03.034] [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: 10/16/2023] [Revised: 02/07/2024] [Accepted: 03/19/2024] [Indexed: 04/19/2024]
Abstract
Learning to discriminate overlapping gustatory stimuli that predict distinct outcomes-a feat known as discrimination learning-can mean the difference between ingesting a poison or a nutritive meal. Despite the obvious importance of this process, very little is known about the neural basis of taste discrimination learning. In other sensory modalities, this form of learning can be mediated by either the sharpening of sensory representations or the enhanced ability of "decision-making" circuits to interpret sensory information. Given the dual role of the gustatory insular cortex (GC) in encoding both sensory and decision-related variables, this region represents an ideal site for investigating how neural activity changes as animals learn a novel taste discrimination. Here, we present results from experiments relying on two-photon calcium imaging of GC neural activity in mice performing a taste-guided mixture discrimination task. The task allows for the recording of neural activity before and after learning induced by training mice to discriminate increasingly similar pairs of taste mixtures. Single-neuron and population analyses show a time-varying pattern of activity, with early sensory responses emerging after taste delivery and binary, choice-encoding responses emerging later in the delay before a decision is made. Our results demonstrate that, while both sensory and decision-related information is encoded by GC in the context of a taste mixture discrimination task, learning and improved performance are associated with a specific enhancement of decision-related responses.
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Affiliation(s)
- Joshua F Kogan
- Graduate Program in Neuroscience, Stony Brook University, Stony Brook, NY 11794, USA; Medical Scientist Training Program, Stony Brook University, Stony Brook, NY 11794, USA; Department of Neurobiology and Behavior, Stony Brook University, Stony Brook, NY 11794, USA.
| | - Alfredo Fontanini
- Graduate Program in Neuroscience, Stony Brook University, Stony Brook, NY 11794, USA; Medical Scientist Training Program, Stony Brook University, Stony Brook, NY 11794, USA; Department of Neurobiology and Behavior, Stony Brook University, Stony Brook, NY 11794, USA.
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3
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Wu Y, Xu Z, Liang S, Wang L, Wang M, Jia H, Chen X, Zhao Z, Liao X. NeuroSeg-III: efficient neuron segmentation in two-photon Ca 2+ imaging data using self-supervised learning. BIOMEDICAL OPTICS EXPRESS 2024; 15:2910-2925. [PMID: 38855703 PMCID: PMC11161377 DOI: 10.1364/boe.521478] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/12/2024] [Revised: 03/28/2024] [Accepted: 03/30/2024] [Indexed: 06/11/2024]
Abstract
Two-photon Ca2+ imaging technology increasingly plays an essential role in neuroscience research. However, the requirement for extensive professional annotation poses a significant challenge to improving the performance of neuron segmentation models. Here, we present NeuroSeg-III, an innovative self-supervised learning approach specifically designed to achieve fast and precise segmentation of neurons in imaging data. This approach consists of two modules: a self-supervised pre-training network and a segmentation network. After pre-training the encoder of the segmentation network via a self-supervised learning method without any annotated data, we only need to fine-tune the segmentation network with a small amount of annotated data. The segmentation network is designed with YOLOv8s, FasterNet, efficient multi-scale attention mechanism (EMA), and bi-directional feature pyramid network (BiFPN), which enhanced the model's segmentation accuracy while reducing the computational cost and parameters. The generalization of our approach was validated across different Ca2+ indicators and scales of imaging data. Significantly, the proposed neuron segmentation approach exhibits exceptional speed and accuracy, surpassing the current state-of-the-art benchmarks when evaluated using a publicly available dataset. The results underscore the effectiveness of NeuroSeg-III, with employing an efficient training strategy tailored for two-photon Ca2+ imaging data and delivering remarkable precision in neuron segmentation.
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Affiliation(s)
- Yukun Wu
- Guangxi Key Laboratory of Special Biomedicine and Advanced Institute for Brain and Intelligence, School of Medicine, Guangxi University, Nanning 530004, China
| | - Zhehao Xu
- Center for Neurointelligence, School of Medicine, Chongqing University, Chongqing 400030, China
| | - Shanshan Liang
- Brain Research Center, State Key Laboratory of Trauma and Chemical Poisoning, Third Military Medical University, Chongqing 400038, China
| | - Lukang Wang
- Brain Research Center, State Key Laboratory of Trauma and Chemical Poisoning, Third Military Medical University, Chongqing 400038, China
| | - Meng Wang
- Center for Neurointelligence, School of Medicine, Chongqing University, Chongqing 400030, China
| | - Hongbo Jia
- Guangxi Key Laboratory of Special Biomedicine and Advanced Institute for Brain and Intelligence, School of Medicine, Guangxi University, Nanning 530004, China
- Brain Research Instrument Innovation Center, Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Sciences, Suzhou 215163, Jiangsu, China
| | - Xiaowei Chen
- Guangxi Key Laboratory of Special Biomedicine and Advanced Institute for Brain and Intelligence, School of Medicine, Guangxi University, Nanning 530004, China
- Chongqing Institute for Brain and Intelligence, Guangyang Bay Laboratory, Chongqing 400064, China
| | - Zhikai Zhao
- Center for Neurointelligence, School of Medicine, Chongqing University, Chongqing 400030, China
| | - Xiang Liao
- Center for Neurointelligence, School of Medicine, Chongqing University, Chongqing 400030, China
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4
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Crown LM, Agyeman KA, Choi W, Zepeda N, Iseri E, Pahlavan P, Siegel SJ, Liu C, Christopoulos V, Lee DJ. Theta-frequency medial septal nucleus deep brain stimulation increases neurovascular activity in MK-801-treated mice. Front Neurosci 2024; 18:1372315. [PMID: 38560047 PMCID: PMC10978728 DOI: 10.3389/fnins.2024.1372315] [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: 01/17/2024] [Accepted: 02/29/2024] [Indexed: 04/04/2024] Open
Abstract
Introduction Deep brain stimulation (DBS) has shown remarkable success treating neurological and psychiatric disorders including Parkinson's disease, essential tremor, dystonia, epilepsy, and obsessive-compulsive disorder. DBS is now being explored to improve cognitive and functional outcomes in other psychiatric conditions, such as those characterized by reduced N-methyl-D-aspartate (NMDA) function (i.e., schizophrenia). While DBS for movement disorders generally involves high-frequency (>100 Hz) stimulation, there is evidence that low-frequency stimulation may have beneficial and persisting effects when applied to cognitive brain networks. Methods In this study, we utilize a novel technology, functional ultrasound imaging (fUSI), to characterize the cerebrovascular impact of medial septal nucleus (MSN) DBS under conditions of NMDA antagonism (pharmacologically using Dizocilpine [MK-801]) in anesthetized male mice. Results Imaging from a sagittal plane across a variety of brain regions within and outside of the septohippocampal circuit, we find that MSN theta-frequency (7.7 Hz) DBS increases hippocampal cerebral blood volume (CBV) during and after stimulation. This effect was not present using standard high-frequency stimulation parameters [i.e., gamma (100 Hz)]. Discussion These results indicate the MSN DBS increases circuit-specific hippocampal neurovascular activity in a frequency-dependent manner and does so in a way that continues beyond the period of electrical stimulation.
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Affiliation(s)
- Lindsey M Crown
- Department of Psychiatry and Behavioral Sciences, Keck School of Medicine, University of Southern California, Los Angeles, CA, United States
| | - Kofi A Agyeman
- Department of Bioengineering, University of California Riverside, Riverside, CA, United States
| | - Wooseong Choi
- Department of Neurological Surgery, Keck School of Medicine, University of Southern California, Los Angeles, CA, United States
| | - Nancy Zepeda
- Department of Neurological Surgery, Keck School of Medicine, University of Southern California, Los Angeles, CA, United States
| | - Ege Iseri
- Department of Bioengineering, University of California Riverside, Riverside, CA, United States
| | - Pooyan Pahlavan
- Department of Bioengineering, University of California Riverside, Riverside, CA, United States
| | - Steven J Siegel
- Department of Psychiatry and Behavioral Sciences, Keck School of Medicine, University of Southern California, Los Angeles, CA, United States
| | - Charles Liu
- Department of Neurological Surgery, Keck School of Medicine, University of Southern California, Los Angeles, CA, United States
- Neurorestoration Center, Keck School of Medicine, University of Southern California, Los Angeles, CA, United States
- Viterbi School of Engineering, University of Southern California, Los Angeles, CA, United States
- Rancho Los Amigos National Rehabilitation Center, Downey, CA, United States
| | - Vasileios Christopoulos
- Department of Bioengineering, University of California Riverside, Riverside, CA, United States
- Neurorestoration Center, Keck School of Medicine, University of Southern California, Los Angeles, CA, United States
- Neuroscience Graduate Program, University of California Riverside, Riverside, CA, United States
| | - Darrin J Lee
- Department of Psychiatry and Behavioral Sciences, Keck School of Medicine, University of Southern California, Los Angeles, CA, United States
- Department of Bioengineering, University of California Riverside, Riverside, CA, United States
- Department of Neurological Surgery, Keck School of Medicine, University of Southern California, Los Angeles, CA, United States
- Neurorestoration Center, Keck School of Medicine, University of Southern California, Los Angeles, CA, United States
- Viterbi School of Engineering, University of Southern California, Los Angeles, CA, United States
- Rancho Los Amigos National Rehabilitation Center, Downey, CA, United States
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5
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Park K, Kohl MM, Kwag J. Memory encoding and retrieval by retrosplenial parvalbumin interneurons are impaired in Alzheimer's disease model mice. Curr Biol 2024; 34:434-443.e4. [PMID: 38157861 DOI: 10.1016/j.cub.2023.12.014] [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: 07/07/2023] [Revised: 10/23/2023] [Accepted: 12/06/2023] [Indexed: 01/03/2024]
Abstract
Memory deficits in Alzheimer's disease (AD) show a strong link with GABAergic interneuron dysfunctions.1,2,3,4,5,6,7 The ensemble dynamics of GABAergic interneurons represent memory encoding and retrieval,8,9,10,11,12 but how GABAergic interneuron dysfunction affects inhibitory ensemble dynamics in AD is unknown. As the retrosplenial cortex (RSC) is critical for episodic memory13,14,15,16 and is affected by β-amyloid accumulation in early AD,17,18,19,20,21 we address this question by performing Ca2+ imaging in RSC parvalbumin (PV)-expressing interneurons during a contextual fear memory task in healthy control mice and the 5XFAD mouse model of AD. We found that populations of PV interneurons responsive to aversive electric foot shocks during contextual fear conditioning (shock-responsive) significantly decreased in the 5XFAD mice, indicating dysfunctions in the recruitment of memory-encoding PV interneurons. In the control mice, ensemble activities of shock-responsive PV interneurons were selectively upregulated during the freezing epoch of the contextual fear memory retrieval, manifested by synaptic potentiation of PV interneuron-mediated inhibition. However, such changes in ensemble dynamics during memory retrieval and synaptic plasticity were both absent in the 5XFAD mice. Optogenetic silencing of PV interneurons during contextual fear conditioning in the control mice mimicked the memory deficits in the 5XFAD mice, while optogenetic activation of PV interneurons in the 5XFAD mice restored memory retrieval. These results demonstrate the critical roles of contextual fear memory-encoding PV interneurons for memory retrieval. Furthermore, synaptic dysfunction of PV interneurons may disrupt the recruitment of PV interneurons and their ensemble dynamics underlying contextual fear memory retrieval, subsequently leading to memory deficits in AD.
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Affiliation(s)
- Kyerl Park
- Department of Brain and Cognitive Sciences, Seoul National University, Gwanak-ro 1, Gwanak-gu, Seoul 08826, Korea; Department of Brain and Cognitive Engineering, Korea University, Anam-ro 145, Seongbuk-gu, Seoul 02841, Korea
| | - Michael M Kohl
- School of Psychology and Neuroscience, University of Glasgow, University Avenue, Glasgow G12 8QQ, UK
| | - Jeehyun Kwag
- Department of Brain and Cognitive Sciences, Seoul National University, Gwanak-ro 1, Gwanak-gu, Seoul 08826, Korea.
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Weiss O, Bounds HA, Adesnik H, Coen-Cagli R. Modeling the diverse effects of divisive normalization on noise correlations. PLoS Comput Biol 2023; 19:e1011667. [PMID: 38033166 PMCID: PMC10715670 DOI: 10.1371/journal.pcbi.1011667] [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: 01/12/2023] [Revised: 12/12/2023] [Accepted: 11/07/2023] [Indexed: 12/02/2023] Open
Abstract
Divisive normalization, a prominent descriptive model of neural activity, is employed by theories of neural coding across many different brain areas. Yet, the relationship between normalization and the statistics of neural responses beyond single neurons remains largely unexplored. Here we focus on noise correlations, a widely studied pairwise statistic, because its stimulus and state dependence plays a central role in neural coding. Existing models of covariability typically ignore normalization despite empirical evidence suggesting it affects correlation structure in neural populations. We therefore propose a pairwise stochastic divisive normalization model that accounts for the effects of normalization and other factors on covariability. We first show that normalization modulates noise correlations in qualitatively different ways depending on whether normalization is shared between neurons, and we discuss how to infer when normalization signals are shared. We then apply our model to calcium imaging data from mouse primary visual cortex (V1), and find that it accurately fits the data, often outperforming a popular alternative model of correlations. Our analysis indicates that normalization signals are often shared between V1 neurons in this dataset. Our model will enable quantifying the relation between normalization and covariability in a broad range of neural systems, which could provide new constraints on circuit mechanisms of normalization and their role in information transmission and representation.
