1
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Ahrens MB. Closing the Experiment-Modeling-Perturbation Loop in Whole-Brain Neuroscience. Neurosci Bull 2024; 40:1212-1214. [PMID: 39014175 DOI: 10.1007/s12264-024-01253-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2024] [Accepted: 06/10/2024] [Indexed: 07/18/2024] Open
Affiliation(s)
- Misha B Ahrens
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA.
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2
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Baier H, Scott EK. The Visual Systems of Zebrafish. Annu Rev Neurosci 2024; 47:255-276. [PMID: 38663429 DOI: 10.1146/annurev-neuro-111020-104854] [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: 08/09/2024]
Abstract
The zebrafish visual system has become a paradigmatic preparation for behavioral and systems neuroscience. Around 40 types of retinal ganglion cells (RGCs) serve as matched filters for stimulus features, including light, optic flow, prey, and objects on a collision course. RGCs distribute their signals via axon collaterals to 12 retinorecipient areas in forebrain and midbrain. The major visuomotor hub, the optic tectum, harbors nine RGC input layers that combine information on multiple features. The retinotopic map in the tectum is locally adapted to visual scene statistics and visual subfield-specific behavioral demands. Tectal projections to premotor centers are topographically organized according to behavioral commands. The known connectivity in more than 20 processing streams allows us to dissect the cellular basis of elementary perceptual and cognitive functions. Visually evoked responses, such as prey capture or loom avoidance, are controlled by dedicated multistation pathways that-at least in the larva-resemble labeled lines. This architecture serves the neuronal code's purpose of driving adaptive behavior.
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Affiliation(s)
- Herwig Baier
- Department of Genes-Circuits-Behavior, Max Planck Institute for Biological Intelligence, Martinsried, Germany;
| | - Ethan K Scott
- Department of Anatomy and Physiology, School of Biomedical Sciences, The University of Melbourne, Parkville, Victoria, Australia
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3
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McNulty P, Wu R, Yamaguchi A, Heckscher ES, Haas A, Nwankpa A, Skanata MM, Gershow M. CRASH2p: Closed-loop Two Photon Imaging in Freely Moving Animals. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.22.595209. [PMID: 38826435 PMCID: PMC11142166 DOI: 10.1101/2024.05.22.595209] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2024]
Abstract
Direct measurement of neural activity in freely moving animals is essential for understanding how the brain controls and represents behaviors. Genetically encoded calcium indicators report neural activity as changes in fluorescence intensity, but brain motion confounds quantitative measurement of fluorescence. Translation, rotation, and deformation of the brain and the movements of intervening scattering or auto-fluorescent tissue all alter the amount of fluorescent light captured by a microscope. Compared to single-photon approaches, two photon microscopy is less sensitive to scattering and off-target fluorescence, but more sensitive to motion, and two photon imaging has always required anchoring the microscope to the brain. We developed a closed-loop resonant axial-scanning high-speed two photon (CRASH2p) microscope for real-time 3D motion correction in unrestrained animals, without implantation of reference markers. We complemented CRASH2p with a novel scanning strategy and a multistage registration pipeline. We performed volumetric ratiometrically corrected functional imaging in the CNS of freely moving Drosophila larvae and discovered previously unknown neural correlates of behavior.
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Affiliation(s)
- Paul McNulty
- Department of Physics,New York University, New York, USA
| | - Rui Wu
- Department of Physics,New York University, New York, USA
| | | | - Ellie S. Heckscher
- Department of Molecular Genetics and Cell Biology, University of Chicago, Chicago, IL
| | - Andrew Haas
- Department of Physics,New York University, New York, USA
| | | | | | - Marc Gershow
- Department of Physics,New York University, New York, USA
- Center for Neural Science,New York University, New York, USA
- Neuroscience Institute, New York University, New York, USA
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4
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Liu Z, Luo X, Yan-Do R, Wang Y, Xie X, Li Z, Cheng SH, Shi P. Vertebrates on a Chip: Noninvasive Electrical and Optical Mapping of Whole Brain Activity Associated with Pharmacological Treatments. ACS Chem Neurosci 2024; 15:2121-2131. [PMID: 38775291 DOI: 10.1021/acschemneuro.4c00158] [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: 06/06/2024] Open
Abstract
Mapping brain activities is necessary for understanding brain physiology and discovering new treatments for neurological disorders. Such efforts have greatly benefited from the advancement in technologies for analyzing neural activity with improving temporal or spatial resolution. Here, we constructed a multielectrode array based brain activity mapping (BAM) system capable of stabilizing and orienting zebrafish larvae for recording electroencephalogram (EEG) like local field potential (LFP) signals and brain-wide calcium dynamics in awake zebrafish. Particularly, we designed a zebrafish trap chip that integrates with an eight-by-eight surface electrode array, so that brain electrophysiology can be noninvasively recorded in an agarose-free and anesthetic-free format with a high temporal resolution of 40 μs, matching the capability typically achieved by invasive LFP recording. Benefiting from the specially designed hybrid system, we can also conduct calcium imaging directly on immobilized awake larval zebrafish, which further supplies us with high spatial resolution brain-wide activity data. All of these innovations reconcile the limitations of sole LFP recording or calcium imaging, emphasizing a synergy of combining electrical and optical modalities within one unified device for activity mapping across a whole vertebrate brain with both improved spatial and temporal resolutions. The compatibility with in vivo drug treatment further makes it suitable for pharmacology studies based on multimodal measurement of brain-wide physiology.
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Affiliation(s)
- Zhen Liu
- Department of Biomedical Engineering, City University of Hong Kong, Kowloon, Hong Kong SAR 999077, China
| | - Xuan Luo
- Department of Biomedical Engineering, City University of Hong Kong, Kowloon, Hong Kong SAR 999077, China
| | - Richard Yan-Do
- Department of Biomedical Engineering, City University of Hong Kong, Kowloon, Hong Kong SAR 999077, China
- Hong Kong Centre for Cerebro-Cardiovascular Health Engineering Hong Kong Science Park, Hong Kong SAR
| | - Yuan Wang
- Department of Biomedical Engineering, City University of Hong Kong, Kowloon, Hong Kong SAR 999077, China
| | - Xi Xie
- State Key Laboratory of Optoelectronic Materials and Technologies, Guangdong Province Key Laboratory of Display Material and Technology School of Electronics and Information Technology, Sun Yat-Sen University, Guangzhou 510006, China
| | - Zhongping Li
- Institute of Environmental Science, Shanxi University, Taiyuan 030006, China
| | - Shuk Han Cheng
- Department of Biomedical Science, City University of Hong Kong, Kowloon, Hong Kong SAR 999077, China
| | - Peng Shi
- Department of Biomedical Engineering, City University of Hong Kong, Kowloon, Hong Kong SAR 999077, China
- Hong Kong Centre for Cerebro-Cardiovascular Health Engineering Hong Kong Science Park, Hong Kong SAR
- Center of Super-Diamond and Advanced Films (COSDAF), City University of Hong Kong Kowloon, Hong Kong SAR
- Shenzhen Research Institute, City University of Hong Kong Shenzhen, Guangdong 518057, China
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5
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Farmen K, Tofiño-Vian M, Wellfelt K, Olson L, Iovino F. Spatio-temporal brain invasion pattern of Streptococcus pneumoniae and dynamic changes in the cellular environment in bacteremia-derived meningitis. Neurobiol Dis 2024; 195:106484. [PMID: 38583642 DOI: 10.1016/j.nbd.2024.106484] [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: 03/18/2024] [Accepted: 03/22/2024] [Indexed: 04/09/2024] Open
Abstract
Streptococcus pneumoniae (the pneumococcus) is the major cause of bacterial meningitis globally, and pneumococcal meningitis is associated with increased risk of long-term neurological sequelae. These include several sensorimotor functions that are controlled by specific brain regions which, during bacterial meningitis, are damaged by a neuroinflammatory response and the deleterious action of bacterial toxins in the brain. However, little is known about the invasion pattern of the pneumococcus into the brain. Using a bacteremia-derived meningitis mouse model, we combined 3D whole brain imaging with brain microdissection to show that all brain regions were equally affected during disease progression, with the presence of pneumococci closely associated to the microvasculature. In the hippocampus, the invasion provoked microglial activation, while the neurogenic niche showed increased proliferation and migration of neuroblasts. Our results indicate that, even before the outbreak of symptoms, the bacterial load throughout the brain is high and causes neuroinflammation and cell death, a pathological scenario which ultimately leads to a failing regeneration of new neurons.
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Affiliation(s)
- Kristine Farmen
- Department of Neuroscience, Karolinska Institutet, Stockholm, Sweden
| | | | - Katrin Wellfelt
- Department of Neuroscience, Karolinska Institutet, Stockholm, Sweden
| | - Lars Olson
- Department of Neuroscience, Karolinska Institutet, Stockholm, Sweden
| | - Federico Iovino
- Department of Neuroscience, Karolinska Institutet, Stockholm, Sweden.
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6
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Lu Z, Zuo S, Shi M, Fan J, Xie J, Xiao G, Yu L, Wu J, Dai Q. Long-term intravital subcellular imaging with confocal scanning light-field microscopy. Nat Biotechnol 2024:10.1038/s41587-024-02249-5. [PMID: 38802562 DOI: 10.1038/s41587-024-02249-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2023] [Accepted: 04/17/2024] [Indexed: 05/29/2024]
Abstract
Long-term observation of subcellular dynamics in living organisms is limited by background fluorescence originating from tissue scattering or dense labeling. Existing confocal approaches face an inevitable tradeoff among parallelization, resolution and phototoxicity. Here we present confocal scanning light-field microscopy (csLFM), which integrates axially elongated line-confocal illumination with the rolling shutter in scanning light-field microscopy (sLFM). csLFM enables high-fidelity, high-speed, three-dimensional (3D) imaging at near-diffraction-limit resolution with both optical sectioning and low phototoxicity. By simultaneous 3D excitation and detection, the excitation intensity can be reduced below 1 mW mm-2, with 15-fold higher signal-to-background ratio over sLFM. We imaged subcellular dynamics over 25,000 timeframes in optically challenging environments in different species, such as migrasome delivery in mouse spleen, retractosome generation in mouse liver and 3D voltage imaging in Drosophila. Moreover, csLFM facilitates high-fidelity, large-scale neural recording with reduced crosstalk, leading to high orientation selectivity to visual stimuli, similar to two-photon microscopy, which aids understanding of neural coding mechanisms.
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Affiliation(s)
- Zhi Lu
- Department of Automation, Tsinghua University, Beijing, China
- Institute for Brain and Cognitive Sciences, Tsinghua University, Beijing, China
- Beijing Key Laboratory of Multi-dimension & Multi-scale Computational Photography (MMCP), Tsinghua University, Beijing, China
- IDG/McGovern Institute for Brain Research, Tsinghua University, Beijing, China
- Zhejiang Hehu Technology, Hangzhou, China
- Hangzhou Zhuoxi Institute of Brain and Intelligence, Hangzhou, China
| | - Siqing Zuo
- Department of Automation, Tsinghua University, Beijing, China
- Institute for Brain and Cognitive Sciences, Tsinghua University, Beijing, China
- Beijing Key Laboratory of Multi-dimension & Multi-scale Computational Photography (MMCP), Tsinghua University, Beijing, China
- IDG/McGovern Institute for Brain Research, Tsinghua University, Beijing, China
| | - Minghui Shi
- State Key Laboratory of Membrane Biology, Tsinghua University-Peking University Joint Center for Life Sciences, Beijing Frontier Research Center for Biological Structure, School of Life Sciences, Tsinghua University, Beijing, China
| | - Jiaqi Fan
- Institute for Brain and Cognitive Sciences, Tsinghua University, Beijing, China
- Tsinghua Shenzhen International Graduate School, Tsinghua University, Shenzhen, China
| | - Jingyu Xie
- Department of Automation, Tsinghua University, Beijing, China
- Institute for Brain and Cognitive Sciences, Tsinghua University, Beijing, China
| | - Guihua Xiao
- Department of Automation, Tsinghua University, Beijing, China
- Institute for Brain and Cognitive Sciences, Tsinghua University, Beijing, China
| | - Li Yu
- State Key Laboratory of Membrane Biology, Tsinghua University-Peking University Joint Center for Life Sciences, Beijing Frontier Research Center for Biological Structure, School of Life Sciences, Tsinghua University, Beijing, China.
| | - Jiamin Wu
- Department of Automation, Tsinghua University, Beijing, China.
- Institute for Brain and Cognitive Sciences, Tsinghua University, Beijing, China.
- Beijing Key Laboratory of Multi-dimension & Multi-scale Computational Photography (MMCP), Tsinghua University, Beijing, China.
- IDG/McGovern Institute for Brain Research, Tsinghua University, Beijing, China.
- Shanghai AI Laboratory, Shanghai, China.
| | - Qionghai Dai
- Department of Automation, Tsinghua University, Beijing, China.
- Institute for Brain and Cognitive Sciences, Tsinghua University, Beijing, China.
- Beijing Key Laboratory of Multi-dimension & Multi-scale Computational Photography (MMCP), Tsinghua University, Beijing, China.
- IDG/McGovern Institute for Brain Research, Tsinghua University, Beijing, China.
- Beijing National Research Center for Information Science and Technology, Tsinghua University, Beijing, China.
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7
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Shang CF, Wang YF, Zhao MT, Fan QX, Zhao S, Qian Y, Xu SJ, Mu Y, Hao J, Du JL. Real-time analysis of large-scale neuronal imaging enables closed-loop investigation of neural dynamics. Nat Neurosci 2024; 27:1014-1018. [PMID: 38467902 DOI: 10.1038/s41593-024-01595-6] [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: 08/25/2022] [Accepted: 02/07/2024] [Indexed: 03/13/2024]
Abstract
Large-scale imaging of neuronal activities is crucial for understanding brain functions. However, it is challenging to analyze large-scale imaging data in real time, preventing closed-loop investigation of neural circuitry. Here we develop a real-time analysis system with a field programmable gate array-graphics processing unit design for an up to 500-megabyte-per-second image stream. Adapted to whole-brain imaging of awake larval zebrafish, the system timely extracts activity from up to 100,000 neurons and enables closed-loop perturbations of neural dynamics.
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Affiliation(s)
- Chun-Feng Shang
- Institute of Neuroscience, State Key Laboratory of Neuroscience, Center for Excellence in Brain Science and Intelligence Technology, Chinese Academy of Sciences, Shanghai, China
- Guangdong-Hongkong-Macau Institute of CNS Regeneration, Ministry of Education CNS Regeneration Collaborative Joint Laboratory, Jinan University, Guangzhou, China
- Shenzhen Institute of Neuroscience, Shenzhen, China
| | - Yu-Fan Wang
- Institute of Neuroscience, State Key Laboratory of Neuroscience, Center for Excellence in Brain Science and Intelligence Technology, Chinese Academy of Sciences, Shanghai, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Mei-Ting Zhao
- Institute of Automation, Chinese Academy of Sciences, Beijing, China
- Guangdong Institute of Artificial Intelligence and Advanced Computing, Guangzhou, China
| | - Qiu-Xiang Fan
- Institute of Automation, Chinese Academy of Sciences, Beijing, China
- Guangdong Institute of Artificial Intelligence and Advanced Computing, Guangzhou, China
| | - Shan Zhao
- Institute of Neuroscience, State Key Laboratory of Neuroscience, Center for Excellence in Brain Science and Intelligence Technology, Chinese Academy of Sciences, Shanghai, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Yu Qian
- Institute of Neuroscience, State Key Laboratory of Neuroscience, Center for Excellence in Brain Science and Intelligence Technology, Chinese Academy of Sciences, Shanghai, China
| | - Sheng-Jin Xu
- Institute of Neuroscience, State Key Laboratory of Neuroscience, Center for Excellence in Brain Science and Intelligence Technology, Chinese Academy of Sciences, Shanghai, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Yu Mu
- Institute of Neuroscience, State Key Laboratory of Neuroscience, Center for Excellence in Brain Science and Intelligence Technology, Chinese Academy of Sciences, Shanghai, China.
- University of Chinese Academy of Sciences, Beijing, China.
| | - Jie Hao
- University of Chinese Academy of Sciences, Beijing, China.
- Institute of Automation, Chinese Academy of Sciences, Beijing, China.
- Guangdong Institute of Artificial Intelligence and Advanced Computing, Guangzhou, China.
| | - Jiu-Lin Du
- Institute of Neuroscience, State Key Laboratory of Neuroscience, Center for Excellence in Brain Science and Intelligence Technology, Chinese Academy of Sciences, Shanghai, China.
- University of Chinese Academy of Sciences, Beijing, China.
- School of Life Science and Technology, ShanghaiTech University, Shanghai, China.
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8
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Song P, Jadan HV, Howe CL, Foust AJ, Dragotti PL. Model-Based Explainable Deep Learning for Light-Field Microscopy Imaging. IEEE TRANSACTIONS ON IMAGE PROCESSING : A PUBLICATION OF THE IEEE SIGNAL PROCESSING SOCIETY 2024; 33:3059-3074. [PMID: 38656840 PMCID: PMC11100862 DOI: 10.1109/tip.2024.3387297] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/20/2023] [Revised: 01/27/2024] [Accepted: 03/12/2024] [Indexed: 04/26/2024]
Abstract
In modern neuroscience, observing the dynamics of large populations of neurons is a critical step of understanding how networks of neurons process information. Light-field microscopy (LFM) has emerged as a type of scanless, high-speed, three-dimensional (3D) imaging tool, particularly attractive for this purpose. Imaging neuronal activity using LFM calls for the development of novel computational approaches that fully exploit domain knowledge embedded in physics and optics models, as well as enabling high interpretability and transparency. To this end, we propose a model-based explainable deep learning approach for LFM. Different from purely data-driven methods, the proposed approach integrates wave-optics theory, sparse representation and non-linear optimization with the artificial neural network. In particular, the architecture of the proposed neural network is designed following precise signal and optimization models. Moreover, the network's parameters are learned from a training dataset using a novel training strategy that integrates layer-wise training with tailored knowledge distillation. Such design allows the network to take advantage of domain knowledge and learned new features. It combines the benefit of both model-based and learning-based methods, thereby contributing to superior interpretability, transparency and performance. By evaluating on both structural and functional LFM data obtained from scattering mammalian brain tissues, we demonstrate the capabilities of the proposed approach to achieve fast, robust 3D localization of neuron sources and accurate neural activity identification.
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Affiliation(s)
- Pingfan Song
- Department of EngineeringUniversity of CambridgeCB2 1PZCambridgeU.K
| | - Herman Verinaz Jadan
- Faculty of Electrical and Computer EngineeringEscuela Superior Politécnica del Litoral (ESPOL)GuayaquilEC090903Ecuador
| | - Carmel L. Howe
- Department of Chemical Physiology and BiochemistryOregon Health and Science UniversityPortlandOR97239USA
| | - Amanda J. Foust
- Center for NeurotechnologyDepartment of BioengineeringImperial College LondonSW7 2AZLondonU.K
| | - Pier Luigi Dragotti
- Department of Electronic and Electrical EngineeringImperial College LondonSW7 2AZLondonUK
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Rué‐Queralt J, Fluhr H, Tourbier S, Aleman‐Gómez Y, Pascucci D, Yerly J, Glomb K, Plomp G, Hagmann P. Connectome spectrum electromagnetic tomography: A method to reconstruct electrical brain source networks at high-spatial resolution. Hum Brain Mapp 2024; 45:e26638. [PMID: 38520365 PMCID: PMC10960556 DOI: 10.1002/hbm.26638] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2023] [Revised: 02/01/2024] [Accepted: 02/13/2024] [Indexed: 03/25/2024] Open
Abstract
Connectome spectrum electromagnetic tomography (CSET) combines diffusion MRI-derived structural connectivity data with well-established graph signal processing tools to solve the M/EEG inverse problem. Using simulated EEG signals from fMRI responses, and two EEG datasets on visual-evoked potentials, we provide evidence supporting that (i) CSET captures realistic neurophysiological patterns with better accuracy than state-of-the-art methods, (ii) CSET can reconstruct brain responses more accurately and with more robustness to intrinsic noise in the EEG signal. These results demonstrate that CSET offers high spatio-temporal accuracy, enabling neuroscientists to extend their research beyond the current limitations of low sampling frequency in functional MRI and the poor spatial resolution of M/EEG.
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Affiliation(s)
- Joan Rué‐Queralt
- Department of RadiologyLausanne University Hospital and University of Lausanne (CHUV‐UNIL)LausanneSwitzerland
- Department of PsychologyUniversity of FribourgFribourgSwitzerland
- Center for ImagingEPFLLausanneSwitzerland
| | - Hugo Fluhr
- Department of RadiologyLausanne University Hospital and University of Lausanne (CHUV‐UNIL)LausanneSwitzerland
| | - Sebastien Tourbier
- Department of RadiologyLausanne University Hospital and University of Lausanne (CHUV‐UNIL)LausanneSwitzerland
| | - Yasser Aleman‐Gómez
- Department of RadiologyLausanne University Hospital and University of Lausanne (CHUV‐UNIL)LausanneSwitzerland
- Department of PsychiatryLausanne University HospitalLausanneSwitzerland
| | | | - Jérôme Yerly
- Department of Diagnostic and Interventional RadiologyLausanne University HospitalLausanneSwitzerland
- Center for Biomedical ImagingEPFLLausanneSwitzerland
| | - Katharina Glomb
- Department of NeurologyCharité University Medicine Berlin and Berlin Institute of HealthBerlinGermany
| | - Gijs Plomp
- Department of PsychologyUniversity of FribourgFribourgSwitzerland
| | - Patric Hagmann
- Department of RadiologyLausanne University Hospital and University of Lausanne (CHUV‐UNIL)LausanneSwitzerland
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10
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Lucon-Xiccato T. Inhibitory control in teleost fish: a methodological and conceptual review. Anim Cogn 2024; 27:27. [PMID: 38530456 DOI: 10.1007/s10071-024-01867-5] [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: 07/11/2023] [Revised: 03/09/2024] [Accepted: 03/11/2024] [Indexed: 03/28/2024]
Abstract
Inhibitory control (IC) plays a central role in behaviour control allowing an individual to resist external lures and internal predispositions. While IC has been consistently investigated in humans, other mammals, and birds, research has only recently begun to explore IC in other vertebrates. This review examines current literature on teleost fish, focusing on both methodological and conceptual aspects. I describe the main paradigms adopted to study IC in fish, identifying well-established tasks that fit various research applications and highlighting their advantages and limitations. In the conceptual analysis, I identify two well-developed lines of research with fish examining IC. The first line focuses on a comparative approach aimed to describe IC at the level of species and to understand the evolution of interspecific differences in relation to ecological specialisation, brain size, and factors affecting cognitive performance. Findings suggest several similarities between fish and previously studied vertebrates. The second line of research focuses on intraspecific variability of IC. Available results indicate substantial variation in fish IC related to sex, personality, genetic, age, and phenotypic plasticity, aligning with what is observed with other vertebrates. Overall, this review suggests that although data on teleosts are still scarce compared to mammals, the contribution of this group to IC research is already substantial and can further increase in various disciplines including comparative psychology, cognitive ecology, and neurosciences, and even in applied fields such as psychiatry research.
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Affiliation(s)
- Tyrone Lucon-Xiccato
- Department of Life Sciences and Biotechnology, University of Ferrara, Ferrara, Italy.
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11
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Manley J, Vaziri A. Whole-brain neural substrates of behavioral variability in the larval zebrafish. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.03.583208. [PMID: 38496592 PMCID: PMC10942351 DOI: 10.1101/2024.03.03.583208] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/19/2024]
Abstract
Animals engaged in naturalistic behavior can exhibit a large degree of behavioral variability even under sensory invariant conditions. Such behavioral variability can include not only variations of the same behavior, but also variability across qualitatively different behaviors driven by divergent cognitive states, such as fight-or-flight decisions. However, the neural circuit mechanisms that generate such divergent behaviors across trials are not well understood. To investigate this question, here we studied the visual-evoked responses of larval zebrafish to moving objects of various sizes, which we found exhibited highly variable and divergent responses across repetitions of the same stimulus. Given that the neuronal circuits underlying such behaviors span sensory, motor, and other brain areas, we built a novel Fourier light field microscope which enables high-resolution, whole-brain imaging of larval zebrafish during behavior. This enabled us to screen for neural loci which exhibited activity patterns correlated with behavioral variability. We found that despite the highly variable activity of single neurons, visual stimuli were robustly encoded at the population level, and the visual-encoding dimensions of neural activity did not explain behavioral variability. This robustness despite apparent single neuron variability was due to the multi-dimensional geometry of the neuronal population dynamics: almost all neural dimensions that were variable across individual trials, i.e. the "noise" modes, were orthogonal to those encoding for sensory information. Investigating this neuronal variability further, we identified two sparsely-distributed, brain-wide neuronal populations whose pre-motor activity predicted whether the larva would respond to a stimulus and, if so, which direction it would turn on a single-trial level. These populations predicted single-trial behavior seconds before stimulus onset, indicating they encoded time-varying internal modulating behavior, perhaps organizing behavior over longer timescales or enabling flexible behavior routines dependent on the animal's internal state. Our results provide the first whole-brain confirmation that sensory, motor, and internal variables are encoded in a highly mixed fashion throughout the brain and demonstrate that de-mixing each of these components at the neuronal population level is critical to understanding the mechanisms underlying the brain's remarkable flexibility and robustness.
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Affiliation(s)
- Jason Manley
- Laboratory of Neurotechnology and Biophysics, The Rockefeller University, New York, NY 10065, USA
- The Kavli Neural Systems Institute, The Rockefeller University, New York, NY 10065, USA
| | - Alipasha Vaziri
- Laboratory of Neurotechnology and Biophysics, The Rockefeller University, New York, NY 10065, USA
- The Kavli Neural Systems Institute, The Rockefeller University, New York, NY 10065, USA
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12
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Hua X, Han K, Mandracchia B, Radmand A, Liu W, Kim H, Yuan Z, Ehrlich SM, Li K, Zheng C, Son J, Silva Trenkle AD, Kwong GA, Zhu C, Dahlman JE, Jia S. Light-field flow cytometry for high-resolution, volumetric and multiparametric 3D single-cell analysis. Nat Commun 2024; 15:1975. [PMID: 38438356 PMCID: PMC10912605 DOI: 10.1038/s41467-024-46250-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2023] [Accepted: 02/15/2024] [Indexed: 03/06/2024] Open
Abstract
Imaging flow cytometry (IFC) combines flow cytometry and fluorescence microscopy to enable high-throughput, multiparametric single-cell analysis with rich spatial details. However, current IFC techniques remain limited in their ability to reveal subcellular information with a high 3D resolution, throughput, sensitivity, and instrumental simplicity. In this study, we introduce a light-field flow cytometer (LFC), an IFC system capable of high-content, single-shot, and multi-color acquisition of up to 5,750 cells per second with a near-diffraction-limited resolution of 400-600 nm in all three dimensions. The LFC system integrates optical, microfluidic, and computational strategies to facilitate the volumetric visualization of various 3D subcellular characteristics through convenient access to commonly used epi-fluorescence platforms. We demonstrate the effectiveness of LFC in assaying, analyzing, and enumerating intricate subcellular morphology, function, and heterogeneity using various phantoms and biological specimens. The advancement offered by the LFC system presents a promising methodological pathway for broad cell biological and translational discoveries, with the potential for widespread adoption in biomedical research.
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Affiliation(s)
- Xuanwen Hua
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, GA, USA
| | - Keyi Han
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, GA, USA
| | - Biagio Mandracchia
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, GA, USA
| | - Afsane Radmand
- Parker H. Petit Institute for Bioengineering and Biosciences, Georgia Institute of Technology, Atlanta, GA, USA
- Department of Chemical Engineering, Georgia Institute of Technology, Atlanta, GA, USA
| | - Wenhao Liu
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, GA, USA
| | - Hyejin Kim
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, GA, USA
| | - Zhou Yuan
- Parker H. Petit Institute for Bioengineering and Biosciences, Georgia Institute of Technology, Atlanta, GA, USA
- Georgia W. Woodruff School of Mechanical Engineering, Georgia Institute of Technology, Atlanta, GA, USA
| | - Samuel M Ehrlich
- Parker H. Petit Institute for Bioengineering and Biosciences, Georgia Institute of Technology, Atlanta, GA, USA
- Georgia W. Woodruff School of Mechanical Engineering, Georgia Institute of Technology, Atlanta, GA, USA
| | - Kaitao Li
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, GA, USA
| | - Corey Zheng
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, GA, USA
| | - Jeonghwan Son
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, GA, USA
| | - Aaron D Silva Trenkle
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, GA, USA
| | - Gabriel A Kwong
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, GA, USA
- Parker H. Petit Institute for Bioengineering and Biosciences, Georgia Institute of Technology, Atlanta, GA, USA
| | - Cheng Zhu
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, GA, USA
- Parker H. Petit Institute for Bioengineering and Biosciences, Georgia Institute of Technology, Atlanta, GA, USA
| | - James E Dahlman
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, GA, USA
- Parker H. Petit Institute for Bioengineering and Biosciences, Georgia Institute of Technology, Atlanta, GA, USA
| | - Shu Jia
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, GA, USA.
- Parker H. Petit Institute for Bioengineering and Biosciences, Georgia Institute of Technology, Atlanta, GA, USA.
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13
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Page Vizcaíno J, Symvoulidis P, Wang Z, Jelten J, Favaro P, Boyden ES, Lasser T. Fast light-field 3D microscopy with out-of-distribution detection and adaptation through conditional normalizing flows. BIOMEDICAL OPTICS EXPRESS 2024; 15:1219-1232. [PMID: 38404325 PMCID: PMC10890860 DOI: 10.1364/boe.504039] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/24/2023] [Revised: 11/09/2023] [Accepted: 11/20/2023] [Indexed: 02/27/2024]
Abstract
Real-time 3D fluorescence microscopy is crucial for the spatiotemporal analysis of live organisms, such as neural activity monitoring. The eXtended field-of-view light field microscope (XLFM), also known as Fourier light field microscope, is a straightforward, single snapshot solution to achieve this. The XLFM acquires spatial-angular information in a single camera exposure. In a subsequent step, a 3D volume can be algorithmically reconstructed, making it exceptionally well-suited for real-time 3D acquisition and potential analysis. Unfortunately, traditional reconstruction methods (like deconvolution) require lengthy processing times (0.0220 Hz), hampering the speed advantages of the XLFM. Neural network architectures can overcome the speed constraints but do not automatically provide a way to certify the realism of their reconstructions, which is essential in the biomedical realm. To address these shortcomings, this work proposes a novel architecture to perform fast 3D reconstructions of live immobilized zebrafish neural activity based on a conditional normalizing flow. It reconstructs volumes at 8 Hz spanning 512x512x96 voxels, and it can be trained in under two hours due to the small dataset requirements (50 image-volume pairs). Furthermore, normalizing flows provides a way to compute the exact likelihood of a sample. This allows us to certify whether the predicted output is in- or ood, and retrain the system when a novel sample is detected. We evaluate the proposed method on a cross-validation approach involving multiple in-distribution samples (genetically identical zebrafish) and various out-of-distribution ones.
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Affiliation(s)
- Josué Page Vizcaíno
- Computational Imaging and Inverse Problems, Department of Computer Science, School of Computation, Information and Technology, Technical University of Munich, Germany
- Munich Institute of Biomedical Engineering, Technical University of Munich, Germany
| | | | - Zeguan Wang
- Synthetic Neurobiology Group, Massachusetts Institute of Technology, USA
| | - Jonas Jelten
- Computational Imaging and Inverse Problems, Department of Computer Science, School of Computation, Information and Technology, Technical University of Munich, Germany
- Munich Institute of Biomedical Engineering, Technical University of Munich, Germany
| | - Paolo Favaro
- Computer Vision Group, University of Bern, Switzerland
| | - Edward S. Boyden
- Synthetic Neurobiology Group, Massachusetts Institute of Technology, USA
| | - Tobias Lasser
- Computational Imaging and Inverse Problems, Department of Computer Science, School of Computation, Information and Technology, Technical University of Munich, Germany
- Munich Institute of Biomedical Engineering, Technical University of Munich, Germany
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14
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Shi W, Quan H, Kong L. High-resolution 3D imaging in light-field microscopy through Stokes matrices and data fusion. OPTICS EXPRESS 2024; 32:3710-3722. [PMID: 38297586 DOI: 10.1364/oe.510728] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/30/2023] [Accepted: 01/08/2024] [Indexed: 02/02/2024]
Abstract
The trade-off between the lateral and vertical resolution has long posed challenges to the efficient and widespread application of Fourier light-field microscopy, a highly scalable 3D imaging tool. Although existing methods for resolution enhancement can improve the measurement result to a certain extent, they come with limitations in terms of accuracy and applicable specimen types. To address these problems, this paper proposed a resolution enhancement scheme utilizing data fusion of polarization Stokes vectors and light-field information for Fourier light-field microscopy system. By introducing the surface normal vector information obtained from polarization measurement and integrating it with the light-field 3D point cloud data, 3D reconstruction results accuracy is highly improved in axial direction. Experimental results with a Fourier light-field 3D imaging microscope demonstrated a substantial enhancement of vertical resolution with a depth resolution to depth of field ratio of 0.19%. This represented approximately 44 times the improvement compared to the theoretical ratio before data fusion, enabling the system to access more detailed information with finer measurement accuracy for test samples. This work not only provides a feasible solution for breaking the limitations imposed by traditional light-field microscope hardware configurations but also offers superior 3D measurement approach in a more cost-effective and practical manner.
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15
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Chai Y, Qi K, Wu Y, Li D, Tan G, Guo Y, Chu J, Mu Y, Shen C, Wen Q. All-optical interrogation of brain-wide activity in freely swimming larval zebrafish. iScience 2024; 27:108385. [PMID: 38205255 PMCID: PMC10776927 DOI: 10.1016/j.isci.2023.108385] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2023] [Revised: 09/22/2023] [Accepted: 10/30/2023] [Indexed: 01/12/2024] Open
Abstract
We introduce an all-optical technique that enables volumetric imaging of brain-wide calcium activity and targeted optogenetic stimulation of specific brain regions in unrestrained larval zebrafish. The system consists of three main components: a 3D tracking module, a dual-color fluorescence imaging module, and a real-time activity manipulation module. Our approach uses a sensitive genetically encoded calcium indicator in combination with a long Stokes shift red fluorescence protein as a reference channel, allowing the extraction of Ca2+ activity from signals contaminated by motion artifacts. The method also incorporates rapid 3D image reconstruction and registration, facilitating real-time selective optogenetic stimulation of different regions of the brain. By demonstrating that selective light activation of the midbrain regions in larval zebrafish could reliably trigger biased turning behavior and changes of brain-wide neural activity, we present a valuable tool for investigating the causal relationship between distributed neural circuit dynamics and naturalistic behavior.
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Affiliation(s)
- Yuming Chai
- Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China
- Hefei National Research Center for Physical Sciences at the Microscale, Center for Integrative Imaging, University of Science and Technology of China, Hefei, China
| | - Kexin Qi
- Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China
- Hefei National Research Center for Physical Sciences at the Microscale, Center for Integrative Imaging, University of Science and Technology of China, Hefei, China
| | - Yubin Wu
- Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China
- Hefei National Research Center for Physical Sciences at the Microscale, Center for Integrative Imaging, University of Science and Technology of China, Hefei, China
| | - Daguang Li
- Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China
- Hefei National Research Center for Physical Sciences at the Microscale, Center for Integrative Imaging, University of Science and Technology of China, Hefei, China
| | - Guodong Tan
- Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China
- Hefei National Research Center for Physical Sciences at the Microscale, Center for Integrative Imaging, University of Science and Technology of China, Hefei, China
| | - Yuqi Guo
- Guangdong Provincial Key Laboratory of Biomedical Optical Imaging Technology and Center for Biomedical Optics and Molecular Imaging, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
| | - Jun Chu
- Guangdong Provincial Key Laboratory of Biomedical Optical Imaging Technology and Center for Biomedical Optics and Molecular Imaging, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
| | - Yu Mu
- Institute of Neuroscience, State Key Laboratory of Neuroscience, Center for Excellence in Brain Science and Intelligence Technology, Chinese Academy of Sciences, Shanghai, China
| | - Chen Shen
- Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China
- Hefei National Research Center for Physical Sciences at the Microscale, Center for Integrative Imaging, University of Science and Technology of China, Hefei, China
| | - Quan Wen
- Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China
- Hefei National Research Center for Physical Sciences at the Microscale, Center for Integrative Imaging, University of Science and Technology of China, Hefei, China
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16
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Robson DN, Li JM. Simultaneous Behavioral and Neuronal Imaging by Tracking Microscopy. Methods Mol Biol 2024; 2707:155-167. [PMID: 37668911 DOI: 10.1007/978-1-0716-3401-1_10] [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: 09/06/2023]
Abstract
Tracking microscopy enables whole-brain cellular resolution imaging in freely swimming animals. This technique enables both structural and functional imaging without immobilizing the animal, and greatly expands the range of the behaviors accessible to neuroscientists. We use infrared imaging to track the target animal in a behavioral arena. Based on the predicted trajectory of the brain, we apply optimal control theory to a motorized stage system to cancel brain motion in three dimensions. We have combined this motion cancellation system with Differential Illumination Focal Filtering (DIFF), a form of structured illumination microscopy, which enables us to image the brain of a freely swimming larval zebrafish for over an hour. Here we describe the typical experimental procedure for data acquisition and processing using the tracking microscope.
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Affiliation(s)
- Drew N Robson
- Max Planck Institute for Biological Cybernetics, Tuebingen, Germany.
| | - Jennifer M Li
- Max Planck Institute for Biological Cybernetics, Tuebingen, Germany
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17
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Wang Z, Zhang J, Symvoulidis P, Guo W, Zhang L, Wilson MA, Boyden ES. Imaging the voltage of neurons distributed across entire brains of larval zebrafish. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.12.15.571964. [PMID: 38168290 PMCID: PMC10760087 DOI: 10.1101/2023.12.15.571964] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/05/2024]
Abstract
Neurons interact in networks distributed throughout the brain. Although much effort has focused on whole-brain calcium imaging, recent advances in genetically encoded voltage indicators (GEVIs) raise the possibility of imaging voltage of neurons distributed across brains. To achieve this, a microscope must image at high volumetric rate and signal-to-noise ratio. We present a remote scanning light-sheet microscope capable of imaging GEVI-expressing neurons distributed throughout entire brains of larval zebrafish at a volumetric rate of 200.8 Hz. We measured voltage of ∼1/3 of the neurons of the brain, distributed throughout. We observed that neurons firing at different times during a sequence were located at different brain locations, for sequences elicited by a visual stimulus, which mapped onto locations throughout the optic tectum, as well as during stimulus-independent bursts, which mapped onto locations in the cerebellum and medulla. Whole-brain voltage imaging may open up frontiers in the fundamental operation of neural systems.
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18
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Lloyd E, Privat M, Sumbre G, Duboué ER, Keene AC. A protocol for whole-brain Ca 2+ imaging in Astyanax mexicanus, a model of comparative evolution. STAR Protoc 2023; 4:102517. [PMID: 37742184 PMCID: PMC10520939 DOI: 10.1016/j.xpro.2023.102517] [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: 11/23/2022] [Revised: 05/17/2023] [Accepted: 07/27/2023] [Indexed: 09/26/2023] Open
Abstract
In this protocol, we describe a comparative approach to study the evolution of brain function in the Mexican tetra, Astyanax mexicanus. We developed surface fish and two independent populations of cavefish with pan-neuronal expression of the Ca2+ sensor GCaMP6s. We describe a methodology to prepare samples and image activity across the optic tectum and olfactory bulb.
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Affiliation(s)
- Evan Lloyd
- Department of Biology, Texas A&M University, College Station, TX 77840, USA.
| | - Martin Privat
- Institut de Biologie de l'ENS (IBENS), Département de Biologie, École Normale Supérieure, CNRS, INSERM, Université PSL, 75005 Paris, France
| | - German Sumbre
- Institut de Biologie de l'ENS (IBENS), Département de Biologie, École Normale Supérieure, CNRS, INSERM, Université PSL, 75005 Paris, France
| | - Erik R Duboué
- Harriet Wilkes Honors College, Florida Atlantic University, Jupiter, FL 33458, USA
| | - Alex C Keene
- Department of Biology, Texas A&M University, College Station, TX 77840, USA.
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19
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Yi C, Zhu L, Sun J, Wang Z, Zhang M, Zhong F, Yan L, Tang J, Huang L, Zhang YH, Li D, Fei P. Video-rate 3D imaging of living cells using Fourier view-channel-depth light field microscopy. Commun Biol 2023; 6:1259. [PMID: 38086994 PMCID: PMC10716377 DOI: 10.1038/s42003-023-05636-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2023] [Accepted: 11/27/2023] [Indexed: 12/18/2023] Open
Abstract
Interrogation of subcellular biological dynamics occurring in a living cell often requires noninvasive imaging of the fragile cell with high spatiotemporal resolution across all three dimensions. It thereby poses big challenges to modern fluorescence microscopy implementations because the limited photon budget in a live-cell imaging task makes the achievable performance of conventional microscopy approaches compromise between their spatial resolution, volumetric imaging speed, and phototoxicity. Here, we incorporate a two-stage view-channel-depth (VCD) deep-learning reconstruction strategy with a Fourier light-field microscope based on diffractive optical element to realize fast 3D super-resolution reconstructions of intracellular dynamics from single diffraction-limited 2D light-filed measurements. This VCD-enabled Fourier light-filed imaging approach (F-VCD), achieves video-rate (50 volumes per second) 3D imaging of intracellular dynamics at a high spatiotemporal resolution of ~180 nm × 180 nm × 400 nm and strong noise-resistant capability, with which light field images with a signal-to-noise ratio (SNR) down to -1.62 dB could be well reconstructed. With this approach, we successfully demonstrate the 4D imaging of intracellular organelle dynamics, e.g., mitochondria fission and fusion, with ~5000 times of observation.
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Affiliation(s)
- Chengqiang Yi
- School of Optical and Electronic Information-Wuhan National Laboratory for Optoelectronics-Advanced Biomedical Imaging Facility, Huazhong University of Science and Technology, Wuhan, 430074, China
| | - Lanxin Zhu
- School of Optical and Electronic Information-Wuhan National Laboratory for Optoelectronics-Advanced Biomedical Imaging Facility, Huazhong University of Science and Technology, Wuhan, 430074, China
| | - Jiahao Sun
- School of Optical and Electronic Information-Wuhan National Laboratory for Optoelectronics-Advanced Biomedical Imaging Facility, Huazhong University of Science and Technology, Wuhan, 430074, China
| | - Zhaofei Wang
- School of Optical and Electronic Information-Wuhan National Laboratory for Optoelectronics-Advanced Biomedical Imaging Facility, Huazhong University of Science and Technology, Wuhan, 430074, China
| | - Meng Zhang
- School of Optical and Electronic Information-Wuhan National Laboratory for Optoelectronics-Advanced Biomedical Imaging Facility, Huazhong University of Science and Technology, Wuhan, 430074, China
- Britton Chance Center for Biomedical Photonics-MoE Key Laboratory for Biomedical Photonics, Advanced Biomedical Imaging Facility-Wuhan National Laboratory for Optoelectronics, Huazhong University of Science and Technology, Wuhan, Hubei, 430074, China
| | - Fenghe Zhong
- School of Optical and Electronic Information-Wuhan National Laboratory for Optoelectronics-Advanced Biomedical Imaging Facility, Huazhong University of Science and Technology, Wuhan, 430074, China
| | - Luxin Yan
- State Education Commission Key Laboratory for Image Processing and Intelligent Control, Huazhong University of Science and Technology, Wuhan, Hubei, 430074, China
| | - Jiang Tang
- School of Optical and Electronic Information-Wuhan National Laboratory for Optoelectronics-Advanced Biomedical Imaging Facility, Huazhong University of Science and Technology, Wuhan, 430074, China
| | - Liang Huang
- Department of Hematology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, 430030, China
| | - Yu-Hui Zhang
- Britton Chance Center for Biomedical Photonics-MoE Key Laboratory for Biomedical Photonics, Advanced Biomedical Imaging Facility-Wuhan National Laboratory for Optoelectronics, Huazhong University of Science and Technology, Wuhan, Hubei, 430074, China
| | - Dongyu Li
- School of Optical and Electronic Information-Wuhan National Laboratory for Optoelectronics-Advanced Biomedical Imaging Facility, Huazhong University of Science and Technology, Wuhan, 430074, China.
| | - Peng Fei
- School of Optical and Electronic Information-Wuhan National Laboratory for Optoelectronics-Advanced Biomedical Imaging Facility, Huazhong University of Science and Technology, Wuhan, 430074, China
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20
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Collier AD, Abdulai AR, Leibowitz SF. Utility of the Zebrafish Model for Studying Neuronal and Behavioral Disturbances Induced by Embryonic Exposure to Alcohol, Nicotine, and Cannabis. Cells 2023; 12:2505. [PMID: 37887349 PMCID: PMC10605371 DOI: 10.3390/cells12202505] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2023] [Revised: 09/28/2023] [Accepted: 09/28/2023] [Indexed: 10/28/2023] Open
Abstract
It is estimated that 5% of pregnant women consume drugs of abuse during pregnancy. Clinical research suggests that intake of drugs during pregnancy, such as alcohol, nicotine and cannabis, disturbs the development of neuronal systems in the offspring, in association with behavioral disturbances early in life and an increased risk of developing drug use disorders. After briefly summarizing evidence in rodents, this review focuses on the zebrafish model and its inherent advantages for studying the effects of embryonic exposure to drugs of abuse on behavioral and neuronal development, with an emphasis on neuropeptides known to promote drug-related behaviors. In addition to stimulating the expression and density of peptide neurons, as in rodents, zebrafish studies demonstrate that embryonic drug exposure has marked effects on the migration, morphology, projections, anatomical location, and peptide co-expression of these neurons. We also describe studies using advanced methodologies that can be applied in vivo in zebrafish: first, to demonstrate a causal relationship between the drug-induced neuronal and behavioral disturbances and second, to discover underlying molecular mechanisms that mediate these effects. The zebrafish model has great potential for providing important information regarding the development of novel and efficacious therapies for ameliorating the effects of early drug exposure.
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Affiliation(s)
| | | | - Sarah F. Leibowitz
- Laboratory of Behavioral Neurobiology, The Rockefeller University, New York, NY 10065, USA
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21
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Sarasamma S, Karim A, Orengo JP. Zebrafish Models of Rare Neurological Diseases like Spinocerebellar Ataxias (SCAs): Advantages and Limitations. BIOLOGY 2023; 12:1322. [PMID: 37887032 PMCID: PMC10604122 DOI: 10.3390/biology12101322] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2023] [Revised: 09/28/2023] [Accepted: 10/06/2023] [Indexed: 10/28/2023]
Abstract
Spinocerebellar ataxia (SCA) is a heterogeneous group of rare familial neurodegenerative disorders that share the key feature of cerebellar ataxia. Clinical heterogeneity, diverse gene mutations and complex neuropathology pose significant challenges for developing effective disease-modifying therapies in SCAs. Without a deep understanding of the molecular mechanisms involved for each SCA, we cannot succeed in developing targeted therapies. Animal models are our best tool to address these issues and several have been generated to study the pathological conditions of SCAs. Among them, zebrafish (Danio rerio) models are emerging as a powerful tool for in vivo study of SCAs, as well as rapid drug screens. In this review, we will summarize recent progress in using zebrafish to study the pathology of SCAs. We will discuss recent advancements on how zebrafish models can further clarify underlying genetic, neuroanatomical, and behavioral pathogenic mechanisms of disease. We highlight their usefulness in rapid drug discovery and large screens. Finally, we will discuss the advantages and limitations of this in vivo model to develop tailored therapeutic strategies for SCA.
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Affiliation(s)
- Sreeja Sarasamma
- Departments of Neurology and Neuroscience, Baylor College of Medicine, Houston, TX 77030, USA
- Department of Fisheries and Wildlife, Michigan State University, East Lansing, MI 48824, USA
| | - Anwarul Karim
- School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
| | - James P. Orengo
- Departments of Neurology and Neuroscience, Baylor College of Medicine, Houston, TX 77030, USA
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22
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Chaoul V, Dib EY, Bedran J, Khoury C, Shmoury O, Harb F, Soueid J. Assessing Drug Administration Techniques in Zebrafish Models of Neurological Disease. Int J Mol Sci 2023; 24:14898. [PMID: 37834345 PMCID: PMC10573323 DOI: 10.3390/ijms241914898] [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: 07/24/2023] [Revised: 08/30/2023] [Accepted: 08/31/2023] [Indexed: 10/15/2023] Open
Abstract
Neurological diseases, including neurodegenerative and neurodevelopmental disorders, affect nearly one in six of the world's population. The burden of the resulting deaths and disability is set to rise during the next few decades as a consequence of an aging population. To address this, zebrafish have become increasingly prominent as a model for studying human neurological diseases and exploring potential therapies. Zebrafish offer numerous benefits, such as genetic homology and brain similarities, complementing traditional mammalian models and serving as a valuable tool for genetic screening and drug discovery. In this comprehensive review, we highlight various drug delivery techniques and systems employed for therapeutic interventions of neurological diseases in zebrafish, and evaluate their suitability. We also discuss the challenges encountered during this process and present potential advancements in innovative techniques.
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Affiliation(s)
- Victoria Chaoul
- Department of Biochemistry and Molecular Genetics, Faculty of Medicine, American University of Beirut, Beirut P.O. Box 11-0236, Lebanon; (V.C.); (J.B.); (O.S.)
| | - Emanuel-Youssef Dib
- Department of Biomedical Sciences, Faculty of Medicine and Medical Sciences, University of Balamand, Kalhat P.O. Box 100, Lebanon; (E.-Y.D.); (C.K.)
| | - Joe Bedran
- Department of Biochemistry and Molecular Genetics, Faculty of Medicine, American University of Beirut, Beirut P.O. Box 11-0236, Lebanon; (V.C.); (J.B.); (O.S.)
| | - Chakib Khoury
- Department of Biomedical Sciences, Faculty of Medicine and Medical Sciences, University of Balamand, Kalhat P.O. Box 100, Lebanon; (E.-Y.D.); (C.K.)
| | - Omar Shmoury
- Department of Biochemistry and Molecular Genetics, Faculty of Medicine, American University of Beirut, Beirut P.O. Box 11-0236, Lebanon; (V.C.); (J.B.); (O.S.)
| | - Frédéric Harb
- Department of Biomedical Sciences, Faculty of Medicine and Medical Sciences, University of Balamand, Kalhat P.O. Box 100, Lebanon; (E.-Y.D.); (C.K.)
| | - Jihane Soueid
- Department of Biochemistry and Molecular Genetics, Faculty of Medicine, American University of Beirut, Beirut P.O. Box 11-0236, Lebanon; (V.C.); (J.B.); (O.S.)
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23
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Ravan A, Feng R, Gruebele M, Chemla YR. Rapid automated 3-D pose estimation of larval zebrafish using a physical model-trained neural network. PLoS Comput Biol 2023; 19:e1011566. [PMID: 37871114 PMCID: PMC10621986 DOI: 10.1371/journal.pcbi.1011566] [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: 01/09/2023] [Revised: 11/02/2023] [Accepted: 10/02/2023] [Indexed: 10/25/2023] Open
Abstract
Quantitative ethology requires an accurate estimation of an organism's postural dynamics in three dimensions plus time. Technological progress over the last decade has made animal pose estimation in challenging scenarios possible with unprecedented detail. Here, we present (i) a fast automated method to record and track the pose of individual larval zebrafish in a 3-D environment, applicable when accurate human labeling is not possible; (ii) a rich annotated dataset of 3-D larval poses for ethologists and the general zebrafish and machine learning community; and (iii) a technique to generate realistic, annotated larval images in different behavioral contexts. Using a three-camera system calibrated with refraction correction, we record diverse larval swims under free swimming conditions and in response to acoustic and optical stimuli. We then employ a convolutional neural network to estimate 3-D larval poses from video images. The network is trained against a set of synthetic larval images rendered using a 3-D physical model of larvae. This 3-D model samples from a distribution of realistic larval poses that we estimate a priori using a template-based pose estimation of a small number of swim bouts. Our network model, trained without any human annotation, performs larval pose estimation three orders of magnitude faster and with accuracy comparable to the template-based approach, capturing detailed kinematics of 3-D larval swims. It also applies accurately to other datasets collected under different imaging conditions and containing behavioral contexts not included in our training.
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Affiliation(s)
- Aniket Ravan
- Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, United States of America
- Center for the Physics of Living Cells, University of Illinois at Urbana-Champaign, Urbana, Illinois, United States of America
| | - Ruopei Feng
- Center for the Physics of Living Cells, University of Illinois at Urbana-Champaign, Urbana, Illinois, United States of America
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois, United States of America
| | - Martin Gruebele
- Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, United States of America
- Center for the Physics of Living Cells, University of Illinois at Urbana-Champaign, Urbana, Illinois, United States of America
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois, United States of America
- Department of Physics, University of Illinois at Urbana-Champaign, Urbana, Illinois, United States of America
| | - Yann R. Chemla
- Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, United States of America
- Center for the Physics of Living Cells, University of Illinois at Urbana-Champaign, Urbana, Illinois, United States of America
- Department of Physics, University of Illinois at Urbana-Champaign, Urbana, Illinois, United States of America
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24
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Mandracchia B, Liu W, Hua X, Forghani P, Lee S, Hou J, Nie S, Xu C, Jia S. Optimal sparsity allows reliable system-aware restoration of fluorescence microscopy images. SCIENCE ADVANCES 2023; 9:eadg9245. [PMID: 37647399 PMCID: PMC10468132 DOI: 10.1126/sciadv.adg9245] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/13/2023] [Accepted: 07/31/2023] [Indexed: 09/01/2023]
Abstract
Fluorescence microscopy is one of the most indispensable and informative driving forces for biological research, but the extent of observable biological phenomena is essentially determined by the content and quality of the acquired images. To address the different noise sources that can degrade these images, we introduce an algorithm for multiscale image restoration through optimally sparse representation (MIRO). MIRO is a deterministic framework that models the acquisition process and uses pixelwise noise correction to improve image quality. Our study demonstrates that this approach yields a remarkable restoration of the fluorescence signal for a wide range of microscopy systems, regardless of the detector used (e.g., electron-multiplying charge-coupled device, scientific complementary metal-oxide semiconductor, or photomultiplier tube). MIRO improves current imaging capabilities, enabling fast, low-light optical microscopy, accurate image analysis, and robust machine intelligence when integrated with deep neural networks. This expands the range of biological knowledge that can be obtained from fluorescence microscopy.
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Affiliation(s)
- Biagio Mandracchia
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, GA, USA
- Scientific-Technical Central Units, Instituto de Salud Carlos III (ISCIII), Majadahonda, Spain
- ETSI Telecomunicación, Universidad de Valladolid, Valladolid, Spain
| | - Wenhao Liu
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, GA, USA
| | - Xuanwen Hua
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, GA, USA
| | - Parvin Forghani
- Department of Pediatrics, School of Medicine, Emory University, Atlanta, GA, USA
| | - Soojung Lee
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, GA, USA
| | - Jessica Hou
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, USA
| | - Shuyi Nie
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, USA
- Parker H. Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, GA, USA
| | - Chunhui Xu
- Department of Pediatrics, School of Medicine, Emory University, Atlanta, GA, USA
- Parker H. Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, GA, USA
| | - Shu Jia
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, GA, USA
- Parker H. Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, GA, USA
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25
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Brynildsen JK, Rajan K, Henderson MX, Bassett DS. Network models to enhance the translational impact of cross-species studies. Nat Rev Neurosci 2023; 24:575-588. [PMID: 37524935 PMCID: PMC10634203 DOI: 10.1038/s41583-023-00720-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/17/2023] [Indexed: 08/02/2023]
Abstract
Neuroscience studies are often carried out in animal models for the purpose of understanding specific aspects of the human condition. However, the translation of findings across species remains a substantial challenge. Network science approaches can enhance the translational impact of cross-species studies by providing a means of mapping small-scale cellular processes identified in animal model studies to larger-scale inter-regional circuits observed in humans. In this Review, we highlight the contributions of network science approaches to the development of cross-species translational research in neuroscience. We lay the foundation for our discussion by exploring the objectives of cross-species translational models. We then discuss how the development of new tools that enable the acquisition of whole-brain data in animal models with cellular resolution provides unprecedented opportunity for cross-species applications of network science approaches for understanding large-scale brain networks. We describe how these tools may support the translation of findings across species and imaging modalities and highlight future opportunities. Our overarching goal is to illustrate how the application of network science tools across human and animal model studies could deepen insight into the neurobiology that underlies phenomena observed with non-invasive neuroimaging methods and could simultaneously further our ability to translate findings across species.
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Affiliation(s)
- Julia K Brynildsen
- Department of Bioengineering, University of Pennsylvania, Philadelphia, PA, USA
| | - Kanaka Rajan
- Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- The Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Michael X Henderson
- Parkinson's Disease Center, Department of Neurodegenerative Science, Van Andel Institute, Grand Rapids, MI, USA
| | - Dani S Bassett
- Department of Bioengineering, University of Pennsylvania, Philadelphia, PA, USA.
- Department of Electrical & Systems Engineering, University of Pennsylvania, Philadelphia, PA, USA.
- Department of Physics & Astronomy, University of Pennsylvania, Philadelphia, PA, USA.
- Department of Neurology, University of Pennsylvania, Philadelphia, PA, USA.
- Department of Psychiatry, University of Pennsylvania, Philadelphia, PA, USA.
- Santa Fe Institute, Santa Fe, NM, USA.
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26
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Ling Z, Han K, Liu W, Hua X, Jia S. Volumetric live-cell autofluorescence imaging using Fourier light-field microscopy. BIOMEDICAL OPTICS EXPRESS 2023; 14:4237-4245. [PMID: 37799690 PMCID: PMC10549745 DOI: 10.1364/boe.495506] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/15/2023] [Revised: 07/13/2023] [Accepted: 07/14/2023] [Indexed: 10/07/2023]
Abstract
This study introduces a rapid, volumetric live-cell imaging technique for visualizing autofluorescent sub-cellular structures and their dynamics by employing high-resolution Fourier light-field microscopy. We demonstrated this method by capturing lysosomal autofluorescence in fibroblasts and HeLa cells. Additionally, we conducted multicolor imaging to simultaneously observe lysosomal autofluorescence and fluorescently-labeled organelles such as lysosomes and mitochondria. We further analyzed the data to quantify the interactions between lysosomes and mitochondria. This research lays the foundation for future exploration of native cellular states and functions in three-dimensional environments, effectively reducing photodamage and eliminating the necessity for exogenous labels.
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Affiliation(s)
- Zhi Ling
- The Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, GA 30332, USA
- Parker H. Petit Institute for Bioengineering and Biosciences, Georgia Institute of Technology, Atlanta, GA 30332, USA
- George W. Woodruff School of Mechanical Engineering, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - Keyi Han
- The Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, GA 30332, USA
| | - Wenhao Liu
- The Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, GA 30332, USA
| | - Xuanwen Hua
- The Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, GA 30332, USA
| | - Shu Jia
- The Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, GA 30332, USA
- Parker H. Petit Institute for Bioengineering and Biosciences, Georgia Institute of Technology, Atlanta, GA 30332, USA
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27
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Yamaguchi A, Wu R, McNulty P, Karagyozov D, Mihovilovic Skanata M, Gershow M. Multi-neuronal recording in unrestrained animals with all acousto-optic random-access line-scanning two-photon microscopy. Front Neurosci 2023; 17:1135457. [PMID: 37389365 PMCID: PMC10303936 DOI: 10.3389/fnins.2023.1135457] [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: 12/31/2022] [Accepted: 05/18/2023] [Indexed: 07/01/2023] Open
Abstract
To understand how neural activity encodes and coordinates behavior, it is desirable to record multi-neuronal activity in freely behaving animals. Imaging in unrestrained animals is challenging, especially for those, like larval Drosophila melanogaster, whose brains are deformed by body motion. A previously demonstrated two-photon tracking microscope recorded from individual neurons in freely crawling Drosophila larvae but faced limits in multi-neuronal recording. Here we demonstrate a new tracking microscope using acousto-optic deflectors (AODs) and an acoustic GRIN lens (TAG lens) to achieve axially resonant 2D random access scanning, sampling along arbitrarily located axial lines at a line rate of 70 kHz. With a tracking latency of 0.1 ms, this microscope recorded activities of various neurons in moving larval Drosophila CNS and VNC including premotor neurons, bilateral visual interneurons, and descending command neurons. This technique can be applied to the existing two-photon microscope to allow for fast 3D tracking and scanning.
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Affiliation(s)
- Akihiro Yamaguchi
- Department of Physics, New York University, New York, NY, United States
| | - Rui Wu
- Department of Physics, New York University, New York, NY, United States
| | - Paul McNulty
- Department of Physics, New York University, New York, NY, United States
| | - Doycho Karagyozov
- Department of Physics, New York University, New York, NY, United States
| | | | - Marc Gershow
- Department of Physics, New York University, New York, NY, United States
- Center for Neural Science, New York University, New York, NY, United States
- Neuroscience Institute, New York University, New York, NY, United States
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28
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Turrini L, Roschi L, de Vito G, Pavone FS, Vanzi F. Imaging Approaches to Investigate Pathophysiological Mechanisms of Brain Disease in Zebrafish. Int J Mol Sci 2023; 24:9833. [PMID: 37372981 DOI: 10.3390/ijms24129833] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2023] [Revised: 06/01/2023] [Accepted: 06/02/2023] [Indexed: 06/29/2023] Open
Abstract
Zebrafish has become an essential model organism in modern biomedical research. Owing to its distinctive features and high grade of genomic homology with humans, it is increasingly employed to model diverse neurological disorders, both through genetic and pharmacological intervention. The use of this vertebrate model has recently enhanced research efforts, both in the optical technology and in the bioengineering fields, aiming at developing novel tools for high spatiotemporal resolution imaging. Indeed, the ever-increasing use of imaging methods, often combined with fluorescent reporters or tags, enable a unique chance for translational neuroscience research at different levels, ranging from behavior (whole-organism) to functional aspects (whole-brain) and down to structural features (cellular and subcellular). In this work, we present a review of the imaging approaches employed to investigate pathophysiological mechanisms underlying functional, structural, and behavioral alterations of human neurological diseases modeled in zebrafish.
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Affiliation(s)
- Lapo Turrini
- European Laboratory for Non-Linear Spectroscopy, Via Nello Carrara 1, 50019 Sesto Fiorentino, Italy
| | - Lorenzo Roschi
- European Laboratory for Non-Linear Spectroscopy, Via Nello Carrara 1, 50019 Sesto Fiorentino, Italy
| | - Giuseppe de Vito
- European Laboratory for Non-Linear Spectroscopy, Via Nello Carrara 1, 50019 Sesto Fiorentino, Italy
- Department of Neuroscience, Psychology, Drug Research and Child Health, University of Florence, Viale Gaetano Pieraccini 6, 50139 Florence, Italy
- Interdepartmental Centre for the Study of Complex Dynamics, University of Florence, Via Giovanni Sansone 1, 50019 Sesto Fiorentino, Italy
| | - Francesco Saverio Pavone
- European Laboratory for Non-Linear Spectroscopy, Via Nello Carrara 1, 50019 Sesto Fiorentino, Italy
- Department of Physics and Astronomy, University of Florence, Via Giovanni Sansone 1, 50019 Sesto Fiorentino, Italy
- National Institute of Optics, National Research Council, Via Nello Carrara 1, 50019 Sesto Fiorentino, Italy
| | - Francesco Vanzi
- European Laboratory for Non-Linear Spectroscopy, Via Nello Carrara 1, 50019 Sesto Fiorentino, Italy
- Department of Biology, University of Florence, Via Madonna del Piano 6, 50019 Sesto Fiorentino, Italy
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29
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Wu Q, Zhang Y. Neural Circuit Mechanisms Involved in Animals' Detection of and Response to Visual Threats. Neurosci Bull 2023; 39:994-1008. [PMID: 36694085 PMCID: PMC10264346 DOI: 10.1007/s12264-023-01021-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2022] [Accepted: 10/30/2022] [Indexed: 01/26/2023] Open
Abstract
Evading or escaping from predators is one of the most crucial issues for survival across the animal kingdom. The timely detection of predators and the initiation of appropriate fight-or-flight responses are innate capabilities of the nervous system. Here we review recent progress in our understanding of innate visually-triggered defensive behaviors and the underlying neural circuit mechanisms, and a comparison among vinegar flies, zebrafish, and mice is included. This overview covers the anatomical and functional aspects of the neural circuits involved in this process, including visual threat processing and identification, the selection of appropriate behavioral responses, and the initiation of these innate defensive behaviors. The emphasis of this review is on the early stages of this pathway, namely, threat identification from complex visual inputs and how behavioral choices are influenced by differences in visual threats. We also briefly cover how the innate defensive response is processed centrally. Based on these summaries, we discuss coding strategies for visual threats and propose a common prototypical pathway for rapid innate defensive responses.
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Affiliation(s)
- Qiwen Wu
- Institute of Neuroscience, Center for Excellence in Brain Science and Intelligence Technology, Chinese Academy of Sciences, Shanghai, 200031, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yifeng Zhang
- Institute of Neuroscience, Center for Excellence in Brain Science and Intelligence Technology, Chinese Academy of Sciences, Shanghai, 200031, China.
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30
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Sung Y. Optical projection tomography of fluorescent microscopic specimens using lateral translation of tube lens. OPTICS LETTERS 2023; 48:2623-2626. [PMID: 37186724 PMCID: PMC10798857 DOI: 10.1364/ol.491499] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/23/2023] [Accepted: 04/21/2023] [Indexed: 05/17/2023]
Abstract
Optical projection tomography (OPT) is a three-dimensional (3D) fluorescence imaging technique, in which projection images are acquired for varying orientations of a sample using a large depth of field. OPT is typically applied to a millimeter-sized specimen, because the rotation of a microscopic specimen is challenging and not compatible with live cell imaging. In this Letter, we demonstrate fluorescence optical tomography of a microscopic specimen by laterally translating the tube lens of a wide-field optical microscope, which allows for high-resolution OPT without rotating the sample. The cost is the reduction of the field of view to about halfway along the direction of the tube lens translation. Using bovine pulmonary artery endothelial cells and 0.1 µm beads, we compare the 3D imaging performance of the proposed method with that of the conventional objective-focus scan method.
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Affiliation(s)
- Yongjin Sung
- College of Engineering & Applied Science, University of Wisconsin, Milwaukee, WI 53211, USA
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31
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Lu Z, Liu Y, Jin M, Luo X, Yue H, Wang Z, Zuo S, Zeng Y, Fan J, Pang Y, Wu J, Yang J, Dai Q. Virtual-scanning light-field microscopy for robust snapshot high-resolution volumetric imaging. Nat Methods 2023; 20:735-746. [PMID: 37024654 PMCID: PMC10172145 DOI: 10.1038/s41592-023-01839-6] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2022] [Accepted: 03/07/2023] [Indexed: 04/08/2023]
Abstract
High-speed three-dimensional (3D) intravital imaging in animals is useful for studying transient subcellular interactions and functions in health and disease. Light-field microscopy (LFM) provides a computational solution for snapshot 3D imaging with low phototoxicity but is restricted by low resolution and reconstruction artifacts induced by optical aberrations, motion and noise. Here, we propose virtual-scanning LFM (VsLFM), a physics-based deep learning framework to increase the resolution of LFM up to the diffraction limit within a snapshot. By constructing a 40 GB high-resolution scanning LFM dataset across different species, we exploit physical priors between phase-correlated angular views to address the frequency aliasing problem. This enables us to bypass hardware scanning and associated motion artifacts. Here, we show that VsLFM achieves ultrafast 3D imaging of diverse processes such as the beating heart in embryonic zebrafish, voltage activity in Drosophila brains and neutrophil migration in the mouse liver at up to 500 volumes per second.
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Affiliation(s)
- Zhi Lu
- Department of Automation, Tsinghua University, Beijing, China
- Institute for Brain and Cognitive Sciences, Tsinghua University, Beijing, China
| | - Yu Liu
- School of Electrical and Information Engineering, Tianjin University, Tianjin, China
| | - Manchang Jin
- School of Electrical and Information Engineering, Tianjin University, Tianjin, China
| | - Xin Luo
- School of Electrical and Information Engineering, Tianjin University, Tianjin, China
| | - Huanjing Yue
- School of Electrical and Information Engineering, Tianjin University, Tianjin, China
| | - Zian Wang
- Department of Automation, Tsinghua University, Beijing, China
| | - Siqing Zuo
- Department of Automation, Tsinghua University, Beijing, China
- Institute for Brain and Cognitive Sciences, Tsinghua University, Beijing, China
| | - Yunmin Zeng
- Department of Automation, Tsinghua University, Beijing, China
- Institute for Brain and Cognitive Sciences, Tsinghua University, Beijing, China
| | - Jiaqi Fan
- Institute for Brain and Cognitive Sciences, Tsinghua University, Beijing, China
| | - Yanwei Pang
- School of Electrical and Information Engineering, Tianjin University, Tianjin, China
| | - Jiamin Wu
- Department of Automation, Tsinghua University, Beijing, China.
- Institute for Brain and Cognitive Sciences, Tsinghua University, Beijing, China.
- IDG/McGovern Institute for Brain Research, Tsinghua University, Beijing, China.
| | - Jingyu Yang
- School of Electrical and Information Engineering, Tianjin University, Tianjin, China.
| | - Qionghai Dai
- Department of Automation, Tsinghua University, Beijing, China.
- Institute for Brain and Cognitive Sciences, Tsinghua University, Beijing, China.
- IDG/McGovern Institute for Brain Research, Tsinghua University, Beijing, China.
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32
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Hasani H, Sun J, Zhu SI, Rong Q, Willomitzer F, Amor R, McConnell G, Cossairt O, Goodhill GJ. Whole-brain imaging of freely-moving zebrafish. Front Neurosci 2023; 17:1127574. [PMID: 37139528 PMCID: PMC10150962 DOI: 10.3389/fnins.2023.1127574] [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: 12/19/2022] [Accepted: 03/28/2023] [Indexed: 05/05/2023] Open
Abstract
One of the holy grails of neuroscience is to record the activity of every neuron in the brain while an animal moves freely and performs complex behavioral tasks. While important steps forward have been taken recently in large-scale neural recording in rodent models, single neuron resolution across the entire mammalian brain remains elusive. In contrast the larval zebrafish offers great promise in this regard. Zebrafish are a vertebrate model with substantial homology to the mammalian brain, but their transparency allows whole-brain recordings of genetically-encoded fluorescent indicators at single-neuron resolution using optical microscopy techniques. Furthermore zebrafish begin to show a complex repertoire of natural behavior from an early age, including hunting small, fast-moving prey using visual cues. Until recently work to address the neural bases of these behaviors mostly relied on assays where the fish was immobilized under the microscope objective, and stimuli such as prey were presented virtually. However significant progress has recently been made in developing brain imaging techniques for zebrafish which are not immobilized. Here we discuss recent advances, focusing particularly on techniques based on light-field microscopy. We also draw attention to several important outstanding issues which remain to be addressed to increase the ecological validity of the results obtained.
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Affiliation(s)
- Hamid Hasani
- Department of Electrical and Computer Engineering, Northwestern University, Evanston, IL, United States
| | - Jipeng Sun
- Department of Computer Science, Northwestern University, Evanston, IL, United States
| | - Shuyu I. Zhu
- Departments of Developmental Biology and Neuroscience, Washington University in St. Louis, St. Louis, MO, United States
| | - Qiangzhou Rong
- Departments of Developmental Biology and Neuroscience, Washington University in St. Louis, St. Louis, MO, United States
| | - Florian Willomitzer
- Wyant College of Optical Sciences, University of Arizona, Tucson, AZ, United States
| | - Rumelo Amor
- Queensland Brain Institute, The University of Queensland, Brisbane, QLD, Australia
| | - Gail McConnell
- Centre for Biophotonics, Strathclyde Institute of Pharmacy and Biomedical Sciences, University of Strathclyde, Glasgow, United Kingdom
| | - Oliver Cossairt
- Department of Computer Science, Northwestern University, Evanston, IL, United States
| | - Geoffrey J. Goodhill
- Departments of Developmental Biology and Neuroscience, Washington University in St. Louis, St. Louis, MO, United States
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33
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Nöbauer T, Zhang Y, Kim H, Vaziri A. Mesoscale volumetric light-field (MesoLF) imaging of neuroactivity across cortical areas at 18 Hz. Nat Methods 2023; 20:600-609. [PMID: 36823333 PMCID: PMC11057224 DOI: 10.1038/s41592-023-01789-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2021] [Accepted: 01/24/2023] [Indexed: 02/25/2023]
Abstract
Various implementations of mesoscopes provide optical access for calcium imaging across multi-millimeter fields of view in the mammalian brain; however, capturing the activity of the neuronal population within such fields of view near-simultaneously and in a volumetric fashion has remained challenging as approaches for imaging scattering brain tissues typically are based on sequential acquisition. Here we present a modular, mesoscale light-field (MesoLF) imaging hardware and software solution that allows recording from thousands of neurons within volumes of ⌀ 4 × 0.2 mm, located at up to 350 µm depth in the mouse cortex, at 18 volumes per second and an effective voxel rate of ~40 megavoxels per second. Using our optical design and computational approach we show recording of ~10,000 neurons across multiple cortical areas in mice using workstation-grade computing resources.
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Affiliation(s)
- Tobias Nöbauer
- Laboratory of Neurotechnology and Biophysics, The Rockefeller University, New York, NY, USA
| | - Yuanlong Zhang
- Laboratory of Neurotechnology and Biophysics, The Rockefeller University, New York, NY, USA
- Department of Automation, Tsinghua University, Beijing, China
| | - Hyewon Kim
- Laboratory of Neurotechnology and Biophysics, The Rockefeller University, New York, NY, USA
| | - Alipasha Vaziri
- Laboratory of Neurotechnology and Biophysics, The Rockefeller University, New York, NY, USA.
- The Kavli Neural Systems Institute, The Rockefeller University, New York, NY, USA.
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34
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Nöbauer T, Zhang Y, Kim H, Vaziri A. Mesoscale volumetric light field (MesoLF) imaging of neuroactivity across cortical areas at 18 Hz. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.03.20.533476. [PMID: 36993596 PMCID: PMC10055306 DOI: 10.1101/2023.03.20.533476] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/31/2023]
Abstract
Various implementations of mesoscopes provide optical access for calcium imaging across multi-millimeter fields-of-view (FOV) in the mammalian brain. However, capturing the activity of the neuronal population within such FOVs near-simultaneously and in a volumetric fashion has remained challenging since approaches for imaging scattering brain tissues typically are based on sequential acquisition. Here, we present a modular, mesoscale light field (MesoLF) imaging hardware and software solution that allows recording from thousands of neurons within volumes of 4000 × 200 μm, located at up to 400 μm depth in the mouse cortex, at 18 volumes per second. Our optical design and computational approach enable up to hour-long recording of ~10,000 neurons across multiple cortical areas in mice using workstation-grade computing resources.
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Affiliation(s)
- Tobias Nöbauer
- Laboratory of Neurotechnology and Biophysics, The Rockefeller University, New York, NY, USA
| | - Yuanlong Zhang
- Laboratory of Neurotechnology and Biophysics, The Rockefeller University, New York, NY, USA
- Department of Automation, Tsinghua University, Beijing, China
| | - Hyewon Kim
- Laboratory of Neurotechnology and Biophysics, The Rockefeller University, New York, NY, USA
| | - Alipasha Vaziri
- Laboratory of Neurotechnology and Biophysics, The Rockefeller University, New York, NY, USA
- The Kavli Neural Systems Institute, The Rockefeller University, New York, NY, USA
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35
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Zhai J, Jin C, Kong L. Compact, Hybrid Light-Sheet and Fourier Light-Field Microscopy with a Single Objective for High-Speed Volumetric Imaging In Vivo. J Phys Chem A 2023; 127:2873-2879. [PMID: 36926932 DOI: 10.1021/acs.jpca.3c00325] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/18/2023]
Abstract
Volumetric imaging of biodynamics at high spatiotemporal resolutions in vivo is vital in biomedical studies, in which Fourier light field microscopy (FLFM) is a promising technique. However, the commonly used wide-field illumination strategy in FLFM introduces intense out of depth-of-field background, which not only degrades the image quality, but also introduces reconstruction artifacts. Employing light sheet illumination is an effective way to alleviate the background and reduce photobleaching in light-field microscopy. Unfortunately, the introduction of light-sheet illumination often requires an extra objective and precise alignment, which increases the system complexity. Here, we propose the compact, hybrid light-sheet and FLFM (CLS-FLFM), which uses only a single objective to achieve both light-sheet illumination and Fourier light-field imaging simultaneously. With a micromirror under the objective, we focus the light sheet, which ensures selective-volume-illumination, on the imaging plane of the FLFM to perform volumetric imaging. We demonstrate the superior performance of CLS-FLFM in inhibiting background in both structural and dynamical imaging of larval zebrafish in vivo. We envision that CLS-FLFM finds wide applications in high-speed, background-inhibited volumetric imaging of biodynamics in vivo.
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Affiliation(s)
- Jiazhen Zhai
- State Key Laboratory of Precision Measurement Technology and Instruments, Department of Precision Instrument, Tsinghua University, Beijing 100084, China
| | - Cheng Jin
- State Key Laboratory of Precision Measurement Technology and Instruments, Department of Precision Instrument, Tsinghua University, Beijing 100084, China
| | - Lingjie Kong
- State Key Laboratory of Precision Measurement Technology and Instruments, Department of Precision Instrument, Tsinghua University, Beijing 100084, China.,IDG/McGovern Institute for Brain Research, Tsinghua University, Beijing 100084, China
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36
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Shainer I, Kuehn E, Laurell E, Al Kassar M, Mokayes N, Sherman S, Larsch J, Kunst M, Baier H. A single-cell resolution gene expression atlas of the larval zebrafish brain. SCIENCE ADVANCES 2023; 9:eade9909. [PMID: 36812331 PMCID: PMC9946346 DOI: 10.1126/sciadv.ade9909] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/21/2022] [Accepted: 12/22/2022] [Indexed: 06/18/2023]
Abstract
The advent of multimodal brain atlases promises to accelerate progress in neuroscience by allowing in silico queries of neuron morphology, connectivity, and gene expression. We used multiplexed fluorescent in situ RNA hybridization chain reaction (HCR) technology to generate expression maps across the larval zebrafish brain for a growing set of marker genes. The data were registered to the Max Planck Zebrafish Brain (mapzebrain) atlas, thus allowing covisualization of gene expression, single-neuron tracings, and expertly curated anatomical segmentations. Using post hoc HCR labeling of the immediate early gene cfos, we mapped responses to prey stimuli and food ingestion across the brain of freely swimming larvae. This unbiased approach revealed, in addition to previously described visual and motor areas, a cluster of neurons in the secondary gustatory nucleus, which express the marker calb2a, as well as a specific neuropeptide Y receptor, and project to the hypothalamus. This discovery exemplifies the power of this new atlas resource for zebrafish neurobiology.
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37
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Chen X, Ginoux F, Carbo-Tano M, Mora T, Walczak AM, Wyart C. Granger causality analysis for calcium transients in neuronal networks, challenges and improvements. eLife 2023; 12:81279. [PMID: 36749019 PMCID: PMC10017105 DOI: 10.7554/elife.81279] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2022] [Accepted: 02/06/2023] [Indexed: 02/08/2023] Open
Abstract
One challenge in neuroscience is to understand how information flows between neurons in vivo to trigger specific behaviors. Granger causality (GC) has been proposed as a simple and effective measure for identifying dynamical interactions. At single-cell resolution however, GC analysis is rarely used compared to directionless correlation analysis. Here, we study the applicability of GC analysis for calcium imaging data in diverse contexts. We first show that despite underlying linearity assumptions, GC analysis successfully retrieves non-linear interactions in a synthetic network simulating intracellular calcium fluctuations of spiking neurons. We highlight the potential pitfalls of applying GC analysis on real in vivo calcium signals, and offer solutions regarding the choice of GC analysis parameters. We took advantage of calcium imaging datasets from motoneurons in embryonic zebrafish to show how the improved GC can retrieve true underlying information flow. Applied to the network of brainstem neurons of larval zebrafish, our pipeline reveals strong driver neurons in the locus of the mesencephalic locomotor region (MLR), driving target neurons matching expectations from anatomical and physiological studies. Altogether, this practical toolbox can be applied on in vivo population calcium signals to increase the selectivity of GC to infer flow of information across neurons.
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Affiliation(s)
- Xiaowen Chen
- Laboratoire de physique de l'École normale supérieure, CNRS, PSL UniversityParisFrance
| | - Faustine Ginoux
- Spinal Sensory Signaling team, Sorbonne Université, Paris Brain Institute (Institut du Cerveau, ICM)ParisFrance
| | - Martin Carbo-Tano
- Spinal Sensory Signaling team, Sorbonne Université, Paris Brain Institute (Institut du Cerveau, ICM)ParisFrance
| | - Thierry Mora
- Laboratoire de physique de l'École normale supérieure, CNRS, PSL UniversityParisFrance
| | - Aleksandra M Walczak
- Laboratoire de physique de l'École normale supérieure, CNRS, PSL UniversityParisFrance
| | - Claire Wyart
- Spinal Sensory Signaling team, Sorbonne Université, Paris Brain Institute (Institut du Cerveau, ICM)ParisFrance
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Zhu SI, Goodhill GJ. From perception to behavior: The neural circuits underlying prey hunting in larval zebrafish. Front Neural Circuits 2023; 17:1087993. [PMID: 36817645 PMCID: PMC9928868 DOI: 10.3389/fncir.2023.1087993] [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: 11/02/2022] [Accepted: 01/10/2023] [Indexed: 02/04/2023] Open
Abstract
A key challenge for neural systems is to extract relevant information from the environment and make appropriate behavioral responses. The larval zebrafish offers an exciting opportunity for studying these sensing processes and sensory-motor transformations. Prey hunting is an instinctual behavior of zebrafish that requires the brain to extract and combine different attributes of the sensory input and form appropriate motor outputs. Due to its small size and transparency the larval zebrafish brain allows optical recording of whole-brain activity to reveal the neural mechanisms involved in prey hunting and capture. In this review we discuss how the larval zebrafish brain processes visual information to identify and locate prey, the neural circuits governing the generation of motor commands in response to prey, how hunting behavior can be modulated by internal states and experience, and some outstanding questions for the field.
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Affiliation(s)
- Shuyu I. Zhu
- Departments of Developmental Biology and Neuroscience, Washington University in St. Louis, St. Louis, MO, United States
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39
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An optofluidic platform for interrogating chemosensory behavior and brainwide neural representation in larval zebrafish. Nat Commun 2023; 14:227. [PMID: 36641479 PMCID: PMC9840631 DOI: 10.1038/s41467-023-35836-2] [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: 02/13/2022] [Accepted: 01/03/2023] [Indexed: 01/15/2023] Open
Abstract
Studying chemosensory processing desires precise chemical cue presentation, behavioral response monitoring, and large-scale neuronal activity recording. Here we present Fish-on-Chips, a set of optofluidic tools for highly-controlled chemical delivery while simultaneously imaging behavioral outputs and whole-brain neuronal activities at cellular resolution in larval zebrafish. These include a fluidics-based swimming arena and an integrated microfluidics-light sheet fluorescence microscopy (µfluidics-LSFM) system, both of which utilize laminar fluid flows to achieve spatiotemporally precise chemical cue presentation. To demonstrate the strengths of the platform, we used the navigation arena to reveal binasal input-dependent behavioral strategies that larval zebrafish adopt to evade cadaverine, a death-associated odor. The µfluidics-LSFM system enables sequential presentation of odor stimuli to individual or both nasal cavities separated by only ~100 µm. This allowed us to uncover brainwide neural representations of cadaverine sensing and binasal input summation in the vertebrate model. Fish-on-Chips is readily generalizable and will empower the investigation of neural coding in the chemical senses.
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Yang E, Zwart MF, James B, Rubinov M, Wei Z, Narayan S, Vladimirov N, Mensh BD, Fitzgerald JE, Ahrens MB. A brainstem integrator for self-location memory and positional homeostasis in zebrafish. Cell 2022; 185:5011-5027.e20. [PMID: 36563666 DOI: 10.1016/j.cell.2022.11.022] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2022] [Revised: 06/28/2022] [Accepted: 11/21/2022] [Indexed: 12/24/2022]
Abstract
To track and control self-location, animals integrate their movements through space. Representations of self-location are observed in the mammalian hippocampal formation, but it is unknown if positional representations exist in more ancient brain regions, how they arise from integrated self-motion, and by what pathways they control locomotion. Here, in a head-fixed, fictive-swimming, virtual-reality preparation, we exposed larval zebrafish to a variety of involuntary displacements. They tracked these displacements and, many seconds later, moved toward their earlier location through corrective swimming ("positional homeostasis"). Whole-brain functional imaging revealed a network in the medulla that stores a memory of location and induces an error signal in the inferior olive to drive future corrective swimming. Optogenetically manipulating medullary integrator cells evoked displacement-memory behavior. Ablating them, or downstream olivary neurons, abolished displacement corrections. These results reveal a multiregional hindbrain circuit in vertebrates that integrates self-motion and stores self-location to control locomotor behavior.
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Affiliation(s)
- En Yang
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA 20147, USA.
| | - Maarten F Zwart
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA 20147, USA; School of Psychology and Neuroscience, Centre for Biophotonics, University of St Andrews, St. Andrews, UK
| | - Ben James
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA 20147, USA
| | - Mikail Rubinov
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA 20147, USA; Department of Biomedical Engineering, Vanderbilt University, Nashville, TN 37235, USA
| | - Ziqiang Wei
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA 20147, USA
| | - Sujatha Narayan
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA 20147, USA
| | - Nikita Vladimirov
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA 20147, USA; URPP Adaptive Brain Circuits in Development and Learning (AdaBD), University of Zurich, Zurich, Switzerland
| | - Brett D Mensh
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA 20147, USA
| | - James E Fitzgerald
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA 20147, USA
| | - Misha B Ahrens
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA 20147, USA.
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41
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Lam PY. Longitudinal in vivo imaging of adult Danionella cerebrum using standard confocal microscopy. Dis Model Mech 2022; 15:283162. [PMID: 36398624 PMCID: PMC9844135 DOI: 10.1242/dmm.049753] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2022] [Accepted: 11/09/2022] [Indexed: 11/19/2022] Open
Abstract
Danionella cerebrum is a new vertebrate model that offers an exciting opportunity to visualize dynamic biological processes in intact adult animals. Key advantages of this model include its small size, life-long optical transparency, genetic amenability and short generation time. Establishing a reliable method for longitudinal in vivo imaging of adult D. cerebrum while maintaining viability will allow in-depth image-based studies of various processes involved in development, disease onset and progression, wound healing, and aging in an intact live animal. Here, a method for both prolonged and longitudinal confocal live imaging of adult D. cerebrum using custom-designed and 3D-printed imaging chambers is described. Two transgenic D. cerebrum lines were created to test the imaging system, i.e. Tg(mpeg1:dendra2) and Tg(kdrl:mCherry-caax). The first line was used to visualize macrophages and microglia, and the second for spatial registration. By using this approach, differences in immune cell morphology and behavior during homeostasis as well as in response to a stab wound or two-photon-induced brain injury were observed in intact adult fish over the course of several days.
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Affiliation(s)
- Pui-Ying Lam
- Neuroscience Research Center, Medical College of Wisconsin, 53226 Milwaukee, WI, USA,Department of Cell Biology, Neurobiology and Anatomy, Medical College of Wisconsin, 53226 Milwaukee, WI, USA,Author for correspondence ()
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Thomson EE, Harfouche M, Kim K, Konda PC, Seitz CW, Cooke C, Xu S, Jacobs WS, Blazing R, Chen Y, Sharma S, Dunn TW, Park J, Horstmeyer RW, Naumann EA. Gigapixel imaging with a novel multi-camera array microscope. eLife 2022; 11:e74988. [PMID: 36515989 PMCID: PMC9917455 DOI: 10.7554/elife.74988] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2021] [Accepted: 11/23/2022] [Indexed: 12/15/2022] Open
Abstract
The dynamics of living organisms are organized across many spatial scales. However, current cost-effective imaging systems can measure only a subset of these scales at once. We have created a scalable multi-camera array microscope (MCAM) that enables comprehensive high-resolution recording from multiple spatial scales simultaneously, ranging from structures that approach the cellular scale to large-group behavioral dynamics. By collecting data from up to 96 cameras, we computationally generate gigapixel-scale images and movies with a field of view over hundreds of square centimeters at an optical resolution of 18 µm. This allows us to observe the behavior and fine anatomical features of numerous freely moving model organisms on multiple spatial scales, including larval zebrafish, fruit flies, nematodes, carpenter ants, and slime mold. Further, the MCAM architecture allows stereoscopic tracking of the z-position of organisms using the overlapping field of view from adjacent cameras. Overall, by removing the bottlenecks imposed by single-camera image acquisition systems, the MCAM provides a powerful platform for investigating detailed biological features and behavioral processes of small model organisms across a wide range of spatial scales.
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Affiliation(s)
- Eric E Thomson
- Department of Neurobiology, Duke School of MedicineDurhamUnited States
| | | | - Kanghyun Kim
- Biomedical Engineering, Duke UniversityDurhamUnited States
| | - Pavan C Konda
- Biomedical Engineering, Duke UniversityDurhamUnited States
| | - Catherine W Seitz
- Department of Neurobiology, Duke School of MedicineDurhamUnited States
| | - Colin Cooke
- Biomedical Engineering, Duke UniversityDurhamUnited States
| | - Shiqi Xu
- Biomedical Engineering, Duke UniversityDurhamUnited States
| | - Whitney S Jacobs
- Department of Neurobiology, Duke School of MedicineDurhamUnited States
| | - Robin Blazing
- Department of Neurobiology, Duke School of MedicineDurhamUnited States
| | - Yang Chen
- Department of Neurobiology, Duke School of MedicineDurhamUnited States
| | | | - Timothy W Dunn
- Biomedical Engineering, Duke UniversityDurhamUnited States
| | | | - Roarke W Horstmeyer
- Ramona Optics IncDurhamUnited States
- Biomedical Engineering, Duke UniversityDurhamUnited States
| | - Eva A Naumann
- Department of Neurobiology, Duke School of MedicineDurhamUnited States
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43
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Computational Analysis of Cardiac Contractile Function. Curr Cardiol Rep 2022; 24:1983-1994. [PMID: 36301405 PMCID: PMC10091868 DOI: 10.1007/s11886-022-01814-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 10/14/2022] [Indexed: 01/11/2023]
Abstract
PURPOSE OF REVIEW Heart failure results in the high incidence and mortality all over the world. Mechanical properties of myocardium are critical determinants of cardiac function, with regional variations in myocardial contractility demonstrated within infarcted ventricles. Quantitative assessment of cardiac contractile function is therefore critical to identify myocardial infarction for the early diagnosis and therapeutic intervention. RECENT FINDINGS Current advancement of cardiac functional assessments is in pace with the development of imaging techniques. The methods tailored to advanced imaging have been widely used in cardiac magnetic resonance, echocardiography, and optical microscopy. In this review, we introduce fundamental concepts and applications of representative methods for each imaging modality used in both fundamental research and clinical investigations. All these methods have been designed or developed to quantify time-dependent 2-dimensional (2D) or 3D cardiac mechanics, holding great potential to unravel global or regional myocardial deformation and contractile function from end-systole to end-diastole. Computational methods to assess cardiac contractile function provide a quantitative insight into the analysis of myocardial mechanics during cardiac development, injury, and remodeling.
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44
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Cho HJ, Lee WS, Jeong J, Lee JS. A review on the impacts of nanomaterials on neuromodulation and neurological dysfunction using a zebrafish animal model. Comp Biochem Physiol C Toxicol Pharmacol 2022; 261:109428. [PMID: 35940544 DOI: 10.1016/j.cbpc.2022.109428] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/04/2022] [Revised: 07/28/2022] [Accepted: 08/03/2022] [Indexed: 11/20/2022]
Abstract
Nanomaterials have been widely employed from industrial to medical fields due to their small sizes and versatile characteristics. However, nanomaterials can also induce unexpected adverse effects on health. In particular, exposure of the nervous system to nanomaterials can cause serious neurological dysfunctions and neurodegenerative diseases. A number of studies have adopted various animal models to evaluate the neurotoxic effects of nanomaterials. Among them, zebrafish has become an attractive animal model for neurotoxicological studies due to several advantages, including the well-characterized nervous system, efficient genome editing, convenient generation of transgenic lines, high-resolution in vivo imaging, and an array of behavioral assays. In this review, we summarize recent studies on the neurotoxicological effects of nanomaterials, particularly engineered nanomaterials and nanoplastics, using zebrafish and discuss key findings with advantages and limitations of the zebrafish model in neurotoxicological studies.
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Affiliation(s)
- Hyun-Ju Cho
- Microbiome Convergence Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), 125 Gwahak-ro, Yuseong-gu, Daejeon 34141, Republic of Korea
| | - Wang Sik Lee
- Environmental Disease Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), 125 Gwahak-ro, Yuseong-gu, Daejeon 34141, Republic of Korea
| | - Jinyoung Jeong
- Environmental Disease Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), 125 Gwahak-ro, Yuseong-gu, Daejeon 34141, Republic of Korea; KRIBB School, University of Science and Technology, Yuseong-gu, Daejeon, 34141, Republic of Korea.
| | - Jeong-Soo Lee
- Microbiome Convergence Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), 125 Gwahak-ro, Yuseong-gu, Daejeon 34141, Republic of Korea; KRIBB School, University of Science and Technology, Yuseong-gu, Daejeon, 34141, Republic of Korea.
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45
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Han K, Hua X, Vasani V, Kim GAR, Liu W, Takayama S, Jia S. 3D super-resolution live-cell imaging with radial symmetry and Fourier light-field microscopy. BIOMEDICAL OPTICS EXPRESS 2022; 13:5574-5584. [PMID: 36733732 PMCID: PMC9872894 DOI: 10.1364/boe.471967] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/02/2022] [Revised: 09/23/2022] [Accepted: 09/26/2022] [Indexed: 06/18/2023]
Abstract
Live-cell imaging reveals the phenotypes and mechanisms of cellular function and their dysfunction that underscore cell physiology, development, and pathology. Here, we report a 3D super-resolution live-cell microscopy method by integrating radiality analysis and Fourier light-field microscopy (rad-FLFM). We demonstrated the method using various live-cell specimens, including actins in Hela cells, microtubules in mammary organoid cells, and peroxisomes in COS-7 cells. Compared with conventional wide-field microscopy, rad-FLFM realizes scanning-free, volumetric 3D live-cell imaging with sub-diffraction-limited resolution of ∼150 nm (x-y) and 300 nm (z), milliseconds volume acquisition time, six-fold extended depth of focus of ∼6 µm, and low photodamage. The method provides a promising avenue to explore spatiotemporal-challenging subcellular processes in a wide range of cell biological research.
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Affiliation(s)
- Keyi Han
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, GA, 30332, USA
| | - Xuanwen Hua
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, GA, 30332, USA
| | - Vishwa Vasani
- George W. Woodruff School of Mechanical Engineering, Georgia Institute of Technology, Atlanta, GA, 30332, USA
| | - Ge-Ah R. Kim
- School of Materials Science and Engineering, Georgia Institute of Technology, Atlanta, GA, 30332, USA
| | - Wenhao Liu
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, GA, 30332, USA
| | - Shuichi Takayama
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, GA, 30332, USA
- Parker H. Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, GA, 30332, USA
| | - Shu Jia
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, GA, 30332, USA
- Parker H. Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, GA, 30332, USA
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46
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Brain milieu induces early microglial maturation through the BAX-Notch axis. Nat Commun 2022; 13:6117. [PMID: 36253375 PMCID: PMC9576735 DOI: 10.1038/s41467-022-33836-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2021] [Accepted: 09/30/2022] [Indexed: 12/24/2022] Open
Abstract
Microglia are derived from primitive myeloid cells and gain their early identity in the embryonic brains. However, the mechanism by which the brain milieu confers microglial maturation signature remains elusive. Here, we demonstrate that the baxcq55 zebrafish and Baxtm1Sjk mouse embryos exhibit similarly defective early microglial maturation. BAX, a typical pro-apoptotic factor, is highly enriched in neuronal cells and regulates microglial maturation through both pro-apoptotic and non-apoptotic mechanisms. BAX regulates dlb via the CaMKII-CREB axis calcium-dependently in living neurons while ensuring the efficient Notch activation in the immigrated pre-microglia by apoptotic neurons. Notch signaling is conserved in supporting embryonic microglia maturation. Compromised microglial development occurred in the Cx3cr1Cre/+Rbpjfl/fl embryonic mice; however, microglia acquire their appropriate signature when incubated with DLL3 in vitro. Thus, our findings elucidate a BAX-CaMKII-CREB-Notch network triggered by the neuronal milieu in microglial development, which may provide innovative insights for targeting microglia in neuronal disorder treatment.
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47
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Wu Y, Wu S, Wang X, Lang C, Zhang Q, Wen Q, Xu T. Rapid detection and recognition of whole brain activity in a freely behaving Caenorhabditis elegans. PLoS Comput Biol 2022; 18:e1010594. [PMID: 36215325 PMCID: PMC9584436 DOI: 10.1371/journal.pcbi.1010594] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2022] [Revised: 10/20/2022] [Accepted: 09/22/2022] [Indexed: 11/07/2022] Open
Abstract
Advanced volumetric imaging methods and genetically encoded activity indicators have permitted a comprehensive characterization of whole brain activity at single neuron resolution in Caenorhabditis elegans. The constant motion and deformation of the nematode nervous system, however, impose a great challenge for consistent identification of densely packed neurons in a behaving animal. Here, we propose a cascade solution for long-term and rapid recognition of head ganglion neurons in a freely moving C. elegans. First, potential neuronal regions from a stack of fluorescence images are detected by a deep learning algorithm. Second, 2-dimensional neuronal regions are fused into 3-dimensional neuron entities. Third, by exploiting the neuronal density distribution surrounding a neuron and relative positional information between neurons, a multi-class artificial neural network transforms engineered neuronal feature vectors into digital neuronal identities. With a small number of training samples, our bottom-up approach is able to process each volume—1024 × 1024 × 18 in voxels—in less than 1 second and achieves an accuracy of 91% in neuronal detection and above 80% in neuronal tracking over a long video recording. Our work represents a step towards rapid and fully automated algorithms for decoding whole brain activity underlying naturalistic behaviors. An important question in neuroscience is to understand the relationship between brain dynamics and naturalistic behaviors when an animal is freely exploring its environment. In the last decade, it has become possible to genetically engineer animals whose neurons produce fluorescence reporters that change their brightness in response to brain activity. In small animals such as the nematode C. elegans, we can now record the fluorescence changes in and thereby infer neural activity from most neurons in the head of a worm, when the animal is freely moving. These neurons are densely packed in a small volume. Since the brain and body are moving and its shape undergoes significant deformation, a human expert, even after long hours of inspection, may still have difficulty to tell where the neurons are and who they are. We sought to develop an automatic method for rapidly detecting and tracking most of these neurons in a moving animal. To do this, we asked a human expert to annotate all head neurons—their locations and digital identities—across a small number of volumes. Then, we trained a computer to learn the locations and digital identities of these neurons across different imaging volumes. Our machine inference method is fast and accurate. While it takes a human expert several hours to complete a sequence of volumes, a machine can finish the task in a few minutes. We hope our method provides a better and more efficient engine for extracting knowledge from whole brain imaging datasets and animal behaviors.
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Affiliation(s)
- Yuxiang Wu
- Chinese Academy of Sciences Key Laboratory of Brain Function and Diseases, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China
- Hefei National Laboratory for Physical Sciences at the Microscale, Center for Integrative Imaging, University of Science and Technology of China, Hefei, China
| | - Shang Wu
- Chinese Academy of Sciences Key Laboratory of Brain Function and Diseases, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China
- Hefei National Laboratory for Physical Sciences at the Microscale, Center for Integrative Imaging, University of Science and Technology of China, Hefei, China
| | - Xin Wang
- John Hopcroft Center for Computer Science, School of electronic information and electrical engineering, Shanghai Jiao Tong University, Shanghai, China
| | - Chengtian Lang
- Department of Electronic Engineering and Information Science, University of Science and Technology of China, Hefei, China
| | - Quanshi Zhang
- John Hopcroft Center for Computer Science, School of electronic information and electrical engineering, Shanghai Jiao Tong University, Shanghai, China
| | - Quan Wen
- Chinese Academy of Sciences Key Laboratory of Brain Function and Diseases, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China
- Hefei National Laboratory for Physical Sciences at the Microscale, Center for Integrative Imaging, University of Science and Technology of China, Hefei, China
- * E-mail: (QW); (TX)
| | - Tianqi Xu
- Chinese Academy of Sciences Key Laboratory of Brain Function and Diseases, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China
- Hefei National Laboratory for Physical Sciences at the Microscale, Center for Integrative Imaging, University of Science and Technology of China, Hefei, China
- * E-mail: (QW); (TX)
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48
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Howe CL, Quicke P, Song P, Verinaz-Jadan H, Dragotti PL, Foust AJ. Comparing synthetic refocusing to deconvolution for the extraction of neuronal calcium transients from light fields. NEUROPHOTONICS 2022; 9:041404. [PMID: 35445141 PMCID: PMC8922050 DOI: 10.1117/1.nph.9.4.041404] [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: 08/03/2021] [Accepted: 02/07/2022] [Indexed: 06/14/2023]
Abstract
Significance: Light-field microscopy (LFM) enables fast, light-efficient, volumetric imaging of neuronal activity with calcium indicators. Calcium transients differ in temporal signal-to-noise ratio (tSNR) and spatial confinement when extracted from volumes reconstructed by different algorithms. Aim: We evaluated the capabilities and limitations of two light-field reconstruction algorithms for calcium fluorescence imaging. Approach: We acquired light-field image series from neurons either bulk-labeled or filled intracellularly with the red-emitting calcium dye CaSiR-1 in acute mouse brain slices. We compared the tSNR and spatial confinement of calcium signals extracted from volumes reconstructed with synthetic refocusing and Richardson-Lucy three-dimensional deconvolution with and without total variation regularization. Results: Both synthetic refocusing and Richardson-Lucy deconvolution resolved calcium signals from single cells and neuronal dendrites in three dimensions. Increasing deconvolution iteration number improved spatial confinement but reduced tSNR compared with synthetic refocusing. Volumetric light-field imaging did not decrease calcium signal tSNR compared with interleaved, widefield image series acquired in matched planes. Conclusions: LFM enables high-volume rate, volumetric imaging of calcium transients in single cell somata (bulk-labeled) and dendrites (intracellularly loaded). The trade-offs identified for tSNR, spatial confinement, and computational cost indicate which of synthetic refocusing or deconvolution can better realize the scientific requirements of future LFM calcium imaging applications.
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Affiliation(s)
- Carmel L. Howe
- Imperial College London, Department of Bioengineering, London, United Kingdom
- Imperial College London, Centre for Neurotechnology, London, United Kingdom
| | - Peter Quicke
- Imperial College London, Department of Bioengineering, London, United Kingdom
- Imperial College London, Centre for Neurotechnology, London, United Kingdom
| | - Pingfan Song
- Imperial College London, Centre for Neurotechnology, London, United Kingdom
- Imperial College London, Department of Electrical and Electronic Engineering, London, United Kingdom
| | - Herman Verinaz-Jadan
- Imperial College London, Centre for Neurotechnology, London, United Kingdom
- Imperial College London, Department of Electrical and Electronic Engineering, London, United Kingdom
| | - Pier Luigi Dragotti
- Imperial College London, Centre for Neurotechnology, London, United Kingdom
- Imperial College London, Department of Electrical and Electronic Engineering, London, United Kingdom
| | - Amanda J. Foust
- Imperial College London, Department of Bioengineering, London, United Kingdom
- Imperial College London, Centre for Neurotechnology, London, United Kingdom
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49
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Zhai J, Shi R, Fan K, Kong L. Background inhibited and speed-loss-free volumetric imaging in vivo based on structured-illumination Fourier light field microscopy. Front Neurosci 2022; 16:1004228. [PMID: 36248666 PMCID: PMC9558295 DOI: 10.3389/fnins.2022.1004228] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2022] [Accepted: 09/14/2022] [Indexed: 11/17/2022] Open
Abstract
Benefiting from its advantages in fast volumetric imaging for recording biodynamics, Fourier light field microscopy (FLFM) has a wide range of applications in biomedical research, especially in neuroscience. However, the imaging quality of the FLFM is always deteriorated by both the out-of-focus background and the strong scattering in biological samples. Here we propose a structured-illumination and interleaved-reconstruction based Fourier light field microscopy (SI-FLFM), in which we can filter out the background fluorescence in FLFM without sacrificing imaging speed. We demonstrate the superiority of our SI-FLFM in high-speed, background-inhibited volumetric imaging of various biodynamics in larval zebrafish and mice in vivo. The signal-to-background ratio (SBR) is improved by tens of times. And the volumetric imaging speed can be up to 40 Hz, avoiding artifacts caused by temporal under-sampling in conventional structured illumination microscopy. These suggest that our SI-FLFM is suitable for applications of weak fluorescence signals but high imaging speed requirements.
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Affiliation(s)
- Jiazhen Zhai
- State Key Laboratory of Precision Measurement Technology and Instruments, Department of Precision Instrument, Tsinghua University, Beijing, China
| | - Ruheng Shi
- State Key Laboratory of Precision Measurement Technology and Instruments, Department of Precision Instrument, Tsinghua University, Beijing, China
| | - Kuikui Fan
- State Key Laboratory of Precision Measurement Technology and Instruments, Department of Precision Instrument, Tsinghua University, Beijing, China
| | - Lingjie Kong
- State Key Laboratory of Precision Measurement Technology and Instruments, Department of Precision Instrument, Tsinghua University, Beijing, China
- IDG/McGovern Institute for Brain Research, Tsinghua University, Beijing, China
- *Correspondence: Lingjie Kong,
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Özsoy Ç, Hotz AL, Rieser NN, Chen Z, Deán-Ben XL, Neuhauss SCF, Razansky D. Volumetric optoacoustic neurobehavioral tracking of epileptic seizures in freely-swimming zebrafish larvae. Front Mol Neurosci 2022; 15:1004518. [PMID: 36176960 PMCID: PMC9514119 DOI: 10.3389/fnmol.2022.1004518] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2022] [Accepted: 08/15/2022] [Indexed: 11/25/2022] Open
Abstract
Fast three-dimensional imaging of freely-swimming zebrafish is essential to understand the link between neuronal activity and behavioral changes during epileptic seizures. Studying the complex spatiotemporal patterns of neuronal activity at the whole-brain or -body level typically requires physical restraint, thus hindering the observation of unperturbed behavior. Here we report on real-time volumetric optoacoustic imaging of aberrant circular swimming activity and calcium transients in freely behaving zebrafish larvae, continuously covering their motion across an entire three-dimensional region. The high spatiotemporal resolution of the technique enables capturing ictal-like epileptic seizure events and quantifying their propagation speed, independently validated with simultaneous widefield fluorescence recordings. The work sets the stage for discerning functional interconnections between zebrafish behavior and neuronal activity for studying fundamental mechanisms of epilepsy and in vivo validation of treatment strategies.
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Affiliation(s)
- Çağla Özsoy
- Faculty of Medicine, Institute of Pharmacology and Toxicology and Institute for Biomedical Engineering, University of Zurich, Zurich, Switzerland
- Department of Information Technology and Electrical Engineering, Institute for Biomedical Engineering, ETH Zurich, Zurich, Switzerland
| | - Adriana L. Hotz
- Department of Molecular Life Sciences, University of Zurich, Zurich, Switzerland
| | - Nicolas N. Rieser
- Department of Molecular Life Sciences, University of Zurich, Zurich, Switzerland
| | - Zhenyue Chen
- Faculty of Medicine, Institute of Pharmacology and Toxicology and Institute for Biomedical Engineering, University of Zurich, Zurich, Switzerland
- Department of Information Technology and Electrical Engineering, Institute for Biomedical Engineering, ETH Zurich, Zurich, Switzerland
| | - Xosé Luís Deán-Ben
- Faculty of Medicine, Institute of Pharmacology and Toxicology and Institute for Biomedical Engineering, University of Zurich, Zurich, Switzerland
- Department of Information Technology and Electrical Engineering, Institute for Biomedical Engineering, ETH Zurich, Zurich, Switzerland
| | | | - Daniel Razansky
- Faculty of Medicine, Institute of Pharmacology and Toxicology and Institute for Biomedical Engineering, University of Zurich, Zurich, Switzerland
- Department of Information Technology and Electrical Engineering, Institute for Biomedical Engineering, ETH Zurich, Zurich, Switzerland
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