1
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Gliko O, Mallory M, Dalley R, Gala R, Gornet J, Zeng H, Sorensen SA, Sümbül U. High-throughput analysis of dendrite and axonal arbors reveals transcriptomic correlates of neuroanatomy. Nat Commun 2024; 15:6337. [PMID: 39068160 PMCID: PMC11283452 DOI: 10.1038/s41467-024-50728-9] [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: 12/01/2023] [Accepted: 07/16/2024] [Indexed: 07/30/2024] Open
Abstract
Neuronal anatomy is central to the organization and function of brain cell types. However, anatomical variability within apparently homogeneous populations of cells can obscure such insights. Here, we report large-scale automation of neuronal morphology reconstruction and analysis on a dataset of 813 inhibitory neurons characterized using the Patch-seq method, which enables measurement of multiple properties from individual neurons, including local morphology and transcriptional signature. We demonstrate that these automated reconstructions can be used in the same manner as manual reconstructions to understand the relationship between some, but not all, cellular properties used to define cell types. We uncover gene expression correlates of laminar innervation on multiple transcriptomically defined neuronal subclasses and types. In particular, our results reveal correlates of the variability in Layer 1 (L1) axonal innervation in a transcriptomically defined subpopulation of Martinotti cells in the adult mouse neocortex.
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Affiliation(s)
| | | | | | | | - James Gornet
- California Institute of Technology, Pasadena, CA, USA
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2
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Feng J, Dong H, Lischinsky JE, Zhou J, Deng F, Zhuang C, Miao X, Wang H, Li G, Cai R, Xie H, Cui G, Lin D, Li Y. Monitoring norepinephrine release in vivo using next-generation GRAB NE sensors. Neuron 2024; 112:1930-1942.e6. [PMID: 38547869 DOI: 10.1016/j.neuron.2024.03.001] [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: 06/15/2023] [Revised: 01/21/2024] [Accepted: 03/01/2024] [Indexed: 06/22/2024]
Abstract
Norepinephrine (NE) is an essential biogenic monoamine neurotransmitter. The first-generation NE sensor makes in vivo, real-time, cell-type-specific and region-specific NE detection possible, but its low NE sensitivity limits its utility. Here, we developed the second-generation GPCR-activation-based NE sensors (GRABNE2m and GRABNE2h) with a superior response and high sensitivity and selectivity to NE both in vitro and in vivo. Notably, these sensors can detect NE release triggered by either optogenetic or behavioral stimuli in freely moving mice, producing robust signals in the locus coeruleus and hypothalamus. With the development of a novel transgenic mouse line, we recorded both NE release and calcium dynamics with dual-color fiber photometry throughout the sleep-wake cycle; moreover, dual-color mesoscopic imaging revealed cell-type-specific spatiotemporal dynamics of NE and calcium during sensory processing and locomotion. Thus, these new GRABNE sensors are valuable tools for monitoring the precise spatiotemporal release of NE in vivo, providing new insights into the physiological and pathophysiological roles of NE.
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Affiliation(s)
- Jiesi Feng
- State Key Laboratory of Membrane Biology, School of Life Sciences, Peking University, Beijing 100871, China; PKU-IDG/McGovern Institute for Brain Research, Beijing 100871, China; Peking-Tsinghua Center for Life Sciences, New Cornerstone Science Laboratory, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing 100871, China.
| | - Hui Dong
- State Key Laboratory of Membrane Biology, School of Life Sciences, Peking University, Beijing 100871, China; PKU-IDG/McGovern Institute for Brain Research, Beijing 100871, China; Peking-Tsinghua Center for Life Sciences, New Cornerstone Science Laboratory, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing 100871, China
| | - Julieta E Lischinsky
- Neuroscience Institute, New York University School of Medicine, New York, NY 10016, USA
| | - Jingheng Zhou
- Neurobiology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC 27709, USA
| | - Fei Deng
- State Key Laboratory of Membrane Biology, School of Life Sciences, Peking University, Beijing 100871, China; PKU-IDG/McGovern Institute for Brain Research, Beijing 100871, China
| | - Chaowei Zhuang
- Department of Automation, Tsinghua University, Beijing 100084, China
| | - Xiaolei Miao
- State Key Laboratory of Membrane Biology, School of Life Sciences, Peking University, Beijing 100871, China; PKU-IDG/McGovern Institute for Brain Research, Beijing 100871, China; Department of Anesthesiology, Beijing Chaoyang Hospital, Capital Medical University, 100020 Beijing, China
| | - Huan Wang
- State Key Laboratory of Membrane Biology, School of Life Sciences, Peking University, Beijing 100871, China; PKU-IDG/McGovern Institute for Brain Research, Beijing 100871, China
| | - Guochuan Li
- State Key Laboratory of Membrane Biology, School of Life Sciences, Peking University, Beijing 100871, China
| | - Ruyi Cai
- State Key Laboratory of Membrane Biology, School of Life Sciences, Peking University, Beijing 100871, China
| | - Hao Xie
- Department of Automation, Tsinghua University, Beijing 100084, China
| | - Guohong Cui
- Neurobiology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC 27709, USA
| | - Dayu Lin
- Neuroscience Institute, New York University School of Medicine, New York, NY 10016, USA
| | - Yulong Li
- State Key Laboratory of Membrane Biology, School of Life Sciences, Peking University, Beijing 100871, China; PKU-IDG/McGovern Institute for Brain Research, Beijing 100871, China; Peking-Tsinghua Center for Life Sciences, New Cornerstone Science Laboratory, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing 100871, China; Chinese Institute for Brain Research, Beijing 102206, China; Institute of Molecular Physiology, Shenzhen Bay Laboratory, Shenzhen, Guangdong 518055, China; National Biomedical Imaging Center, Peking University, Beijing 100871, China.
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3
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Papale AE, Harish M, Paletzki RF, O’Connor NJ, Eastwood BS, Seal RP, Williamson RS, Gerfen CR, Hooks BM. Symmetry in frontal but not motor and somatosensory cortical projections. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.06.02.543431. [PMID: 37398221 PMCID: PMC10312571 DOI: 10.1101/2023.06.02.543431] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/04/2023]
Abstract
Neocortex and striatum are topographically organized for sensory and motor functions. While sensory and motor areas are lateralized for touch and motor control, respectively, frontal areas are involved in decision making, where lateralization of function may be less important. This study contrasted the topographic precision of cell type-specific ipsilateral and contralateral cortical projections while varying the injection site location in transgenic mice of both sexes. While sensory cortical areas had strongly topographic outputs to ipsilateral cortex and striatum, they were weaker and not as topographically precise to contralateral targets. Motor cortex had somewhat stronger projections, but still relatively weak contralateral topography. In contrast, frontal cortical areas had high degrees of topographic similarity for both ipsilateral and contralateral projections to cortex and striatum. Corticothalamic organization is mainly ipsilateral, with weaker, more medial contralateral projections. Corticostriatal computations might integrate input outside closed basal ganglia loops using contralateral projections, enabling the two hemispheres to act as a unit to converge on one result in motor planning and decision making.
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Affiliation(s)
- Andrew E. Papale
- Department of Psychiatry, University of Pittsburgh School of Medicine, Pittsburgh, PA
| | - Madhumita Harish
- Department of Neurobiology, University of Pittsburgh School of Medicine, Pittsburgh, PA
| | | | | | | | - Rebecca P. Seal
- Department of Neurobiology, University of Pittsburgh School of Medicine, Pittsburgh, PA
| | - Ross S. Williamson
- Department of Otolaryngology, University of Pittsburgh School of Medicine, Pittsburgh, PA
| | | | - Bryan M. Hooks
- Department of Neurobiology, University of Pittsburgh School of Medicine, Pittsburgh, PA
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4
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Piluso S, Souedet N, Jan C, Hérard AS, Clouchoux C, Delzescaux T. giRAff: an automated atlas segmentation tool adapted to single histological slices. Front Neurosci 2024; 17:1230814. [PMID: 38274499 PMCID: PMC10808556 DOI: 10.3389/fnins.2023.1230814] [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: 05/29/2023] [Accepted: 10/31/2023] [Indexed: 01/27/2024] Open
Abstract
Conventional histology of the brain remains the gold standard in the analysis of animal models. In most biological studies, standard protocols usually involve producing a limited number of histological slices to be analyzed. These slices are often selected into a specific anatomical region of interest or around a specific pathological lesion. Due to the lack of automated solutions to analyze such single slices, neurobiologists perform the segmentation of anatomical regions manually most of the time. Because the task is long, tedious, and operator-dependent, we propose an automated atlas segmentation method called giRAff, which combines rigid and affine registrations and is suitable for conventional histological protocols involving any number of single slices from a given mouse brain. In particular, the method has been tested on several routine experimental protocols involving different anatomical regions of different sizes and for several brains. For a given set of single slices, the method can automatically identify the corresponding slices in the mouse Allen atlas template with good accuracy and segmentations comparable to those of an expert. This versatile and generic method allows the segmentation of any single slice without additional anatomical context in about 1 min. Basically, our proposed giRAff method is an easy-to-use, rapid, and automated atlas segmentation tool compliant with a wide variety of standard histological protocols.
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Affiliation(s)
- Sébastien Piluso
- Université Paris-Saclay, CEA, CNRS, MIRCen, Laboratoire des Maladies Neurodégénératives, Fontenay-aux-Roses, France
- WITSEE, Paris, France
| | - Nicolas Souedet
- Université Paris-Saclay, CEA, CNRS, MIRCen, Laboratoire des Maladies Neurodégénératives, Fontenay-aux-Roses, France
| | - Caroline Jan
- Université Paris-Saclay, CEA, CNRS, MIRCen, Laboratoire des Maladies Neurodégénératives, Fontenay-aux-Roses, France
| | - Anne-Sophie Hérard
- Université Paris-Saclay, CEA, CNRS, MIRCen, Laboratoire des Maladies Neurodégénératives, Fontenay-aux-Roses, France
| | | | - Thierry Delzescaux
- Université Paris-Saclay, CEA, CNRS, MIRCen, Laboratoire des Maladies Neurodégénératives, Fontenay-aux-Roses, France
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5
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Koelle S, Mastrovito D, Whitesell JD, Hirokawa KE, Zeng H, Meila M, Harris JA, Mihalas S. Modeling the cell-type-specific mesoscale murine connectome with anterograde tracing experiments. Netw Neurosci 2023; 7:1497-1512. [PMID: 38144695 PMCID: PMC10745083 DOI: 10.1162/netn_a_00337] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2021] [Accepted: 09/10/2023] [Indexed: 12/26/2023] Open
Abstract
The Allen Mouse Brain Connectivity Atlas consists of anterograde tracing experiments targeting diverse structures and classes of projecting neurons. Beyond regional anterograde tracing done in C57BL/6 wild-type mice, a large fraction of experiments are performed using transgenic Cre-lines. This allows access to cell-class-specific whole-brain connectivity information, with class defined by the transgenic lines. However, even though the number of experiments is large, it does not come close to covering all existing cell classes in every area where they exist. Here, we study how much we can fill in these gaps and estimate the cell-class-specific connectivity function given the simplifying assumptions that nearby voxels have smoothly varying projections, but that these projection tensors can change sharply depending on the region and class of the projecting cells. This paper describes the conversion of Cre-line tracer experiments into class-specific connectivity matrices representing the connection strengths between source and target structures. We introduce and validate a novel statistical model for creation of connectivity matrices. We extend the Nadaraya-Watson kernel learning method that we previously used to fill in spatial gaps to also fill in gaps in cell-class connectivity information. To do this, we construct a "cell-class space" based on class-specific averaged regionalized projections and combine smoothing in 3D space as well as in this abstract space to share information between similar neuron classes. Using this method, we construct a set of connectivity matrices using multiple levels of resolution at which discontinuities in connectivity are assumed. We show that the connectivities obtained from this model display expected cell-type- and structure-specific connectivities. We also show that the wild-type connectivity matrix can be factored using a sparse set of factors, and analyze the informativeness of this latent variable model.
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Affiliation(s)
- Samson Koelle
- Allen Institute for Brain Science, Seattle, WA, USA
- Department of Statistics, University of Washington, Seattle, WA, USA
| | | | | | | | - Hongkui Zeng
- Allen Institute for Brain Science, Seattle, WA, USA
| | - Marina Meila
- Department of Statistics, University of Washington, Seattle, WA, USA
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6
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Chen C, Tassou A, Morales V, Scherrer G. Graph theory analysis reveals an assortative pain network vulnerable to attacks. Sci Rep 2023; 13:21985. [PMID: 38082002 PMCID: PMC10713541 DOI: 10.1038/s41598-023-49458-7] [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: 07/12/2023] [Accepted: 12/08/2023] [Indexed: 12/18/2023] Open
Abstract
The neural substrate of pain experience has been described as a dense network of connected brain regions. However, the connectivity pattern of these brain regions remains elusive, precluding a deeper understanding of how pain emerges from the structural connectivity. Here, we employ graph theory to systematically characterize the architecture of a comprehensive pain network, including both cortical and subcortical brain areas. This structural brain network consists of 49 nodes denoting pain-related brain areas, linked by edges representing their relative incoming and outgoing axonal projection strengths. Within this network, 63% of brain areas share reciprocal connections, reflecting a dense network. The clustering coefficient, a measurement of the probability that adjacent nodes are connected, indicates that brain areas in the pain network tend to cluster together. Community detection, the process of discovering cohesive groups in complex networks, successfully reveals two known subnetworks that specifically mediate the sensory and affective components of pain, respectively. Assortativity analysis, which evaluates the tendency of nodes to connect with other nodes that have similar features, indicates that the pain network is assortative. Finally, robustness, the resistance of a complex network to failures and perturbations, indicates that the pain network displays a high degree of error tolerance (local failure rarely affects the global information carried by the network) but is vulnerable to attacks (selective removal of hub nodes critically changes network connectivity). Taken together, graph theory analysis unveils an assortative structural pain network in the brain that processes nociceptive information. Furthermore, the vulnerability of this network to attack presents the possibility of alleviating pain by targeting the most connected brain areas in the network.
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Affiliation(s)
- Chong Chen
- Department of Cell Biology and Physiology, The University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA.
- UNC Neuroscience Center, The University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA.
- Department of Pharmacology, The University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA.
| | - Adrien Tassou
- Department of Cell Biology and Physiology, The University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
- UNC Neuroscience Center, The University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
- Department of Pharmacology, The University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Valentina Morales
- Department of Cell Biology and Physiology, The University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
- UNC Neuroscience Center, The University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
- Department of Pharmacology, The University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Grégory Scherrer
- Department of Cell Biology and Physiology, The University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA.
- UNC Neuroscience Center, The University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA.
- Department of Pharmacology, The University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA.
- New York Stem Cell Foundation ‒ Robertson Investigator, Chapel Hill, NC, 27599, USA.
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7
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Cecyn MN, Abrahao KP. Where do you measure the Bregma for rodent stereotaxic surgery? IBRO Neurosci Rep 2023; 15:143-148. [PMID: 38204571 PMCID: PMC10776314 DOI: 10.1016/j.ibneur.2023.07.003] [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: 02/03/2023] [Accepted: 07/26/2023] [Indexed: 01/12/2024] Open
Abstract
The advent of the stereotaxic apparatus developed by Clarke and Horsley revolutionized neuroscience research, enabling precise 3D navigation along the skull mediolateral, anteroposterior, and dorsoventral axes. In rodents, the Bregma is widely used as the origin reference point for the stereotaxic coordinates, but the specific procedure for its measurement varies among different laboratories. Notably, the renowned brain atlas developed by Paxinos and Franklin lacks explicit instructions on the Bregma determination. Recent studies have found discrepancies in skull and brain landmark measurements. This review describes the commonly used brain atlases and highlights the limitations in accurately measuring the stereotaxic coordinates. In addition, we propose alternative and more reliable approaches to measure the Bregma. It is imperative to address the misconceptions about the accuracy of stereotaxic surgeries, as it can significantly impact a substantial portion of neuroscience research.
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Affiliation(s)
- Marianna Nogueira Cecyn
- Departamento de Psicobiologia, Escola Paulista de Medicina, Universidade Federal de São Paulo, São Paulo, SP, Brazil
| | - Karina Possa Abrahao
- Departamento de Psicobiologia, Escola Paulista de Medicina, Universidade Federal de São Paulo, São Paulo, SP, Brazil
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8
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Carey H, Pegios M, Martin L, Saleeba C, Turner AJ, Everett NA, Bjerke IE, Puchades MA, Bjaalie JG, McMullan S. DeepSlice: rapid fully automatic registration of mouse brain imaging to a volumetric atlas. Nat Commun 2023; 14:5884. [PMID: 37735467 PMCID: PMC10514056 DOI: 10.1038/s41467-023-41645-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2023] [Accepted: 09/12/2023] [Indexed: 09/23/2023] Open
Abstract
Registration of data to a common frame of reference is an essential step in the analysis and integration of diverse neuroscientific data. To this end, volumetric brain atlases enable histological datasets to be spatially registered and analyzed, yet accurate registration remains expertise-dependent and slow. In order to address this limitation, we have trained a neural network, DeepSlice, to register mouse brain histological images to the Allen Brain Common Coordinate Framework, retaining registration accuracy while improving speed by >1000 fold.
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Affiliation(s)
- Harry Carey
- Macquarie Medical School, Faculty of Medicine, Health & Human Sciences, Macquarie University, Marsfield, NSW, Australia
- Department of Molecular Medicine, Institute of Basic Medical Sciences, University of Oslo, Oslo, Norway
| | - Michael Pegios
- Macquarie Medical School, Faculty of Medicine, Health & Human Sciences, Macquarie University, Marsfield, NSW, Australia
| | | | - Chris Saleeba
- Macquarie Medical School, Faculty of Medicine, Health & Human Sciences, Macquarie University, Marsfield, NSW, Australia
| | - Anita J Turner
- Macquarie Medical School, Faculty of Medicine, Health & Human Sciences, Macquarie University, Marsfield, NSW, Australia
| | | | - Ingvild E Bjerke
- Department of Molecular Medicine, Institute of Basic Medical Sciences, University of Oslo, Oslo, Norway
| | - Maja A Puchades
- Department of Molecular Medicine, Institute of Basic Medical Sciences, University of Oslo, Oslo, Norway
| | - Jan G Bjaalie
- Department of Molecular Medicine, Institute of Basic Medical Sciences, University of Oslo, Oslo, Norway
| | - Simon McMullan
- Macquarie Medical School, Faculty of Medicine, Health & Human Sciences, Macquarie University, Marsfield, NSW, Australia.
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9
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Andrianova L, Yanakieva S, Margetts-Smith G, Kohli S, Brady ES, Aggleton JP, Craig MT. No evidence from complementary data sources of a direct glutamatergic projection from the mouse anterior cingulate area to the hippocampal formation. eLife 2023; 12:e77364. [PMID: 37545394 PMCID: PMC10425170 DOI: 10.7554/elife.77364] [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: 01/26/2022] [Accepted: 08/03/2023] [Indexed: 08/08/2023] Open
Abstract
The connectivity and interplay between the prefrontal cortex and hippocampus underpin various key cognitive processes, with changes in these interactions being implicated in both neurodevelopmental and neurodegenerative conditions. Understanding the precise cellular connections through which this circuit is organised is, therefore, vital for understanding these same processes. Overturning earlier findings, a recent study described a novel excitatory projection from anterior cingulate area to dorsal hippocampus. We sought to validate this unexpected finding using multiple, complementary methods: anterograde and retrograde anatomical tracing, using anterograde and retrograde adeno-associated viral vectors, monosynaptic rabies tracing, and the Fast Blue classical tracer. Additionally, an extensive data search of the Allen Projection Brain Atlas database was conducted to find the stated projection within any of the deposited anatomical studies as an independent verification of our own results. However, we failed to find any evidence of a direct, monosynaptic glutamatergic projection from mouse anterior cingulate cortex to the hippocampus proper.
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Affiliation(s)
- Lilya Andrianova
- Institute of Biomedical and Clinical Science, University of Exeter Medical SchoolExeterUnited Kingdom
- School of Psychology & Neuroscience, College of Medical, Veterinary and Life Sciences, University of GlasgowGlasgowUnited Kingdom
- School of Infection & Immunity, College of Medical, Veterinary and Life Sciences, University of GlasgowGlasgowUnited Kingdom
| | - Steliana Yanakieva
- School of Infection & Immunity, College of Medical, Veterinary and Life Sciences, University of GlasgowGlasgowUnited Kingdom
| | - Gabriella Margetts-Smith
- Institute of Biomedical and Clinical Science, University of Exeter Medical SchoolExeterUnited Kingdom
| | - Shivali Kohli
- Institute of Biomedical and Clinical Science, University of Exeter Medical SchoolExeterUnited Kingdom
| | - Erica S Brady
- Institute of Biomedical and Clinical Science, University of Exeter Medical SchoolExeterUnited Kingdom
| | - John P Aggleton
- School of Psychology, Cardiff UniversityCardiffUnited Kingdom
| | - Michael T Craig
- Institute of Biomedical and Clinical Science, University of Exeter Medical SchoolExeterUnited Kingdom
- School of Psychology & Neuroscience, College of Medical, Veterinary and Life Sciences, University of GlasgowGlasgowUnited Kingdom
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10
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Skibbe H, Rachmadi MF, Nakae K, Gutierrez CE, Hata J, Tsukada H, Poon C, Schlachter M, Doya K, Majka P, Rosa MGP, Okano H, Yamamori T, Ishii S, Reisert M, Watakabe A. The Brain/MINDS Marmoset Connectivity Resource: An open-access platform for cellular-level tracing and tractography in the primate brain. PLoS Biol 2023; 21:e3002158. [PMID: 37384809 DOI: 10.1371/journal.pbio.3002158] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2023] [Accepted: 05/11/2023] [Indexed: 07/01/2023] Open
Abstract
The primate brain has unique anatomical characteristics, which translate into advanced cognitive, sensory, and motor abilities. Thus, it is important that we gain insight on its structure to provide a solid basis for models that will clarify function. Here, we report on the implementation and features of the Brain/MINDS Marmoset Connectivity Resource (BMCR), a new open-access platform that provides access to high-resolution anterograde neuronal tracer data in the marmoset brain, integrated to retrograde tracer and tractography data. Unlike other existing image explorers, the BMCR allows visualization of data from different individuals and modalities in a common reference space. This feature, allied to an unprecedented high resolution, enables analyses of features such as reciprocity, directionality, and spatial segregation of connections. The present release of the BMCR focuses on the prefrontal cortex (PFC), a uniquely developed region of the primate brain that is linked to advanced cognition, including the results of 52 anterograde and 164 retrograde tracer injections in the cortex of the marmoset. Moreover, the inclusion of tractography data from diffusion MRI allows systematic analyses of this noninvasive modality against gold-standard cellular connectivity data, enabling detection of false positives and negatives, which provide a basis for future development of tractography. This paper introduces the BMCR image preprocessing pipeline and resources, which include new tools for exploring and reviewing the data.
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Affiliation(s)
- Henrik Skibbe
- Brain Image Analysis Unit, RIKEN Center for Brain Science, Wako, Saitama, Japan
| | | | - Ken Nakae
- Exploratory Research Center on Life and Living Systems (ExCELLS), National Institutes of Natural Sciences, Aichi, Japan
| | - Carlos Enrique Gutierrez
- Neural Computation Unit, Okinawa Institute of Science and Technology Graduate University, Onna Village, Japan
| | - Junichi Hata
- Laboratory for Marmoset Neural Architecture, RIKEN Center for Brain Science, Wako, Saitama, Japan
- Department of Physiology, Keio University School of Medicine, Tokyo, Japan
| | - Hiromichi Tsukada
- Neural Computation Unit, Okinawa Institute of Science and Technology Graduate University, Onna Village, Japan
- Center for Mathematical Science and Artificial Intelligence, Chubu University, Kasugai, Aichi, Japan
| | - Charissa Poon
- Brain Image Analysis Unit, RIKEN Center for Brain Science, Wako, Saitama, Japan
| | - Matthias Schlachter
- Brain Image Analysis Unit, RIKEN Center for Brain Science, Wako, Saitama, Japan
| | - Kenji Doya
- Neural Computation Unit, Okinawa Institute of Science and Technology Graduate University, Onna Village, Japan
| | - Piotr Majka
- Laboratory of Neuroinformatics, Nencki Institute of Experimental Biology of Polish Academy of Sciences, Warsaw, Poland
- Australian Research Council, Centre of Excellence for Integrative Brain Function, Monash University Node, Clayton, Australia
- Neuroscience Program, Biomedicine Discovery Institute and Department of Physiology, Monash University, Clayton, Australia
| | - Marcello G P Rosa
- Australian Research Council, Centre of Excellence for Integrative Brain Function, Monash University Node, Clayton, Australia
- Neuroscience Program, Biomedicine Discovery Institute and Department of Physiology, Monash University, Clayton, Australia
| | - Hideyuki Okano
- Laboratory for Marmoset Neural Architecture, RIKEN Center for Brain Science, Wako, Saitama, Japan
- Department of Physiology, Keio University School of Medicine, Tokyo, Japan
| | - Tetsuo Yamamori
- Laboratory of Haptic Perception and Cognitive Physiology, RIKEN Center for Brain Science, Wako, Saitama, Japan
- Department of Marmoset Biology and Medicine, Central Institute for Experimental Animals, Kawasaki, Japan
| | - Shin Ishii
- Department of Systems Science, Kyoto University, Kyoto, Japan
| | - Marco Reisert
- Brain Image Analysis Unit, RIKEN Center for Brain Science, Wako, Saitama, Japan
- Department of Stereotactic and Functional Neurosurgery, Medical Center of the University of Freiburg, Freiburg Im Breisgau, Germany
- Medical Faculty of the University of Freiburg, Freiburg Im Breisgau, Germany
- Department of Diagnostic and Interventional Radiology, Medical Physics, Medical Center-University of Freiburg, Freiburg Im Breisgau, Germany
| | - Akiya Watakabe
- Laboratory of Haptic Perception and Cognitive Physiology, RIKEN Center for Brain Science, Wako, Saitama, Japan
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11
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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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12
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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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13
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Chen C, Tassou A, Morales V, Scherrer G. Graph theory analysis reveals an assortative pain network vulnerable to attacks. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.03.08.531580. [PMID: 36945626 PMCID: PMC10028857 DOI: 10.1101/2023.03.08.531580] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/12/2023]
Abstract
The neural substrate of pain experience has been described as a dense network of connected brain regions. However, the connectivity pattern of these brain regions remains elusive, precluding a deeper understanding of how pain emerges from the structural connectivity. Here, we use graph theory to systematically characterize the architecture of a comprehensive pain network, including both cortical and subcortical brain areas. This structural brain network consists of 49 nodes denoting pain-related brain areas, linked by edges representing their relative incoming and outgoing axonal projection strengths. Sixty-three percent of brain areas in this structural pain network share reciprocal connections, reflecting a dense network. The clustering coefficient, a measurement of the probability that adjacent nodes are connected, indicates that brain areas in the pain network tend to cluster together. Community detection, the process of discovering cohesive groups in complex networks, successfully reveals two known subnetworks that specifically mediate the sensory and affective components of pain, respectively. Assortativity analysis, which evaluates the tendency of nodes to connect with other nodes with similar features, indicates that the pain network is assortative. Finally, robustness, the resistance of a complex network to failures and perturbations, indicates that the pain network displays a high degree of error tolerance (local failure rarely affects the global information carried by the network) but is vulnerable to attacks (selective removal of hub nodes critically changes network connectivity). Taken together, graph theory analysis unveils an assortative structural pain network in the brain processing nociceptive information, and the vulnerability of this network to attack opens up the possibility of alleviating pain by targeting the most connected brain areas in the network.
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14
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Perens J, Salinas CG, Roostalu U, Skytte JL, Gundlach C, Hecksher-Sørensen J, Dahl AB, Dyrby TB. Multimodal 3D Mouse Brain Atlas Framework with the Skull-Derived Coordinate System. Neuroinformatics 2023; 21:269-286. [PMID: 36809643 DOI: 10.1007/s12021-023-09623-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/01/2023] [Indexed: 02/23/2023]
Abstract
Magnetic resonance imaging (MRI) and light-sheet fluorescence microscopy (LSFM) are technologies that enable non-disruptive 3-dimensional imaging of whole mouse brains. A combination of complementary information from both modalities is desirable for studying neuroscience in general, disease progression and drug efficacy. Although both technologies rely on atlas mapping for quantitative analyses, the translation of LSFM recorded data to MRI templates has been complicated by the morphological changes inflicted by tissue clearing and the enormous size of the raw data sets. Consequently, there is an unmet need for tools that will facilitate fast and accurate translation of LSFM recorded brains to in vivo, non-distorted templates. In this study, we have developed a bidirectional multimodal atlas framework that includes brain templates based on both imaging modalities, region delineations from the Allen's Common Coordinate Framework, and a skull-derived stereotaxic coordinate system. The framework also provides algorithms for bidirectional transformation of results obtained using either MR or LSFM (iDISCO cleared) mouse brain imaging while the coordinate system enables users to easily assign in vivo coordinates across the different brain templates.
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Affiliation(s)
- Johanna Perens
- Gubra ApS, Hørsholm, Denmark.,Section for Visual Computing, Department of Applied Mathematics and Computer Science, Technical University Denmark, Kongens Lyngby, Denmark.,Danish Research Centre for Magnetic Resonance, Centre for Functional and Diagnostic Imaging and Research, Copenhagen University Hospital Amager and Hvidovre, Copenhagen, Denmark
| | | | | | | | - Carsten Gundlach
- Neutrons and X-rays for Materials Physics, Department of Physics, Technical University Denmark, Kongens Lyngby, Denmark
| | | | - Anders Bjorholm Dahl
- Section for Visual Computing, Department of Applied Mathematics and Computer Science, Technical University Denmark, Kongens Lyngby, Denmark
| | - Tim B Dyrby
- Section for Visual Computing, Department of Applied Mathematics and Computer Science, Technical University Denmark, Kongens Lyngby, Denmark.,Danish Research Centre for Magnetic Resonance, Centre for Functional and Diagnostic Imaging and Research, Copenhagen University Hospital Amager and Hvidovre, Copenhagen, Denmark
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15
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Yao S, Wang Q, Hirokawa KE, Ouellette B, Ahmed R, Bomben J, Brouner K, Casal L, Caldejon S, Cho A, Dotson NI, Daigle TL, Egdorf T, Enstrom R, Gary A, Gelfand E, Gorham M, Griffin F, Gu H, Hancock N, Howard R, Kuan L, Lambert S, Lee EK, Luviano J, Mace K, Maxwell M, Mortrud MT, Naeemi M, Nayan C, Ngo NK, Nguyen T, North K, Ransford S, Ruiz A, Seid S, Swapp J, Taormina MJ, Wakeman W, Zhou T, Nicovich PR, Williford A, Potekhina L, McGraw M, Ng L, Groblewski PA, Tasic B, Mihalas S, Harris JA, Cetin A, Zeng H. A whole-brain monosynaptic input connectome to neuron classes in mouse visual cortex. Nat Neurosci 2023; 26:350-364. [PMID: 36550293 PMCID: PMC10039800 DOI: 10.1038/s41593-022-01219-x] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2021] [Accepted: 10/27/2022] [Indexed: 12/24/2022]
Abstract
Identification of structural connections between neurons is a prerequisite to understanding brain function. Here we developed a pipeline to systematically map brain-wide monosynaptic input connections to genetically defined neuronal populations using an optimized rabies tracing system. We used mouse visual cortex as the exemplar system and revealed quantitative target-specific, layer-specific and cell-class-specific differences in its presynaptic connectomes. The retrograde connectivity indicates the presence of ventral and dorsal visual streams and further reveals topographically organized and continuously varying subnetworks mediated by different higher visual areas. The visual cortex hierarchy can be derived from intracortical feedforward and feedback pathways mediated by upper-layer and lower-layer input neurons. We also identify a new role for layer 6 neurons in mediating reciprocal interhemispheric connections. This study expands our knowledge of the visual system connectomes and demonstrates that the pipeline can be scaled up to dissect connectivity of different cell populations across the mouse brain.
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Affiliation(s)
- Shenqin Yao
- Allen Institute for Brain Science, Seattle, WA, USA.
| | - Quanxin Wang
- Allen Institute for Brain Science, Seattle, WA, USA
| | - Karla E Hirokawa
- Allen Institute for Brain Science, Seattle, WA, USA
- Cajal Neuroscience, Seattle, WA, USA
| | | | | | | | | | - Linzy Casal
- Allen Institute for Brain Science, Seattle, WA, USA
| | | | - Andy Cho
- Allen Institute for Brain Science, Seattle, WA, USA
| | | | | | - Tom Egdorf
- Allen Institute for Brain Science, Seattle, WA, USA
| | | | - Amanda Gary
- Allen Institute for Brain Science, Seattle, WA, USA
| | | | | | | | - Hong Gu
- Allen Institute for Brain Science, Seattle, WA, USA
| | | | | | - Leonard Kuan
- Allen Institute for Brain Science, Seattle, WA, USA
| | | | | | | | - Kyla Mace
- Allen Institute for Brain Science, Seattle, WA, USA
| | | | | | | | | | | | | | - Kat North
- Allen Institute for Brain Science, Seattle, WA, USA
- Cajal Neuroscience, Seattle, WA, USA
| | | | | | - Sam Seid
- Allen Institute for Brain Science, