1
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Gou L, Wang Y, Gao L, Zhong Y, Xie L, Wang H, Zha X, Shao Y, Xu H, Xu X, Yan J. Gapr for large-scale collaborative single-neuron reconstruction. Nat Methods 2024; 21:1926-1935. [PMID: 38961277 DOI: 10.1038/s41592-024-02345-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Accepted: 06/06/2024] [Indexed: 07/05/2024]
Abstract
Whole-brain analysis of single-neuron morphology is crucial for unraveling the complex structure of the brain. However, large-scale neuron reconstruction from terabyte and even petabyte data of mammalian brains generated by state-of-the-art light microscopy is a daunting task. Here, we developed 'Gapr' (Gapr accelerates projectome reconstruction) that streamlines deep learning-based automatic reconstruction, 'automatic proofreading' that reduces human workloads at high-confidence sites, and high-throughput collaborative proofreading by crowd users through the Internet. Furthermore, Gapr offers a seamless user interface that ensures high proofreading speed per annotator, on-demand conversion for handling large datasets, flexible workflows tailored to diverse datasets and rigorous error tracking for quality control. Finally, we demonstrated Gapr's efficacy by reconstructing over 4,000 neurons in mouse brains, revealing the morphological diversity in cortical interneurons and hypothalamic neurons. Here, we present Gapr as a solution for large-scale single-neuron reconstruction projects.
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Affiliation(s)
- Lingfeng Gou
- Institute of Neuroscience, State Key Laboratory of Neuroscience, CAS Center for Excellence in Brain Science and Intelligence Technology, Chinese Academy of Sciences, Shanghai, China
| | - Yanzhi Wang
- Institute of Neuroscience, State Key Laboratory of Neuroscience, CAS Center for Excellence in Brain Science and Intelligence Technology, Chinese Academy of Sciences, Shanghai, China
- University of Chinese Academy of Sciences, Shanghai, China
| | - Le Gao
- Institute of Neuroscience, State Key Laboratory of Neuroscience, CAS Center for Excellence in Brain Science and Intelligence Technology, Chinese Academy of Sciences, Shanghai, China
| | - Yiting Zhong
- Institute of Neuroscience, State Key Laboratory of Neuroscience, CAS Center for Excellence in Brain Science and Intelligence Technology, Chinese Academy of Sciences, Shanghai, China
- University of Chinese Academy of Sciences, Shanghai, China
| | - Lucheng Xie
- Institute of Neuroscience, State Key Laboratory of Neuroscience, CAS Center for Excellence in Brain Science and Intelligence Technology, Chinese Academy of Sciences, Shanghai, China
| | - Haifang Wang
- Institute of Neuroscience, State Key Laboratory of Neuroscience, CAS Center for Excellence in Brain Science and Intelligence Technology, Chinese Academy of Sciences, Shanghai, China
| | - Xi Zha
- Institute of Neuroscience, State Key Laboratory of Neuroscience, CAS Center for Excellence in Brain Science and Intelligence Technology, Chinese Academy of Sciences, Shanghai, China
| | - Yinqi Shao
- Institute of Neuroscience, State Key Laboratory of Neuroscience, CAS Center for Excellence in Brain Science and Intelligence Technology, Chinese Academy of Sciences, Shanghai, China
| | - Huatai Xu
- Institute of Neuroscience, State Key Laboratory of Neuroscience, CAS Center for Excellence in Brain Science and Intelligence Technology, Chinese Academy of Sciences, Shanghai, China
- Shanghai Center for Brain Science and Brain-Inspired Intelligence Technology, Shanghai, China
| | - Xiaohong Xu
- Institute of Neuroscience, State Key Laboratory of Neuroscience, CAS Center for Excellence in Brain Science and Intelligence Technology, Chinese Academy of Sciences, Shanghai, China
- Shanghai Center for Brain Science and Brain-Inspired Intelligence Technology, Shanghai, China
| | - Jun Yan
- Institute of Neuroscience, State Key Laboratory of Neuroscience, CAS Center for Excellence in Brain Science and Intelligence Technology, Chinese Academy of Sciences, Shanghai, China.
- Shanghai Center for Brain Science and Brain-Inspired Intelligence Technology, Shanghai, China.
- School of Future Technology, University of Chinese Academy of Sciences, Beijing, China.
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2
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Zheng WL, Wu Z, Hummos A, Yang GR, Halassa MM. Rapid context inference in a thalamocortical model using recurrent neural networks. Nat Commun 2024; 15:8275. [PMID: 39333467 PMCID: PMC11436643 DOI: 10.1038/s41467-024-52289-3] [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: 07/14/2023] [Accepted: 08/29/2024] [Indexed: 09/29/2024] Open
Abstract
Cognitive flexibility is a fundamental ability that enables humans and animals to exhibit appropriate behaviors in various contexts. The thalamocortical interactions between the prefrontal cortex (PFC) and the mediodorsal thalamus (MD) have been identified as crucial for inferring temporal context, a critical component of cognitive flexibility. However, the neural mechanism responsible for context inference remains unknown. To address this issue, we propose a PFC-MD neural circuit model that utilizes a Hebbian plasticity rule to support rapid, online context inference. Specifically, the model MD thalamus can infer temporal contexts from prefrontal inputs within a few trials. This is achieved through the use of PFC-to-MD synaptic plasticity with pre-synaptic traces and adaptive thresholding, along with winner-take-all normalization in the MD. Furthermore, our model thalamus gates context-irrelevant neurons in the PFC, thus facilitating continual learning. We evaluate our model performance by having it sequentially learn various cognitive tasks. Incorporating an MD-like component alleviates catastrophic forgetting of previously learned contexts and demonstrates the transfer of knowledge to future contexts. Our work provides insight into how biological properties of thalamocortical circuits can be leveraged to achieve rapid context inference and continual learning.
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Affiliation(s)
- Wei-Long Zheng
- Department of Computer Science and Engineering, Shanghai Jiao Tong University, Shanghai, China.
- Institute of Medical Robotics, Shanghai Jiao Tong University, Shanghai, China.
- Department of Brain and Cognitive Science, Massachusetts Institute of Technology, Cambridge, MA, USA.
| | - Zhongxuan Wu
- Department of Neuroscience, The University of Texas at Austin, Austin, TX, USA
| | - Ali Hummos
- Department of Brain and Cognitive Science, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Guangyu Robert Yang
- Department of Brain and Cognitive Science, Massachusetts Institute of Technology, Cambridge, MA, USA
- Altera.AL, Inc., Menlo Park, CA, USA
| | - Michael M Halassa
- Department of Neuroscience, Tufts University School of Medicine, Boston, MA, USA.
- Department of Psychiatry, Tufts University School of Medicine, Boston, MA, USA.
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3
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Li XH, Shi W, Zhao ZX, Matsuura T, Lu JS, Che J, Chen QY, Zhou Z, Xue M, Hao S, Xu F, Bi GQ, Kaang BK, Collingridge GL, Zhuo M. Increased GluK1 Subunit Receptors in Corticostriatal Projection from the Anterior Cingulate Cortex Contributed to Seizure-Like Activities. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024:e2308444. [PMID: 39225597 DOI: 10.1002/advs.202308444] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/06/2023] [Revised: 07/26/2024] [Indexed: 09/04/2024]
Abstract
The corticostriatal connection plays a crucial role in cognitive, emotional, and motor control. However, the specific roles and synaptic transmissions of corticostriatal connection are less studied, especially the corticostriatal transmission from the anterior cingulate cortex (ACC). Here, a direct glutamatergic excitatory synaptic transmission in the corticostriatal projection from the ACC is found. Kainate receptors (KAR)-mediated synaptic transmission is increased in this corticostriatal connection both in vitro and in vivo seizure-like activities. GluK1 containing KARs and downstream calcium-stimulated adenylyl cyclase subtype 1 (AC1) are involved in the upregulation of KARs following seizure-like activities. Inhibiting the activities of ACC or its corticostriatal connection significantly attenuated pentylenetetrazole (PTZ)-induced seizure. Additionally, injection of GluK1 receptor antagonist UBP310 or the AC1 inhibitor NB001 both show antiepileptic effects. The studies provide direct evidence that KARs are involved in seizure activity in the corticostriatal connection and the KAR-AC1 signaling pathway is a potential novel antiepileptic strategy.
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Affiliation(s)
- Xu-Hui Li
- Center for Neuron and Disease, Frontier Institute of Science and Technology, Xi'an Jiaotong University, Xi'an, Shaanxi, 710049, China
- Department of Physiology, Faculty of Medicine, University of Toronto, Medical Science Building, 1 King's College Circle, Toronto, Ontario, M5S 1A8, Canada
| | - Wantong Shi
- Center for Neuron and Disease, Frontier Institute of Science and Technology, Xi'an Jiaotong University, Xi'an, Shaanxi, 710049, China
| | - Zhi-Xia Zhao
- Center for Neuron and Disease, Frontier Institute of Science and Technology, Xi'an Jiaotong University, Xi'an, Shaanxi, 710049, China
| | - Takanori Matsuura
- Department of Physiology, Faculty of Medicine, University of Toronto, Medical Science Building, 1 King's College Circle, Toronto, Ontario, M5S 1A8, Canada
- Department of Orthopaedics, School of Medicine, University of Occupational and Environmental Health, Yahatanishi-ku, Kitakyushu, 807-8555, Japan
| | - Jing-Shan Lu
- Center for Neuron and Disease, Frontier Institute of Science and Technology, Xi'an Jiaotong University, Xi'an, Shaanxi, 710049, China
| | - Jingmin Che
- Shaanxi Provincial Key Laboratory of Infection and Immune Diseases, Shaanxi Provincial People's Hospital, Xi'an, Shaanxi, 710068, China
| | - Qi-Yu Chen
- CAS Key Laboratory of Brain Connectome and Manipulation, Interdisciplinary Center for Brain Information, The Brain Cognition and Brain Disease Institute, Shenzhen Institute of Advanced Technology, Shenzhen, Guangdong, 518055, China
| | - Zhaoxiang Zhou
- Department of Physiology, Faculty of Medicine, University of Toronto, Medical Science Building, 1 King's College Circle, Toronto, Ontario, M5S 1A8, Canada
- Department of Neurology, First Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong, 510130, China
| | - Man Xue
- Center for Neuron and Disease, Frontier Institute of Science and Technology, Xi'an Jiaotong University, Xi'an, Shaanxi, 710049, China
| | - Shun Hao
- Department of Pharmacology, Qingdao University School of Pharmacy, Qingdao, Shandong, 266071, China
| | - Fang Xu
- CAS Key Laboratory of Brain Connectome and Manipulation, Interdisciplinary Center for Brain Information, The Brain Cognition and Brain Disease Institute, Shenzhen Institute of Advanced Technology, Shenzhen, Guangdong, 518055, China
| | - Guo-Qiang Bi
- CAS Key Laboratory of Brain Connectome and Manipulation, Interdisciplinary Center for Brain Information, The Brain Cognition and Brain Disease Institute, Shenzhen Institute of Advanced Technology, Shenzhen, Guangdong, 518055, China
| | - Bong-Kiun Kaang
- Department of Biological Sciences, College of Natural Sciences, Seoul National University, Seoul, 151-746, South Korea
| | - Graham L Collingridge
- Department of Physiology, Faculty of Medicine, University of Toronto, Medical Science Building, 1 King's College Circle, Toronto, Ontario, M5S 1A8, Canada
| | - Min Zhuo
- Center for Neuron and Disease, Frontier Institute of Science and Technology, Xi'an Jiaotong University, Xi'an, Shaanxi, 710049, China
- Department of Physiology, Faculty of Medicine, University of Toronto, Medical Science Building, 1 King's College Circle, Toronto, Ontario, M5S 1A8, Canada
- Department of Neurology, First Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong, 510130, China
- Department of Pharmacology, Qingdao University School of Pharmacy, Qingdao, Shandong, 266071, China
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4
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Chen G, Lai S, Jiang S, Li F, Sun K, Wu X, Zhou K, Liu Y, Deng X, Chen Z, Xu F, Xu Y, Wang K, Cao G, Xu F, Bi GQ, Zhu Y. Cellular and circuit architecture of the lateral septum for reward processing. Neuron 2024; 112:2783-2798.e9. [PMID: 38959892 DOI: 10.1016/j.neuron.2024.06.004] [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: 12/05/2023] [Revised: 04/29/2024] [Accepted: 06/06/2024] [Indexed: 07/05/2024]
Abstract
The lateral septum (LS) is composed of heterogeneous cell types that are important for various motivated behaviors. However, the transcriptional profiles, spatial arrangement, function, and connectivity of these cell types have not been systematically studied. Using single-nucleus RNA sequencing, we delineated diverse genetically defined cell types in the LS that play distinct roles in reward processing. Notably, we found that estrogen receptor 1 (Esr1)-expressing neurons in the ventral LS (LSEsr1) are key drivers of reward seeking via projections to the ventral tegmental area, and these neurons play an essential role in methamphetamine (METH) reward and METH-seeking behavior. Extended exposure to METH increases the excitability of LSEsr1 neurons by upregulating hyperpolarization-activated cyclic nucleotide-gated (HCN) channels, thereby contributing to METH-induced locomotor sensitization. These insights not only elucidate the intricate molecular, circuit, and functional architecture of the septal region in reward processing but also reveal a neural pathway critical for METH reward and behavioral sensitization.
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Affiliation(s)
- Gaowei Chen
- Shenzhen Key Laboratory of Drug Addiction, The Brain Cognition and Brain Disease Institute, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China; University of Chinese Academy of Sciences, Beijing 100049, China; Shenzhen Neher Neural Plasticity Laboratory, Shenzhen-Hong Kong Institute of Brain Science, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
| | - Shishi Lai
- Yunnan University School of Medicine, Yunnan University, Kunming 650091, China; Southwest United Graduate School, Kunming 650092, China
| | - Shaolei Jiang
- University of Shanghai for Science and Technology, Shanghai 200093, China
| | - Fengling Li
- Shenzhen Key Laboratory of Drug Addiction, The Brain Cognition and Brain Disease Institute, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China; Shenzhen Neher Neural Plasticity Laboratory, Shenzhen-Hong Kong Institute of Brain Science, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
| | - Kaige Sun
- Shenzhen Key Laboratory of Drug Addiction, The Brain Cognition and Brain Disease Institute, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China; Shandong Normal University, Jinan 250014, China
| | - Xiaocong Wu
- Department of Gastrointestinal and Hernia Surgery, First Affiliated Hospital of Kunming Medical University, Kunming 650032, China
| | - Kuikui Zhou
- University of Health and Rehabilitation Sciences, Qingdao 266000, China
| | - Yutong Liu
- Shenzhen Key Laboratory of Drug Addiction, The Brain Cognition and Brain Disease Institute, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China; Shenzhen Neher Neural Plasticity Laboratory, Shenzhen-Hong Kong Institute of Brain Science, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
| | - Xiaofei Deng
- Shenzhen Key Laboratory of Drug Addiction, The Brain Cognition and Brain Disease Institute, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China; Shenzhen Neher Neural Plasticity Laboratory, Shenzhen-Hong Kong Institute of Brain Science, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
| | - Zijun Chen
- Shenzhen Key Laboratory of Drug Addiction, The Brain Cognition and Brain Disease Institute, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China; Shenzhen Neher Neural Plasticity Laboratory, Shenzhen-Hong Kong Institute of Brain Science, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
| | - Fang Xu
- Interdisciplinary Center for Brain Information, the Brain Cognition and Brain Disease Institute, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
| | - Yu Xu
- Yunnan Technological Innovation Centre of Drug Addiction Medicine, Yunnan University, Kunming 650091, China
| | - Kunhua Wang
- Yunnan Technological Innovation Centre of Drug Addiction Medicine, Yunnan University, Kunming 650091, China
| | - Gang Cao
- Faculty of Life and Health Sciences, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
| | - Fuqiang Xu
- Faculty of Life and Health Sciences, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China; CAS Key Laboratory of Brain Connectome and Manipulation, the Brain Cognition and Brain Disease Institute, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
| | - Guo-Qiang Bi
- Interdisciplinary Center for Brain Information, the Brain Cognition and Brain Disease Institute, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
| | - Yingjie Zhu
- Shenzhen Key Laboratory of Drug Addiction, The Brain Cognition and Brain Disease Institute, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China; University of Chinese Academy of Sciences, Beijing 100049, China; Shenzhen Neher Neural Plasticity Laboratory, Shenzhen-Hong Kong Institute of Brain Science, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China; Faculty of Life and Health Sciences, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China; CAS Key Laboratory of Brain Connectome and Manipulation, the Brain Cognition and Brain Disease Institute, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China.
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5
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Wang W, Ruan X, Liu G, Milkie DE, Li W, Betzig E, Upadhyayula S, Gao R. Nanoscale volumetric fluorescence imaging via photochemical sectioning. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.08.01.605857. [PMID: 39149407 PMCID: PMC11326139 DOI: 10.1101/2024.08.01.605857] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 08/17/2024]
Abstract
Optical nanoscopy of intact biological specimens has been transformed by recent advancements in hydrogel-based tissue clearing and expansion, enabling the imaging of cellular and subcellular structures with molecular contrast. However, existing high-resolution fluorescence microscopes have limited imaging depth, which prevents the study of whole-mount specimens without physical sectioning. To address this challenge, we developed "photochemical sectioning," a spatially precise, light-based sample sectioning process. By combining photochemical sectioning with volumetric lattice light-sheet imaging and petabyte-scale computation, we imaged and reconstructed axons and myelination sheaths across entire mouse olfactory bulbs at nanoscale resolution. An olfactory-bulb-wide analysis of myelinated and unmyelinated axons revealed distinctive patterns of axon degeneration and de-/dysmyelination in the neurodegenerative mouse, highlighting the potential for peta- to exabyte-scale super-resolution studies using this approach.
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Affiliation(s)
- Wei Wang
- Department of Chemistry, University of Illinois Chicago; Chicago, IL 60607, USA
| | - Xiongtao Ruan
- Department of Molecular and Cell Biology, University of California, Berkeley; Berkeley, CA 94720, USA
| | - Gaoxiang Liu
- Department of Molecular and Cell Biology, University of California, Berkeley; Berkeley, CA 94720, USA
| | - Daniel E. Milkie
- Howard Hughes Medical Institute, Janelia Research Campus; Ashburn, VA 20417, USA
| | - Wenping Li
- Department of Chemistry, University of Illinois Chicago; Chicago, IL 60607, USA
| | - Eric Betzig
- Department of Molecular and Cell Biology, University of California, Berkeley; Berkeley, CA 94720, USA
- Howard Hughes Medical Institute, Janelia Research Campus; Ashburn, VA 20417, USA
- Department of Physics, Howard Hughes Medical Institute, Helen Wills Neuroscience Institute, University of California, Berkeley; Berkeley, CA 94720, USA
| | - Srigokul Upadhyayula
- Department of Molecular and Cell Biology, University of California, Berkeley; Berkeley, CA 94720, USA
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory; Berkeley, CA 94720, USA
- Chan Zuckerberg Biohub; San Francisco, CA 94158, USA
| | - Ruixuan Gao
- Department of Chemistry, University of Illinois Chicago; Chicago, IL 60607, USA
- Department of Biological Sciences, University of Illinois Chicago; Chicago, IL 60607, USA
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6
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Glaser A, Chandrashekar J, Vasquez S, Arshadi C, Ouellette N, Jiang X, Baka J, Kovacs G, Woodard M, Seshamani S, Cao K, Clack N, Recknagel A, Grim A, Balaram P, Turschak E, Hooper M, Liddell A, Rohde J, Hellevik A, Takasaki K, Erion Barner L, Logsdon M, Chronopoulos C, de Vries S, Ting J, Perlmutter S, Kalmbach B, Dembrow N, Tasic B, Reid RC, Feng D, Svoboda K. Expansion-assisted selective plane illumination microscopy for nanoscale imaging of centimeter-scale tissues. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.06.08.544277. [PMID: 37425699 PMCID: PMC10327101 DOI: 10.1101/2023.06.08.544277] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/11/2023]
Abstract
Recent advances in tissue processing, labeling, and fluorescence microscopy are providing unprecedented views of the structure of cells and tissues at sub-diffraction resolutions and near single molecule sensitivity, driving discoveries in diverse fields of biology, including neuroscience. Biological tissue is organized over scales of nanometers to centimeters. Harnessing molecular imaging across intact, three-dimensional samples on this scale requires new types of microscopes with larger fields of view and working distance, as well as higher throughput. We present a new expansion-assisted selective plane illumination microscope (ExA-SPIM) with aberration-free 1×1×3 μm optical resolution over a large field of view (10.6×8.0 mm 2 ) and working distance (35 mm) at speeds up to 946 megavoxels/sec. Combined with new tissue clearing and expansion methods, the microscope allows imaging centimeter-scale samples with 250×250×750 nm optical resolution (4× expansion), including entire mouse brains, with high contrast and without sectioning. We illustrate ExA-SPIM by reconstructing individual neurons across the mouse brain, imaging cortico-spinal neurons in the macaque motor cortex, and visualizing axons in human white matter.
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7
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Leiwe MN, Fujimoto S, Baba T, Moriyasu D, Saha B, Sakaguchi R, Inagaki S, Imai T. Automated neuronal reconstruction with super-multicolour Tetbow labelling and threshold-based clustering of colour hues. Nat Commun 2024; 15:5279. [PMID: 38918382 PMCID: PMC11199630 DOI: 10.1038/s41467-024-49455-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2022] [Accepted: 06/06/2024] [Indexed: 06/27/2024] Open
Abstract
Fluorescence imaging is widely used for the mesoscopic mapping of neuronal connectivity. However, neurite reconstruction is challenging, especially when neurons are densely labelled. Here, we report a strategy for the fully automated reconstruction of densely labelled neuronal circuits. Firstly, we establish stochastic super-multicolour labelling with up to seven different fluorescent proteins using the Tetbow method. With this method, each neuron is labelled with a unique combination of fluorescent proteins, which are then imaged and separated by linear unmixing. We also establish an automated neurite reconstruction pipeline based on the quantitative analysis of multiple dyes (QDyeFinder), which identifies neurite fragments with similar colour combinations. To classify colour combinations, we develop unsupervised clustering algorithm, dCrawler, in which data points in multi-dimensional space are clustered based on a given threshold distance. Our strategy allows the reconstruction of neurites for up to hundreds of neurons at the millimetre scale without using their physical continuity.
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Affiliation(s)
- Marcus N Leiwe
- Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
- MetaCell LCC, LTD, Cambridge, MA, USA
| | - Satoshi Fujimoto
- Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Toshikazu Baba
- Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Daichi Moriyasu
- Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Biswanath Saha
- Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Richi Sakaguchi
- Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Shigenori Inagaki
- Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
| | - Takeshi Imai
- Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan.
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8
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Park J, Wang J, Guan W, Gjesteby LA, Pollack D, Kamentsky L, Evans NB, Stirman J, Gu X, Zhao C, Marx S, Kim ME, Choi SW, Snyder M, Chavez D, Su-Arcaro C, Tian Y, Park CS, Zhang Q, Yun DH, Moukheiber M, Feng G, Yang XW, Keene CD, Hof PR, Ghosh SS, Frosch MP, Brattain LJ, Chung K. Integrated platform for multiscale molecular imaging and phenotyping of the human brain. Science 2024; 384:eadh9979. [PMID: 38870291 DOI: 10.1126/science.adh9979] [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: 03/28/2023] [Accepted: 04/22/2024] [Indexed: 06/15/2024]
Abstract
Understanding cellular architectures and their connectivity is essential for interrogating system function and dysfunction. However, we lack technologies for mapping the multiscale details of individual cells and their connectivity in the human organ-scale system. We developed a platform that simultaneously extracts spatial, molecular, morphological, and connectivity information of individual cells from the same human brain. The platform includes three core elements: a vibrating microtome for ultraprecision slicing of large-scale tissues without losing cellular connectivity (MEGAtome), a polymer hydrogel-based tissue processing technology for multiplexed multiscale imaging of human organ-scale tissues (mELAST), and a computational pipeline for reconstructing three-dimensional connectivity across multiple brain slabs (UNSLICE). We applied this platform for analyzing human Alzheimer's disease pathology at multiple scales and demonstrating scalable neural connectivity mapping in the human brain.
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Affiliation(s)
- Juhyuk Park
- Institute for Medical Engineering and Science, Massachusetts Institute of Technology (MIT), Cambridge, MA 02139, USA
- Department of Chemical Engineering, MIT, Cambridge, MA 02139, USA
- Picower Institute for Learning and Memory, MIT, Cambridge, MA 02139, USA
- Center for Nanomedicine, Institute for Basic Science, Seoul 03722, Republic of Korea
| | - Ji Wang
- Institute for Medical Engineering and Science, Massachusetts Institute of Technology (MIT), Cambridge, MA 02139, USA
- Picower Institute for Learning and Memory, MIT, Cambridge, MA 02139, USA
| | - Webster Guan
- Department of Chemical Engineering, MIT, Cambridge, MA 02139, USA
| | | | | | - Lee Kamentsky
- Institute for Medical Engineering and Science, Massachusetts Institute of Technology (MIT), Cambridge, MA 02139, USA
- Picower Institute for Learning and Memory, MIT, Cambridge, MA 02139, USA
| | - Nicholas B Evans
- Institute for Medical Engineering and Science, Massachusetts Institute of Technology (MIT), Cambridge, MA 02139, USA
- Picower Institute for Learning and Memory, MIT, Cambridge, MA 02139, USA
| | - Jeff Stirman
- LifeCanvas Technologies, Cambridge, MA 02141, USA
| | - Xinyi Gu
- Department of Electrical Engineering and Computer Science, MIT, Cambridge, MA 02139, USA
| | - Chuanxi Zhao
- Picower Institute for Learning and Memory, MIT, Cambridge, MA 02139, USA
| | - Slayton Marx
- Picower Institute for Learning and Memory, MIT, Cambridge, MA 02139, USA
| | - Minyoung E Kim
- Department of Brain and Cognitive Sciences, MIT, Cambridge, MA 02139, USA
| | - Seo Woo Choi
- Department of Chemical Engineering, MIT, Cambridge, MA 02139, USA
| | | | - David Chavez
- MIT Lincoln Laboratory, Lexington, MA 02421, USA
| | - Clover Su-Arcaro
- Picower Institute for Learning and Memory, MIT, Cambridge, MA 02139, USA
| | - Yuxuan Tian
- Department of Chemical Engineering, MIT, Cambridge, MA 02139, USA
| | - Chang Sin Park
- Department of Psychiatry and Biobehavioral Sciences, David Geffen School of Medicine at UCLA, Los Angeles, CA 90095, USA
- Center for Neurobehavioral Genetics, Jane and Terry Semel Institute for Neuroscience, University of California, Los Angeles, CA 90024, USA
| | - Qiangge Zhang
- McGovern Institute for Brain Research, MIT, Cambridge, MA 02139, USA
| | - Dae Hee Yun
- Department of Brain and Cognitive Sciences, MIT, Cambridge, MA 02139, USA
| | - Mira Moukheiber
- Picower Institute for Learning and Memory, MIT, Cambridge, MA 02139, USA
| | - Guoping Feng
- Department of Brain and Cognitive Sciences, MIT, Cambridge, MA 02139, USA
- McGovern Institute for Brain Research, MIT, Cambridge, MA 02139, USA
| | - X William Yang
- Department of Psychiatry and Biobehavioral Sciences, David Geffen School of Medicine at UCLA, Los Angeles, CA 90095, USA
- Center for Neurobehavioral Genetics, Jane and Terry Semel Institute for Neuroscience, University of California, Los Angeles, CA 90024, USA
| | - C Dirk Keene
- Department of Laboratory Medicine and Pathology, University of Washington School of Medicine, Seattle, WA 98115, USA
| | - Patrick R Hof
- Nash Family Department of Neuroscience, Center for Discovery and Innovation, and Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10019, USA
| | - Satrajit S Ghosh
- Department of Brain and Cognitive Sciences, MIT, Cambridge, MA 02139, USA
- McGovern Institute for Brain Research, MIT, Cambridge, MA 02139, USA
- Department of Otolaryngology, Harvard Medical School, Boston, MA 02114, USA
| | - Matthew P Frosch
- C. S. Kubik Laboratory for Neuropathology, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA
| | | | - Kwanghun Chung
- Institute for Medical Engineering and Science, Massachusetts Institute of Technology (MIT), Cambridge, MA 02139, USA
- Department of Chemical Engineering, MIT, Cambridge, MA 02139, USA
- Picower Institute for Learning and Memory, MIT, Cambridge, MA 02139, USA
- Department of Brain and Cognitive Sciences, MIT, Cambridge, MA 02139, USA
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9
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Torres R, Takasaki K, Gliko O, Laughland C, Yu WQ, Turschak E, Hellevik A, Balaram P, Perlman E, Sümbül U, Reid RC. A scalable and modular computational pipeline for axonal connectomics: automated tracing and assembly of axons across serial sections. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.11.598365. [PMID: 38915568 PMCID: PMC11195148 DOI: 10.1101/2024.06.11.598365] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/26/2024]
Abstract
Progress in histological methods and in microscope technology has enabled dense staining and imaging of axons over large brain volumes, but tracing axons over such volumes requires new computational tools for 3D reconstruction of data acquired from serial sections. We have developed a computational pipeline for automated tracing and volume assembly of densely stained axons imaged over serial sections, which leverages machine learning-based segmentation to enable stitching and alignment with the axon traces themselves. We validated this segmentation-driven approach to volume assembly and alignment of individual axons over centimeter-scale serial sections and show the application of the output traces for analysis of local orientation and for proofreading over aligned volumes. The pipeline is scalable, and combined with recent advances in experimental approaches, should enable new studies of mesoscale connectivity and function over the whole human brain.
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10
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Choi YK, Feng L, Jeong WK, Kim J. Connecto-informatics at the mesoscale: current advances in image processing and analysis for mapping the brain connectivity. Brain Inform 2024; 11:15. [PMID: 38833195 DOI: 10.1186/s40708-024-00228-9] [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: 03/29/2024] [Accepted: 05/08/2024] [Indexed: 06/06/2024] Open
Abstract
Mapping neural connections within the brain has been a fundamental goal in neuroscience to understand better its functions and changes that follow aging and diseases. Developments in imaging technology, such as microscopy and labeling tools, have allowed researchers to visualize this connectivity through high-resolution brain-wide imaging. With this, image processing and analysis have become more crucial. However, despite the wealth of neural images generated, access to an integrated image processing and analysis pipeline to process these data is challenging due to scattered information on available tools and methods. To map the neural connections, registration to atlases and feature extraction through segmentation and signal detection are necessary. In this review, our goal is to provide an updated overview of recent advances in these image-processing methods, with a particular focus on fluorescent images of the mouse brain. Our goal is to outline a pathway toward an integrated image-processing pipeline tailored for connecto-informatics. An integrated workflow of these image processing will facilitate researchers' approach to mapping brain connectivity to better understand complex brain networks and their underlying brain functions. By highlighting the image-processing tools available for fluroscent imaging of the mouse brain, this review will contribute to a deeper grasp of connecto-informatics, paving the way for better comprehension of brain connectivity and its implications.
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Affiliation(s)
- Yoon Kyoung Choi
- Brain Science Institute, Korea Institute of Science and Technology (KIST), Seoul, South Korea
- Department of Computer Science and Engineering, Korea University, Seoul, South Korea
| | | | - Won-Ki Jeong
- Department of Computer Science and Engineering, Korea University, Seoul, South Korea
| | - Jinhyun Kim
- Brain Science Institute, Korea Institute of Science and Technology (KIST), Seoul, South Korea.
- Department of Computer Science and Engineering, Korea University, Seoul, South Korea.
- KIST-SKKU Brain Research Center, SKKU Institute for Convergence, Sungkyunkwan University, Suwon, South Korea.
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11
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Liu Z, Li A, Gong H, Yang X, Luo Q, Feng Z, Li X. The cytoarchitectonic landscape revealed by deep learning method facilitated precise positioning in mouse neocortex. Cereb Cortex 2024; 34:bhae229. [PMID: 38836835 DOI: 10.1093/cercor/bhae229] [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: 03/19/2024] [Revised: 05/13/2024] [Accepted: 05/23/2024] [Indexed: 06/06/2024] Open
Abstract
Neocortex is a complex structure with different cortical sublayers and regions. However, the precise positioning of cortical regions can be challenging due to the absence of distinct landmarks without special preparation. To address this challenge, we developed a cytoarchitectonic landmark identification pipeline. The fluorescence micro-optical sectioning tomography method was employed to image the whole mouse brain stained by general fluorescent nucleotide dye. A fast 3D convolution network was subsequently utilized to segment neuronal somas in entire neocortex. By approach, the cortical cytoarchitectonic profile and the neuronal morphology were analyzed in 3D, eliminating the influence of section angle. And the distribution maps were generated that visualized the number of neurons across diverse morphological types, revealing the cytoarchitectonic landscape which characterizes the landmarks of cortical regions, especially the typical signal pattern of barrel cortex. Furthermore, the cortical regions of various ages were aligned using the generated cytoarchitectonic landmarks suggesting the structural changes of barrel cortex during the aging process. Moreover, we observed the spatiotemporally gradient distributions of spindly neurons, concentrated in the deep layer of primary visual area, with their proportion decreased over time. These findings could improve structural understanding of neocortex, paving the way for further exploration with this method.
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Affiliation(s)
- Zhixiang Liu
- Britton Chance Center for Biomedical Photonics, Wuhan National Laboratory for Optoelectronics, MoE Key Laboratory for Biomedical Photonics, Huazhong University of Science and Technology, No. 1037 Luoyu Road, Wuhan 430070, China
| | - Anan Li
- Britton Chance Center for Biomedical Photonics, Wuhan National Laboratory for Optoelectronics, MoE Key Laboratory for Biomedical Photonics, Huazhong University of Science and Technology, No. 1037 Luoyu Road, Wuhan 430070, China
- Key Laboratory of Biomedical Engineering of Hainan Province, School of Biomedical Engineering, Hainan University, No. 58 Renmin Road, Haikou 570228, China
- HUST-Suzhou Institute for Brainsmatics, Jiangsu Industrial Technology Research Institute, No. 388 Ruoshui Road, Suzhou 215000, China
| | - Hui Gong
- Britton Chance Center for Biomedical Photonics, Wuhan National Laboratory for Optoelectronics, MoE Key Laboratory for Biomedical Photonics, Huazhong University of Science and Technology, No. 1037 Luoyu Road, Wuhan 430070, China
- HUST-Suzhou Institute for Brainsmatics, Jiangsu Industrial Technology Research Institute, No. 388 Ruoshui Road, Suzhou 215000, China
| | - Xiaoquan Yang
- Key Laboratory of Biomedical Engineering of Hainan Province, School of Biomedical Engineering, Hainan University, No. 58 Renmin Road, Haikou 570228, China
- HUST-Suzhou Institute for Brainsmatics, Jiangsu Industrial Technology Research Institute, No. 388 Ruoshui Road, Suzhou 215000, China
| | - Qingming Luo
- Key Laboratory of Biomedical Engineering of Hainan Province, School of Biomedical Engineering, Hainan University, No. 58 Renmin Road, Haikou 570228, China
| | - Zhao Feng
- Key Laboratory of Biomedical Engineering of Hainan Province, School of Biomedical Engineering, Hainan University, No. 58 Renmin Road, Haikou 570228, China
- HUST-Suzhou Institute for Brainsmatics, Jiangsu Industrial Technology Research Institute, No. 388 Ruoshui Road, Suzhou 215000, China
| | - Xiangning Li
- Key Laboratory of Biomedical Engineering of Hainan Province, School of Biomedical Engineering, Hainan University, No. 58 Renmin Road, Haikou 570228, China
- HUST-Suzhou Institute for Brainsmatics, Jiangsu Industrial Technology Research Institute, No. 388 Ruoshui Road, Suzhou 215000, China
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12
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Liu Z, Feng Z, Liu G, Li A, Gong H, Yang X, Li X. A complementary approach for neocortical cytoarchitecture inspection with cellular resolution imaging at whole brain scale. Front Neuroanat 2024; 18:1388084. [PMID: 38846539 PMCID: PMC11153794 DOI: 10.3389/fnana.2024.1388084] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2024] [Accepted: 04/26/2024] [Indexed: 06/09/2024] Open
Abstract
Cytoarchitecture, the organization of cells within organs and tissues, serves as a crucial anatomical foundation for the delineation of various regions. It enables the segmentation of the cortex into distinct areas with unique structural and functional characteristics. While traditional 2D atlases have focused on cytoarchitectonic mapping of cortical regions through individual sections, the intricate cortical gyri and sulci demands a 3D perspective for unambiguous interpretation. In this study, we employed fluorescent micro-optical sectioning tomography to acquire architectural datasets of the entire macaque brain at a resolution of 0.65 μm × 0.65 μm × 3 μm. With these volumetric data, the cortical laminar textures were remarkably presented in appropriate view planes. Additionally, we established a stereo coordinate system to represent the cytoarchitectonic information as surface-based tomograms. Utilizing these cytoarchitectonic features, we were able to three-dimensionally parcel the macaque cortex into multiple regions exhibiting contrasting architectural patterns. The whole-brain analysis was also conducted on mice that clearly revealed the presence of barrel cortex and reflected biological reasonability of this method. Leveraging these high-resolution continuous datasets, our method offers a robust tool for exploring the organizational logic and pathological mechanisms of the brain's 3D anatomical structure.
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Affiliation(s)
- Zhixiang Liu
- Britton Chance Center for Biomedical Photonics, Wuhan National Laboratory for Optoelectronics, MoE Key Laboratory for Biomedical Photonics, Huazhong University of Science and Technology, Wuhan, China
| | - Zhao Feng
- Key Laboratory of Biomedical Engineering of Hainan Province, School of Biomedical Engineering, Hainan University, Haikou, China
- Research Unit of Multimodal Cross Scale Neural Signal Detection and Imaging, Chinese Academy of Medical Sciences, HUST-Suzhou Institute for Brainsmatics, JITRI, Suzhou, China
| | - Guangcai Liu
- Britton Chance Center for Biomedical Photonics, Wuhan National Laboratory for Optoelectronics, MoE Key Laboratory for Biomedical Photonics, Huazhong University of Science and Technology, Wuhan, China
| | - Anan Li
- Britton Chance Center for Biomedical Photonics, Wuhan National Laboratory for Optoelectronics, MoE Key Laboratory for Biomedical Photonics, Huazhong University of Science and Technology, Wuhan, China
- Research Unit of Multimodal Cross Scale Neural Signal Detection and Imaging, Chinese Academy of Medical Sciences, HUST-Suzhou Institute for Brainsmatics, JITRI, Suzhou, China
| | - Hui Gong
- Britton Chance Center for Biomedical Photonics, Wuhan National Laboratory for Optoelectronics, MoE Key Laboratory for Biomedical Photonics, Huazhong University of Science and Technology, Wuhan, China
- Research Unit of Multimodal Cross Scale Neural Signal Detection and Imaging, Chinese Academy of Medical Sciences, HUST-Suzhou Institute for Brainsmatics, JITRI, Suzhou, China
| | - Xiaoquan Yang
- Britton Chance Center for Biomedical Photonics, Wuhan National Laboratory for Optoelectronics, MoE Key Laboratory for Biomedical Photonics, Huazhong University of Science and Technology, Wuhan, China
- Research Unit of Multimodal Cross Scale Neural Signal Detection and Imaging, Chinese Academy of Medical Sciences, HUST-Suzhou Institute for Brainsmatics, JITRI, Suzhou, China
| | - Xiangning Li
- Key Laboratory of Biomedical Engineering of Hainan Province, School of Biomedical Engineering, Hainan University, Haikou, China
- Research Unit of Multimodal Cross Scale Neural Signal Detection and Imaging, Chinese Academy of Medical Sciences, HUST-Suzhou Institute for Brainsmatics, JITRI, Suzhou, China
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13
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Deng Y, Zhu J, Liu X, Dai J, Yu T, Zhu D. A robust vessel-labeling pipeline with high tissue clearing compatibility for 3D mapping of vascular networks. iScience 2024; 27:109730. [PMID: 38706842 PMCID: PMC11068851 DOI: 10.1016/j.isci.2024.109730] [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: 11/15/2023] [Revised: 02/23/2024] [Accepted: 04/09/2024] [Indexed: 05/07/2024] Open
Abstract
The combination of vessel-labeling, tissue-clearing, and light-sheet imaging techniques provides a potent tool for accurately mapping vascular networks, enabling the assessment of vascular remodeling in vascular-related disorders. However, most vascular labeling methods face challenges such as inadequate labeling efficiency or poor compatibility with current tissue clearing technology, which significantly undermines the image quality. To address this limitation, we introduce a vessel-labeling pipeline, termed Ultralabel, which relies on a specially designed dye hydrogel containing lysine-fixable dextran and gelatins for double enhancement. Ultralabel demonstrates not only excellent vessel-labeling capability but also strong compatibility with all tissue clearing methods tested, which outperforms other vessel-labeling methods. Consequently, Ultralabel enables fine mapping of vascular networks in diverse organs, as well as multi-color labeling alongside other labeling techniques. Ultralabel should provide a robust and user-friendly method for obtaining 3D vascular networks in different biomedical applications.
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Affiliation(s)
- Yating Deng
- 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 430074, Hubei, China
| | - Jingtan Zhu
- 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 430074, Hubei, China
| | - Xiaomei Liu
- 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 430074, Hubei, China
| | - Junyao Dai
- 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 430074, Hubei, China
| | - Tingting Yu
- 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 430074, Hubei, China
| | - Dan Zhu
- 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 430074, Hubei, China
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14
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Zheng W, Mu H, Chen Z, Liu J, Xia D, Cheng Y, Jing Q, Lau PM, Tang J, Bi GQ, Wu F, Wang H. NEATmap: a high-efficiency deep learning approach for whole mouse brain neuronal activity trace mapping. Natl Sci Rev 2024; 11:nwae109. [PMID: 38831937 PMCID: PMC11145917 DOI: 10.1093/nsr/nwae109] [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: 09/13/2023] [Revised: 01/26/2024] [Accepted: 02/25/2024] [Indexed: 06/05/2024] Open
Abstract
Quantitative analysis of activated neurons in mouse brains by a specific stimulation is usually a primary step to locate the responsive neurons throughout the brain. However, it is challenging to comprehensively and consistently analyze the neuronal activity trace in whole brains of a large cohort of mice from many terabytes of volumetric imaging data. Here, we introduce NEATmap, a deep learning-based high-efficiency, high-precision and user-friendly software for whole-brain neuronal activity trace mapping by automated segmentation and quantitative analysis of immunofluorescence labeled c-Fos+ neurons. We applied NEATmap to study the brain-wide differentiated neuronal activation in response to physical and psychological stressors in cohorts of mice.
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Affiliation(s)
- Weijie Zheng
- AHU-IAI AI Joint Laboratory, Anhui University, Hefei 230039, China
- Anhui Province Key Laboratory of Biomedical Imaging and Intelligent Processing, Institute of Artificial Intelligence, Hefei Comprehensive National Science Center, Hefei 230088, China
- National Engineering Laboratory for Brain-inspired Intelligence Technology and Application, School of Information Science and Technology, University of Science and Technology of China, Hefei 230026, China
| | - Huawei Mu
- Anhui Province Key Laboratory of Biomedical Imaging and Intelligent Processing, Institute of Artificial Intelligence, Hefei Comprehensive National Science Center, Hefei 230088, China
- Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230026, China
| | - Zhiyi Chen
- Anhui Province Key Laboratory of Biomedical Imaging and Intelligent Processing, Institute of Artificial Intelligence, Hefei Comprehensive National Science Center, Hefei 230088, China
- National Engineering Laboratory for Brain-inspired Intelligence Technology and Application, School of Information Science and Technology, University of Science and Technology of China, Hefei 230026, China
| | - Jiajun Liu
- Anhui Province Key Laboratory of Biomedical Imaging and Intelligent Processing, Institute of Artificial Intelligence, Hefei Comprehensive National Science Center, Hefei 230088, China
- National Engineering Laboratory for Brain-inspired Intelligence Technology and Application, School of Information Science and Technology, University of Science and Technology of China, Hefei 230026, China
| | - Debin Xia
- Anhui Province Key Laboratory of Biomedical Imaging and Intelligent Processing, Institute of Artificial Intelligence, Hefei Comprehensive National Science Center, Hefei 230088, China
- National Engineering Laboratory for Brain-inspired Intelligence Technology and Application, School of Information Science and Technology, University of Science and Technology of China, Hefei 230026, China
| | - Yuxiao Cheng
- Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230026, China
| | - Qi Jing
- Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230026, China
| | - Pak-Ming Lau
- Anhui Province Key Laboratory of Biomedical Imaging and Intelligent Processing, Institute of Artificial Intelligence, Hefei Comprehensive National Science Center, Hefei 230088, China
- Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230026, China
- Interdisciplinary Center for Brain Information, Brain Cognition and Brain Disease Institute, Shenzhen-Hong Kong Institute of Brain Science-Shenzhen Fundamental Research Institutions, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
| | - Jin Tang
- AHU-IAI AI Joint Laboratory, Anhui University, Hefei 230039, China
- Anhui Province Key Laboratory of Biomedical Imaging and Intelligent Processing, Institute of Artificial Intelligence, Hefei Comprehensive National Science Center, Hefei 230088, China
| | - Guo-Qiang Bi
- Anhui Province Key Laboratory of Biomedical Imaging and Intelligent Processing, Institute of Artificial Intelligence, Hefei Comprehensive National Science Center, Hefei 230088, China
- Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230026, China
- Interdisciplinary Center for Brain Information, Brain Cognition and Brain Disease Institute, Shenzhen-Hong Kong Institute of Brain Science-Shenzhen Fundamental Research Institutions, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
| | - Feng Wu
- Anhui Province Key Laboratory of Biomedical Imaging and Intelligent Processing, Institute of Artificial Intelligence, Hefei Comprehensive National Science Center, Hefei 230088, China
- National Engineering Laboratory for Brain-inspired Intelligence Technology and Application, School of Information Science and Technology, University of Science and Technology of China, Hefei 230026, China
| | - Hao Wang
- Anhui Province Key Laboratory of Biomedical Imaging and Intelligent Processing, Institute of Artificial Intelligence, Hefei Comprehensive National Science Center, Hefei 230088, China
- National Engineering Laboratory for Brain-inspired Intelligence Technology and Application, School of Information Science and Technology, University of Science and Technology of China, Hefei 230026, China
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15
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Fei Y, Wu Q, Zhao S, Song K, Han J, Liu C. Diverse and asymmetric patterns of single-neuron projectome in regulating interhemispheric connectivity. Nat Commun 2024; 15:3403. [PMID: 38649683 PMCID: PMC11035633 DOI: 10.1038/s41467-024-47762-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2023] [Accepted: 04/11/2024] [Indexed: 04/25/2024] Open
Abstract
The corpus callosum, historically considered primarily for homotopic connections, supports many heterotopic connections, indicating complex interhemispheric connectivity. Understanding this complexity is crucial yet challenging due to diverse cell-specific wiring patterns. Here, we utilized public AAV bulk tracing and single-neuron tracing data to delineate the anatomical connection patterns of mouse brains and conducted wide-field calcium imaging to assess functional connectivity across various brain states in male mice. The single-neuron data uncovered complex and dense interconnected patterns, particularly for interhemispheric-heterotopic connections. We proposed a metric "heterogeneity" to quantify the complexity of the connection patterns. Computational modeling of these patterns suggested that the heterogeneity of upstream projections impacted downstream homotopic functional connectivity. Furthermore, higher heterogeneity observed in interhemispheric-heterotopic projections would cause lower strength but higher stability in functional connectivity than their intrahemispheric counterparts. These findings were corroborated by our wide-field functional imaging data, underscoring the important role of heterotopic-projection heterogeneity in interhemispheric communication.
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Affiliation(s)
- Yao Fei
- School of Automation, Northwestern Polytechnical University, Xi'an, China
- CAS Center for Excellence in Brain Science and Intelligence Technology, Institute of Neuroscience, Chinese Academy of Sciences, Shanghai, 200031, China
| | - Qihang Wu
- CAS Center for Excellence in Brain Science and Intelligence Technology, Institute of Neuroscience, Chinese Academy of Sciences, Shanghai, 200031, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Shijie Zhao
- School of Automation, Northwestern Polytechnical University, Xi'an, China.
- Research & Development, Institute of Northwestern Polytechnical University in Shenzhen, Shenzhen, China.
| | - Kun Song
- CAS Center for Excellence in Brain Science and Intelligence Technology, Institute of Neuroscience, Chinese Academy of Sciences, Shanghai, 200031, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Junwei Han
- School of Automation, Northwestern Polytechnical University, Xi'an, China.
- Research & Development, Institute of Northwestern Polytechnical University in Shenzhen, Shenzhen, China.
| | - Cirong Liu
- CAS Center for Excellence in Brain Science and Intelligence Technology, Institute of Neuroscience, Chinese Academy of Sciences, Shanghai, 200031, China.
- University of Chinese Academy of Sciences, Beijing, 100049, China.
- Key Laboratory of Genetic Evolution & Animal Models, Chinese Academy of Sciences, Shanghai, China.
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16
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Qi H, Duan S, Xu Y, Zhang H. Frontiers and future perspectives of neuroimmunology. FUNDAMENTAL RESEARCH 2024; 4:206-217. [PMID: 38933499 PMCID: PMC11197808 DOI: 10.1016/j.fmre.2022.10.002] [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: 08/13/2022] [Revised: 08/16/2022] [Accepted: 10/11/2022] [Indexed: 11/06/2022] Open
Abstract
Neuroimmunology is an interdisciplinary branch of biomedical science that emerges from the intersection of studies on the nervous system and the immune system. The complex interplay between the two systems has long been recognized. Research efforts directed at the underlying functional interface and associated pathophysiology, however, have garnered attention only in recent decades. In this narrative review, we highlight significant advances in research on neuroimmune interplay and modulation. A particular focus is on early- and middle-career neuroimmunologists in China and their achievements in frontier areas of "neuroimmune interface", "neuro-endocrine-immune network and modulation", "neuroimmune interactions in diseases", "meningeal lymphatic and glymphatic systems in health and disease", and "tools and methodologies in neuroimmunology research". Key scientific questions and future directions for potential breakthroughs in neuroimmunology research are proposed.
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Affiliation(s)
- Hai Qi
- School of Medicine, Tsinghua University, Beijing 100084, China
| | - Shumin Duan
- Faculty of Medicine and Pharmaceutical Sciences, Zhejiang University, Hangzhou 310014, China
| | - Yanying Xu
- Department of Life Sciences, National Natural Science Foundation of China, Beijing 100085, China
| | - Hongliang Zhang
- Department of Life Sciences, National Natural Science Foundation of China, Beijing 100085, China
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17
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Yi Y, Li Y, Zhang S, Men Y, Wang Y, Jing D, Ding J, Zhu Q, Chen Z, Chen X, Li JL, Wang Y, Wang J, Peng H, Zhang L, Luo W, Feng JQ, He Y, Ge WP, Zhao H. Mapping of individual sensory nerve axons from digits to spinal cord with the transparent embedding solvent system. Cell Res 2024; 34:124-139. [PMID: 38168640 PMCID: PMC10837210 DOI: 10.1038/s41422-023-00867-3] [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: 02/22/2023] [Accepted: 08/07/2023] [Indexed: 01/05/2024] Open
Abstract
Achieving uniform optical resolution for a large tissue sample is a major challenge for deep imaging. For conventional tissue clearing methods, loss of resolution and quality in deep regions is inevitable due to limited transparency. Here we describe the Transparent Embedding Solvent System (TESOS) method, which combines tissue clearing, transparent embedding, sectioning and block-face imaging. We used TESOS to acquire volumetric images of uniform resolution for an adult mouse whole-body sample. The TESOS method is highly versatile and can be combined with different microscopy systems to achieve uniformly high resolution. With a light sheet microscope, we imaged the whole body of an adult mouse, including skin, at a uniform 0.8 × 0.8 × 3.5 μm3 voxel resolution within 120 h. With a confocal microscope and a 40×/1.3 numerical aperture objective, we achieved a uniform sub-micron resolution in the whole sample to reveal a complete projection of individual nerve axons within the central or peripheral nervous system. Furthermore, TESOS allowed the first mesoscale connectome mapping of individual sensory neuron axons spanning 5 cm from adult mouse digits to the spinal cord at a uniform sub-micron resolution.
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Affiliation(s)
- Yating Yi
- State Key Laboratory of Oral Diseases, National Center for Stomatology, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, Sichuan, China
- Department of Orthodontics, West China Hospital of Stomatology, Sichuan University, Chengdu, Sichuan, China
- Chinese Institute for Brain Research, Beijing, China
| | - Youqi Li
- Chinese Institute for Brain Research, Beijing, China
- Department of Neurology, Beijing Tiantan Hospital, Capital Medical University, Beijing, China
- School of Basic Medical Sciences, Capital Medical University, Beijing, China
| | - Shiwen Zhang
- State Key Laboratory of Oral Diseases, National Center for Stomatology, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, Sichuan, China
- Department of Oral Implantology, West China Hospital of Stomatology, Sichuan University, Chengdu, Sichuan, China
| | - Yi Men
- State Key Laboratory of Oral Diseases, National Center for Stomatology, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, Sichuan, China
- Department of Head and Neck Oncology, West China Hospital of Stomatology, Sichuan University, Chengdu, Sichuan, China
| | - Yuhong Wang
- West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Dian Jing
- Department of Orthodontics, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine; College of Stomatology, Shanghai Jiao Tong University; National Center for Stomatology; National Clinical Research Center for Oral Diseases; Shanghai Key Laboratory of Stomatology; Shanghai Research Institute of Stomatology, Shanghai, China
| | - Jiayi Ding
- Chinese Institute for Brain Research, Beijing, China
- Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, China
| | - Qingjie Zhu
- Chinese Institute for Brain Research, Beijing, China
| | - Zexi Chen
- Chinese Institute for Brain Research, Beijing, China
| | - Xingjun Chen
- Chinese Institute for Brain Research, Beijing, China
- Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, China
| | - Jun-Liszt Li
- Chinese Institute for Brain Research, Beijing, China
- Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, China
| | - Yilong Wang
- Chinese Institute for Brain Research, Beijing, China
- Department of Neurology, Beijing Tiantan Hospital, Capital Medical University, Beijing, China
| | - Jun Wang
- State Key Laboratory of Oral Diseases, National Center for Stomatology, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, Sichuan, China
- Department of Orthodontics, West China Hospital of Stomatology, Sichuan University, Chengdu, Sichuan, China
| | - Hanchuan Peng
- SEU-ALLEN Joint Center, Institute for Brain and Intelligence, Southeast University, Nanjing, Jiangsu, China
| | - Li Zhang
- Chinese Institute for Brain Research, Beijing, China
| | | | - Jian Q Feng
- Texas A&M University, College of Dentistry, Dallas, TX, USA
| | - Yongwen He
- Qujing Medical College, Qujing, Yunnan, China.
| | - Woo-Ping Ge
- Chinese Institute for Brain Research, Beijing, China.
| | - Hu Zhao
- Chinese Institute for Brain Research, Beijing, China.