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Affiliation(s)
- Oren Weiss
- Department of Systems and Computational Biology, Albert Einstein College of Medicine, Bronx, New York, United States of America
| | - Hayley A. Bounds
- Helen Wills Neuroscience Institute, University of California, Berkeley, Berkeley, California, United States of America
| | - Hillel Adesnik
- Helen Wills Neuroscience Institute, University of California, Berkeley, Berkeley, California, United States of America
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, California, United States of America
| | - Ruben Coen-Cagli
- Department of Systems and Computational Biology, Albert Einstein College of Medicine, Bronx, New York, United States of America
- Dominick P. Purpura Department of Neuroscience, Albert Einstein College of Medicine, Bronx, New York, United States of America
- Department of Ophthalmology and Visual Sciences, Albert Einstein College of Medicine, Bronx, New York, United States of America
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7
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Leng Y, Li X, Zheng F, Liu H, Wang C, Wang X, Liao Y, Liu J, Meng K, Yu J, Zhang J, Wang B, Tan Y, Liu M, Jia X, Li D, Li Y, Gu Z, Fan Y. Advances in In Vitro Models of Neuromuscular Junction: Focusing on Organ-on-a-Chip, Organoids, and Biohybrid Robotics. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2023; 35:e2211059. [PMID: 36934404 DOI: 10.1002/adma.202211059] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/27/2022] [Revised: 02/18/2023] [Indexed: 06/18/2023]
Abstract
The neuromuscular junction (NMJ) is a peripheral synaptic connection between presynaptic motor neurons and postsynaptic skeletal muscle fibers that enables muscle contraction and voluntary motor movement. Many traumatic, neurodegenerative, and neuroimmunological diseases are classically believed to mainly affect either the neuronal or the muscle side of the NMJ, and treatment options are lacking. Recent advances in novel techniques have helped develop in vitro physiological and pathophysiological models of the NMJ as well as enable precise control and evaluation of its functions. This paper reviews the recent developments in in vitro NMJ models with 2D or 3D cultures, from organ-on-a-chip and organoids to biohybrid robotics. Related derivative techniques are introduced for functional analysis of the NMJ, such as the patch-clamp technique, microelectrode arrays, calcium imaging, and stimulus methods, particularly optogenetic-mediated light stimulation, microelectrode-mediated electrical stimulation, and biochemical stimulation. Finally, the applications of the in vitro NMJ models as disease models or for drug screening related to suitable neuromuscular diseases are summarized and their future development trends and challenges are discussed.
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Affiliation(s)
- Yubing Leng
- Key Laboratory for Biomechanics and Mechanobiology of Ministry of Education, Beijing Advanced Innovation Center for Biomedical Engineering, School of Biological Science and Medical Engineering, and with the School of Engineering Medicine, Beihang University, Beijing, 100083, China
| | - Xiaorui Li
- Key Laboratory for Biomechanics and Mechanobiology of Ministry of Education, Beijing Advanced Innovation Center for Biomedical Engineering, School of Biological Science and Medical Engineering, and with the School of Engineering Medicine, Beihang University, Beijing, 100083, China
| | - Fuyin Zheng
- Key Laboratory for Biomechanics and Mechanobiology of Ministry of Education, Beijing Advanced Innovation Center for Biomedical Engineering, School of Biological Science and Medical Engineering, and with the School of Engineering Medicine, Beihang University, Beijing, 100083, China
| | - Hui Liu
- Key Laboratory for Biomechanics and Mechanobiology of Ministry of Education, Beijing Advanced Innovation Center for Biomedical Engineering, School of Biological Science and Medical Engineering, and with the School of Engineering Medicine, Beihang University, Beijing, 100083, China
| | - Chunyan Wang
- State Key Laboratory of Space Medicine Fundamentals and Application, China Astronaut Research and Training Center, Beijing, 100094, China
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing, 210096, China
| | - Xudong Wang
- Key Laboratory for Biomechanics and Mechanobiology of Ministry of Education, Beijing Advanced Innovation Center for Biomedical Engineering, School of Biological Science and Medical Engineering, and with the School of Engineering Medicine, Beihang University, Beijing, 100083, China
| | - Yulong Liao
- Key Laboratory for Biomechanics and Mechanobiology of Ministry of Education, Beijing Advanced Innovation Center for Biomedical Engineering, School of Biological Science and Medical Engineering, and with the School of Engineering Medicine, Beihang University, Beijing, 100083, China
| | - Jiangyue Liu
- Key Laboratory for Biomechanics and Mechanobiology of Ministry of Education, Beijing Advanced Innovation Center for Biomedical Engineering, School of Biological Science and Medical Engineering, and with the School of Engineering Medicine, Beihang University, Beijing, 100083, China
| | - Kaiqi Meng
- Key Laboratory for Biomechanics and Mechanobiology of Ministry of Education, Beijing Advanced Innovation Center for Biomedical Engineering, School of Biological Science and Medical Engineering, and with the School of Engineering Medicine, Beihang University, Beijing, 100083, China
| | - Jiaheng Yu
- Key Laboratory for Biomechanics and Mechanobiology of Ministry of Education, Beijing Advanced Innovation Center for Biomedical Engineering, School of Biological Science and Medical Engineering, and with the School of Engineering Medicine, Beihang University, Beijing, 100083, China
| | - Jingyi Zhang
- Key Laboratory for Biomechanics and Mechanobiology of Ministry of Education, Beijing Advanced Innovation Center for Biomedical Engineering, School of Biological Science and Medical Engineering, and with the School of Engineering Medicine, Beihang University, Beijing, 100083, China
| | - Binyu Wang
- Key Laboratory for Biomechanics and Mechanobiology of Ministry of Education, Beijing Advanced Innovation Center for Biomedical Engineering, School of Biological Science and Medical Engineering, and with the School of Engineering Medicine, Beihang University, Beijing, 100083, China
| | - Yingjun Tan
- State Key Laboratory of Space Medicine Fundamentals and Application, China Astronaut Research and Training Center, Beijing, 100094, China
| | - Meili Liu
- Key Laboratory for Biomechanics and Mechanobiology of Ministry of Education, Beijing Advanced Innovation Center for Biomedical Engineering, School of Biological Science and Medical Engineering, and with the School of Engineering Medicine, Beihang University, Beijing, 100083, China
| | - Xiaoling Jia
- Key Laboratory for Biomechanics and Mechanobiology of Ministry of Education, Beijing Advanced Innovation Center for Biomedical Engineering, School of Biological Science and Medical Engineering, and with the School of Engineering Medicine, Beihang University, Beijing, 100083, China
| | - Deyu Li
- Key Laboratory for Biomechanics and Mechanobiology of Ministry of Education, Beijing Advanced Innovation Center for Biomedical Engineering, School of Biological Science and Medical Engineering, and with the School of Engineering Medicine, Beihang University, Beijing, 100083, China
| | - Yinghui Li
- State Key Laboratory of Space Medicine Fundamentals and Application, China Astronaut Research and Training Center, Beijing, 100094, China
| | - Zhongze Gu
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing, 210096, China
| | - Yubo Fan
- Key Laboratory for Biomechanics and Mechanobiology of Ministry of Education, Beijing Advanced Innovation Center for Biomedical Engineering, School of Biological Science and Medical Engineering, and with the School of Engineering Medicine, Beihang University, Beijing, 100083, China
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8
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Sibener LJ, Mosberger AC, Chen TX, Athalye VR, Murray JM, Costa RM. Dissociable roles of thalamic nuclei in the refinement of reaches to spatial targets. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.09.20.558560. [PMID: 37790555 PMCID: PMC10542479 DOI: 10.1101/2023.09.20.558560] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/05/2023]
Abstract
Reaches are complex movements that are critical for survival, and encompass the control of different aspects such as direction, speed, and endpoint precision. Complex movements have been postulated to be learned and controlled through distributed motor networks, of which the thalamus is a highly connected node. Still, the role of different thalamic circuits in learning and controlling specific aspects of reaches has not been investigated. We report dissociable roles of two distinct thalamic nuclei - the parafascicular (Pf) and ventroanterior/ventrolateral (VAL) nuclei - in the refinement of spatial target reaches in mice. Using 2-photon calcium imaging in a head-fixed joystick task where mice learned to reach to a target in space, we found that glutamatergic neurons in both areas were most active during reaches early in learning. Reach-related activity in both areas decreased late in learning, as movement direction was refined and reaches increased in accuracy. Furthermore, the population dynamics of Pf, but not VAL, covaried in different subspaces in early and late learning, but eventually stabilized in late learning. The neural activity in Pf, but not VAL, encoded the direction of reaches in early but not late learning. Accordingly, bilateral lesions of Pf before, but not after learning, strongly and specifically impaired the refinement of reach direction. VAL lesions did not impact direction refinement, but instead resulted in increased speed and target overshoot. Our findings provide new evidence that the thalamus is a critical motor node in the learning and control of reaching movements, with specific subnuclei controlling distinct aspects of the reach early in learning.
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9
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van den Boom BJG, Elhazaz-Fernandez A, Rasmussen PA, van Beest EH, Parthasarathy A, Denys D, Willuhn I. Unraveling the mechanisms of deep-brain stimulation of the internal capsule in a mouse model. Nat Commun 2023; 14:5385. [PMID: 37666830 PMCID: PMC10477328 DOI: 10.1038/s41467-023-41026-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2023] [Accepted: 08/17/2023] [Indexed: 09/06/2023] Open
Abstract
Deep-brain stimulation (DBS) is an effective treatment for patients suffering from otherwise therapy-resistant psychiatric disorders, including obsessive-compulsive disorder. Modulation of cortico-striatal circuits has been suggested as a mechanism of action. To gain mechanistic insight, we monitored neuronal activity in cortico-striatal regions in a mouse model for compulsive behavior, while systematically varying clinically-relevant parameters of internal-capsule DBS. DBS showed dose-dependent effects on both brain and behavior: An increasing, yet balanced, number of excited and inhibited neurons was recruited, scattered throughout cortico-striatal regions, while excessive grooming decreased. Such neuronal recruitment did not alter basic brain function such as resting-state activity, and only occurred in awake animals, indicating a dependency on network activity. In addition to these widespread effects, we observed specific involvement of the medial orbitofrontal cortex in therapeutic outcomes, which was corroborated by optogenetic stimulation. Together, our findings provide mechanistic insight into how DBS exerts its therapeutic effects on compulsive behaviors.
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Affiliation(s)
- Bastijn J G van den Boom
- Netherlands Institute for Neuroscience, Royal Netherlands Academy of Arts and Sciences, Amsterdam, The Netherlands.
- Department of Psychiatry, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands.
| | - Alfredo Elhazaz-Fernandez
- Netherlands Institute for Neuroscience, Royal Netherlands Academy of Arts and Sciences, Amsterdam, The Netherlands
| | - Peter A Rasmussen
- Netherlands Institute for Neuroscience, Royal Netherlands Academy of Arts and Sciences, Amsterdam, The Netherlands
| | - Enny H van Beest
- Netherlands Institute for Neuroscience, Royal Netherlands Academy of Arts and Sciences, Amsterdam, The Netherlands
| | - Aishwarya Parthasarathy
- Netherlands Institute for Neuroscience, Royal Netherlands Academy of Arts and Sciences, Amsterdam, The Netherlands
- Department of Psychiatry, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands
| | - Damiaan Denys
- Department of Psychiatry, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands
| | - Ingo Willuhn
- Netherlands Institute for Neuroscience, Royal Netherlands Academy of Arts and Sciences, Amsterdam, The Netherlands.
- Department of Psychiatry, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands.
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10
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Zhao M, Kwon SE. Interneuron-Targeted Disruption of SYNGAP1 Alters Sensory Representations in the Neocortex and Impairs Sensory Learning. J Neurosci 2023; 43:6212-6226. [PMID: 37558489 PMCID: PMC10476640 DOI: 10.1523/jneurosci.1997-22.2023] [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: 10/25/2022] [Revised: 07/18/2023] [Accepted: 07/20/2023] [Indexed: 08/11/2023] Open
Abstract
SYNGAP1 haploinsufficiency in humans leads to severe neurodevelopmental disorders characterized by intellectual disability, autism, epilepsy, and sensory processing deficits. However, the circuit mechanisms underlying these disorders are not well understood. In mice, a decrease of SynGAP levels results in cognitive deficits by interfering with the development of excitatory glutamatergic connections. Recent evidence suggests that SynGAP also plays a crucial role in the development and function of GABAergic inhibitory interneurons. Nevertheless, it remains uncertain whether and to what extent the expression of SYNGAP1 in inhibitory interneurons contributes to cortical circuit function and related behaviors. The activity of cortical neurons has not been measured simultaneously with behavior. To address these gaps, we recorded from layer 2/3 neurons in the primary whisker somatosensory cortex (wS1) of mice while they learned to perform a whisker tactile detection task. Our results demonstrate that mice with interneuron-specific SYNGAP1 haploinsufficiency exhibit learning deficits characterized by heightened behavioral responses in the absence of relevant sensory input and premature responses to unrelated sensory stimuli not associated with reward acquisition. These behavioral deficits are accompanied by specific circuit abnormalities within wS1. Interneuron-specific SYNGAP1 haploinsufficiency increases detrimental neuronal correlations directly related to task performance and enhances responses to irrelevant sensory stimuli unrelated to the reward acquisition. In summary, our findings indicate that a reduction of SynGAP in inhibitory interneurons impairs sensory representation in the primary sensory cortex by disrupting neuronal correlations, which likely contributes to the observed cognitive deficits in mice with pan-neuronal SYNGAP1 haploinsufficiency.SIGNIFICANCE STATEMENT SYNGAP1 haploinsufficiency leads to severe neurodevelopmental disorders. The exact nature of neural circuit dysfunction caused by SYNGAP1 haploinsufficiency remains poorly understood. SynGAP plays a critical role in the function of GABAergic inhibitory interneurons as well as glutamatergic pyramidal neurons in the neocortex. Whether and how decreasing SYNGAP1 level in inhibitory interneurons disrupts a behaviorally relevant circuit remains unclear. We measure neural activity and behavior in mice learning a perceptual task. Mice with interneuron-targeted disruption of SYNGAP1 display increased detrimental neuronal correlations and elevated responses to irrelevant sensory inputs, which are related to impaired task performance. These results show that cortical interneuron dysfunction contributes to sensory deficits in SYNGAP1 haploinsufficiency with important implications for identifying therapeutic targets.
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Affiliation(s)
- Meiling Zhao
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, Michigan 48109
| | - Sung Eun Kwon
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, Michigan 48109
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11
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Hassan SI, Bigler S, Siegelbaum SA. Social odor discrimination and its enhancement by associative learning in the hippocampal CA2 region. Neuron 2023; 111:2232-2246.e5. [PMID: 37192623 PMCID: PMC10524117 DOI: 10.1016/j.neuron.2023.04.026] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2021] [Revised: 10/25/2022] [Accepted: 04/21/2023] [Indexed: 05/18/2023]
Abstract
Although the hippocampus is crucial for social memory, how social sensory information is combined with contextual information to form episodic social memories remains unknown. Here, we investigated the mechanisms for social sensory information processing using two-photon calcium imaging from hippocampal CA2 pyramidal neurons (PNs)-which are crucial for social memory-in awake head-fixed mice exposed to social and non-social odors. We found that CA2 PNs represent social odors of individual conspecifics and that these representations are refined during associative social odor-reward learning to enhance the discrimination of rewarded compared with unrewarded odors. Moreover, the structure of the CA2 PN population activity enables CA2 to generalize along categories of rewarded versus unrewarded and social versus non-social odor stimuli. Finally, we found that CA2 is important for learning social but not non-social odor-reward associations. These properties of CA2 odor representations provide a likely substrate for the encoding of episodic social memory.
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Affiliation(s)
- Sami I Hassan
- Department of Neuroscience, Mortimer B. Zuckerman Mind Brain Behavior Institute, The Kavli Institute for Brain Science, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY 10027, USA.
| | - Shivani Bigler
- Department of Neuroscience, Mortimer B. Zuckerman Mind Brain Behavior Institute, The Kavli Institute for Brain Science, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY 10027, USA
| | - Steven A Siegelbaum
- Department of Neuroscience, Mortimer B. Zuckerman Mind Brain Behavior Institute, The Kavli Institute for Brain Science, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY 10027, USA.
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12
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Schmitt TTX, Andrea KMA, Wadle SL, Hirtz JJ. Distinct topographic organization and network activity patterns of corticocollicular neurons within layer 5 auditory cortex. Front Neural Circuits 2023; 17:1210057. [PMID: 37521334 PMCID: PMC10372447 DOI: 10.3389/fncir.2023.1210057] [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: 04/21/2023] [Accepted: 06/22/2023] [Indexed: 08/01/2023] Open
Abstract
The auditory cortex (AC) modulates the activity of upstream pathways in the auditory brainstem via descending (corticofugal) projections. This feedback system plays an important role in the plasticity of the auditory system by shaping response properties of neurons in many subcortical nuclei. The majority of layer (L) 5 corticofugal neurons project to the inferior colliculus (IC). This corticocollicular (CC) pathway is involved in processing of complex sounds, auditory-related learning, and defense behavior. Partly due to their location in deep cortical layers, CC neuron population activity patterns within neuronal AC ensembles remain poorly understood. We employed two-photon imaging to record the activity of hundreds of L5 neurons in anesthetized as well as awake animals. CC neurons are broader tuned than other L5 pyramidal neurons and display weaker topographic order in core AC subfields. Network activity analyses revealed stronger clusters of CC neurons compared to non-CC neurons, which respond more reliable and integrate information over larger distances. However, results obtained from secondary auditory cortex (A2) differed considerably. Here CC neurons displayed similar or higher topography, depending on the subset of neurons analyzed. Furthermore, specifically in A2, CC activity clusters formed in response to complex sounds were spatially more restricted compared to other L5 neurons. Our findings indicate distinct network mechanism of CC neurons in analyzing sound properties with pronounced subfield differences, demonstrating that the topography of sound-evoked responses within AC is neuron-type dependent.
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13
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Zhou Z, Yip HM, Tsimring K, Sur M, Ip JPK, Tin C. Effective and efficient neural networks for spike inference from in vivo calcium imaging. CELL REPORTS METHODS 2023; 3:100462. [PMID: 37323579 PMCID: PMC10261900 DOI: 10.1016/j.crmeth.2023.100462] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Revised: 02/21/2023] [Accepted: 03/31/2023] [Indexed: 06/17/2023]
Abstract
Calcium imaging provides advantages in monitoring large populations of neuronal activities simultaneously. However, it lacks the signal quality provided by neural spike recording in traditional electrophysiology. To address this issue, we developed a supervised data-driven approach to extract spike information from calcium signals. We propose the ENS2 (effective and efficient neural networks for spike inference from calcium signals) system for spike-rate and spike-event predictions using ΔF/F0 calcium inputs based on a U-Net deep neural network. When testing on a large, ground-truth public database, it consistently outperformed state-of-the-art algorithms in both spike-rate and spike-event predictions with reduced computational load. We further demonstrated that ENS2 can be applied to analyses of orientation selectivity in primary visual cortex neurons. We conclude that it would be a versatile inference system that may benefit diverse neuroscience studies.
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Affiliation(s)
- Zhanhong Zhou
- Department of Biomedical Engineering, City University of Hong Kong, Hong Kong SAR, China
| | - Hei Matthew Yip
- School of Biomedical Sciences, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Katya Tsimring
- Department of Brain and Cognitive Sciences, Picower Institute for Learning and Memory, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, USA
| | - Mriganka Sur
- Department of Brain and Cognitive Sciences, Picower Institute for Learning and Memory, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, USA
| | - Jacque Pak Kan Ip
- School of Biomedical Sciences, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Chung Tin
- Department of Biomedical Engineering, City University of Hong Kong, Hong Kong SAR, China
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14
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Chen YT, Jewell SW, Witten DM. Quantifying uncertainty in spikes estimated from calcium imaging data. Biostatistics 2023; 24:481-501. [PMID: 34654923 PMCID: PMC10449000 DOI: 10.1093/biostatistics/kxab034] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2021] [Revised: 07/28/2021] [Accepted: 09/04/2021] [Indexed: 11/12/2022] Open
Abstract
In recent years, a number of methods have been proposed to estimate the times at which a neuron spikes on the basis of calcium imaging data. However, quantifying the uncertainty associated with these estimated spikes remains an open problem. We consider a simple and well-studied model for calcium imaging data, which states that calcium decays exponentially in the absence of a spike, and instantaneously increases when a spike occurs. We wish to test the null hypothesis that the neuron did not spike-i.e., that there was no increase in calcium-at a particular timepoint at which a spike was estimated. In this setting, classical hypothesis tests lead to inflated Type I error, because the spike was estimated on the same data used for testing. To overcome this problem, we propose a selective inference approach. We describe an efficient algorithm to compute finite-sample $p$-values that control selective Type I error, and confidence intervals with correct selective coverage, for spikes estimated using a recent proposal from the literature. We apply our proposal in simulation and on calcium imaging data from the $\texttt{spikefinder}$ challenge.
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Affiliation(s)
- Yiqun T Chen
- Department of Biostatistics, University of Washington,
Seattle, WA 98195, USA
| | - Sean W Jewell
- Department of Statistics, University of Washington, Seattle,
WA 98195, USA
| | - Daniela M Witten
- Departments of Statistics & Biostatistics, University of
Washington, Seattle, WA 98195, USA
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15
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Sit KK, Goard MJ. Coregistration of heading to visual cues in retrosplenial cortex. Nat Commun 2023; 14:1992. [PMID: 37031198 PMCID: PMC10082791 DOI: 10.1038/s41467-023-37704-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2022] [Accepted: 03/28/2023] [Indexed: 04/10/2023] Open
Abstract
Spatial cognition depends on an accurate representation of orientation within an environment. Head direction cells in distributed brain regions receive a range of sensory inputs, but visual input is particularly important for aligning their responses to environmental landmarks. To investigate how population-level heading responses are aligned to visual input, we recorded from retrosplenial cortex (RSC) of head-fixed mice in a moving environment using two-photon calcium imaging. We show that RSC neurons are tuned to the animal's relative orientation in the environment, even in the absence of head movement. Next, we found that RSC receives functionally distinct projections from visual and thalamic areas and contains several functional classes of neurons. While some functional classes mirror RSC inputs, a newly discovered class coregisters visual and thalamic signals. Finally, decoding analyses reveal unique contributions to heading from each class. Our results suggest an RSC circuit for anchoring heading representations to environmental visual landmarks.
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Affiliation(s)
- Kevin K Sit
- Department of Psychological and Brain Sciences University of California, Santa Barbara, Santa Barbara, CA, 93106, USA
| | - Michael J Goard
- Department of Psychological and Brain Sciences University of California, Santa Barbara, Santa Barbara, CA, 93106, USA.
- Department of Molecular, Cellular, and Developmental Biology University of California, Santa Barbara, Santa Barbara, CA, 93106, USA.
- Neuroscience Research Institute University of California Santa Barbara, Santa Barbara, CA, 93106, USA.
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16
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Chen Z, Blair GJ, Cao C, Zhou J, Aharoni D, Golshani P, Blair HT, Cong J. FPGA-Based In-Vivo Calcium Image Decoding for Closed-Loop Feedback Applications. IEEE TRANSACTIONS ON BIOMEDICAL CIRCUITS AND SYSTEMS 2023; 17:169-179. [PMID: 37071510 PMCID: PMC10414190 DOI: 10.1109/tbcas.2023.3268130] [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] [Indexed: 05/11/2023]
Abstract
Miniaturized calcium imaging is an emerging neural recording technique that has been widely used for monitoring neural activity on a large scale at a specific brain region of rats or mice. Most existing calcium-image analysis pipelines operate offline. This results in long processing latency, making it difficult to realize closed-loop feedback stimulation for brain research. In recent work, we have proposed an FPGA-based real-time calcium image processing pipeline for closed-loop feedback applications. It can perform real-time calcium image motion correction, enhancement, fast trace extraction, and real-time decoding from extracted traces. Here, we extend this work by proposing a variety of neural network based methods for real-time decoding and evaluate the tradeoff among these decoding methods and accelerator designs. We introduce the implementation of the neural network based decoders on the FPGA, and show their speedup against the implementation on the ARM processor. Our FPGA implementation enables the real-time calcium image decoding with sub-ms processing latency for closed-loop feedback applications.
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17
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Yang JY, O'Connell TF, Hsu WMM, Bauer MS, Dylla KV, Sharpee TO, Hong EJ. Restructuring of olfactory representations in the fly brain around odor relationships in natural sources. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.02.15.528627. [PMID: 36824890 PMCID: PMC9949042 DOI: 10.1101/2023.02.15.528627] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
A core challenge of olfactory neuroscience is to understand how neural representations of odor are generated and progressively transformed across different layers of the olfactory circuit into formats that support perception and behavior. The encoding of odor by odorant receptors in the input layer of the olfactory system reflects, at least in part, the chemical relationships between odor compounds. Neural representations of odor in higher order associative olfactory areas, generated by random feedforward networks, are expected to largely preserve these input odor relationships1-3. We evaluated these ideas by examining how odors are represented at different stages of processing in the olfactory circuit of the vinegar fly D. melanogaster. We found that representations of odor in the mushroom body (MB), a third-order associative olfactory area in the fly brain, are indeed structured and invariant across flies. However, the structure of MB representational space diverged significantly from what is expected in a randomly connected network. In addition, odor relationships encoded in the MB were better correlated with a metric of the similarity of their distribution across natural sources compared to their similarity with respect to chemical features, and the converse was true for odor relationships encoded in primary olfactory receptor neurons (ORNs). Comparison of odor coding at primary, secondary, and tertiary layers of the circuit revealed that odors were significantly regrouped with respect to their representational similarity across successive stages of olfactory processing, with the largest changes occurring in the MB. The non-linear reorganization of odor relationships in the MB indicates that unappreciated structure exists in the fly olfactory circuit, and this structure may facilitate the generalization of odors with respect to their co-occurence in natural sources.
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Affiliation(s)
- Jie-Yoon Yang
- These authors contributed equally
- Division of Biology & Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Thomas F O'Connell
- These authors contributed equally
- Division of Biology & Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Wei-Mien M Hsu
- Computational Neurobiology Laboratory, Salk Institute for Biological Studies, La Jolla, CA, USA; Department of Physics, University of California, San Diego, La Jolla, CA, USA
| | - Matthew S Bauer
- Division of Biology & Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Kristina V Dylla
- Division of Biology & Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Tatyana O Sharpee
- Computational Neurobiology Laboratory, Salk Institute for Biological Studies, La Jolla, CA, USA; Department of Physics, University of California, San Diego, La Jolla, CA, USA
| | - Elizabeth J Hong
- Division of Biology & Biological Engineering, California Institute of Technology, Pasadena, CA, USA
- Lead contact
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18
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Sun Z. A Simple Ca 2+-Imaging Approach of Network-Activity Analyses for Human Neurons. Methods Mol Biol 2023; 2683:247-258. [PMID: 37300781 DOI: 10.1007/978-1-0716-3287-1_20] [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: 06/12/2023]
Abstract
Rapid advances in light microscopy and development of all-optical electrophysiological imaging tools have greatly leveraged the speed and the depth of neurobiology studies. Calcium imaging is a common method that is useful for measuring calcium signals in cells and has been used as a functional proxy for neuronal activity. Here I describe a simple, stimulation-free approach that measures neuronal network activity and single-neuron dynamics in human neurons. This protocol provides the experimental workflow that includes step-wise illustrations of sample preparations, data processing, and analyses that can be used for quick phenotypical assessment and serves as a quick functional readout for mutagenesis or screen effort for neurodegenerative studies.
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Affiliation(s)
- Zijun Sun
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA, USA.
- Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, CA, USA.
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19
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Xu Z, Wu Y, Guan J, Liang S, Pan J, Wang M, Hu Q, Jia H, Chen X, Liao X. NeuroSeg-II: A deep learning approach for generalized neuron segmentation in two-photon Ca 2+ imaging. Front Cell Neurosci 2023; 17:1127847. [PMID: 37091918 PMCID: PMC10117760 DOI: 10.3389/fncel.2023.1127847] [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: 12/20/2022] [Accepted: 03/20/2023] [Indexed: 04/25/2023] Open
Abstract
The development of two-photon microscopy and Ca2+ indicators has enabled the recording of multiscale neuronal activities in vivo and thus advanced the understanding of brain functions. However, it is challenging to perform automatic, accurate, and generalized neuron segmentation when processing a large amount of imaging data. Here, we propose a novel deep-learning-based neural network, termed as NeuroSeg-II, to conduct automatic neuron segmentation for in vivo two-photon Ca2+ imaging data. This network architecture is based on Mask region-based convolutional neural network (R-CNN) but has enhancements of an attention mechanism and modified feature hierarchy modules. We added an attention mechanism module to focus the computation on neuron regions in imaging data. We also enhanced the feature hierarchy to extract feature information at diverse levels. To incorporate both spatial and temporal information in our data processing, we fused the images from average projection and correlation map extracting the temporal information of active neurons, and the integrated information was expressed as two-dimensional (2D) images. To achieve a generalized neuron segmentation, we conducted a hybrid learning strategy by training our model with imaging data from different labs, including multiscale data with different Ca2+ indicators. The results showed that our approach achieved promising segmentation performance across different imaging scales and Ca2+ indicators, even including the challenging data of large field-of-view mesoscopic images. By comparing state-of-the-art neuron segmentation methods for two-photon Ca2+ imaging data, we showed that our approach achieved the highest accuracy with a publicly available dataset. Thus, NeuroSeg-II enables good segmentation accuracy and a convenient training and testing process.
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Affiliation(s)
- Zhehao Xu
- Advanced Institute for Brain and Intelligence, Medical College, Guangxi University, Nanning, China
| | - Yukun Wu
- Advanced Institute for Brain and Intelligence, Medical College, Guangxi University, Nanning, China
| | - Jiangheng Guan
- Department of Neurosurgery, The General Hospital of Chinese PLA Central Theater Command, Wuhan, China
| | - Shanshan Liang
- 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
- Center for Neurointelligence, School of Medicine, Chongqing University, Chongqing, China
| | - Qianshuo Hu
- School of Artificial Intelligence, Chongqing University of Technology, Chongqing, China
| | - Hongbo Jia
- Advanced Institute for Brain and Intelligence, Medical College, Guangxi University, Nanning, China
- Brain Research Instrument Innovation Center, Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Sciences, Suzhou, Jiangsu, China
| | - Xiaowei Chen
- Advanced Institute for Brain and Intelligence, Medical College, Guangxi University, Nanning, China
- Brain Research Center and State Key Laboratory of Trauma, Burns, and Combined Injury, Third Military Medical University, Chongqing, China
- Guangyang Bay Laboratory, Chongqing Institute for Brain and Intelligence, Chongqing, China
- *Correspondence: Xiaowei Chen,
| | - Xiang Liao
- Center for Neurointelligence, School of Medicine, Chongqing University, Chongqing, China
- Xiang Liao,
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20
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Shani-Narkiss H, Beniaguev D, Segev I, Mizrahi A. Stability and flexibility of odor representations in the mouse olfactory bulb. Front Neural Circuits 2023; 17:1157259. [PMID: 37151358 PMCID: PMC10157098 DOI: 10.3389/fncir.2023.1157259] [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: 02/02/2023] [Accepted: 03/27/2023] [Indexed: 05/09/2023] Open
Abstract
Dynamic changes in sensory representations have been basic tenants of studies in neural coding and plasticity. In olfaction, relatively little is known about the dynamic range of changes in odor representations under different brain states and over time. Here, we used time-lapse in vivo two-photon calcium imaging to describe changes in odor representation by mitral cells, the output neurons of the mouse olfactory bulb. Using anesthetics as a gross manipulation to switch between different brain states (wakefulness and under anesthesia), we found that odor representations by mitral cells undergo significant re-shaping across states but not over time within state. Odor representations were well balanced across the population in the awake state yet highly diverse under anesthesia. To evaluate differences in odor representation across states, we used linear classifiers to decode odor identity in one state based on training data from the other state. Decoding across states resulted in nearly chance-level accuracy. In contrast, repeating the same procedure for data recorded within the same state but in different time points, showed that time had a rather minor impact on odor representations. Relative to the differences across states, odor representations remained stable over months. Thus, single mitral cells can change dynamically across states but maintain robust representations across months. These findings have implications for sensory coding and plasticity in the mammalian brain.
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Affiliation(s)
- Haran Shani-Narkiss
- The Edmond and Lily Safra Center for Brain Sciences, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - David Beniaguev
- The Edmond and Lily Safra Center for Brain Sciences, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Idan Segev
- The Edmond and Lily Safra Center for Brain Sciences, The Hebrew University of Jerusalem, Jerusalem, Israel
- Department of Neurobiology, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Adi Mizrahi
- The Edmond and Lily Safra Center for Brain Sciences, The Hebrew University of Jerusalem, Jerusalem, Israel
- Department of Neurobiology, The Hebrew University of Jerusalem, Jerusalem, Israel
- *Correspondence: Adi Mizrahi,
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21
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Gare S, Chel S, Abhinav TK, Dhyani V, Jana S, Giri L. Mapping of structural arrangement of cells and collective calcium transients: an integrated framework combining live cell imaging using confocal microscopy and UMAP-assisted HDBSCAN-based approach. Integr Biol (Camb) 2022; 14:184-203. [PMID: 36670549 DOI: 10.1093/intbio/zyac017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2022] [Revised: 11/22/2022] [Accepted: 11/30/2022] [Indexed: 01/22/2023]
Abstract
Live cell calcium (Ca2+) imaging is one of the important tools to record cellular activity during in vitro and in vivo preclinical studies. Specially, high-resolution microscopy can provide valuable dynamic information at the single cell level. One of the major challenges in the implementation of such imaging schemes is to extract quantitative information in the presence of significant heterogeneity in Ca2+ responses attained due to variation in structural arrangement and drug distribution. To fill this gap, we propose time-lapse imaging using spinning disk confocal microscopy and machine learning-enabled framework for automated grouping of Ca2+ spiking patterns. Time series analysis is performed to correlate the drug induced cellular responses to self-assembly pattern present in multicellular systems. The framework is designed to reduce the large-scale dynamic responses using uniform manifold approximation and projection (UMAP). In particular, we propose the suitability of hierarchical DBSCAN (HDBSCAN) in view of reduced number of hyperparameters. We find UMAP-assisted HDBSCAN outperforms existing approaches in terms of clustering accuracy in segregation of Ca2+ spiking patterns. One of the novelties includes the application of non-linear dimension reduction in segregation of the Ca2+ transients with statistical similarity. The proposed pipeline for automation was also proved to be a reproducible and fast method with minimal user input. The algorithm was used to quantify the effect of cellular arrangement and stimulus level on collective Ca2+ responses induced by GPCR targeting drug. The analysis revealed a significant increase in subpopulation containing sustained oscillation corresponding to higher packing density. In contrast to traditional measurement of rise time and decay ratio from Ca2+ transients, the proposed pipeline was used to classify the complex patterns with longer duration and cluster-wise model fitting. The two-step process has a potential implication in deciphering biophysical mechanisms underlying the Ca2+ oscillations in context of structural arrangement between cells.
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Affiliation(s)
- Suman Gare
- Department of Chemical Engineering, Indian Institute of Technology, Hyderabad, India
| | - Soumita Chel
- Department of Chemical Engineering, Indian Institute of Technology, Hyderabad, India
| | - T K Abhinav
- Department of Chemical Engineering, Indian Institute of Technology, Hyderabad, India
| | - Vaibhav Dhyani
- Department of Chemical Engineering, Indian Institute of Technology, Hyderabad, India
| | - Soumya Jana
- Department of Electrical Engineering, Indian Institute of Technology, Hyderabad, India
| | - Lopamudra Giri
- Department of Chemical Engineering, Indian Institute of Technology, Hyderabad, India
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22
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Krishnan S, Heer C, Cherian C, Sheffield MEJ. Reward expectation extinction restructures and degrades CA1 spatial maps through loss of a dopaminergic reward proximity signal. Nat Commun 2022; 13:6662. [PMID: 36333323 PMCID: PMC9636178 DOI: 10.1038/s41467-022-34465-5] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2022] [Accepted: 10/25/2022] [Indexed: 11/06/2022] Open
Abstract
Hippocampal place cells support reward-related spatial memories by forming a cognitive map that over-represents reward locations. The strength of these memories is modulated by the extent of reward expectation during encoding. However, the circuit mechanisms underlying this modulation are unclear. Here we find that when reward expectation is extinguished in mice, they remain engaged with their environment, yet place cell over-representation of rewards vanishes, place field remapping throughout the environment increases, and place field trial-to-trial reliability decreases. Interestingly, Ventral Tegmental Area (VTA) dopaminergic axons in CA1 exhibit a ramping reward-proximity signal that depends on reward expectation and inhibiting VTA dopaminergic neurons largely replicates the effects of extinguishing reward expectation. We conclude that changing reward expectation restructures CA1 cognitive maps and determines map reliability by modulating the dopaminergic VTA-CA1 reward-proximity signal. Thus, internal states of high reward expectation enhance encoding of spatial memories by reinforcing hippocampal cognitive maps associated with reward.
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Affiliation(s)
- Seetha Krishnan
- Department of Neurobiology and Institute for Neuroscience, University of Chicago, Chicago, IL, 60637, USA
| | - Chad Heer
- Department of Neurobiology and Institute for Neuroscience, University of Chicago, Chicago, IL, 60637, USA
| | - Chery Cherian
- Department of Neurobiology and Institute for Neuroscience, University of Chicago, Chicago, IL, 60637, USA
| | - Mark E J Sheffield
- Department of Neurobiology and Institute for Neuroscience, University of Chicago, Chicago, IL, 60637, USA.
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23
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Cai Y, Wu J, Dai Q. Review on data analysis methods for mesoscale neural imaging in vivo. NEUROPHOTONICS 2022; 9:041407. [PMID: 35450225 PMCID: PMC9010663 DOI: 10.1117/1.nph.9.4.041407] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/30/2021] [Accepted: 03/23/2022] [Indexed: 06/14/2023]
Abstract
Significance: Mesoscale neural imaging in vivo has gained extreme popularity in neuroscience for its capacity of recording large-scale neurons in action. Optical imaging with single-cell resolution and millimeter-level field of view in vivo has been providing an accumulated database of neuron-behavior correspondence. Meanwhile, optical detection of neuron signals is easily contaminated by noises, background, crosstalk, and motion artifacts, while neural-level signal processing and network-level coordinate are extremely complicated, leading to laborious and challenging signal processing demands. The existing data analysis procedure remains unstandardized, which could be daunting to neophytes or neuroscientists without computational background. Aim: We hope to provide a general data analysis pipeline of mesoscale neural imaging shared between imaging modalities and systems. Approach: We divide the pipeline into two main stages. The first stage focuses on extracting high-fidelity neural responses at single-cell level from raw images, including motion registration, image denoising, neuron segmentation, and signal extraction. The second stage focuses on data mining, including neural functional mapping, clustering, and brain-wide network deduction. Results: Here, we introduce the general pipeline of processing the mesoscale neural images. We explain the principles of these procedures and compare different approaches and their application scopes with detailed discussions about the shortcomings and remaining challenges. Conclusions: There are great challenges and opportunities brought by the large-scale mesoscale data, such as the balance between fidelity and efficiency, increasing computational load, and neural network interpretability. We believe that global circuits on single-neuron level will be more extensively explored in the future.
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Affiliation(s)
- Yeyi Cai
- Tsinghua University, Department of Automation, Beijing, China
| | - Jiamin Wu
- Tsinghua University, Department of Automation, Beijing, China
| | - Qionghai Dai
- Tsinghua University, Department of Automation, Beijing, China
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Benisty H, Song A, Mishne G, Charles AS. Review of data processing of functional optical microscopy for neuroscience. NEUROPHOTONICS 2022; 9:041402. [PMID: 35937186 PMCID: PMC9351186 DOI: 10.1117/1.nph.9.4.041402] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/04/2022] [Accepted: 07/15/2022] [Indexed: 05/04/2023]
Abstract
Functional optical imaging in neuroscience is rapidly growing with the development of optical systems and fluorescence indicators. To realize the potential of these massive spatiotemporal datasets for relating neuronal activity to behavior and stimuli and uncovering local circuits in the brain, accurate automated processing is increasingly essential. We cover recent computational developments in the full data processing pipeline of functional optical microscopy for neuroscience data and discuss ongoing and emerging challenges.
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Affiliation(s)
- Hadas Benisty
- Yale Neuroscience, New Haven, Connecticut, United States
| | - Alexander Song
- Max Planck Institute for Intelligent Systems, Stuttgart, Germany
| | - Gal Mishne
- UC San Diego, Halıcığlu Data Science Institute, Department of Electrical and Computer Engineering and the Neurosciences Graduate Program, La Jolla, California, United States
| | - Adam S. Charles
- Johns Hopkins University, Kavli Neuroscience Discovery Institute, Center for Imaging Science, Department of Biomedical Engineering, Department of Neuroscience, and Mathematical Institute for Data Science, Baltimore, Maryland, United States
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25
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Lee JJ, Krumin M, Harris KD, Carandini M. Task specificity in mouse parietal cortex. Neuron 2022; 110:2961-2969.e5. [PMID: 35963238 PMCID: PMC9616730 DOI: 10.1016/j.neuron.2022.07.017] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Revised: 01/16/2022] [Accepted: 07/15/2022] [Indexed: 11/26/2022]
Abstract
Parietal cortex is implicated in a variety of behavioral processes, but it is unknown whether and how its individual neurons participate in multiple tasks. We trained head-fixed mice to perform two visual decision tasks involving a steering wheel or a virtual T-maze and recorded from the same parietal neurons during these two tasks. Neurons that were active during the T-maze task were typically inactive during the steering-wheel task and vice versa. Recording from the same neurons in the same apparatus without task stimuli yielded the same specificity as in the task, suggesting that task specificity depends on physical context. To confirm this, we trained some mice in a third task combining the steering wheel context with the visual environment of the T-maze. This hybrid task engaged the same neurons as those engaged in the steering-wheel task. Thus, participation by neurons in mouse parietal cortex is task specific, and this specificity is determined by physical context.
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Affiliation(s)
- Julie J Lee
- UCL Institute of Ophthalmology, University College London, Gower Street, London WC1E 6AE, UK.
| | - Michael Krumin
- UCL Institute of Ophthalmology, University College London, Gower Street, London WC1E 6AE, UK
| | - Kenneth D Harris
- UCL Queen Square Institute of Neurology, University College London, Gower Street, London WC1E 6AE, UK
| | - Matteo Carandini
- UCL Institute of Ophthalmology, University College London, Gower Street, London WC1E 6AE, UK
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26
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Grienberger C, Giovannucci A, Zeiger W, Portera-Cailliau C. Two-photon calcium imaging of neuronal activity. NATURE REVIEWS. METHODS PRIMERS 2022; 2:67. [PMID: 38124998 PMCID: PMC10732251 DOI: 10.1038/s43586-022-00147-1] [Citation(s) in RCA: 26] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 07/07/2022] [Indexed: 12/23/2023]
Abstract
In vivo two-photon calcium imaging (2PCI) is a technique used for recording neuronal activity in the intact brain. It is based on the principle that, when neurons fire action potentials, intracellular calcium levels rise, which can be detected using fluorescent molecules that bind to calcium. This Primer is designed for scientists who are considering embarking on experiments with 2PCI. We provide the reader with a background on the basic concepts behind calcium imaging and on the reasons why 2PCI is an increasingly powerful and versatile technique in neuroscience. The Primer explains the different steps involved in experiments with 2PCI, provides examples of what ideal preparations should look like and explains how data are analysed. We also discuss some of the current limitations of the technique, and the types of solutions to circumvent them. Finally, we conclude by anticipating what the future of 2PCI might look like, emphasizing some of the analysis pipelines that are being developed and international efforts for data sharing.
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Affiliation(s)
- Christine Grienberger
- Department of Biology and Volen National Center for Complex Systems, Brandeis University, Waltham, MA, USA
| | - Andrea Giovannucci
- Joint Department of Biomedical Engineering University of North Carolina at Chapel Hill and North Carolina State University, Chapel Hill, NC, USA
- UNC Neuroscience Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - William Zeiger
- Department of Neurology, David Geffen School of Medicine at UCLA, Los Angeles, CA, USA
| | - Carlos Portera-Cailliau
- Department of Neurology, David Geffen School of Medicine at UCLA, Los Angeles, CA, USA
- Department of Neurobiology, David Geffen School of Medicine at UCLA, Los Angeles, CA, USA
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27
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Koukouli F, Montmerle M, Aguirre A, De Brito Van Velze M, Peixoto J, Choudhary V, Varilh M, Julio-Kalajzic F, Allene C, Mendéz P, Zerlaut Y, Marsicano G, Schlüter OM, Rebola N, Bacci A, Lourenço J. Visual-area-specific tonic modulation of GABA release by endocannabinoids sets the activity and coordination of neocortical principal neurons. Cell Rep 2022; 40:111202. [PMID: 36001978 PMCID: PMC9433882 DOI: 10.1016/j.celrep.2022.111202] [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: 09/03/2021] [Revised: 05/24/2022] [Accepted: 07/21/2022] [Indexed: 12/01/2022] Open
Abstract
Perisomatic inhibition of pyramidal neurons (PNs) coordinates cortical network activity during sensory processing, and this role is mainly attributed to parvalbumin-expressing basket cells (BCs). However, cannabinoid receptor type 1 (CB1)-expressing interneurons are also BCs, but the connectivity and function of these elusive but prominent neocortical inhibitory neurons are unclear. We find that their connectivity pattern is visual area specific. Persistently active CB1 signaling suppresses GABA release from CB1 BCs in the medial secondary visual cortex (V2M), but not in the primary visual cortex (V1). Accordingly, in vivo, tonic CB1 signaling is responsible for higher but less coordinated PN activity in the V2M than in the V1. These differential firing dynamics in the V1 and V2M can be captured by a computational network model that incorporates visual-area-specific properties. Our results indicate a differential CB1-mediated mechanism controlling PN activity, suggesting an alternative connectivity scheme of a specific GABAergic circuit in different cortical areas. CB1+ basket cells exhibit visual-area-specific morphology and connectivity patterns Tonic CB1 signaling underlies high pyramidal neurons (PN) activity in V2M but not V1 Tonic CB1 signaling differentially modulates PN-correlated activity in V1 and V2M Numerical simulations capture specific CB1-dependent firing dynamics of V1 and V2M
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Affiliation(s)
- Fani Koukouli
- ICM - Institut du Cerveau, Sorbonne Université, INSERM, CNRS, Paris, France
| | - Martin Montmerle
- ICM - Institut du Cerveau, Sorbonne Université, INSERM, CNRS, Paris, France
| | - Andrea Aguirre
- ICM - Institut du Cerveau, Sorbonne Université, INSERM, CNRS, Paris, France
| | | | - Jérémy Peixoto
- ICM - Institut du Cerveau, Sorbonne Université, INSERM, CNRS, Paris, France
| | - Vikash Choudhary
- ICM - Institut du Cerveau, Sorbonne Université, INSERM, CNRS, Paris, France
| | - Marjorie Varilh
- INSERM, U1215 NeuroCentre Magendie, University of Bordeaux, 33077 Bordeaux, France
| | | | - Camille Allene
- ICM - Institut du Cerveau, Sorbonne Université, INSERM, CNRS, Paris, France
| | | | - Yann Zerlaut
- ICM - Institut du Cerveau, Sorbonne Université, INSERM, CNRS, Paris, France
| | - Giovanni Marsicano
- INSERM, U1215 NeuroCentre Magendie, University of Bordeaux, 33077 Bordeaux, France
| | - Oliver M Schlüter
- Department of Psychiatry and Psychotherapy, University Medical Center Göttingen, Göttingen, Germany; Department of Neuroscience, University of Pittsburgh, Pittsburgh, PA, USA
| | - Nelson Rebola
- ICM - Institut du Cerveau, Sorbonne Université, INSERM, CNRS, Paris, France
| | - Alberto Bacci
- ICM - Institut du Cerveau, Sorbonne Université, INSERM, CNRS, Paris, France.
| | - Joana Lourenço
- ICM - Institut du Cerveau, Sorbonne Université, INSERM, CNRS, Paris, France.
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28
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Xue X, Buccino AP, Saseendran Kumar S, Hierlemann A, Bartram J. Inferring monosynaptic connections from paired dendritic spine Ca 2+imaging and large-scale recording of extracellular spiking. J Neural Eng 2022; 19. [PMID: 35931040 DOI: 10.1088/1741-2552/ac8765] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2022] [Accepted: 08/05/2022] [Indexed: 11/12/2022]
Abstract
Techniques to identify monosynaptic connections between neurons have been vital for neuroscience research, facilitating important advancements concerning network topology, synaptic plasticity, and synaptic integration, among others. Here, we introduce a novel approach to identify and monitor monosynaptic connections using high-resolution dendritic spine Ca2+imaging combined with simultaneous large-scale recording of extracellular electrical activity by means of high-density microelectrode arrays (HD-MEAs). We introduce an easily adoptable analysis pipeline that associates the imaged spine with its presynaptic unit and test it onin vitrorecordings. The method is further validated and optimized by simulating synaptically-evoked spine Ca2+transients based on measured spike trains in order to obtain simulated ground-truth connections. The proposed approach offers unique advantages asi) it can be used to identify monosynaptic connections with an accurate localization of the synapse within the dendritic tree,ii) it provides precise information of presynaptic spiking, andiii) postsynaptic spine Ca2+signals and, finally,iv) the non-invasive nature of the proposed method allows for long-term measurements. The analysis toolkit together with the rich data sets that were acquired are made publicly available for further exploration by the research community.
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Affiliation(s)
- Xiaohan Xue
- D-BSSE, ETH Zürich, Mattenstrasse 26, Basel, 4058, SWITZERLAND
| | | | | | | | - Julian Bartram
- D-BSSE, ETH Zürich, Mattenstrasse 26, Basel, 4058, SWITZERLAND
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29
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Kang S, Park J, Kim K, Lim SH, Kim S, Choi JH, Rah JC, Choi JW. ICoRD: Iterative correlation-based ROI detection method for the extraction of neural signals in calcium imaging. J Neural Eng 2022; 19. [PMID: 35896100 DOI: 10.1088/1741-2552/ac84aa] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2022] [Accepted: 07/27/2022] [Indexed: 11/12/2022]
Abstract
OBJECTIVE In vivo calcium imaging is a standard neuroimaging technique that allows selective observation of target neuronal activities. In calcium imaging, neuron activation signals provide key information for the investigation of neural circuits. For efficient extraction of the calcium signals of neurons, selective detection of the region of interest (ROI) pixels corresponding to the active subcellular region of the target neuron is essential. However, current ROI detection methods for calcium imaging data exhibit a relatively low signal extraction performance from neurons with a low signal-to-noise power ratio (SNR). This is problematic because a low SNR is unavoidable in many biological experiments. APPROACH Therefore, we propose an iterative correlation-based ROI detection (ICoRD) method that robustly extracts the calcium signal of the target neuron from a calcium imaging series with severe noise. MAIN RESULTS ICoRD extracts calcium signals closer to the ground-truth calcium signal than the conventional method from simulated calcium imaging data in all low SNR ranges. Additionally, this study confirmed that ICoRD robustly extracts activation signals against noise, even within in vivo environments. SIGNIFICANCE ICoRD showed reliable detection from neurons with a low SNR and sparse activation, which were not detected by conventional methods. ICoRD will facilitate our understanding of neural circuit activity by providing significantly improved ROI detection in noisy images.
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Affiliation(s)
- Seongtak Kang
- Department of Information & Communication Engineering, Daegu Gyeongbuk Institute of Science & Technology, 333 Techno Jungang-daero, Hyeonpung-eup, Dalseong-gun, Daegu, 42988, Korea (the Republic of)
| | - Jiho Park
- Department of Information & Communication Engineering, Daegu Gyeongbuk Institute of Science & Technology, 333 Techno Jungang-daero, Hyeonpung-eup, Dalseong-gun, Daegu, 42988, Korea (the Republic of)
| | - Kyungsoo Kim
- Department of Neurology, University of California San Francisco, 1651 4th St, San Francisco, California, 94158, UNITED STATES
| | - Sung-Ho Lim
- KEPCO Engineering and Construction Company Inc, 269, Hyeoksin-ro, Gimcheon-si, Gyeongsangbuk-do, Gimcheon, 39660, Korea (the Republic of)
| | - Samhwan Kim
- Brain Engineering Convergence Research Center (BCC), Daegu Gyeongbuk Institute of Science & Technology, 333, Techno jungang-daero, Hyeonpung-eup, Dalseong-gun, Daegu, 42988, Korea (the Republic of)
| | - Joon Ho Choi
- Laboratory of Neurophysiology, Korea Brain Research Institute, 61, Cheomdan-ro, Dong-gu, Daegu, 41062, Korea (the Republic of)
| | - Jong-Cheol Rah
- Laboratory of Neurophysiology, Korea Brain Research Institute, 61, Cheomdan-ro, Dong-gu, Daegu, 41062, Korea (the Republic of)
| | - Ji-Woong Choi
- Department of Information & Communication Engineering, Daegu Gyeongbuk Institute of Science & Technology, 333 Techno Jungang-daero, Hyeonpung-eup, Dalseong-gun, Daegu, 42988, Korea (the Republic of)
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30
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Computational Methods for Neuron Segmentation in Two-Photon Calcium Imaging Data: A Survey. APPLIED SCIENCES-BASEL 2022. [DOI: 10.3390/app12146876] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Calcium imaging has rapidly become a methodology of choice for real-time in vivo neuron analysis. Its application to large sets of data requires automated tools to annotate and segment cells, allowing scalable image segmentation under reproducible criteria. In this paper, we review and summarize the most recent methods for computational segmentation of calcium imaging. The contributions of the paper are three-fold: we provide an overview of the main algorithms taxonomized in three categories (signal processing, matrix factorization and machine learning-based approaches), we highlight the main advantages and disadvantages of each category and we provide a summary of the performance of the methods that have been tested on public benchmarks (with links to the public code when available).
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31
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Flores-Valle A, Seelig JD. Axial motion estimation and correction for simultaneous multi-plane two-photon calcium imaging. BIOMEDICAL OPTICS EXPRESS 2022; 13:2035-2049. [PMID: 35519241 PMCID: PMC9045928 DOI: 10.1364/boe.445775] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/13/2021] [Revised: 12/16/2021] [Accepted: 02/01/2022] [Indexed: 06/14/2023]
Abstract
Two-photon imaging in behaving animals is typically accompanied by brain motion. For functional imaging experiments, for example with genetically encoded calcium indicators, such brain motion induces changes in fluorescence intensity. These motion-related intensity changes or motion artifacts can typically not be separated from neural activity-induced signals. While lateral motion, within the focal plane, can be corrected by computationally aligning images, axial motion, out of the focal plane, cannot easily be corrected. Here, we developed an algorithm for axial motion correction for non-ratiometric calcium indicators taking advantage of simultaneous multi-plane imaging. Using temporally multiplexed beams, recording simultaneously from at least two focal planes at different z positions, and recording a z-stack for each beam as a calibration step, the algorithm separates motion-related and neural activity-induced changes in fluorescence intensity. The algorithm is based on a maximum likelihood optimisation approach; it assumes (as a first order approximation) that no distortions of the sample occurs during axial motion and that neural activity increases uniformly along the optical axis in each region of interest. The developed motion correction approach allows axial motion estimation and correction at high frame rates for isolated structures in the imaging volume in vivo, such as sparse expression patterns in the fruit fly brain.
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Affiliation(s)
- Andres Flores-Valle
- Max Planck Institute for Neurobiology of Behavior - caesar (MPINB), Bonn, Germany
- International Max Planck Research School for Brain and Behavior, Bonn, Germany
| | - Johannes D Seelig
- Max Planck Institute for Neurobiology of Behavior - caesar (MPINB), Bonn, Germany
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32
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Zong W, Obenhaus HA, Skytøen ER, Eneqvist H, de Jong NL, Vale R, Jorge MR, Moser MB, Moser EI. Large-scale two-photon calcium imaging in freely moving mice. Cell 2022; 185:1240-1256.e30. [PMID: 35305313 PMCID: PMC8970296 DOI: 10.1016/j.cell.2022.02.017] [Citation(s) in RCA: 92] [Impact Index Per Article: 46.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2021] [Revised: 01/12/2022] [Accepted: 02/14/2022] [Indexed: 11/29/2022]
Abstract
We developed a miniaturized two-photon microscope (MINI2P) for fast, high-resolution, multiplane calcium imaging of over 1,000 neurons at a time in freely moving mice. With a microscope weight below 3 g and a highly flexible connection cable, MINI2P allowed stable imaging with no impediment of behavior in a variety of assays compared to untethered, unimplanted animals. The improved cell yield was achieved through a optical system design featuring an enlarged field of view (FOV) and a microtunable lens with increased z-scanning range and speed that allows fast and stable imaging of multiple interleaved planes, as well as 3D functional imaging. Successive imaging across multiple, adjacent FOVs enabled recordings from more than 10,000 neurons in the same animal. Large-scale proof-of-principle data were obtained from cell populations in visual cortex, medial entorhinal cortex, and hippocampus, revealing spatial tuning of cells in all areas. We made a light-weight 2-photon miniscope for calcium imaging in freely moving mice Stable high-quality imaging was observed during a wide spectrum of behaviors Activity can be monitored in volumes of over 1,000 visual or entorhinal-cortex cells A custom-designed z-scanning module allows fast imaging across multiple planes
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Affiliation(s)
- Weijian Zong
- Kavli Institute for Systems Neuroscience and Centre for Neural Computation, Norwegian University of Science and Technology (NTNU), Trondheim NO-7491, Norway.
| | - Horst A Obenhaus
- Kavli Institute for Systems Neuroscience and Centre for Neural Computation, Norwegian University of Science and Technology (NTNU), Trondheim NO-7491, Norway
| | - Emilie R Skytøen
- Kavli Institute for Systems Neuroscience and Centre for Neural Computation, Norwegian University of Science and Technology (NTNU), Trondheim NO-7491, Norway
| | - Hanna Eneqvist
- Kavli Institute for Systems Neuroscience and Centre for Neural Computation, Norwegian University of Science and Technology (NTNU), Trondheim NO-7491, Norway
| | - Nienke L de Jong
- Kavli Institute for Systems Neuroscience and Centre for Neural Computation, Norwegian University of Science and Technology (NTNU), Trondheim NO-7491, Norway
| | - Ruben Vale
- Kavli Institute for Systems Neuroscience and Centre for Neural Computation, Norwegian University of Science and Technology (NTNU), Trondheim NO-7491, Norway
| | - Marina R Jorge
- Kavli Institute for Systems Neuroscience and Centre for Neural Computation, Norwegian University of Science and Technology (NTNU), Trondheim NO-7491, Norway
| | - May-Britt Moser
- Kavli Institute for Systems Neuroscience and Centre for Neural Computation, Norwegian University of Science and Technology (NTNU), Trondheim NO-7491, Norway
| | - Edvard I Moser
- Kavli Institute for Systems Neuroscience and Centre for Neural Computation, Norwegian University of Science and Technology (NTNU), Trondheim NO-7491, Norway.
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Calcium Imaging and Electrophysiology of hippocampal Activity under Anesthesia and natural Sleep in Mice. Sci Data 2022; 9:113. [PMID: 35351935 PMCID: PMC8964694 DOI: 10.1038/s41597-022-01244-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2021] [Accepted: 03/04/2022] [Indexed: 11/08/2022] Open
Abstract
AbstractThe acute effects of anesthesia and their underlying mechanisms are still not fully understood. Thus, comprehensive analysis and efficient generalization require their description in various brain regions. Here we describe a large-scale, annotated collection of 2-photon calcium imaging data and multi-electrode, extracellular electrophysiological recordings in CA1 of the murine hippocampus under three distinct anesthetics (Isoflurane, Ketamine/Xylazine and Medetomidine/Midazolam/Fentanyl), during natural sleep, and wakefulness. We cover several aspects of data quality standardization and provide a set of tools for autonomous validation, along with analysis workflows for reuse and data exploration. The datasets described here capture various aspects of neural activity in hundreds of pyramidal cells at single cell resolution. In addition to relevance for basic biological research, the dataset may find utility in computational neuroscience as a benchmark for models of anesthesia and sleep.
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34
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To deconvolve, or not to deconvolve: Inferences of neuronal activities using calcium imaging data. J Neurosci Methods 2022; 366:109431. [PMID: 34856319 DOI: 10.1016/j.jneumeth.2021.109431] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2021] [Revised: 11/25/2021] [Accepted: 11/26/2021] [Indexed: 01/19/2023]
Abstract
BACKGROUND With the increasing popularity of calcium imaging in neuroscience research, choosing the right methods to analyze calcium imaging data is critical to address various scientific questions. Unlike spike trains measured using electrodes, fluorescence intensity traces provide an indirect and noisy measurement of the underlying neuronal activities. The observed calcium traces are either analyzed directly or deconvolved to spike trains to infer neuronal activities. When both approaches are applicable, it is unclear whether deconvolving calcium traces is a necessary step. METHODS In this article, we compare the performance of using calcium traces or their deconvolved spike trains for three common analyses: clustering, principal component analysis (PCA), and population decoding. RESULTS We found that (1) the two approaches lead to diverging results; (2) estimated spike trains, when smoothed or binned appropriately, usually lead to satisfactory performances, such as more accurate estimation of cluster membership; (3) although estimate spike train produce results more similar to true spike data than trace data, we found that the PCA results from trace data might better reflect the underlying neuronal ensembles (clusters); and (4) for both approaches, decobability can be improved by using denoising or smoothing methods. COMPARISON WITH EXISTING METHODS Our simulations and applications to real data suggest that estimated spike data outperform trace data in cluster analysis and give comparable results for population decoding. In addition, the decobability of estimated spike data can be slightly better than that of calcium trace data with appropriate filtering / smoothing methods. CONCLUSION We conclude that spike detection might be a useful pre-processing step for certain problems such as clustering; however, the continuous nature of calcium imaging data provides a natural smoothness that might be helpful for problems such as dimensional reduction.
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Meamardoost S, Bhattacharya M, Hwang EJ, Komiyama T, Mewes C, Wang L, Zhang Y, Gunawan R. FARCI: Fast and Robust Connectome Inference. Brain Sci 2021; 11:1556. [PMID: 34942857 PMCID: PMC8699247 DOI: 10.3390/brainsci11121556] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2021] [Revised: 11/12/2021] [Accepted: 11/18/2021] [Indexed: 11/17/2022] Open
Abstract
The inference of neuronal connectome from large-scale neuronal activity recordings, such as two-photon Calcium imaging, represents an active area of research in computational neuroscience. In this work, we developed FARCI (Fast and Robust Connectome Inference), a MATLAB package for neuronal connectome inference from high-dimensional two-photon Calcium fluorescence data. We employed partial correlations as a measure of the functional association strength between pairs of neurons to reconstruct a neuronal connectome. We demonstrated using in silico datasets from the Neural Connectomics Challenge (NCC) and those generated using the state-of-the-art simulator of Neural Anatomy and Optimal Microscopy (NAOMi) that FARCI provides an accurate connectome and its performance is robust to network sizes, missing neurons, and noise levels. Moreover, FARCI is computationally efficient and highly scalable to large networks. In comparison with the best performing connectome inference algorithm in the NCC, Generalized Transfer Entropy (GTE), and Fluorescence Single Neuron and Network Analysis Package (FluoroSNNAP), FARCI produces more accurate networks over different network sizes, while providing significantly better computational speed and scaling.
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Affiliation(s)
- Saber Meamardoost
- Department of Chemical and Biological Engineering, University at Buffalo, Buffalo, NY 14260, USA;
| | | | - Eun Jung Hwang
- Neurobiology Section, Center for Neural Circuits and Behavior, Department of Neurosciences, University of California San Diego, La Jolla, CA 92093, USA; (E.J.H.); (T.K.)
- Cell Biology and Anatomy Discipline, Center for Brain Function and Repair, Chicago Medical School, Rosalind Franklin University of Medicine and Science, North Chicago, IL 60064, USA
| | - Takaki Komiyama
- Neurobiology Section, Center for Neural Circuits and Behavior, Department of Neurosciences, University of California San Diego, La Jolla, CA 92093, USA; (E.J.H.); (T.K.)
| | - Claudia Mewes
- Department of Physics and Astronomy, University of Alabama, Tuscaloosa, AL 35487, USA;
| | - Linbing Wang
- Department of Civil and Environmental Engineering, Virginia Polytechnic Institute and State University, Blacksburg, VA 24061, USA;
| | - Ying Zhang
- Department of Cell and Molecular Biology, University of Rhode Island, Kingston, RI 02881, USA;
| | - Rudiyanto Gunawan
- Department of Chemical and Biological Engineering, University at Buffalo, Buffalo, NY 14260, USA;
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Leonardi AA, Lo Faro MJ, Fazio B, Spinella C, Conoci S, Livreri P, Irrera A. Fluorescent Biosensors Based on Silicon Nanowires. NANOMATERIALS (BASEL, SWITZERLAND) 2021; 11:2970. [PMID: 34835735 PMCID: PMC8624671 DOI: 10.3390/nano11112970] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/28/2021] [Revised: 10/27/2021] [Accepted: 11/03/2021] [Indexed: 01/05/2023]
Abstract
Nanostructures are arising as novel biosensing platforms promising to surpass current performance in terms of sensitivity, selectivity, and affordability of standard approaches. However, for several nanosensors, the material and synthesis used make the industrial transfer of such technologies complex. Silicon nanowires (NWs) are compatible with Si-based flat architecture fabrication and arise as a hopeful solution to couple their interesting physical properties and surface-to-volume ratio to an easy commercial transfer. Among all the transduction methods, fluorescent probes and sensors emerge as some of the most used approaches thanks to their easy data interpretation, measure affordability, and real-time in situ analysis. In fluorescent sensors, Si NWs are employed as substrate and coupled with several fluorophores, NWs can be used as quenchers in stem-loop configuration, and have recently been used for direct fluorescent sensing. In this review, an overview on fluorescent sensors based on Si NWs is presented, analyzing the literature of the field and highlighting the advantages and drawbacks for each strategy.
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Affiliation(s)
- Antonio Alessio Leonardi
- Dipartimento di Fisica e Astronomia “Ettore Majorana”, Università degli Studi di Catania, Via S. Sofia 64, 95123 Catania, Italy; (A.A.L.); (M.J.L.F.)
- Istituto per i Processi Chimico-Fisici, Consiglio Nazionale delle Ricerche (CNR-IPCF), Viale F. Stagno D’Alcontres 37, 98158 Messina, Italy;
- Istituto per la Microelettronica e Microsistemi, Consiglio Nazionale delle Ricerche (CNR-IMM) UoS Catania, Via S. Sofia 64, 95123 Catania, Italy
- Lab SENS, Beyond NANO, Dipartimento di Scienze Chimiche, Biologiche, Farmaceutiche, ed Ambientali, Università Degli Studi di Messina, Viale Ferdinando Stagno d’Alcontres, 98166 Messina, Italy; (C.S.); (S.C.)
| | - Maria José Lo Faro
- Dipartimento di Fisica e Astronomia “Ettore Majorana”, Università degli Studi di Catania, Via S. Sofia 64, 95123 Catania, Italy; (A.A.L.); (M.J.L.F.)
- Istituto per la Microelettronica e Microsistemi, Consiglio Nazionale delle Ricerche (CNR-IMM) UoS Catania, Via S. Sofia 64, 95123 Catania, Italy
| | - Barbara Fazio
- Istituto per i Processi Chimico-Fisici, Consiglio Nazionale delle Ricerche (CNR-IPCF), Viale F. Stagno D’Alcontres 37, 98158 Messina, Italy;
- Lab SENS, Beyond NANO, Dipartimento di Scienze Chimiche, Biologiche, Farmaceutiche, ed Ambientali, Università Degli Studi di Messina, Viale Ferdinando Stagno d’Alcontres, 98166 Messina, Italy; (C.S.); (S.C.)
| | - Corrado Spinella
- Lab SENS, Beyond NANO, Dipartimento di Scienze Chimiche, Biologiche, Farmaceutiche, ed Ambientali, Università Degli Studi di Messina, Viale Ferdinando Stagno d’Alcontres, 98166 Messina, Italy; (C.S.); (S.C.)
- Istituto per la Microelettronica e Microsistemi, Consiglio Nazionale delle Ricerche (CNR-IMM) Zona Industriale, VIII Strada 5, 95121 Catania, Italy
| | - Sabrina Conoci
- Lab SENS, Beyond NANO, Dipartimento di Scienze Chimiche, Biologiche, Farmaceutiche, ed Ambientali, Università Degli Studi di Messina, Viale Ferdinando Stagno d’Alcontres, 98166 Messina, Italy; (C.S.); (S.C.)
- Istituto per la Microelettronica e Microsistemi, Consiglio Nazionale delle Ricerche (CNR-IMM) Zona Industriale, VIII Strada 5, 95121 Catania, Italy
- Dipartimento di Scienze Chimiche, Biologiche, Farmaceutiche, ed Ambientali, Università Degli Studi di Messina, Viale Ferdinando Stagno d’Alcontres, 98166 Messina, Italy
| | - Patrizia Livreri
- Dipartimento di ingegneria, Università degli Studi di Palermo, Viale delle Scienze BLDG 9, 90128 Palermo, Italy;
| | - Alessia Irrera
- Istituto per i Processi Chimico-Fisici, Consiglio Nazionale delle Ricerche (CNR-IPCF), Viale F. Stagno D’Alcontres 37, 98158 Messina, Italy;
- Lab SENS, Beyond NANO, Dipartimento di Scienze Chimiche, Biologiche, Farmaceutiche, ed Ambientali, Università Degli Studi di Messina, Viale Ferdinando Stagno d’Alcontres, 98166 Messina, Italy; (C.S.); (S.C.)
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Reliable Sensory Processing in Mouse Visual Cortex through Cooperative Interactions between Somatostatin and Parvalbumin Interneurons. J Neurosci 2021; 41:8761-8778. [PMID: 34493543 DOI: 10.1523/jneurosci.3176-20.2021] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Revised: 08/16/2021] [Accepted: 08/23/2021] [Indexed: 11/21/2022] Open
Abstract
Intrinsic neuronal variability significantly limits information encoding in the primary visual cortex (V1). However, under certain conditions, neurons can respond reliably with highly precise responses to the same visual stimuli from trial to trial. This suggests that there exists intrinsic neural circuit mechanisms that dynamically modulate the intertrial variability of visual cortical neurons. Here, we sought to elucidate the role of different inhibitory interneurons (INs) in reliable coding in mouse V1. To study the interactions between somatostatin-expressing interneurons (SST-INs) and parvalbumin-expressing interneurons (PV-INs), we used a dual-color calcium imaging technique that allowed us to simultaneously monitor these two neural ensembles while awake mice, of both sexes, passively viewed natural movies. SST neurons were more active during epochs of reliable pyramidal neuron firing, whereas PV neurons were more active during epochs of unreliable firing. SST neuron activity lagged that of PV neurons, consistent with a feedback inhibitory SST→PV circuit. To dissect the role of this circuit in pyramidal neuron activity, we used temporally limited optogenetic activation and inactivation of SST and PV interneurons during periods of reliable and unreliable pyramidal cell firing. Transient firing of SST neurons increased pyramidal neuron reliability by actively suppressing PV neurons, a proposal that was supported by a rate-based model of V1 neurons. These results identify a cooperative functional role for the SST→PV circuit in modulating the reliability of pyramidal neuron activity.SIGNIFICANCE STATEMENT Cortical neurons often respond to identical sensory stimuli with large variability. However, under certain conditions, the same neurons can also respond highly reliably. The circuit mechanisms that contribute to this modulation remain unknown. Here, we used novel dual-wavelength calcium imaging and temporally selective optical perturbation to identify an inhibitory neural circuit in visual cortex that can modulate the reliability of pyramidal neurons to naturalistic visual stimuli. Our results, supported by computational models, suggest that somatostatin interneurons increase pyramidal neuron reliability by suppressing parvalbumin interneurons via the inhibitory SST→PV circuit. These findings reveal a novel role of the SST→PV circuit in modulating the fidelity of neural coding critical for visual perception.
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The habenula clock influences response to a stressor. Neurobiol Stress 2021; 15:100403. [PMID: 34632007 PMCID: PMC8488752 DOI: 10.1016/j.ynstr.2021.100403] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2021] [Revised: 09/17/2021] [Accepted: 09/19/2021] [Indexed: 12/12/2022] Open
Abstract
The response of an animal to a sensory stimulus depends on the nature of the stimulus and on expectations, which are mediated by spontaneous activity. Here, we ask how circadian variation in the expectation of danger, and thus the response to a potential threat, is controlled. We focus on the habenula, a mediator of threat response that functions by regulating neuromodulator release, and use zebrafish as the experimental system. Single cell transcriptomics indicates that multiple clock genes are expressed throughout the habenula, while quantitative in situ hybridization confirms that the clock oscillates. Two-photon calcium imaging indicates a circadian change in spontaneous activity of habenula neurons. To assess the role of this clock, a truncated clocka gene was specifically expressed in the habenula. This partially inhibited the clock, as shown by changes in per3 expression as well as altered day-night variation in dopamine, serotonin and acetylcholine levels. Behaviourally, anxiety-like responses evoked by an alarm pheromone were reduced. Circadian effects of the pheromone were disrupted, such that responses in the day resembled those at night. Behaviours that are regulated by the pineal clock and not triggered by stressors were unaffected. We suggest that the habenula clock regulates the expectation of danger, thus providing one mechanism for circadian change in the response to a stressor.
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Lee CCY, Kheradpezhouh E, Diamond ME, Arabzadeh E. State-Dependent Changes in Perception and Coding in the Mouse Somatosensory Cortex. Cell Rep 2021; 32:108197. [PMID: 32997984 DOI: 10.1016/j.celrep.2020.108197] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2020] [Revised: 07/07/2020] [Accepted: 09/03/2020] [Indexed: 12/24/2022] Open
Abstract
An animal's behavioral state is reflected in the dynamics of cortical population activity and its capacity to process sensory information. To better understand the relationship between behavioral states and information processing, mice are trained to detect varying amplitudes of whisker-deflection under two-photon calcium imaging. Layer 2/3 neurons in the vibrissal primary somatosensory cortex are imaged across different behavioral states, defined based on detection performance (low to high-state) and pupil diameter. The neurometric curve in each behavioral state mirrors the corresponding psychometric performance, with calcium signals predictive of the animal's choice. High behavioral states are associated with lower network synchrony, extending over shorter cortical distances. The decrease in correlation across neurons in high state results in enhanced information transmission capacity at the population level. The observed state-dependent changes suggest that the coding regime within the first stage of cortical processing may underlie adaptive routing of relevant information through the sensorimotor system.
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Affiliation(s)
- Conrad C Y Lee
- Eccles Institute of Neuroscience, John Curtin School of Medical Research, The Australian National University, Canberra, ACT 2601, Australia; Australian Research Council Centre of Excellence for Integrative Brain Function, The Australian National University Node, Canberra, ACT 2601, Australia.
| | - Ehsan Kheradpezhouh
- Eccles Institute of Neuroscience, John Curtin School of Medical Research, The Australian National University, Canberra, ACT 2601, Australia; Australian Research Council Centre of Excellence for Integrative Brain Function, The Australian National University Node, Canberra, ACT 2601, Australia
| | - Mathew E Diamond
- Australian Research Council Centre of Excellence for Integrative Brain Function, The Australian National University Node, Canberra, ACT 2601, Australia; Cognitive Neuroscience, International School for Advanced Studies (SISSA), Trieste, Italy
| | - Ehsan Arabzadeh
- Eccles Institute of Neuroscience, John Curtin School of Medical Research, The Australian National University, Canberra, ACT 2601, Australia; Australian Research Council Centre of Excellence for Integrative Brain Function, The Australian National University Node, Canberra, ACT 2601, Australia
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40
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Song A, Gauthier JL, Pillow JW, Tank DW, Charles AS. Neural anatomy and optical microscopy (NAOMi) simulation for evaluating calcium imaging methods. J Neurosci Methods 2021; 358:109173. [PMID: 33839190 PMCID: PMC8217135 DOI: 10.1016/j.jneumeth.2021.109173] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2020] [Revised: 03/21/2021] [Accepted: 03/24/2021] [Indexed: 11/20/2022]
Abstract
BACKGROUND The past decade has seen a multitude of new in vivo functional imaging methodologies. However, the lack of ground-truth comparisons or evaluation metrics makes the large-scale, systematic validation vital to the continued development and use of optical microscopy impossible. NEW-METHOD We provide a new framework for evaluating two-photon microscopy methods via in silico Neural Anatomy and Optical Microscopy (NAOMi) simulation. Our computationally efficient model generates large anatomical volumes of mouse cortex, simulates neural activity, and incorporates optical propagation and scanning to create realistic calcium imaging datasets. RESULTS We verify NAOMi simulations against in vivo two-photon recordings from mouse cortex. We leverage this in silico ground truth to directly compare different segmentation algorithms and optical designs. We find modern segmentation algorithms extract strong neural time-courses comparable to estimation using oracle spatial information, but with an increase in the false positive rate. Comparison between optical setups demonstrate improved resilience to motion artifacts in sparsely labeled samples using Bessel beams, increased signal-to-noise ratio and cell-count using low numerical aperture Gaussian beams and nuclear GCaMP, and more uniform spatial sampling with temporal focusing versus multi-plane imaging. COMPARISON WITH EXISTING METHODS NAOMi is a first-of-its kind framework for assessing optical imaging modalities. Existing methods are either anatomical simulations or do not address functional imaging. Thus there is no competing method for simulating realistic functional optical microscopy data. CONCLUSIONS By leveraging the rich accumulated knowledge of neural anatomy and optical physics, we provide a powerful new tool to assess and develop important methods in neural imaging.
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Affiliation(s)
- Alexander Song
- Princeton Neuroscience Institute, Princeton University, Princeton, 08540 NJ, USA; Department of Physics, Princeton University, Princeton, 08540 NJ, USA
| | - Jeff L Gauthier
- Princeton Neuroscience Institute, Princeton University, Princeton, 08540 NJ, USA
| | - Jonathan W Pillow
- Princeton Neuroscience Institute, Princeton University, Princeton, 08540 NJ, USA; Department of Psychology, Princeton University, Princeton, 08540 NJ, USA
| | - David W Tank
- Princeton Neuroscience Institute, Princeton University, Princeton, 08540 NJ, USA; Bezos Center for Neural Circuit Dynamics, Princeton University, Princeton, 08540 NJ, USA; Department of Molecular Biology, Princeton University, Princeton, 08540 NJ, USA
| | - Adam S Charles
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, 21218, MD, USA; Mathematical Institute for Data Science, Johns Hopkins University, Baltimore, 21218, MD, USA; Center for Imaging Science, Johns Hopkins University, Baltimore, 21218, MD, USA; Kavli Neuroscience Discovery Institute, Johns Hopkins University, Baltimore, 21218, MD, USA
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41
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Rupasinghe A, Francis N, Liu J, Bowen Z, Kanold PO, Babadi B. Direct extraction of signal and noise correlations from two-photon calcium imaging of ensemble neuronal activity. eLife 2021; 10:68046. [PMID: 34180397 PMCID: PMC8354639 DOI: 10.7554/elife.68046] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2021] [Accepted: 06/27/2021] [Indexed: 12/21/2022] Open
Abstract
Neuronal activity correlations are key to understanding how populations of neurons collectively encode information. While two-photon calcium imaging has created a unique opportunity to record the activity of large populations of neurons, existing methods for inferring correlations from these data face several challenges. First, the observations of spiking activity produced by two-photon imaging are temporally blurred and noisy. Secondly, even if the spiking data were perfectly recovered via deconvolution, inferring network-level features from binary spiking data is a challenging task due to the non-linear relation of neuronal spiking to endogenous and exogenous inputs. In this work, we propose a methodology to explicitly model and directly estimate signal and noise correlations from two-photon fluorescence observations, without requiring intermediate spike deconvolution. We provide theoretical guarantees on the performance of the proposed estimator and demonstrate its utility through applications to simulated and experimentally recorded data from the mouse auditory cortex.
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Affiliation(s)
- Anuththara Rupasinghe
- Department of Electrical and Computer Engineering, University of Maryland, College Park, United States
| | - Nikolas Francis
- The Institute for Systems Research, University of Maryland, College Park, United States.,Department of Biology, University of Maryland, College Park, United States
| | - Ji Liu
- The Institute for Systems Research, University of Maryland, College Park, United States.,Department of Biology, University of Maryland, College Park, United States
| | - Zac Bowen
- The Institute for Systems Research, University of Maryland, College Park, United States.,Department of Biology, University of Maryland, College Park, United States
| | - Patrick O Kanold
- The Institute for Systems Research, University of Maryland, College Park, United States.,Department of Biology, University of Maryland, College Park, United States.,Department of Biomedical Engineering, Johns Hopkins University, Baltimore, United States
| | - Behtash Babadi
- Department of Electrical and Computer Engineering, University of Maryland, College Park, United States
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42
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Romero S, Hight AE, Clayton KK, Resnik J, Williamson RS, Hancock KE, Polley DB. Cellular and Widefield Imaging of Sound Frequency Organization in Primary and Higher Order Fields of the Mouse Auditory Cortex. Cereb Cortex 2021; 30:1603-1622. [PMID: 31667491 DOI: 10.1093/cercor/bhz190] [Citation(s) in RCA: 49] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
The mouse auditory cortex (ACtx) contains two core fields-primary auditory cortex (A1) and anterior auditory field (AAF)-arranged in a mirror reversal tonotopic gradient. The best frequency (BF) organization and naming scheme for additional higher order fields remain a matter of debate, as does the correspondence between smoothly varying global tonotopy and heterogeneity in local cellular tuning. Here, we performed chronic widefield and two-photon calcium imaging from the ACtx of awake Thy1-GCaMP6s reporter mice. Data-driven parcellation of widefield maps identified five fields, including a previously unidentified area at the ventral posterior extreme of the ACtx (VPAF) and a tonotopically organized suprarhinal auditory field (SRAF) that extended laterally as far as ectorhinal cortex. Widefield maps were stable over time, where single pixel BFs fluctuated by less than 0.5 octaves throughout a 1-month imaging period. After accounting for neuropil signal and frequency tuning strength, BF organization in neighboring layer 2/3 neurons was intermediate to the heterogeneous salt and pepper organization and the highly precise local organization that have each been described in prior studies. Multiscale imaging data suggest there is no ultrasonic field or secondary auditory cortex in the mouse. Instead, VPAF and a dorsal posterior (DP) field emerged as the strongest candidates for higher order auditory areas.
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Affiliation(s)
- Sandra Romero
- Eaton-Peabody Laboratories, Massachusetts Eye and Ear Infirmary, Boston, MA 02114, USA
| | - Ariel E Hight
- Eaton-Peabody Laboratories, Massachusetts Eye and Ear Infirmary, Boston, MA 02114, USA
| | - Kameron K Clayton
- Eaton-Peabody Laboratories, Massachusetts Eye and Ear Infirmary, Boston, MA 02114, USA
| | - Jennifer Resnik
- Eaton-Peabody Laboratories, Massachusetts Eye and Ear Infirmary, Boston, MA 02114, USA.,Department of Otolaryngology, Harvard Medical School, Boston, MA 02114, USA
| | - Ross S Williamson
- Eaton-Peabody Laboratories, Massachusetts Eye and Ear Infirmary, Boston, MA 02114, USA.,Department of Otolaryngology, Harvard Medical School, Boston, MA 02114, USA
| | - Kenneth E Hancock
- Eaton-Peabody Laboratories, Massachusetts Eye and Ear Infirmary, Boston, MA 02114, USA.,Department of Otolaryngology, Harvard Medical School, Boston, MA 02114, USA
| | - Daniel B Polley
- Eaton-Peabody Laboratories, Massachusetts Eye and Ear Infirmary, Boston, MA 02114, USA.,Department of Otolaryngology, Harvard Medical School, Boston, MA 02114, USA
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43
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Spellman T, Svei M, Kaminsky J, Manzano-Nieves G, Liston C. Prefrontal deep projection neurons enable cognitive flexibility via persistent feedback monitoring. Cell 2021; 184:2750-2766.e17. [PMID: 33861951 DOI: 10.1016/j.cell.2021.03.047] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2020] [Revised: 02/16/2021] [Accepted: 03/23/2021] [Indexed: 12/20/2022]
Abstract
Cognitive flexibility, the ability to alter strategy according to changing stimulus-response-reward relationships, is critical for updating learned behavior. Attentional set-shifting, a test of cognitive flexibility, depends on the activity of prefrontal cortex (PFC). It remains unclear, however, what role PFC neurons play to support set-shifting. Using optogenetics and two-photon calcium imaging, we demonstrate that medial PFC activity does not bias sensorimotor responses during set-shifting, but rather enables set-shifting by encoding trial feedback information, a role it has been known to play in other contexts. Unexpectedly, the functional properties of PFC cells did not vary with their efferent projection targets. Instead, representations of trial feedback formed a topological gradient, with cells more strongly selective for feedback information located further from the pial surface, where afferent input from the anterior cingulate cortex was denser. These findings identify a critical role for deep PFC projection neurons in enabling set-shifting through behavioral feedback monitoring.
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Affiliation(s)
- Timothy Spellman
- Feil Family Brain and Mind Research Institute, Weill Cornell Medicine, New York, NY 10021, USA; Department of Psychiatry, Weill Cornell Medicine, New York, NY 10021, USA.
| | - Malka Svei
- Feil Family Brain and Mind Research Institute, Weill Cornell Medicine, New York, NY 10021, USA; Department of Psychiatry, Weill Cornell Medicine, New York, NY 10021, USA
| | - Jesse Kaminsky
- Feil Family Brain and Mind Research Institute, Weill Cornell Medicine, New York, NY 10021, USA; Department of Psychiatry, Weill Cornell Medicine, New York, NY 10021, USA
| | - Gabriela Manzano-Nieves
- Feil Family Brain and Mind Research Institute, Weill Cornell Medicine, New York, NY 10021, USA; Department of Psychiatry, Weill Cornell Medicine, New York, NY 10021, USA
| | - Conor Liston
- Feil Family Brain and Mind Research Institute, Weill Cornell Medicine, New York, NY 10021, USA; Department of Psychiatry, Weill Cornell Medicine, New York, NY 10021, USA.
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44
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Affiliation(s)
- Adrienne L Fairhall
- Department of Physiology and Biophysics, Computational Neuroscience Center, University of Washington, Seattle, WA 98195
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45
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Vanwalleghem G, Constantin L, Scott EK. Calcium Imaging and the Curse of Negativity. Front Neural Circuits 2021; 14:607391. [PMID: 33488363 PMCID: PMC7815594 DOI: 10.3389/fncir.2020.607391] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2020] [Accepted: 12/02/2020] [Indexed: 12/17/2022] Open
Abstract
The imaging of neuronal activity using calcium indicators has become a staple of modern neuroscience. However, without ground truths, there is a real risk of missing a significant portion of the real responses. Here, we show that a common assumption, the non-negativity of the neuronal responses as detected by calcium indicators, biases all levels of the frequently used analytical methods for these data. From the extraction of meaningful fluorescence changes to spike inference and the analysis of inferred spikes, each step risks missing real responses because of the assumption of non-negativity. We first show that negative deviations from baseline can exist in calcium imaging of neuronal activity. Then, we use simulated data to test three popular algorithms for image analysis, CaImAn, suite2p, and CellSort, finding that suite2p may be the best suited to large datasets. We also tested the spike inference algorithms included in CaImAn, suite2p, and Cellsort, as well as the dedicated inference algorithms MLspike and CASCADE, and found each to have limitations in dealing with inhibited neurons. Among these spike inference algorithms, FOOPSI, from CaImAn, performed the best on inhibited neurons, but even this algorithm inferred spurious spikes upon the return of the fluorescence signal to baseline. As such, new approaches will be needed before spikes can be sensitively and accurately inferred from calcium data in inhibited neurons. We further suggest avoiding data analysis approaches that, by assuming non-negativity, ignore inhibited responses. Instead, we suggest a first exploratory step, using k-means or PCA for example, to detect whether meaningful negative deviations are present. Taking these steps will ensure that inhibition, as well as excitation, is detected in calcium imaging datasets.
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Affiliation(s)
- Gilles Vanwalleghem
- Neural Circuits and Behavior Laboratory, Queensland Brain Institute, The University of Queensland, St Lucia, QLD, Australia
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46
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Roth RH, Ding JB. From Neurons to Cognition: Technologies for Precise Recording of Neural Activity Underlying Behavior. BME FRONTIERS 2020; 2020:7190517. [PMID: 37849967 PMCID: PMC10521756 DOI: 10.34133/2020/7190517] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2020] [Accepted: 10/27/2020] [Indexed: 10/19/2023] Open
Abstract
Understanding how brain activity encodes information and controls behavior is a long-standing question in neuroscience. This complex problem requires converging efforts from neuroscience and engineering, including technological solutions to perform high-precision and large-scale recordings of neuronal activity in vivo as well as unbiased methods to reliably measure and quantify behavior. Thanks to advances in genetics, molecular biology, engineering, and neuroscience, in recent decades, a variety of optical imaging and electrophysiological approaches for recording neuronal activity in awake animals have been developed and widely applied in the field. Moreover, sophisticated computer vision and machine learning algorithms have been developed to analyze animal behavior. In this review, we provide an overview of the current state of technology for neuronal recordings with a focus on optical and electrophysiological methods in rodents. In addition, we discuss areas that future technological development will need to cover in order to further our understanding of the neural activity underlying behavior.
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Affiliation(s)
- Richard H Roth
- Department of Neurosurgery, Stanford University, Stanford, CA 94305, USA
| | - Jun B Ding
- Department of Neurosurgery, Stanford University, Stanford, CA 94305, USA
- Department of Neurology and Neurological Sciences, Stanford University, Stanford, CA 94305, USA
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47
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Abstract
Quantitative analysis of neuronal morphologies usually begins with choosing a particular feature representation in order to make individual morphologies amenable to standard statistics tools and machine learning algorithms. Many different feature representations have been suggested in the literature, ranging from density maps to intersection profiles, but they have never been compared side by side. Here we performed a systematic comparison of various representations, measuring how well they were able to capture the difference between known morphological cell types. For our benchmarking effort, we used several curated data sets consisting of mouse retinal bipolar cells and cortical inhibitory neurons. We found that the best performing feature representations were two-dimensional density maps, two-dimensional persistence images and morphometric statistics, which continued to perform well even when neurons were only partially traced. Combining these feature representations together led to further performance increases suggesting that they captured non-redundant information. The same representations performed well in an unsupervised setting, implying that they can be suitable for dimensionality reduction or clustering.
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48
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Hoang H, Sato MA, Shinomoto S, Tsutsumi S, Hashizume M, Ishikawa T, Kano M, Ikegaya Y, Kitamura K, Kawato M, Toyama K. Improved hyperacuity estimation of spike timing from calcium imaging. Sci Rep 2020; 10:17844. [PMID: 33082425 PMCID: PMC7576127 DOI: 10.1038/s41598-020-74672-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2020] [Accepted: 10/01/2020] [Indexed: 01/08/2023] Open
Abstract
Two-photon imaging is a major recording technique used in neuroscience. However, it suffers from several limitations, including a low sampling rate, the nonlinearity of calcium responses, the slow dynamics of calcium dyes and a low SNR, all of which severely limit the potential of two-photon imaging to elucidate neuronal dynamics with high temporal resolution. We developed a hyperacuity algorithm (HA_time) based on an approach that combines a generative model and machine learning to improve spike detection and the precision of spike time inference. Bayesian inference was performed to estimate the calcium spike model, assuming constant spike shape and size. A support vector machine using this information and a jittering method maximizing the likelihood of estimated spike times enhanced spike time estimation precision approximately fourfold (range, 2–7; mean, 3.5–4.0; 2SEM, 0.1–0.25) compared to the sampling interval. Benchmark scores of HA_time for biological data from three different brain regions were among the best of the benchmark algorithms. Simulation of broader data conditions indicated that our algorithm performed better than others with high firing rate conditions. Furthermore, HA_time exhibited comparable performance for conditions with and without ground truths. Thus HA_time is a useful tool for spike reconstruction from two-photon imaging.
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Affiliation(s)
- Huu Hoang
- ATR Brain Information Communication Research Laboratory Group, Advanced Telecommunications Research Institute International, Kyoto, Japan
| | - Masa-Aki Sato
- ATR Brain Information Communication Research Laboratory Group, Advanced Telecommunications Research Institute International, Kyoto, Japan
| | - Shigeru Shinomoto
- ATR Brain Information Communication Research Laboratory Group, Advanced Telecommunications Research Institute International, Kyoto, Japan.,Department of Physics, Kyoto University, Kyoto, Japan
| | - Shinichiro Tsutsumi
- Laboratory for Multi-scale Biological Psychiatry, RIKEN Center for Brain Science, 2-1 Hirosawa, Wako city, 351-0198, Saitama, Japan
| | - Miki Hashizume
- Department of Biochemistry, Faculty of Medicine, Saitama Medical University, Saitama, Japan
| | - Tomoe Ishikawa
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, Tokyo, Japan
| | - Masanobu Kano
- Department of Neurophysiology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Yuji Ikegaya
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, Tokyo, Japan
| | - Kazuo Kitamura
- Department of Neurophysiology, Faculty of Medicine, University of Yamanashi, Yamanashi, Japan
| | - Mitsuo Kawato
- ATR Brain Information Communication Research Laboratory Group, Advanced Telecommunications Research Institute International, Kyoto, Japan
| | - Keisuke Toyama
- ATR Brain Information Communication Research Laboratory Group, Advanced Telecommunications Research Institute International, Kyoto, Japan.
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Werginz P, Wang BY, Chen ZC, Palanker D. On optimal coupling of the 'electronic photoreceptors' into the degenerate retina. J Neural Eng 2020; 17:045008. [PMID: 32613948 PMCID: PMC10948023 DOI: 10.1088/1741-2552/aba0d2] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Objective To restore sight in atrophic age-related macular degeneration, the lost photoreceptors can be replaced with electronic implants, which replicate their two major functions: (1) converting light into an electric signal, and (2) transferring visual information to the secondary neurons in the retinal neural network—the bipolar cells (BC). We study the selectivity of BC activation by subretinal implants and dynamics of their response to pulsatile waveforms in order to optimize the electrical stimulation scheme such that retinal signal processing with 'electronic photoreceptors' remains as close to natural as possible. Approach A multicompartmental model of a BC was implemented to simulate responses of the voltage-gated calcium channels and subsequent synaptic vesicle release under continuous and pulsatile stimuli. We compared the predicted response under various frequencies, pulse durations, and alternating gratings to the corresponding experimental measurements. In addition, electric field was computed for various electrode configurations in a 3-d finite element model to assess the stimulation selectivity via spatial confinement of the field. Main results The modeled BC-mediated retinal responses were, in general, in good agreement with previously published experimental results. Kinetics of the calcium pumps and of the neurotransmitter release in ribbon synapses, which underpin the BC's temporal filtering and rectifying functions, allow mimicking the natural BC response with high frequency pulsatile stimulation, thereby preserving features of the retinal signal processing, such as flicker fusion, adaptation to static stimuli and non-linear summation of subunits in receptive field. Selectivity of the BC stimulation while avoiding direct activation of the downstream neurons (amacrine and ganglion cells—RGCs) is improved with local return electrodes. Significance If the retinal neural network is preserved to a large extent in age-related macular degeneration, selective stimulation of BCs with proper spatial and temporal modulation of the extracellular electric field may retain many features of the natural retinal signal processing and hence allow highly functional restoration of sight.
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Affiliation(s)
- Paul Werginz
- Institute for Analysis and Scientific Computing, Vienna University of Technology, Vienna, Austria. Author to whom any correspondence should be adressed
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Lee Y, Xie J, Lee E, Sudarsanan S, Lin DT, Chen R, Bhattacharyya SS. Real-Time Neuron Detection and Neural Signal Extraction Platform for Miniature Calcium Imaging. Front Comput Neurosci 2020; 14:43. [PMID: 32676021 PMCID: PMC7333463 DOI: 10.3389/fncom.2020.00043] [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: 03/07/2019] [Accepted: 04/28/2020] [Indexed: 12/03/2022] Open
Abstract
Real-time neuron detection and neural activity extraction are critical components of real-time neural decoding. In this paper, we propose a novel real-time neuron detection and activity extraction system using a dataflow framework to provide real-time performance and adaptability to new algorithms and hardware platforms. The proposed system was evaluated on simulated calcium imaging data, calcium imaging data with manual annotation, and calcium imaging data of the anterior lateral motor cortex. We found that the proposed system accurately detected neurons and extracted neural activities in real time without any requirement for expensive, cumbersome, or special-purpose computing hardware. We expect that the system will enable cost-effective, real-time calcium imaging-based neural decoding, leading to precise neuromodulation.
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Affiliation(s)
- Yaesop Lee
- Department of Electrical and Computer Engineering, University of Maryland at College Park, College Park, MD, United States
| | - Jing Xie
- Department of Electrical and Computer Engineering, University of Maryland at College Park, College Park, MD, United States
| | - Eungjoo Lee
- Department of Electrical and Computer Engineering, University of Maryland at College Park, College Park, MD, United States
| | - Srijesh Sudarsanan
- Department of Electrical and Computer Engineering, University of Maryland at College Park, College Park, MD, United States
| | - Da-Ting Lin
- National Institute on Drug Abuse, National Institutes of Health (NIH), Baltimore, MD, United States
| | - Rong Chen
- Department of Electrical and Computer Engineering, University of Maryland at College Park, College Park, MD, United States.,Department of Diagnostic Radiology and Nuclear Medicine, University of Maryland at Baltimore, Baltimore, MD, United States
| | - Shuvra S Bhattacharyya
- Department of Electrical and Computer Engineering, University of Maryland at College Park, College Park, MD, United States.,Institute for Advanced Computer Studies (UMIACS), University of Maryland at College Park, College Park, MD, United States
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