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18
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Xue F, Li F, Zhang KM, Ding L, Wang Y, Zhao X, Xu F, Zhang D, Sun M, Lau PM, Zhu Q, Zhou P, Bi GQ. Multi-region calcium imaging in freely behaving mice with ultra-compact head-mounted fluorescence microscopes. Natl Sci Rev 2024; 11:nwad294. [PMID: 38288367 PMCID: PMC10824555 DOI: 10.1093/nsr/nwad294] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2023] [Revised: 09/26/2023] [Accepted: 11/23/2023] [Indexed: 01/31/2024] Open
Abstract
To investigate the circuit-level neural mechanisms of behavior, simultaneous imaging of neuronal activity in multiple cortical and subcortical regions is highly desired. Miniature head-mounted microscopes offer the capability of calcium imaging in freely behaving animals. However, implanting multiple microscopes on a mouse brain remains challenging due to space constraints and the cumbersome weight of the equipment. Here, we present TINIscope, a Tightly Integrated Neuronal Imaging microscope optimized for electronic and opto-mechanical design. With its compact and lightweight design of 0.43 g, TINIscope enables unprecedented simultaneous imaging of behavior-relevant activity in up to four brain regions in mice. Proof-of-concept experiments with TINIscope recorded over 1000 neurons in four hippocampal subregions and revealed concurrent activity patterns spanning across these regions. Moreover, we explored potential multi-modal experimental designs by integrating additional modules for optogenetics, electrical stimulation or local field potential recordings. Overall, TINIscope represents a timely and indispensable tool for studying the brain-wide interregional coordination that underlies unrestrained behaviors.
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Affiliation(s)
- Feng Xue
- Department of Precision Machinery and Precision Instruments, University of Science and Technology of China, Hefei 230026, China
- Hefei National Laboratory for Physical Sciences at the Microscale, University of Science and Technology of China, Hefei 230026, China
| | - Fei Li
- Interdisciplinary Center for Brain Information, the Brain Cognition and Brain Disease Institute, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
- Faculty of Life and Health Sciences, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
| | - Ke-ming Zhang
- Hefei National Laboratory for Physical Sciences at the Microscale, University of Science and Technology of China, Hefei 230026, China
- School of Life Sciences, University of Science and Technology of China, Hefei 230026, China
| | - Lufeng Ding
- Interdisciplinary Center for Brain Information, the Brain Cognition and Brain Disease Institute, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
- School of Life Sciences, University of Science and Technology of China, Hefei 230026, China
| | - Yang Wang
- Institute of Semiconductors, Chinese Academy of Sciences, Beijing 100083, China
| | - Xingtao Zhao
- Department of Modern Life Sciences and Biotecnology, Xiongan Institute of Innovation, Xiongan New Area, Xiongan 071899, China
| | - Fang Xu
- Interdisciplinary Center for Brain Information, the Brain Cognition and Brain Disease Institute, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
- Faculty of Life and Health Sciences, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
- Shenzhen-Hong Kong Institute of Brain Science-Shenzhen Fundamental Research Institutions, Shenzhen 518055, China
| | - Danke Zhang
- Interdisciplinary Center for Brain Information, the Brain Cognition and Brain Disease Institute, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
| | - Mingzhai Sun
- Suzhou Institute for Advanced Research, University of Science and Technology of China, Suzhou 215123, China
| | - Pak-Ming Lau
- Hefei National Laboratory for Physical Sciences at the Microscale, University of Science and Technology of China, Hefei 230026, China
- Interdisciplinary Center for Brain Information, the Brain Cognition and Brain Disease Institute, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
- School of Life Sciences, University of Science and Technology of China, Hefei 230026, China
- Shenzhen-Hong Kong Institute of Brain Science-Shenzhen Fundamental Research Institutions, Shenzhen 518055, China
- Institute of Artificial Intelligence, Hefei Comprehensive National Science Center, Hefei 230088, China
| | - Qingyuan Zhu
- Hefei National Laboratory for Physical Sciences at the Microscale, University of Science and Technology of China, Hefei 230026, China
| | - Pengcheng Zhou
- Interdisciplinary Center for Brain Information, the Brain Cognition and Brain Disease Institute, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
- Faculty of Life and Health Sciences, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
| | - Guo-Qiang Bi
- Hefei National Laboratory for Physical Sciences at the Microscale, University of Science and Technology of China, Hefei 230026, China
- Interdisciplinary Center for Brain Information, the Brain Cognition and Brain Disease Institute, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
- School of Life Sciences, University of Science and Technology of China, Hefei 230026, China
- Shenzhen-Hong Kong Institute of Brain Science-Shenzhen Fundamental Research Institutions, Shenzhen 518055, China
- Institute of Artificial Intelligence, Hefei Comprehensive National Science Center, Hefei 230088, China
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19
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Li Y, Di C, Song S, Zhang Y, Lu Y, Liao J, Lei B, Zhong J, Guo K, Zhang N, Su S. Choroid plexus mast cells drive tumor-associated hydrocephalus. Cell 2023; 186:5719-5738.e28. [PMID: 38056463 DOI: 10.1016/j.cell.2023.11.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2023] [Revised: 09/04/2023] [Accepted: 11/01/2023] [Indexed: 12/08/2023]
Abstract
Tumor-associated hydrocephalus (TAH) is a common and lethal complication of brain metastases. Although other factors beyond mechanical obstructions have been suggested, the exact mechanisms are unknown. Using single-nucleus RNA sequencing and spatial transcriptomics, we find that a distinct population of mast cells locate in the choroid plexus and dramatically increase during TAH. Genetic fate tracing and intracranial mast-cell-specific tryptase knockout showed that choroid plexus mast cells (CPMCs) disrupt cilia of choroid plexus epithelia via the tryptase-PAR2-FoxJ1 pathway and consequently increase cerebrospinal fluid production. Mast cells are also found in the human choroid plexus. Levels of tryptase in cerebrospinal fluid are closely associated with clinical severity of TAH. BMS-262084, an inhibitor of tryptase, can cross the blood-brain barrier, inhibit TAH in vivo, and alleviate mast-cell-induced damage of epithelial cilia in a human pluripotent stem-cell-derived choroid plexus organoid model. Collectively, we uncover the function of CPMCs and provide an attractive therapy for TAH.
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Affiliation(s)
- Yiye Li
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Medical Research Center, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou 510120, China; Breast Tumor Center, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou 510120, China
| | - Can Di
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Medical Research Center, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou 510120, China; Breast Tumor Center, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou 510120, China
| | - Shijian Song
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Medical Research Center, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou 510120, China; Breast Tumor Center, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou 510120, China
| | - Yubo Zhang
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Medical Research Center, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou 510120, China; Breast Tumor Center, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou 510120, China
| | - Yiwen Lu
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Medical Research Center, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou 510120, China; Breast Tumor Center, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou 510120, China
| | - Jianyou Liao
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Medical Research Center, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou 510120, China
| | - Bingxi Lei
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Medical Research Center, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou 510120, China; Department of Neurosurgery, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou 510120, China
| | - Jian Zhong
- Department of Neurosurgery, The First Affiliated Hospital of Sun Yat-Sen University, Guangdong Provincial Key Laboratory of Brain Function and Disease, Guangdong Translational Medicine Innovation Platform, Guangzhou 510080, China
| | - Kaihua Guo
- Department of Anatomy and Physiology, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou 510080, China
| | - Nu Zhang
- Department of Neurosurgery, The First Affiliated Hospital of Sun Yat-Sen University, Guangdong Provincial Key Laboratory of Brain Function and Disease, Guangdong Translational Medicine Innovation Platform, Guangzhou 510080, China; Department of Anatomy and Physiology, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou 510080, China
| | - Shicheng Su
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Medical Research Center, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou 510120, China; Breast Tumor Center, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou 510120, China; Department of Immunology and Microbiology, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou 510080, China; Biotherapy Center, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou 510120, China.
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20
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Li XH, Shi W, Chen QY, Hao S, Miao HH, Miao Z, Xu F, Bi GQ, Zhuo M. Activation of the glutamatergic cingulate cortical-cortical connection facilitates pain in adult mice. Commun Biol 2023; 6:1247. [PMID: 38071375 PMCID: PMC10710420 DOI: 10.1038/s42003-023-05589-1] [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: 03/16/2023] [Accepted: 11/14/2023] [Indexed: 12/18/2023] Open
Abstract
The brain consists of the left and right cerebral hemispheres and both are connected by callosal projections. Less is known about the basic mechanism of this cortical-cortical connection and its functional importance. Here we investigate the cortical-cortical connection between the bilateral anterior cingulate cortex (ACC) by using the classic electrophysiological and optogenetic approach. We find that there is a direct synaptic projection from one side ACC to the contralateral ACC. Glutamate is the major excitatory transmitter for bilateral ACC connection, including projections to pyramidal cells in superficial (II/III) and deep (V/VI) layers of the ACC. Both AMPA and kainate receptors contribute to synaptic transmission. Repetitive stimulation of the projection also evoked postsynaptic Ca2+ influx in contralateral ACC pyramidal neurons. Behaviorally, light activation of the ACC-ACC connection facilitated behavioral withdrawal responses to mechanical stimuli and noxious heat. In an animal model of neuropathic pain, light inhibitory of ACC-ACC connection reduces both primary and secondary hyperalgesia. Our findings provide strong direct evidence for the excitatory or facilitatory contribution of ACC-ACC connection to pain perception, and this mechanism may provide therapeutic targets for future treatment of chronic pain and related emotional disorders.
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Affiliation(s)
- Xu-Hui Li
- Center for Neuron and Disease, Frontier Institute of Science and Technology, Xi'an Jiaotong University, Xi'an, Shaanxi, 710049, China
- Department of Physiology, Faculty of Medicine, University of Toronto, Medical Science Building, 1 King's College Circle, Toronto, Ontario, M5S 1A8, Canada
- Institute of Brain Research, Qingdao International Academician Park, Qingdao, Shandong, 266000, China
| | - Wantong Shi
- Center for Neuron and Disease, Frontier Institute of Science and Technology, Xi'an Jiaotong University, Xi'an, Shaanxi, 710049, China
- Institute of Brain Research, Qingdao International Academician Park, Qingdao, Shandong, 266000, China
| | - Qi-Yu Chen
- Institute of Brain Research, Qingdao International Academician Park, Qingdao, Shandong, 266000, China
- CAS Key Laboratory of Brain Connectome and Manipulation, Interdisciplinary Center for Brain Information, The Brain Cognition and Brain Disease Institute, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen-Hong Kong Institute of Brain Science Shenzhen Fundamental Research Institutions, Shenzhen, Guangdong, 518055, China
| | - Shun Hao
- Institute of Brain Research, Qingdao International Academician Park, Qingdao, Shandong, 266000, China
| | - Hui-Hui Miao
- Department of Physiology, Faculty of Medicine, University of Toronto, Medical Science Building, 1 King's College Circle, Toronto, Ontario, M5S 1A8, Canada
- Department of Anesthesiology, Beijing Shijitan Hospital, Capital Medical University, 10th Tieyi Road, Haidian District, Beijing, 100038, China
| | - Zhuang Miao
- Department of Physiology, Faculty of Medicine, University of Toronto, Medical Science Building, 1 King's College Circle, Toronto, Ontario, M5S 1A8, Canada
| | - Fang Xu
- CAS Key Laboratory of Brain Connectome and Manipulation, Interdisciplinary Center for Brain Information, The Brain Cognition and Brain Disease Institute, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen-Hong Kong Institute of Brain Science Shenzhen Fundamental Research Institutions, Shenzhen, Guangdong, 518055, China
| | - Guo-Qiang Bi
- CAS Key Laboratory of Brain Connectome and Manipulation, Interdisciplinary Center for Brain Information, The Brain Cognition and Brain Disease Institute, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen-Hong Kong Institute of Brain Science Shenzhen Fundamental Research Institutions, Shenzhen, Guangdong, 518055, China
| | - Min Zhuo
- Center for Neuron and Disease, Frontier Institute of Science and Technology, Xi'an Jiaotong University, Xi'an, Shaanxi, 710049, China.
- Department of Physiology, Faculty of Medicine, University of Toronto, Medical Science Building, 1 King's College Circle, Toronto, Ontario, M5S 1A8, Canada.
- Institute of Brain Research, Qingdao International Academician Park, Qingdao, Shandong, 266000, China.
- Department of Neurology, First Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong, 510130, China.
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21
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Timonidis N, Bakker R, Rubio-Teves M, Alonso-Martínez C, Garcia-Amado M, Clascá F, Tiesinga PHE. Translating single-neuron axonal reconstructions into meso-scale connectivity statistics in the mouse somatosensory thalamus. Front Neuroinform 2023; 17:1272243. [PMID: 38107469 PMCID: PMC10722239 DOI: 10.3389/fninf.2023.1272243] [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: 08/03/2023] [Accepted: 11/13/2023] [Indexed: 12/19/2023] Open
Abstract
Characterizing the connectomic and morphological diversity of thalamic neurons is key for better understanding how the thalamus relays sensory inputs to the cortex. The recent public release of complete single-neuron morphological reconstructions enables the analysis of previously inaccessible connectivity patterns from individual neurons. Here we focus on the Ventral Posteromedial (VPM) nucleus and characterize the full diversity of 257 VPM neurons, obtained by combining data from the MouseLight and Braintell projects. Neurons were clustered according to their most dominantly targeted cortical area and further subdivided by their jointly targeted areas. We obtained a 2D embedding of morphological diversity using the dissimilarity between all pairs of axonal trees. The curved shape of the embedding allowed us to characterize neurons by a 1-dimensional coordinate. The coordinate values were aligned both with the progression of soma position along the dorsal-ventral and lateral-medial axes and with that of axonal terminals along the posterior-anterior and medial-lateral axes, as well as with an increase in the number of branching points, distance from soma and branching width. Taken together, we have developed a novel workflow for linking three challenging aspects of connectomics, namely the topography, higher order connectivity patterns and morphological diversity, with VPM as a test-case. The workflow is linked to a unified access portal that contains the morphologies and integrated with 2D cortical flatmap and subcortical visualization tools. The workflow and resulting processed data have been made available in Python, and can thus be used for modeling and experimentally validating new hypotheses on thalamocortical connectivity.
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Affiliation(s)
- Nestor Timonidis
- Neuroinformatics Department, Donders Centre for Neuroscience, Radboud University Nijmegen, Nijmegen, Netherlands
| | - Rembrandt Bakker
- Neuroinformatics Department, Donders Centre for Neuroscience, Radboud University Nijmegen, Nijmegen, Netherlands
- Institute of Neuroscience and Medicine (INM-6) and Institute for Advanced Simulation (IAS-6) and JARA BRAIN Institute I, Jülich Research Centre, Jülich, Germany
| | - Mario Rubio-Teves
- Department of Anatomy and Neuroscience, School of Medicine, Autónoma de Madrid University, Madrid, Spain
| | - Carmen Alonso-Martínez
- Department of Anatomy and Neuroscience, School of Medicine, Autónoma de Madrid University, Madrid, Spain
| | - Maria Garcia-Amado
- Department of Anatomy and Neuroscience, School of Medicine, Autónoma de Madrid University, Madrid, Spain
| | - Francisco Clascá
- Institute of Neuroscience and Medicine (INM-6) and Institute for Advanced Simulation (IAS-6) and JARA BRAIN Institute I, Jülich Research Centre, Jülich, Germany
| | - Paul H. E. Tiesinga
- Neuroinformatics Department, Donders Centre for Neuroscience, Radboud University Nijmegen, Nijmegen, Netherlands
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22
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Jiang T, Gong H, Yuan J. Whole-brain Optical Imaging: A Powerful Tool for Precise Brain Mapping at the Mesoscopic Level. Neurosci Bull 2023; 39:1840-1858. [PMID: 37715920 PMCID: PMC10661546 DOI: 10.1007/s12264-023-01112-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Accepted: 05/08/2023] [Indexed: 09/18/2023] Open
Abstract
The mammalian brain is a highly complex network that consists of millions to billions of densely-interconnected neurons. Precise dissection of neural circuits at the mesoscopic level can provide important structural information for understanding the brain. Optical approaches can achieve submicron lateral resolution and achieve "optical sectioning" by a variety of means, which has the natural advantage of allowing the observation of neural circuits at the mesoscopic level. Automated whole-brain optical imaging methods based on tissue clearing or histological sectioning surpass the limitation of optical imaging depth in biological tissues and can provide delicate structural information in a large volume of tissues. Combined with various fluorescent labeling techniques, whole-brain optical imaging methods have shown great potential in the brain-wide quantitative profiling of cells, circuits, and blood vessels. In this review, we summarize the principles and implementations of various whole-brain optical imaging methods and provide some concepts regarding their future development.
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Affiliation(s)
- Tao Jiang
- Huazhong University of Science and Technology-Suzhou Institute for Brainsmatics, Jiangsu Industrial Technology Research Institute, Suzhou, 215123, China
| | - Hui Gong
- Huazhong University of Science and Technology-Suzhou Institute for Brainsmatics, Jiangsu Industrial Technology Research Institute, Suzhou, 215123, China
- Wuhan National Laboratory for Optoelectronics, Huazhong University of Science and Technology, Wuhan, 430074, China
| | - Jing Yuan
- Huazhong University of Science and Technology-Suzhou Institute for Brainsmatics, Jiangsu Industrial Technology Research Institute, Suzhou, 215123, China.
- Wuhan National Laboratory for Optoelectronics, Huazhong University of Science and Technology, Wuhan, 430074, China.
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23
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Li S, Xu X, Li C, Xu Z, Wu K, Ye Q, Zhang Y, Jiang X, Cang C, Tian C, Wen J. In vivo labeling and quantitative imaging of neuronal populations using MRI. Neuroimage 2023; 281:120374. [PMID: 37729795 DOI: 10.1016/j.neuroimage.2023.120374] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2023] [Revised: 08/30/2023] [Accepted: 09/10/2023] [Indexed: 09/22/2023] Open
Abstract
The study of neural circuits, which underlies perception, cognition, emotion, and behavior, is essential for understanding the mammalian brain, a complex organ consisting of billions of neurons. To study the structure and function of the brain, in vivo neuronal labeling and imaging techniques are crucial as they provide true physiological information that ex vivo methods cannot offer. In this paper, we present a new strategy for in vivo neuronal labeling and quantification using MRI. We demonstrate the efficacy of this method by delivering the oatp1a1 gene to the target neurons using rAAV2-retro virus. OATP1A1 protein expression on the neuronal membrane increased the uptake of a specific MRI contrast agent (Gd-EOB-DTPA), leading to hyperintense signals on T1W images of labeled neuronal populations. We also used dynamic contrast enhancement-based methods to obtain quantitative information on labeled neuronal populations in vivo.
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Affiliation(s)
- Shana Li
- The First Affiliated Hospital of USTC (Anhui Provincial Hospital), Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, PR China
| | - Xiang Xu
- The First Affiliated Hospital of USTC (Anhui Provincial Hospital), Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, PR China
| | - Canjun Li
- School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, PR China
| | - Ziyan Xu
- School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, PR China
| | - Ke Wu
- The First Affiliated Hospital of USTC (Anhui Provincial Hospital), Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, PR China
| | - Qiong Ye
- Key Laboratory of High Field Magnetic Resonance Image of Anhui Province, High Magnetic Field Laboratory, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei, Anhui, PR China
| | - Yan Zhang
- The First Affiliated Hospital of USTC (Anhui Provincial Hospital), Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, PR China
| | - Xiaohua Jiang
- The First Affiliated Hospital of USTC (Anhui Provincial Hospital), Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, PR China
| | - Chunlei Cang
- School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, PR China
| | - Changlin Tian
- The First Affiliated Hospital of USTC (Anhui Provincial Hospital), Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, PR China; School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, PR China; Key Laboratory of High Field Magnetic Resonance Image of Anhui Province, High Magnetic Field Laboratory, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei, Anhui, PR China.
| | - Jie Wen
- The First Affiliated Hospital of USTC (Anhui Provincial Hospital), Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, PR China.
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24
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Ma C, Xia D, Huang S, Du Q, Liu J, Zhang B, Zhu Q, Bi G, Wang H, Xu RX. High precision vibration sectioning for 3D imaging of the whole central nervous system. J Neurosci Methods 2023; 399:109966. [PMID: 37666283 DOI: 10.1016/j.jneumeth.2023.109966] [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: 03/26/2023] [Revised: 06/21/2023] [Accepted: 08/30/2023] [Indexed: 09/06/2023]
Abstract
BACKGROUND Imaging and reconstruction of the morphology of neurons within the entire central nervous system (CNS) is important for deciphering the neural circuitry and related brain functions. With combination of tissue clearing and light sheet microscopy, previous studies have imaged the mouse CNS at cellular resolution, while remaining single axons unresolvable due to the tradeoff between sample size and imaging resolution. This could be improved by sectioning the sample into thick slices and imaged with high resolution light sheet microscopy as described in our previous study. However, the achievable quality for 3D imaging of serial thick slices is often hindered by surface undulation and other artifacts introduced by sectioning and handling limitations. NEW METHODS In order to improve the imaging quality for mouse CNS, we develop a high-performance vibratome system for sample sectioning and handling automation. The sectioning mechanism of the system was modeled theoretically and verified experimentally. The effects of process parameters and sample properties on sectioning accuracy were studied to optimize the sectioning outcome. The resultant imaging outcome was demonstrated on mouse samples. RESULTS Our theoretical model of vibratome effectively depicts the relationship between the sample surface undulation errors and the sectioning parameters. With the guidance of the theoretical model, the vibratome is able to achieve a local surface undulation error of ±0.5 µm and a surface arithmetic mean deviation (Sa) of 220 nm for 300-μm-thick tissue slices. Imaging results of mouse CNS show the continuous sectioning capability of the vibratome. COMPARISON WITH EXISTING METHOD Our automatic sectioning and handling system is able to process serial thick slices for 3D imaging of the whole CNS at a single-axon resolution, superior to the commercially available vibratome devices. CONCLUSION Our automatic sectioning and handling system can be optimized to prepare thick sample slices with minimal surface undulation and manual manipulation in support of 3D brain mapping with high-throughput and high-accuracy.
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Affiliation(s)
- Canzhen Ma
- School of Engineering Science, University of Science and Technology of China, Hefei 230027, China; Institute of Artificial Intelligence, Hefei Comprehensive National Science Center, Hefei 230088, China; School of Biomedical Engineering, University of Science and Technology of China, Suzhou 215123, China
| | - Debin Xia
- Institute of Artificial Intelligence, Hefei Comprehensive National Science Center, Hefei 230088, China; National Engineering Laboratory for Brain-inspired Intelligence Technology and Application, University of Science and Technology of China, Hefei 230027, China
| | - Shichang Huang
- Hefei National Laboratory for Physical Sciences at the Microscale, and School of Life Sciences, University of Science and Technology of China, Hefei, Anhui 230027, China
| | - Qing Du
- Institute of Artificial Intelligence, Hefei Comprehensive National Science Center, Hefei 230088, China
| | - Jiajun Liu
- Institute of Artificial Intelligence, Hefei Comprehensive National Science Center, Hefei 230088, China; National Engineering Laboratory for Brain-inspired Intelligence Technology and Application, University of Science and Technology of China, Hefei 230027, China
| | - Bo Zhang
- Institute of Artificial Intelligence, Hefei Comprehensive National Science Center, Hefei 230088, China; National Engineering Laboratory for Brain-inspired Intelligence Technology and Application, University of Science and Technology of China, Hefei 230027, China
| | - Qingyuan Zhu
- Hefei National Laboratory for Physical Sciences at the Microscale, and School of Life Sciences, University of Science and Technology of China, Hefei, Anhui 230027, China
| | - Guoqiang Bi
- Institute of Artificial Intelligence, Hefei Comprehensive National Science Center, Hefei 230088, China; Hefei National Laboratory for Physical Sciences at the Microscale, and School of Life Sciences, University of Science and Technology of China, Hefei, Anhui 230027, China
| | - Hao Wang
- Institute of Artificial Intelligence, Hefei Comprehensive National Science Center, Hefei 230088, China; National Engineering Laboratory for Brain-inspired Intelligence Technology and Application, University of Science and Technology of China, Hefei 230027, China.
| | - Ronald X Xu
- School of Engineering Science, University of Science and Technology of China, Hefei 230027, China; School of Biomedical Engineering, University of Science and Technology of China, Suzhou 215123, China.
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25
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Han X, Guo S, Ji N, Li T, Liu J, Ye X, Wang Y, Yun Z, Xiong F, Rong J, Liu D, Ma H, Wang Y, Huang Y, Zhang P, Wu W, Ding L, Hawrylycz M, Lein E, Ascoli GA, Xie W, Liu L, Zhang L, Peng H. Whole human-brain mapping of single cortical neurons for profiling morphological diversity and stereotypy. SCIENCE ADVANCES 2023; 9:eadf3771. [PMID: 37824619 PMCID: PMC10569712 DOI: 10.1126/sciadv.adf3771] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/29/2022] [Accepted: 04/18/2023] [Indexed: 10/14/2023]
Abstract
Quantifying neuron morphology and distribution at the whole-brain scale is essential to understand the structure and diversity of cell types. It is exceedingly challenging to reuse recent technologies of single-cell labeling and whole-brain imaging to study human brains. We propose adaptive cell tomography (ACTomography), a low-cost, high-throughput, and high-efficacy tomography approach, based on adaptive targeting of individual cells. We established a platform to inject dyes into cortical neurons in surgical tissues of 18 patients with brain tumors or other conditions and one donated fresh postmortem brain. We collected three-dimensional images of 1746 cortical neurons, of which 852 neurons were reconstructed to quantify local dendritic morphology, and mapped to standard atlases. In our data, human neurons are more diverse across brain regions than by subject age or gender. The strong stereotypy within cohorts of brain regions allows generating a statistical tensor field of neuron morphology to characterize anatomical modularity of a human brain.
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Affiliation(s)
- Xiaofeng Han
- Institute for Brain and Intelligence, Southeast University, Nanjing, China
| | - Shuxia Guo
- Institute for Brain and Intelligence, Southeast University, Nanjing, China
| | - Nan Ji
- Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, Beijing, China
- China National Clinical Research Center for Neurological Diseases, Beijing, China
- Beijing Key Laboratory of Brain Tumor, Beijing, China
| | - Tian Li
- Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, Beijing, China
| | - Jian Liu
- Institute for Brain and Intelligence, Southeast University, Nanjing, China
| | - Xiangqiao Ye
- Institute for Brain and Intelligence, Southeast University, Nanjing, China
| | - Yi Wang
- Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, Beijing, China
| | - Zhixi Yun
- Institute for Brain and Intelligence, Southeast University, Nanjing, China
| | - Feng Xiong
- Institute for Brain and Intelligence, Southeast University, Nanjing, China
| | - Jing Rong
- Institute for Brain and Intelligence, Southeast University, Nanjing, China
| | - Di Liu
- Institute for Brain and Intelligence, Southeast University, Nanjing, China
| | - Hui Ma
- Institute for Brain and Intelligence, Southeast University, Nanjing, China
| | - Yujin Wang
- Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, Beijing, China
| | - Yue Huang
- China National Clinical Research Center for Neurological Diseases, Beijing, China
| | - Peng Zhang
- Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, Beijing, China
| | - Wenhao Wu
- Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, Beijing, China
| | - Liya Ding
- Institute for Brain and Intelligence, Southeast University, Nanjing, China
| | | | - Ed Lein
- Allen Institute for Brain Science, Seattle, WA, USA
| | - Giorgio A. Ascoli
- Center for Neural Informatics, Krasnow Institute for Advanced Studies and Bioengineering Department, College of Engineering and Computing, George Mason University, Fairfax, VA, USA
| | - Wei Xie
- Institute for Brain and Intelligence, Southeast University, Nanjing, China
- The Key Laboratory of Developmental Genes and Human Disease, Ministry of Education, School of Life Science and Technology, Southeast University, Nanjing, China
| | - Lijuan Liu
- Institute for Brain and Intelligence, Southeast University, Nanjing, China
| | - Liwei Zhang
- Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, Beijing, China
- China National Clinical Research Center for Neurological Diseases, Beijing, China
- Beijing Key Laboratory of Brain Tumor, Beijing, China
| | - Hanchuan Peng
- Institute for Brain and Intelligence, Southeast University, Nanjing, China
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26
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Li Z, Shang Z, Liu J, Zhen H, Zhu E, Zhong S, Sturgess RN, Zhou Y, Hu X, Zhao X, Wu Y, Li P, Lin R, Ren J. D-LMBmap: a fully automated deep-learning pipeline for whole-brain profiling of neural circuitry. Nat Methods 2023; 20:1593-1604. [PMID: 37770711 PMCID: PMC10555838 DOI: 10.1038/s41592-023-01998-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2022] [Accepted: 08/02/2023] [Indexed: 09/30/2023]
Abstract
Recent proliferation and integration of tissue-clearing methods and light-sheet fluorescence microscopy has created new opportunities to achieve mesoscale three-dimensional whole-brain connectivity mapping with exceptionally high throughput. With the rapid generation of large, high-quality imaging datasets, downstream analysis is becoming the major technical bottleneck for mesoscale connectomics. Current computational solutions are labor intensive with limited applications because of the exhaustive manual annotation and heavily customized training. Meanwhile, whole-brain data analysis always requires combining multiple packages and secondary development by users. To address these challenges, we developed D-LMBmap, an end-to-end package providing an integrated workflow containing three modules based on deep-learning algorithms for whole-brain connectivity mapping: axon segmentation, brain region segmentation and whole-brain registration. D-LMBmap does not require manual annotation for axon segmentation and achieves quantitative analysis of whole-brain projectome in a single workflow with superior accuracy for multiple cell types in all of the modalities tested.
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Affiliation(s)
- Zhongyu Li
- Division of Neurobiology, MRC Laboratory of Molecular Biology, Cambridge, UK
| | - Zengyi Shang
- School of Software Engineering, Xi'an Jiaotong University, Xi'an, China
| | - Jingyi Liu
- School of Software Engineering, Xi'an Jiaotong University, Xi'an, China
| | - Haotian Zhen
- School of Software Engineering, Xi'an Jiaotong University, Xi'an, China
| | - Entao Zhu
- School of Software Engineering, Xi'an Jiaotong University, Xi'an, China
| | - Shilin Zhong
- National Institute of Biological Sciences (NIBS), Beijing, China
| | - Robyn N Sturgess
- Division of Neurobiology, MRC Laboratory of Molecular Biology, Cambridge, UK
| | - Yitian Zhou
- School of Software Engineering, Xi'an Jiaotong University, Xi'an, China
| | - Xuemeng Hu
- School of Software Engineering, Xi'an Jiaotong University, Xi'an, China
| | - Xingyue Zhao
- School of Software Engineering, Xi'an Jiaotong University, Xi'an, China
| | - Yi Wu
- School of Software Engineering, Xi'an Jiaotong University, Xi'an, China
| | - Peiqi Li
- School of Software Engineering, Xi'an Jiaotong University, Xi'an, China
| | - Rui Lin
- National Institute of Biological Sciences (NIBS), Beijing, China
| | - Jing Ren
- Division of Neurobiology, MRC Laboratory of Molecular Biology, Cambridge, UK.
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27
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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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28
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Georgiadis M, Menzel M, Reuter JA, Born DE, Kovacevich SR, Alvarez D, Taghavi HM, Schroeter A, Rudin M, Gao Z, Guizar-Sicairos M, Weiss TM, Axer M, Rajkovic I, Zeineh MM. Imaging crossing fibers in mouse, pig, monkey, and human brain using small-angle X-ray scattering. Acta Biomater 2023; 164:317-331. [PMID: 37098400 PMCID: PMC10811447 DOI: 10.1016/j.actbio.2023.04.029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2022] [Revised: 04/15/2023] [Accepted: 04/18/2023] [Indexed: 04/27/2023]
Abstract
Myelinated axons (nerve fibers) efficiently transmit signals throughout the brain via action potentials. Multiple methods that are sensitive to axon orientations, from microscopy to magnetic resonance imaging, aim to reconstruct the brain's structural connectome. As billions of nerve fibers traverse the brain with various possible geometries at each point, resolving fiber crossings is necessary to generate accurate structural connectivity maps. However, doing so with specificity is a challenging task because signals originating from oriented fibers can be influenced by brain (micro)structures unrelated to myelinated axons. X-ray scattering can specifically probe myelinated axons due to the periodicity of the myelin sheath, which yields distinct peaks in the scattering pattern. Here, we show that small-angle X-ray scattering (SAXS) can be used to detect myelinated, axon-specific fiber crossings. We first demonstrate the capability using strips of human corpus callosum to create artificial double- and triple-crossing fiber geometries, and we then apply the method in mouse, pig, vervet monkey, and human brains. We compare results to polarized light imaging (3D-PLI), tracer experiments, and to outputs from diffusion MRI that sometimes fails to detect crossings. Given its specificity, capability of 3-dimensional sampling and high resolution, SAXS could serve as a ground truth for validating fiber orientations derived using diffusion MRI as well as microscopy-based methods. STATEMENT OF SIGNIFICANCE: To study how the nerve fibers in our brain are interconnected, scientists need to visualize their trajectories, which often cross one another. Here, we show the unique capacity of small-angle X-ray scattering (SAXS) to study these fiber crossings without use of labeling, taking advantage of SAXS's specificity to myelin - the insulating sheath that is wrapped around nerve fibers. We use SAXS to detect double and triple crossing fibers and unveil intricate crossings in mouse, pig, vervet monkey, and human brains. This non-destructive method can uncover complex fiber trajectories and validate other less specific imaging methods (e.g., MRI or microscopy), towards accurate mapping of neuronal connectivity in the animal and human brain.
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Affiliation(s)
- Marios Georgiadis
- Department of Radiology, Stanford School of Medicine, Stanford, CA, USA; Institute for Biomedical Engineering, ETH Zurich and University of Zurich, Zurich, Switzerland.
| | - Miriam Menzel
- Institute of Neuroscience and Medicine (INM-1), Forschungszentrum Jülich GmbH, Jülich 52425, Germany; Department of Imaging Physics, Delft University of Technology, Delft, the Netherlands
| | - Jan A Reuter
- Institute of Neuroscience and Medicine (INM-1), Forschungszentrum Jülich GmbH, Jülich 52425, Germany
| | - Donald E Born
- Department of Pathology, Stanford School of Medicine, Stanford, CA, USA
| | | | - Dario Alvarez
- Department of Radiology, Stanford School of Medicine, Stanford, CA, USA
| | | | - Aileen Schroeter
- Institute for Biomedical Engineering, ETH Zurich and University of Zurich, Zurich, Switzerland
| | - Markus Rudin
- Institute for Biomedical Engineering, ETH Zurich and University of Zurich, Zurich, Switzerland
| | - Zirui Gao
- Institute for Biomedical Engineering, ETH Zurich and University of Zurich, Zurich, Switzerland
| | | | - Thomas M Weiss
- SLAC National Accelerator Laboratory, Stanford Synchrotron Radiation Lightsource, USA
| | - Markus Axer
- Institute of Neuroscience and Medicine (INM-1), Forschungszentrum Jülich GmbH, Jülich 52425, Germany
| | - Ivan Rajkovic
- SLAC National Accelerator Laboratory, Stanford Synchrotron Radiation Lightsource, USA
| | - Michael M Zeineh
- Department of Radiology, Stanford School of Medicine, Stanford, CA, USA
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29
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Arefin TM, Lee CH, Liang Z, Rallapalli H, Wadghiri YZ, Turnbull DH, Zhang J. Towards reliable reconstruction of the mouse brain corticothalamic connectivity using diffusion MRI. Neuroimage 2023; 273:120111. [PMID: 37060936 PMCID: PMC10149621 DOI: 10.1016/j.neuroimage.2023.120111] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2022] [Revised: 03/29/2023] [Accepted: 04/12/2023] [Indexed: 04/17/2023] Open
Abstract
Diffusion magnetic resonance imaging (dMRI) tractography has yielded intriguing insights into brain circuits and their relationship to behavior in response to gene mutations or neurological diseases across a number of species. Still, existing tractography approaches suffer from limited sensitivity and specificity, leading to uncertain interpretation of the reconstructed connections. Hence, in this study, we aimed to optimize the imaging and computational pipeline to achieve the best possible spatial overlaps between the tractography and tracer-based axonal projection maps within the mouse brain corticothalamic network. We developed a dMRI-based atlas of the mouse forebrain with structural labels imported from the Allen Mouse Brain Atlas (AMBA). Using the atlas and dMRI tractography, we first reconstructed detailed node-to-node mouse brain corticothalamic structural connectivity matrices using different imaging and tractography parameters. We then investigated the effects of each condition for accurate reconstruction of the corticothalamic projections by quantifying the similarities between the tractography and the tracer data from the Allen Mouse Brain Connectivity Atlas (AMBCA). Our results suggest that these parameters significantly affect tractography outcomes and our atlas can be used to investigate macroscopic structural connectivity in the mouse brain. Furthermore, tractography in mouse brain gray matter still face challenges and need improved imaging and tractography methods.
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Affiliation(s)
- Tanzil Mahmud Arefin
- Bernard and Irene Schwartz Center for Biomedical Imaging (CBI), Center for Advanced Imaging Innovation and Research (CAI2R), Department of Radiology, New York University Grossman School of Medicine, 660 First Ave., New York City, NY, United States; Center for Neurotechnology in Mental Health Research, Department of Biomedical Engineering, The Pennsylvania State University, University Park, PA, United States
| | - Choong Heon Lee
- Bernard and Irene Schwartz Center for Biomedical Imaging (CBI), Center for Advanced Imaging Innovation and Research (CAI2R), Department of Radiology, New York University Grossman School of Medicine, 660 First Ave., New York City, NY, United States
| | - Zifei Liang
- Bernard and Irene Schwartz Center for Biomedical Imaging (CBI), Center for Advanced Imaging Innovation and Research (CAI2R), Department of Radiology, New York University Grossman School of Medicine, 660 First Ave., New York City, NY, United States
| | - Harikrishna Rallapalli
- Bernard and Irene Schwartz Center for Biomedical Imaging (CBI), Center for Advanced Imaging Innovation and Research (CAI2R), Department of Radiology, New York University Grossman School of Medicine, 660 First Ave., New York City, NY, United States
| | - Youssef Z Wadghiri
- Bernard and Irene Schwartz Center for Biomedical Imaging (CBI), Center for Advanced Imaging Innovation and Research (CAI2R), Department of Radiology, New York University Grossman School of Medicine, 660 First Ave., New York City, NY, United States
| | - Daniel H Turnbull
- Bernard and Irene Schwartz Center for Biomedical Imaging (CBI), Center for Advanced Imaging Innovation and Research (CAI2R), Department of Radiology, New York University Grossman School of Medicine, 660 First Ave., New York City, NY, United States
| | - Jiangyang Zhang
- Bernard and Irene Schwartz Center for Biomedical Imaging (CBI), Center for Advanced Imaging Innovation and Research (CAI2R), Department of Radiology, New York University Grossman School of Medicine, 660 First Ave., New York City, NY, United States.
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30
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Zhu X, Yan H, Zhan Y, Feng F, Wei C, Yao YG, Liu C. An anatomical and connectivity atlas of the marmoset cerebellum. Cell Rep 2023; 42:112480. [PMID: 37163375 DOI: 10.1016/j.celrep.2023.112480] [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: 10/18/2022] [Revised: 02/01/2023] [Accepted: 04/20/2023] [Indexed: 05/12/2023] Open
Abstract
The cerebellum is essential for motor control and cognitive functioning, engaging in bidirectional communication with the cerebral cortex. The common marmoset, a small non-human primate, offers unique advantages for studying cerebello-cerebral circuits. However, the marmoset cerebellum is not well described in published resources. In this study, we present a comprehensive atlas of the marmoset cerebellum comprising (1) fine-detailed anatomical atlases and surface-analysis tools of the cerebellar cortex based on ultra-high-resolution ex vivo MRI, (2) functional connectivity and gradient patterns of the cerebellar cortex revealed by awake resting-state fMRI, and (3) structural-connectivity mapping of cerebellar nuclei using high-resolution diffusion MRI tractography. The atlas elucidates the anatomical details of the marmoset cerebellum, reveals distinct gradient patterns of intra-cerebellar and cerebello-cerebral functional connectivity, and maps the topological relationship of cerebellar nuclei in cerebello-cerebral circuits. As version 5 of the Marmoset Brain Mapping project, this atlas is publicly available at https://marmosetbrainmapping.org/MBMv5.html.
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Affiliation(s)
- Xiaojia Zhu
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences and Yunnan Province, and KIZ-CUHK Joint Laboratory of Bioresources and Molecular Research in Common Diseases, National Research Facility for Phenotypic & Genetic Analysis of Model Animals (Primate Facility), National Resource Center for Non-Human Primates, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650201, China; Institute of Neuroscience, CAS Center for Excellence in Brain Science and Intelligence Technology, CAS Key Laboratory of Primate Neurobiology, State Key Laboratory of Neuroscience, Chinese Academy of Sciences, Shanghai 200031, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Haotian Yan
- Institute of Neuroscience, CAS Center for Excellence in Brain Science and Intelligence Technology, CAS Key Laboratory of Primate Neurobiology, State Key Laboratory of Neuroscience, Chinese Academy of Sciences, Shanghai 200031, China
| | - Yafeng Zhan
- Institute of Neuroscience, CAS Center for Excellence in Brain Science and Intelligence Technology, CAS Key Laboratory of Primate Neurobiology, State Key Laboratory of Neuroscience, Chinese Academy of Sciences, Shanghai 200031, China
| | - Furui Feng
- Institute of Neuroscience, CAS Center for Excellence in Brain Science and Intelligence Technology, CAS Key Laboratory of Primate Neurobiology, State Key Laboratory of Neuroscience, Chinese Academy of Sciences, Shanghai 200031, China
| | - Chuanyao Wei
- Institute of Neuroscience, CAS Center for Excellence in Brain Science and Intelligence Technology, CAS Key Laboratory of Primate Neurobiology, State Key Laboratory of Neuroscience, Chinese Academy of Sciences, Shanghai 200031, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yong-Gang Yao
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences and Yunnan Province, and KIZ-CUHK Joint Laboratory of Bioresources and Molecular Research in Common Diseases, National Research Facility for Phenotypic & Genetic Analysis of Model Animals (Primate Facility), National Resource Center for Non-Human Primates, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650201, China; University of Chinese Academy of Sciences, Beijing 100049, China.
| | - Cirong Liu
- Institute of Neuroscience, CAS Center for Excellence in Brain Science and Intelligence Technology, CAS Key Laboratory of Primate Neurobiology, State Key Laboratory of Neuroscience, Chinese Academy of Sciences, Shanghai 200031, China; University of Chinese Academy of Sciences, Beijing 100049, China; Shanghai Center for Brain Science and Brain-Inspired Intelligence Technology, Shanghai, China.
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31
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Liang Z, Arefin TM, Lee CH, Zhang J. Using mesoscopic tract-tracing data to guide the estimation of fiber orientation distributions in the mouse brain from diffusion MRI. Neuroimage 2023; 270:119999. [PMID: 36871795 PMCID: PMC10052941 DOI: 10.1016/j.neuroimage.2023.119999] [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: 12/30/2022] [Revised: 02/21/2023] [Accepted: 02/28/2023] [Indexed: 03/07/2023] Open
Abstract
Diffusion MRI (dMRI) tractography is the only tool for non-invasive mapping of macroscopic structural connectivity over the entire brain. Although it has been successfully used to reconstruct large white matter tracts in the human and animal brains, the sensitivity and specificity of dMRI tractography remained limited. In particular, the fiber orientation distributions (FODs) estimated from dMRI signals, key to tractography, may deviate from histologically measured fiber orientation in crossing fibers and gray matter regions. In this study, we demonstrated that a deep learning network, trained using mesoscopic tract-tracing data from the Allen Mouse Brain Connectivity Atlas, was able to improve the estimation of FODs from mouse brain dMRI data. Tractography results based on the network generated FODs showed improved specificity while maintaining sensitivity comparable to results based on FOD estimated using a conventional spherical deconvolution method. Our result is a proof-of-concept of how mesoscale tract-tracing data can guide dMRI tractography and enhance our ability to characterize brain connectivity.
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Affiliation(s)
- Zifei Liang
- Department of Radiology, Bernard and Irene Schwartz Center for Biomedical Imaging, New York University School of Medicine, 660 First Ave, New York, NY 10016, USA
| | - Tanzil Mahmud Arefin
- Department of Radiology, Bernard and Irene Schwartz Center for Biomedical Imaging, New York University School of Medicine, 660 First Ave, New York, NY 10016, USA
| | - Choong H Lee
- Department of Radiology, Bernard and Irene Schwartz Center for Biomedical Imaging, New York University School of Medicine, 660 First Ave, New York, NY 10016, USA
| | - Jiangyang Zhang
- Department of Radiology, Bernard and Irene Schwartz Center for Biomedical Imaging, New York University School of Medicine, 660 First Ave, New York, NY 10016, USA.
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32
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Chen G, Lai S, Bao G, Ke J, Meng X, Lu S, Wu X, Xu H, Wu F, Xu Y, Xu F, Bi GQ, Peng G, Zhou K, Zhu Y. Distinct reward processing by subregions of the nucleus accumbens. Cell Rep 2023; 42:112069. [PMID: 36753418 DOI: 10.1016/j.celrep.2023.112069] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2022] [Revised: 12/11/2022] [Accepted: 01/19/2023] [Indexed: 02/09/2023] Open
Abstract
The nucleus accumbens (NAc) plays an important role in motivation and reward processing. Recent studies suggest that different NAc subnuclei differentially contribute to reward-related behaviors. However, how reward is encoded in individual NAc neurons remains unclear. Using in vivo single-cell resolution calcium imaging, we find diverse patterns of reward encoding in the medial and lateral shell subdivision of the NAc (NAcMed and NAcLat, respectively). Reward consumption increases NAcLat activity but decreases NAcMed activity, albeit with high variability among neurons. The heterogeneity in reward encoding could be attributed to differences in their synaptic inputs and transcriptional profiles. Specific optogenetic activation of Nts-positive neurons in the NAcLat promotes positive reinforcement, while activation of Cartpt-positive neurons in the NAcMed induces behavior aversion. Collectively, our study shows the organizational and transcriptional differences in NAc subregions and provides a framework for future dissection of NAc subregions in physiological and pathological conditions.
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Affiliation(s)
- Gaowei Chen
- Shenzhen Key Laboratory of Drug Addiction, Shenzhen Neher Neural Plasticity Laboratory, the Brain Cognition and Brain Disease Institute, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China; University of Chinese Academy of Sciences, Beijing 100049, China; Shenzhen-Hong Kong Institute of Brain Science-Shenzhen Fundamental Research Institutions, Shenzhen 518055, China
| | - Shishi Lai
- Shenzhen Key Laboratory of Drug Addiction, Shenzhen Neher Neural Plasticity Laboratory, the Brain Cognition and Brain Disease Institute, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China; Shenzhen-Hong Kong Institute of Brain Science-Shenzhen Fundamental Research Institutions, Shenzhen 518055, China; Yunnan University School of Medicine, Yunnan University, Kunming 650091, China
| | - Guo Bao
- Shenzhen Key Laboratory of Drug Addiction, Shenzhen Neher Neural Plasticity Laboratory, the Brain Cognition and Brain Disease Institute, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China; Shenzhen-Hong Kong Institute of Brain Science-Shenzhen Fundamental Research Institutions, Shenzhen 518055, China
| | - Jincan Ke
- University of Chinese Academy of Sciences, Beijing 100049, China; CAS Key Laboratory of Regenerative Biology, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, GIBH-HKU Guangdong-Hong Kong Stem Cell and Regenerative Medicine Research Centre, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China
| | - Xiaogao Meng
- CAS Key Laboratory of Regenerative Biology, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, GIBH-HKU Guangdong-Hong Kong Stem Cell and Regenerative Medicine Research Centre, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China; University of Science and Technology of China, Hefei 230026, China
| | - Shanshan Lu
- Shenzhen Key Laboratory of Drug Addiction, Shenzhen Neher Neural Plasticity Laboratory, the Brain Cognition and Brain Disease Institute, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China; University of Chinese Academy of Sciences, Beijing 100049, China; Shenzhen-Hong Kong Institute of Brain Science-Shenzhen Fundamental Research Institutions, Shenzhen 518055, China
| | - Xiaocong Wu
- NHC Key Laboratory of Drug Addiction Medicine, Kunming Medical University, Kunming 650032, China
| | - Hua Xu
- Shenzhen Key Laboratory of Drug Addiction, Shenzhen Neher Neural Plasticity Laboratory, the Brain Cognition and Brain Disease Institute, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China; Shenzhen-Hong Kong Institute of Brain Science-Shenzhen Fundamental Research Institutions, Shenzhen 518055, China
| | - Fengyi Wu
- Interdisciplinary Center for Brain Information, The Brain Cognition and Brain Disease Institute, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
| | - Yu Xu
- NHC Key Laboratory of Drug Addiction Medicine, Kunming Medical University, Kunming 650032, China
| | - Fang Xu
- University of Chinese Academy of Sciences, Beijing 100049, China; Shenzhen-Hong Kong Institute of Brain Science-Shenzhen Fundamental Research Institutions, Shenzhen 518055, China; Interdisciplinary Center for Brain Information, The Brain Cognition and Brain Disease Institute, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
| | - Guo-Qiang Bi
- University of Chinese Academy of Sciences, Beijing 100049, China; Shenzhen-Hong Kong Institute of Brain Science-Shenzhen Fundamental Research Institutions, Shenzhen 518055, China; Interdisciplinary Center for Brain Information, The Brain Cognition and Brain Disease Institute, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
| | - Guangdun Peng
- University of Chinese Academy of Sciences, Beijing 100049, China; CAS Key Laboratory of Regenerative Biology, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, GIBH-HKU Guangdong-Hong Kong Stem Cell and Regenerative Medicine Research Centre, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China
| | - Kuikui Zhou
- Shenzhen Key Laboratory of Drug Addiction, Shenzhen Neher Neural Plasticity Laboratory, the Brain Cognition and Brain Disease Institute, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China; University of Chinese Academy of Sciences, Beijing 100049, China; Shenzhen-Hong Kong Institute of Brain Science-Shenzhen Fundamental Research Institutions, Shenzhen 518055, China; School of Health and Life Sciences, University of Health and Rehabilitation Sciences, Qingdao 266071, China.
| | - Yingjie Zhu
- Shenzhen Key Laboratory of Drug Addiction, Shenzhen Neher Neural Plasticity Laboratory, the Brain Cognition and Brain Disease Institute, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China; University of Chinese Academy of Sciences, Beijing 100049, China; Shenzhen-Hong Kong Institute of Brain Science-Shenzhen Fundamental Research Institutions, Shenzhen 518055, China; Faculty of Life and Health Sciences, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China; CAS Key Laboratory of Brain Connectome and Manipulation, the Brain Cognition and Brain Disease Institute (BCBDI), Shenzhen Institute of Advanced Technology (SIAT), Chinese Academy of Sciences, Shenzhen 518055, China; CAS Center for Excellence in Brain Science and Intelligence Technology, Chinese Academy of Sciences, Shanghai 200031, China.
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33
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Rockland KS. A brief sketch across multiscale and comparative neuroanatomical features. Front Neuroanat 2023; 17:1108363. [PMID: 36861111 PMCID: PMC9968756 DOI: 10.3389/fnana.2023.1108363] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2022] [Accepted: 01/10/2023] [Indexed: 02/16/2023] Open
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34
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Real-time denoising enables high-sensitivity fluorescence time-lapse imaging beyond the shot-noise limit. Nat Biotechnol 2023; 41:282-292. [PMID: 36163547 PMCID: PMC9931589 DOI: 10.1038/s41587-022-01450-8] [Citation(s) in RCA: 34] [Impact Index Per Article: 34.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2022] [Accepted: 07/29/2022] [Indexed: 11/09/2022]
Abstract
A fundamental challenge in fluorescence microscopy is the photon shot noise arising from the inevitable stochasticity of photon detection. Noise increases measurement uncertainty and limits imaging resolution, speed and sensitivity. To achieve high-sensitivity fluorescence imaging beyond the shot-noise limit, we present DeepCAD-RT, a self-supervised deep learning method for real-time noise suppression. Based on our previous framework DeepCAD, we reduced the number of network parameters by 94%, memory consumption by 27-fold and processing time by a factor of 20, allowing real-time processing on a two-photon microscope. A high imaging signal-to-noise ratio can be acquired with tenfold fewer photons than in standard imaging approaches. We demonstrate the utility of DeepCAD-RT in a series of photon-limited experiments, including in vivo calcium imaging of mice, zebrafish larva and fruit flies, recording of three-dimensional (3D) migration of neutrophils after acute brain injury and imaging of 3D dynamics of cortical ATP release. DeepCAD-RT will facilitate the morphological and functional interrogation of biological dynamics with a minimal photon budget.
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Chen Z, Zheng W, Pang K, Xia D, Guo L, Chen X, Wu F, Wang H. Weakly supervised learning analysis of Aβ plaque distribution in the whole rat brain. Front Neurosci 2023; 16:1097019. [PMID: 36741048 PMCID: PMC9892753 DOI: 10.3389/fnins.2022.1097019] [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: 11/13/2022] [Accepted: 12/30/2022] [Indexed: 01/20/2023] Open
Abstract
Alzheimer's disease (AD) is a great challenge for the world and hardly to be cured, partly because of the lack of animal models that fully mimic pathological progress. Recently, a rat model exhibiting the most pathological symptoms of AD has been reported. However, high-resolution imaging and accurate quantification of beta-amyloid (Aβ) plaques in the whole rat brain have not been fulfilled due to substantial technical challenges. In this paper, a high-efficiency data analysis pipeline is proposed to quantify Aβ plaques in whole rat brain through several terabytes of image data acquired by a high-speed volumetric imaging approach we have developed previously. A novel segmentation framework applying a high-performance weakly supervised learning method which can dramatically reduce the human labeling consumption is described in this study. The effectiveness of our segmentation framework is validated with different metrics. The segmented Aβ plaques were mapped to a standard rat brain atlas for quantitative analysis of the Aβ distribution in each brain area. This pipeline may also be applied to the segmentation and accurate quantification of other non-specific morphology objects.
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Affiliation(s)
- Zhiyi Chen
- National Engineering Laboratory for Brain-Inspired Intelligence Technology and Application, School of Information Science and Technology, University of Science and Technology of China, Hefei, China,Institute of Artificial Intelligence, Hefei Comprehensive National Science Center, Hefei, China
| | - Weijie Zheng
- Institute of Artificial Intelligence, Hefei Comprehensive National Science Center, Hefei, China,AHU-IAI AI Joint Laboratory, Anhui University, Hefei, China
| | - Keliang Pang
- School of Pharmaceutical Sciences, IDG/McGovern Institute for Brain Research, Tsinghua University-Peking University Joint Center for Life Sciences, Tsinghua University, Beijing, China,*Correspondence: Keliang Pang,
| | - Debin Xia
- National Engineering Laboratory for Brain-Inspired Intelligence Technology and Application, School of Information Science and Technology, University of Science and Technology of China, Hefei, China,Institute of Artificial Intelligence, Hefei Comprehensive National Science Center, Hefei, China
| | - Lingxiao Guo
- Institute of Artificial Intelligence, Hefei Comprehensive National Science Center, Hefei, China
| | - Xuejin Chen
- National Engineering Laboratory for Brain-Inspired Intelligence Technology and Application, School of Information Science and Technology, University of Science and Technology of China, Hefei, China,Institute of Artificial Intelligence, Hefei Comprehensive National Science Center, Hefei, China
| | - Feng Wu
- National Engineering Laboratory for Brain-Inspired Intelligence Technology and Application, School of Information Science and Technology, University of Science and Technology of China, Hefei, China,Institute of Artificial Intelligence, Hefei Comprehensive National Science Center, Hefei, China
| | - Hao Wang
- National Engineering Laboratory for Brain-Inspired Intelligence Technology and Application, School of Information Science and Technology, University of Science and Technology of China, Hefei, China,Institute of Artificial Intelligence, Hefei Comprehensive National Science Center, Hefei, China,Hao Wang,
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36
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Dandekar T, Kunz M. How Is Our Own Extremely Powerful Brain Constructed? Bioinformatics 2023. [DOI: 10.1007/978-3-662-65036-3_15] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/06/2023] Open
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37
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Pi C, Tang W, Li Z, Liu Y, Jing Q, Dai W, Wang T, Yang C, Yu S. Cortical pain induced by optogenetic cortical spreading depression: from whole brain activity mapping. Mol Brain 2022; 15:99. [PMID: 36471383 PMCID: PMC9721019 DOI: 10.1186/s13041-022-00985-w] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Accepted: 11/22/2022] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND Cortical spreading depression (CSD) is an electrophysiological event underlying migraine aura. Traditional CSD models are invasive and often cause injuries. The aim of the study was to establish a minimally invasive optogenetic CSD model and identify the active networks after CSD using whole-brain activity mapping. METHODS CSD was induced in mice by light illumination, and their periorbital thresholds and behaviours in the open field, elevated plus-maze and light-aversion were recorded. Using c-fos, we mapped the brain activity after CSD. The whole brain was imaged, reconstructed and analyzed using the Volumetric Imaging with Synchronized on-the-fly-scan and Readout technique. To ensure the accuracy of the results, the immunofluorescence staining method was used to verify the imaging results. RESULTS The optogenetic CSD model showed significantly decreased periorbital thresholds, increased facial grooming and freezing behaviours and prominent light-aversion behaviours. Brain activity mapping revealed that the somatosensory, primary sensory, olfactory, basal ganglia and default mode networks were activated. However, the thalamus and trigeminal nucleus caudalis were not activated. CONCLUSIONS Optogenetic CSD model could mimic the behaviours of headache and photophobia. Moreover, the optogenetic CSD could activate multiple sensory cortical regions without the thalamus or trigeminal nucleus caudalis to induce cortical pain.
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Affiliation(s)
- Chenghui Pi
- grid.216938.70000 0000 9878 7032College of Medicine, Nankai University, Tianjin, China ,grid.414252.40000 0004 1761 8894Department of Neurology, The First Medical Centre, Chinese PLA General Hospital, Beijing, China
| | - Wenjing Tang
- grid.414252.40000 0004 1761 8894Department of Neurology, The First Medical Centre, Chinese PLA General Hospital, Beijing, China
| | - Zhishuai Li
- grid.9227.e0000000119573309The State Key Laboratory for Management and Control of Complex Systems, Institute of Automation, Chinese Academy of Sciences, Beijing, China
| | - Yang Liu
- grid.414252.40000 0004 1761 8894Department of Neurology, The First Medical Centre, Chinese PLA General Hospital, Beijing, China
| | - Qi Jing
- grid.59053.3a0000000121679639School of Life Sciences, University of Science and Technology of China, Hefei, China
| | - Wei Dai
- grid.414252.40000 0004 1761 8894Department of Neurology, The First Medical Centre, Chinese PLA General Hospital, Beijing, China
| | - Tao Wang
- grid.414252.40000 0004 1761 8894Department of Neurology, The First Medical Centre, Chinese PLA General Hospital, Beijing, China
| | - Chunxiao Yang
- grid.216938.70000 0000 9878 7032College of Medicine, Nankai University, Tianjin, China ,grid.414252.40000 0004 1761 8894Department of Neurology, The First Medical Centre, Chinese PLA General Hospital, Beijing, China
| | - Shengyuan Yu
- grid.216938.70000 0000 9878 7032College of Medicine, Nankai University, Tianjin, China ,grid.414252.40000 0004 1761 8894Department of Neurology, The First Medical Centre, Chinese PLA General Hospital, Beijing, China
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Liu Q, Wu Y, Wang H, Jia F, Xu F. Viral Tools for Neural Circuit Tracing. Neurosci Bull 2022; 38:1508-1518. [PMID: 36136267 PMCID: PMC9723069 DOI: 10.1007/s12264-022-00949-z] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2022] [Accepted: 06/09/2022] [Indexed: 10/14/2022] Open
Abstract
Neural circuits provide an anatomical basis for functional networks. Therefore, dissecting the structure of neural circuits is essential to understanding how the brain works. Recombinant neurotropic viruses are important tools for neural circuit tracing with many advantages over non-viral tracers: they allow for anterograde, retrograde, and trans-synaptic delivery of tracers in a cell type-specific, circuit-selective manner. In this review, we summarize the recent developments in the viral tools for neural circuit tracing, discuss the key principles of using viral tools in neuroscience research, and highlight innovations for developing and optimizing viral tools for neural circuit tracing across diverse animal species, including nonhuman primates.
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Affiliation(s)
- Qing Liu
- The Brain Cognition and Brain Disease Institute (BCBDI), Shenzhen Key Laboratory of Viral Vectors for Biomedicine, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen-Hong Kong Institute of Brain Science-Shenzhen Fundamental Research Institutions, NMPA Key Laboratory for Research and Evaluation of Viral Vector Technology in Cell and Gene Therapy Medicinal Products, Shenzhen Key Laboratory of Quality Control Technology for Virus-Based Therapeutics, Guangdong Provincial Medical Products Administration, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yang Wu
- State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, Key Laboratory of Magnetic Resonance in Biological Systems, Wuhan Center for Magnetic Resonance, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences, Wuhan, 430071, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Huadong Wang
- The Brain Cognition and Brain Disease Institute (BCBDI), Shenzhen Key Laboratory of Viral Vectors for Biomedicine, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen-Hong Kong Institute of Brain Science-Shenzhen Fundamental Research Institutions, NMPA Key Laboratory for Research and Evaluation of Viral Vector Technology in Cell and Gene Therapy Medicinal Products, Shenzhen Key Laboratory of Quality Control Technology for Virus-Based Therapeutics, Guangdong Provincial Medical Products Administration, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Fan Jia
- The Brain Cognition and Brain Disease Institute (BCBDI), Shenzhen Key Laboratory of Viral Vectors for Biomedicine, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen-Hong Kong Institute of Brain Science-Shenzhen Fundamental Research Institutions, NMPA Key Laboratory for Research and Evaluation of Viral Vector Technology in Cell and Gene Therapy Medicinal Products, Shenzhen Key Laboratory of Quality Control Technology for Virus-Based Therapeutics, Guangdong Provincial Medical Products Administration, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Fuqiang Xu
- The Brain Cognition and Brain Disease Institute (BCBDI), Shenzhen Key Laboratory of Viral Vectors for Biomedicine, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen-Hong Kong Institute of Brain Science-Shenzhen Fundamental Research Institutions, NMPA Key Laboratory for Research and Evaluation of Viral Vector Technology in Cell and Gene Therapy Medicinal Products, Shenzhen Key Laboratory of Quality Control Technology for Virus-Based Therapeutics, Guangdong Provincial Medical Products Administration, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China.
- State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, Key Laboratory of Magnetic Resonance in Biological Systems, Wuhan Center for Magnetic Resonance, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences, Wuhan, 430071, China.
- 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.
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Han T, Wu J, Luo W, Wang H, Jin Z, Qu L. Review of Generative Adversarial Networks in mono- and cross-modal biomedical image registration. Front Neuroinform 2022; 16:933230. [PMID: 36483313 PMCID: PMC9724825 DOI: 10.3389/fninf.2022.933230] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2022] [Accepted: 10/13/2022] [Indexed: 09/19/2023] Open
Abstract
Biomedical image registration refers to aligning corresponding anatomical structures among different images, which is critical to many tasks, such as brain atlas building, tumor growth monitoring, and image fusion-based medical diagnosis. However, high-throughput biomedical image registration remains challenging due to inherent variations in the intensity, texture, and anatomy resulting from different imaging modalities, different sample preparation methods, or different developmental stages of the imaged subject. Recently, Generative Adversarial Networks (GAN) have attracted increasing interest in both mono- and cross-modal biomedical image registrations due to their special ability to eliminate the modal variance and their adversarial training strategy. This paper provides a comprehensive survey of the GAN-based mono- and cross-modal biomedical image registration methods. According to the different implementation strategies, we organize the GAN-based mono- and cross-modal biomedical image registration methods into four categories: modality translation, symmetric learning, adversarial strategies, and joint training. The key concepts, the main contributions, and the advantages and disadvantages of the different strategies are summarized and discussed. Finally, we analyze the statistics of all the cited works from different points of view and reveal future trends for GAN-based biomedical image registration studies.
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Affiliation(s)
- Tingting Han
- Ministry of Education Key Laboratory of Intelligent Computing and Signal Processing, Information Materials and Intelligent Sensing Laboratory of Anhui Province, Anhui University, Hefei, China
| | - Jun Wu
- Ministry of Education Key Laboratory of Intelligent Computing and Signal Processing, Information Materials and Intelligent Sensing Laboratory of Anhui Province, Anhui University, Hefei, China
| | - Wenting Luo
- Ministry of Education Key Laboratory of Intelligent Computing and Signal Processing, Information Materials and Intelligent Sensing Laboratory of Anhui Province, Anhui University, Hefei, China
| | - Huiming Wang
- Ministry of Education Key Laboratory of Intelligent Computing and Signal Processing, Information Materials and Intelligent Sensing Laboratory of Anhui Province, Anhui University, Hefei, China
| | - Zhe Jin
- School of Artificial Intelligence, Anhui University, Hefei, China
| | - Lei Qu
- Ministry of Education Key Laboratory of Intelligent Computing and Signal Processing, Information Materials and Intelligent Sensing Laboratory of Anhui Province, Anhui University, Hefei, China
- Institute of Artificial Intelligence, Hefei Comprehensive National Science Center, Hefei, China
- SEU-ALLEN Joint Center, Institute for Brain and Intelligence, Southeast University, Nanjing, China
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40
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Sun L, Xu M, Shi Y, Xu Y, Chen J, He L. Decoding psychosis: from national genome project to national brain project. Gen Psychiatr 2022; 35:e100889. [PMID: 36248024 PMCID: PMC9511649 DOI: 10.1136/gpsych-2022-100889] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Accepted: 09/05/2022] [Indexed: 11/17/2022] Open
Abstract
The mind has puzzled humans for centuries, and its disorders, such as psychoses, have caused tremendous difficulties. However, relatively recent biotechnological breakthroughs, such as DNA technology and neuroimaging, have empowered scientists to explore the more fundamental aspects of psychosis. From searching for psychosis-causing genes to imaging the depths of the brain, scientists worldwide seek novel methods to understand the mind and the causes of its disorders. This article will briefly review the history of understanding and managing psychosis and the main findings of modern genetic research and then attempt to stimulate thought for decoding the biological mechanisms of psychosis in the present era of brain science.
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Affiliation(s)
- Liya Sun
- Shanghai Mental Health Center Editorial Office, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders, Ministry of Education, Shanghai Jiao Tong University, Shanghai, China
| | - Manfei Xu
- Shanghai Mental Health Center Editorial Office, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Yongyong Shi
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders, Ministry of Education, Shanghai Jiao Tong University, Shanghai, China
| | - Yifeng Xu
- Shanghai Mental Health Center Editorial Office, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Shanghai Key Laboratory of Psychotic Disorders, Shanghai Mental Health Centre, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Jinghong Chen
- Shanghai Mental Health Center Editorial Office, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Shanghai Key Laboratory of Psychotic Disorders, Shanghai Mental Health Centre, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Lin He
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders, Ministry of Education, Shanghai Jiao Tong University, Shanghai, China
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41
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Poo MM. Transcriptome, connectome and neuromodulation of the primate brain. Cell 2022; 185:2636-2639. [PMID: 35732175 DOI: 10.1016/j.cell.2022.05.011] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2022] [Revised: 05/12/2022] [Accepted: 05/13/2022] [Indexed: 01/21/2023]
Abstract
Single-cell transcriptomic analysis has facilitated cell type identification in the brain and mapping of cell type-specific connectomes, helping to elucidate neural circuits underlying brain functions and to treat brain disorders by neuromodulation. Yet, we lack a consensual definition of neuronal types/subtypes and clear distinction between cause and effect within interconnected networks.
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Affiliation(s)
- Mu-Ming Poo
- Institute of Neuroscience, Chinese Academy of Sciences; Shanghai Center for Brain Science and Brain-inspired Technology, Lingang Laboratory, Shanghai, China.
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42
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Shen Y, Ding LF, Yang CY, Xu F, Lau PM, Bi GQ. Mapping big brains at subcellular resolution in the era of big data in zoology. Zool Res 2022; 43:597-599. [PMID: 35726585 PMCID: PMC9336455 DOI: 10.24272/j.issn.2095-8137.2022.138] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2022] [Accepted: 06/15/2022] [Indexed: 11/07/2022] Open
Affiliation(s)
- Yan Shen
- Interdisciplinary Center for Brain Information, Brain Cognition and Brain Disease Institute, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences
- Shenzhen-Hong Kong Institute of Brain Science-Shenzhen Fundamental Research Institutions, Shenzhen, Guangdong 518000, China
| | - Lu-Feng Ding
- Interdisciplinary Center for Brain Information, Brain Cognition and Brain Disease Institute, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences
- Shenzhen-Hong Kong Institute of Brain Science-Shenzhen Fundamental Research Institutions, Shenzhen, Guangdong 518000, China
| | - Chao-Yu Yang
- Interdisciplinary Center for Brain Information, Brain Cognition and Brain Disease Institute, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences
- Shenzhen-Hong Kong Institute of Brain Science-Shenzhen Fundamental Research Institutions, Shenzhen, Guangdong 518000, China
- Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui 230001, China
| | - Fang Xu
- Interdisciplinary Center for Brain Information, Brain Cognition and Brain Disease Institute, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences
- Shenzhen-Hong Kong Institute of Brain Science-Shenzhen Fundamental Research Institutions, Shenzhen, Guangdong 518000, China
| | - Pak-Ming Lau
- Interdisciplinary Center for Brain Information, Brain Cognition and Brain Disease Institute, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences
- Shenzhen-Hong Kong Institute of Brain Science-Shenzhen Fundamental Research Institutions, Shenzhen, Guangdong 518000, China
- Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui 230001, China
- Institute of Artificial Intelligence, Hefei Comprehensive National Science Center, Hefei, Anhui 230001, China
| | - Guo-Qiang Bi
- Interdisciplinary Center for Brain Information, Brain Cognition and Brain Disease Institute, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences
- Shenzhen-Hong Kong Institute of Brain Science-Shenzhen Fundamental Research Institutions, Shenzhen, Guangdong 518000, China
- Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui 230001, China
- Institute of Artificial Intelligence, Hefei Comprehensive National Science Center, Hefei, Anhui 230001, China. E-mail:
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43
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Wang XJ. Theory of the Multiregional Neocortex: Large-Scale Neural Dynamics and Distributed Cognition. Annu Rev Neurosci 2022; 45:533-560. [PMID: 35803587 DOI: 10.1146/annurev-neuro-110920-035434] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
The neocortex is a complex neurobiological system with many interacting regions. How these regions work together to subserve flexible behavior and cognition has become increasingly amenable to rigorous research. Here, I review recent experimental and theoretical work on the modus operandi of a multiregional cortex. These studies revealed several general principles for the neocortical interareal connectivity, low-dimensional macroscopic gradients of biological properties across cortical areas, and a hierarchy of timescales for information processing. Theoretical work suggests testable predictions regarding differential excitation and inhibition along feedforward and feedback pathways in the cortical hierarchy. Furthermore, modeling of distributed working memory and simple decision-making has given rise to a novel mathematical concept, dubbed bifurcation in space, that potentially explains how different cortical areas, with a canonical circuit organization but gradients of biological heterogeneities, are able to subserve their respective (e.g., sensory coding versus executive control) functions in a modularly organized brain.
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Affiliation(s)
- Xiao-Jing Wang
- Center for Neural Science, New York University, New York, NY, USA;
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44
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Kolluru C, Todd A, Upadhye AR, Liu Y, Berezin MY, Fereidouni F, Levenson RM, Wang Y, Shoffstall AJ, Jenkins MW, Wilson DL. Imaging peripheral nerve micro-anatomy with MUSE, 2D and 3D approaches. Sci Rep 2022; 12:10205. [PMID: 35715554 PMCID: PMC9205958 DOI: 10.1038/s41598-022-14166-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2022] [Accepted: 06/02/2022] [Indexed: 01/25/2023] Open
Abstract
Understanding peripheral nerve micro-anatomy can assist in the development of safe and effective neuromodulation devices. However, current approaches for imaging nerve morphology at the fiber level are either cumbersome, require substantial instrumentation, have a limited volume of view, or are limited in resolution/contrast. We present alternative methods based on MUSE (Microscopy with Ultraviolet Surface Excitation) imaging to investigate peripheral nerve morphology, both in 2D and 3D. For 2D imaging, fixed samples are imaged on a conventional MUSE system either label free (via auto-fluorescence) or after staining with fluorescent dyes. This method provides a simple and rapid technique to visualize myelinated nerve fibers at specific locations along the length of the nerve and perform measurements of fiber morphology (e.g., axon diameter and g-ratio). For 3D imaging, a whole-mount staining and MUSE block-face imaging method is developed that can be used to characterize peripheral nerve micro-anatomy and improve the accuracy of computational models in neuromodulation. Images of rat sciatic and human cadaver tibial nerves are presented, illustrating the applicability of the method in different preclinical models.
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Affiliation(s)
- Chaitanya Kolluru
- grid.67105.350000 0001 2164 3847Department of Biomedical Engineering, Case Western Reserve University, Cleveland, OH 44106 USA
| | - Austin Todd
- grid.267309.90000 0001 0629 5880University of Texas Health Science Center at San Antonio, San Antonio, TX 78229 USA
| | - Aniruddha R. Upadhye
- grid.67105.350000 0001 2164 3847Department of Biomedical Engineering, Case Western Reserve University, Cleveland, OH 44106 USA ,grid.410349.b0000 0004 5912 6484APT Center, Louis Stokes Cleveland VA Medical Center, Cleveland, OH 44106 USA
| | - Yehe Liu
- grid.67105.350000 0001 2164 3847Department of Biomedical Engineering, Case Western Reserve University, Cleveland, OH 44106 USA
| | - Mikhail Y. Berezin
- grid.4367.60000 0001 2355 7002Department of Radiology, Washington University in St. Louis, St. Louis, MO 63110 USA
| | - Farzad Fereidouni
- grid.416958.70000 0004 0413 7653Department of Pathology and Laboratory Medicine, UC Davis Health, Sacramento, CA 95817 USA
| | - Richard M. Levenson
- grid.416958.70000 0004 0413 7653Department of Pathology and Laboratory Medicine, UC Davis Health, Sacramento, CA 95817 USA
| | - Yanming Wang
- grid.67105.350000 0001 2164 3847Department of Radiology, Case Western Reserve University, Cleveland, OH 44106 USA
| | - Andrew J. Shoffstall
- grid.67105.350000 0001 2164 3847Department of Biomedical Engineering, Case Western Reserve University, Cleveland, OH 44106 USA ,grid.410349.b0000 0004 5912 6484APT Center, Louis Stokes Cleveland VA Medical Center, Cleveland, OH 44106 USA
| | - Michael W. Jenkins
- grid.67105.350000 0001 2164 3847Department of Biomedical Engineering, Case Western Reserve University, Cleveland, OH 44106 USA ,grid.67105.350000 0001 2164 3847Department of Pediatrics, Case Western Reserve University, Cleveland, OH 44106 USA
| | - David L. Wilson
- grid.67105.350000 0001 2164 3847Department of Biomedical Engineering, Case Western Reserve University, Cleveland, OH 44106 USA ,grid.67105.350000 0001 2164 3847Department of Radiology, Case Western Reserve University, Cleveland, OH 44106 USA
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Guo S, Xue J, Liu J, Ye X, Guo Y, Liu D, Zhao X, Xiong F, Han X, Peng H. Smart imaging to empower brain-wide neuroscience at single-cell levels. Brain Inform 2022; 9:10. [PMID: 35543774 PMCID: PMC9095808 DOI: 10.1186/s40708-022-00158-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Accepted: 04/12/2022] [Indexed: 11/10/2022] Open
Abstract
A deep understanding of the neuronal connectivity and networks with detailed cell typing across brain regions is necessary to unravel the mechanisms behind the emotional and memorial functions as well as to find the treatment of brain impairment. Brain-wide imaging with single-cell resolution provides unique advantages to access morphological features of a neuron and to investigate the connectivity of neuron networks, which has led to exciting discoveries over the past years based on animal models, such as rodents. Nonetheless, high-throughput systems are in urgent demand to support studies of neural morphologies at larger scale and more detailed level, as well as to enable research on non-human primates (NHP) and human brains. The advances in artificial intelligence (AI) and computational resources bring great opportunity to 'smart' imaging systems, i.e., to automate, speed up, optimize and upgrade the imaging systems with AI and computational strategies. In this light, we review the important computational techniques that can support smart systems in brain-wide imaging at single-cell resolution.
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Affiliation(s)
- Shuxia Guo
- Institute for Brain and Intelligence, Southeast University, Nanjing, 210096, Jiangsu, China.
| | - Jie Xue
- Institute for Brain and Intelligence, Southeast University, Nanjing, 210096, Jiangsu, China
| | - Jian Liu
- Institute for Brain and Intelligence, Southeast University, Nanjing, 210096, Jiangsu, China
| | - Xiangqiao Ye
- Institute for Brain and Intelligence, Southeast University, Nanjing, 210096, Jiangsu, China
| | - Yichen Guo
- Institute for Brain and Intelligence, Southeast University, Nanjing, 210096, Jiangsu, China
| | - Di Liu
- Institute for Brain and Intelligence, Southeast University, Nanjing, 210096, Jiangsu, China
| | - Xuan Zhao
- Institute for Brain and Intelligence, Southeast University, Nanjing, 210096, Jiangsu, China
| | - Feng Xiong
- Institute for Brain and Intelligence, Southeast University, Nanjing, 210096, Jiangsu, China
| | - Xiaofeng Han
- Institute for Brain and Intelligence, Southeast University, Nanjing, 210096, Jiangsu, China.
| | - Hanchuan Peng
- Institute for Brain and Intelligence, Southeast University, Nanjing, 210096, Jiangsu, China
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46
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Shi W, Xue M, Wu F, Fan K, Chen QY, Xu F, Li X, Bi G, Lu J, Zhuo M. Whole-brain mapping of efferent projections of the anterior cingulate cortex in adult male mice. Mol Pain 2022; 18:17448069221094529. [PMID: 35354345 PMCID: PMC9083044 DOI: 10.1177/17448069221094529] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The anterior cingulate cortex (ACC) is a key cortical region that plays an important role in pain perception and emotional functions. Previous studies of the ACC projections have been collected primarily from monkeys, rabbits and rats. Due to technological advances, such as gene manipulation, recent progress has been made in our understanding of the molecular and cellular mechanisms of the ACC-related chronic pain and emotion is mainly obtained from adult mice. Few anatomic studies have examined the whole-brain projections of the ACC in adult mice. In the present study, we examined the continuous axonal outputs of the ACC in the whole brain of adult male mice. We used the virus anterograde tracing technique and an ultrahigh-speed imaging method of Volumetric Imaging with Synchronized on-the-fly-scan and Readout (VISoR). We created a three-dimensional (3D) reconstruction of mouse brains. We found that the ACC projected ipsilaterally primarily to the caudate putamen (CPu), ventral thalamic nucleus, zona incerta (ZI), periaqueductal gray (PAG), superior colliculus (SC), interpolar spinal trigeminal nucleus (Sp5I), and dorsal medullary reticular nucleus (MdD). The ACC also projected to contralateral brain regions, including the ACC, reuniens thalamic nucleus (Re), PAG, Sp5I, and MdD. Our results provide a whole-brain mapping of efferent projections from the ACC in adult male mice, and these findings are critical for future studies of the molecular and synaptic mechanisms of the ACC and its related network in mouse models of brain diseases.
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Affiliation(s)
| | - Man Xue
- 12480Xi'an Jiaotong University
| | - Fengyi Wu
- 85411Chinese Academy of Sciences Shenzhen Institutes of Advanced Technology
| | - Kexin Fan
- 598900Xi'an Jiaotong University School of Basic Medical Sciences
| | - Qi-Yu Chen
- 85411Chinese Academy of Sciences Shenzhen Institutes of Advanced Technology
| | - Fang Xu
- 85411Chinese Academy of Sciences Shenzhen Institutes of Advanced Technology
| | | | - Guoqiang Bi
- 85411Chinese Academy of Sciences Shenzhen Institutes of Advanced Technology
| | | | - Min Zhuo
- Physiology7938University of Toronto
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Xue M, Shi W, Zhou S, Li Y, Wu F, Chen QY, Liu RH, Zhou Z, Zhang YX, Chen Y, Xu F, Bi G, Li X, Lu J, Zhuo M. Mapping thalamic-anterior cingulate monosynaptic inputs in adult mice. Mol Pain 2022; 18:17448069221087034. [PMID: 35240879 PMCID: PMC9009153 DOI: 10.1177/17448069221087034] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
The anterior cingulate cortex (ACC) is located in the frontal part of the
cingulate cortex, and plays important roles in pain perception and emotion. The
thalamocortical pathway is the major sensory input to the ACC. Previous studies
have show that several different thalamic nuclei receive projection fibers from
spinothalamic tract, that in turn send efferents to the ACC by using neural
tracers and optical imaging methods. Most of these studies were performed in
monkeys, cats, and rats, few studies were reported systematically in adult mice.
Adult mice, especially genetically modified mice, have provided molecular and
synaptic mechanisms for cortical plasticity and modulation in the ACC. In the
present study, we utilized rabies virus-based retrograde tracing system to map
thalamic-anterior cingulate monosynaptic inputs in adult mice. We also combined
with a new high-throughput VISoR imaging technique to generate a
three-dimensional whole-brain reconstruction, especially the thalamus. We found
that cortical neurons in the ACC received direct projections from different
sub-nuclei in the thalamus, including the anterior, ventral, medial, lateral,
midline, and intralaminar thalamic nuclei. These findings provide key anatomic
evidences for the connection between the thalamus and ACC.
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Affiliation(s)
- Man Xue
- 12480Xi'an Jiaotong University
| | | | - Sibo Zhou
- 528996Xi'an Jiaotong University Frontier Institute of Science and Technology
| | | | | | | | | | | | | | | | | | | | | | | | - Min Zhuo
- Qingdao International Academician Park
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48
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Xu R, Bichot NP, Takahashi A, Desimone R. The cortical connectome of primate lateral prefrontal cortex. Neuron 2022; 110:312-327.e7. [PMID: 34739817 PMCID: PMC8776613 DOI: 10.1016/j.neuron.2021.10.018] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2021] [Revised: 09/09/2021] [Accepted: 10/11/2021] [Indexed: 01/21/2023]
Abstract
The lateral prefrontal cortex (LPFC) of primates plays an important role in executive control, but how it interacts with the rest of the cortex remains unclear. To address this, we densely mapped the cortical connectome of LPFC, using electrical microstimulation combined with functional MRI (EM-fMRI). We found isomorphic mappings between LPFC and five major processing domains composing most of the cerebral cortex except early sensory and motor areas. An LPFC grid of ∼200 stimulation sites topographically mapped to separate grids of activation sites in the five domains, coarsely resembling how the visual cortex maps the retina. The temporal and parietal maps largely overlapped in LPFC, suggesting topographically organized convergence of the ventral and dorsal streams, and the other maps overlapped at least partially. Thus, the LPFC contains overlapping, millimeter-scale maps that mirror the organization of major cortical processing domains, supporting LPFC's role in coordinating activity within and across these domains.
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Affiliation(s)
- Rui Xu
- Department of Brain and Cognitive Sciences, McGovern Institute for Brain Research, Massachusetts Institute of Technology, Cambridge, MA, USA.
| | - Narcisse P Bichot
- Department of Brain and Cognitive Sciences, McGovern Institute for Brain Research, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Atsushi Takahashi
- Department of Brain and Cognitive Sciences, McGovern Institute for Brain Research, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Robert Desimone
- Department of Brain and Cognitive Sciences, McGovern Institute for Brain Research, Massachusetts Institute of Technology, Cambridge, MA, USA
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49
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Newmaster KT, Kronman FA, Wu YT, Kim Y. Seeing the Forest and Its Trees Together: Implementing 3D Light Microscopy Pipelines for Cell Type Mapping in the Mouse Brain. Front Neuroanat 2022; 15:787601. [PMID: 35095432 PMCID: PMC8794814 DOI: 10.3389/fnana.2021.787601] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2021] [Accepted: 12/02/2021] [Indexed: 12/14/2022] Open
Abstract
The brain is composed of diverse neuronal and non-neuronal cell types with complex regional connectivity patterns that create the anatomical infrastructure underlying cognition. Remarkable advances in neuroscience techniques enable labeling and imaging of these individual cell types and their interactions throughout intact mammalian brains at a cellular resolution allowing neuroscientists to examine microscopic details in macroscopic brain circuits. Nevertheless, implementing these tools is fraught with many technical and analytical challenges with a need for high-level data analysis. Here we review key technical considerations for implementing a brain mapping pipeline using the mouse brain as a primary model system. Specifically, we provide practical details for choosing methods including cell type specific labeling, sample preparation (e.g., tissue clearing), microscopy modalities, image processing, and data analysis (e.g., image registration to standard atlases). We also highlight the need to develop better 3D atlases with standardized anatomical labels and nomenclature across species and developmental time points to extend the mapping to other species including humans and to facilitate data sharing, confederation, and integrative analysis. In summary, this review provides key elements and currently available resources to consider while developing and implementing high-resolution mapping methods.
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Affiliation(s)
- Kyra T Newmaster
- Department of Neural and Behavioral Sciences, The Pennsylvania State University, Hershey, PA, United States
| | - Fae A Kronman
- Department of Neural and Behavioral Sciences, The Pennsylvania State University, Hershey, PA, United States
| | - Yuan-Ting Wu
- Department of Neural and Behavioral Sciences, The Pennsylvania State University, Hershey, PA, United States
| | - Yongsoo Kim
- Department of Neural and Behavioral Sciences, The Pennsylvania State University, Hershey, PA, United States
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50
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Qu L, Li Y, Xie P, Liu L, Wang Y, Wu J, Liu Y, Wang T, Li L, Guo K, Wan W, Ouyang L, Xiong F, Kolstad AC, Wu Z, Xu F, Zheng Y, Gong H, Luo Q, Bi G, Dong H, Hawrylycz M, Zeng H, Peng H. Cross-modal coherent registration of whole mouse brains. Nat Methods 2022; 19:111-118. [PMID: 34887551 DOI: 10.1038/s41592-021-01334-w] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2021] [Accepted: 10/28/2021] [Indexed: 01/04/2023]
Abstract
Recent whole-brain mapping projects are collecting large-scale three-dimensional images using modalities such as serial two-photon tomography, fluorescence micro-optical sectioning tomography, light-sheet fluorescence microscopy, volumetric imaging with synchronous on-the-fly scan and readout or magnetic resonance imaging. Registration of these multi-dimensional whole-brain images onto a standard atlas is essential for characterizing neuron types and constructing brain wiring diagrams. However, cross-modal image registration is challenging due to intrinsic variations of brain anatomy and artifacts resulting from different sample preparation methods and imaging modalities. We introduce a cross-modal registration method, mBrainAligner, which uses coherent landmark mapping and deep neural networks to align whole mouse brain images to the standard Allen Common Coordinate Framework atlas. We build a brain atlas for the fluorescence micro-optical sectioning tomography modality to facilitate single-cell mapping, and used our method to generate a whole-brain map of three-dimensional single-neuron morphology and neuron cell types.
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Affiliation(s)
- Lei Qu
- Ministry of Education Key Laboratory of Intelligent Computation & Signal Processing, Information Materials and Intelligent Sensing Laboratory of Anhui Province, School of Electronics and Information Engineering, Anhui University, Hefei, China
- SEU-ALLEN Joint Center, Institute for Brain and Intelligence, Southeast University, Nanjing, China
- Institute of Artificial Intelligence, Hefei Comprehensive National Science Center, Hefei, China
| | - Yuanyuan Li
- Ministry of Education Key Laboratory of Intelligent Computation & Signal Processing, Information Materials and Intelligent Sensing Laboratory of Anhui Province, School of Electronics and Information Engineering, Anhui University, Hefei, China
| | - Peng Xie
- SEU-ALLEN Joint Center, Institute for Brain and Intelligence, Southeast University, Nanjing, China
| | - Lijuan Liu
- SEU-ALLEN Joint Center, Institute for Brain and Intelligence, Southeast University, Nanjing, China
- Ministry of Education Key Laboratory of Developmental Genes and Human Disease, School of Life Science and Technology, Southeast University, Nanjing, China
| | - Yimin Wang
- SEU-ALLEN Joint Center, Institute for Brain and Intelligence, Southeast University, Nanjing, China
- School of Computer Engineering and Science, Shanghai University, Shanghai, China
| | - Jun Wu
- Ministry of Education Key Laboratory of Intelligent Computation & Signal Processing, Information Materials and Intelligent Sensing Laboratory of Anhui Province, School of Electronics and Information Engineering, Anhui University, Hefei, China
| | - Yu Liu
- Ministry of Education Key Laboratory of Intelligent Computation & Signal Processing, Information Materials and Intelligent Sensing Laboratory of Anhui Province, School of Electronics and Information Engineering, Anhui University, Hefei, China
| | - Tao Wang
- Ministry of Education Key Laboratory of Intelligent Computation & Signal Processing, Information Materials and Intelligent Sensing Laboratory of Anhui Province, School of Electronics and Information Engineering, Anhui University, Hefei, China
| | - Longfei Li
- Ministry of Education Key Laboratory of Intelligent Computation & Signal Processing, Information Materials and Intelligent Sensing Laboratory of Anhui Province, School of Electronics and Information Engineering, Anhui University, Hefei, China
| | - Kaixuan Guo
- Ministry of Education Key Laboratory of Intelligent Computation & Signal Processing, Information Materials and Intelligent Sensing Laboratory of Anhui Province, School of Electronics and Information Engineering, Anhui University, Hefei, China
| | - Wan Wan
- Ministry of Education Key Laboratory of Intelligent Computation & Signal Processing, Information Materials and Intelligent Sensing Laboratory of Anhui Province, School of Electronics and Information Engineering, Anhui University, Hefei, China
| | - Lei Ouyang
- Ministry of Education Key Laboratory of Intelligent Computation & Signal Processing, Information Materials and Intelligent Sensing Laboratory of Anhui Province, School of Electronics and Information Engineering, Anhui University, Hefei, China
| | - Feng Xiong
- SEU-ALLEN Joint Center, Institute for Brain and Intelligence, Southeast University, Nanjing, China
| | - Anna C Kolstad
- Department of Cell, Developmental & Regenerative Biology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Zhuhao Wu
- Department of Cell, Developmental & Regenerative Biology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Fang Xu
- CAS Key Laboratory of Brain Connectome and Manipulation, Interdisciplinary Center for Brain Information, The Brain Cognition and Brain Disease Institute, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen-Hong Kong Institute of Brain Science-Shenzhen Fundamental Research Institutions, Shenzhen, China
| | | | - Hui Gong
- Britton Chance Center for Biomedical Photonics, Wuhan National Laboratory for Optoelectronics, MoE Key Laboratory for Biomedical Photonics, Huazhong University of Science and Technology, Wuhan, China
- HUST-Suzhou Institute for Brainsmatics, JITRI Institute for Brainsmatics, Suzhou, China
- CAS Center for Excellence in Brain Science and Intelligence Technology, Chinese Academy of Science, Shanghai, China
| | - Qingming Luo
- Britton Chance Center for Biomedical Photonics, Wuhan National Laboratory for Optoelectronics, MoE Key Laboratory for Biomedical Photonics, Huazhong University of Science and Technology, Wuhan, China
- HUST-Suzhou Institute for Brainsmatics, JITRI Institute for Brainsmatics, Suzhou, China
- CAS Center for Excellence in Brain Science and Intelligence Technology, Chinese Academy of Science, Shanghai, China
- School of Biomedical Engineering, Hainan University, Haikou, China
| | - Guoqiang Bi
- Institute of Artificial Intelligence, Hefei Comprehensive National Science Center, Hefei, China
- CAS Key Laboratory of Brain Connectome and Manipulation, Interdisciplinary Center for Brain Information, The Brain Cognition and Brain Disease Institute, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen-Hong Kong Institute of Brain Science-Shenzhen Fundamental Research Institutions, Shenzhen, China
- Center for Integrative Imaging, Hefei National Laboratory for Physical Sciences at the Microscale, and School of Life Sciences, University of Science and Technology of China, Hefei, China
| | - Hongwei Dong
- Center for Integrative Connectomics, Department of Neurobiology, David Geffen School of Medicine at UCLA, Los Angeles, CA, USA
| | | | - Hongkui Zeng
- Allen Institute for Brain Science, Seattle, WA, USA
| | - Hanchuan Peng
- SEU-ALLEN Joint Center, Institute for Brain and Intelligence, Southeast University, Nanjing, China.
- Allen Institute for Brain Science, Seattle, WA, USA.
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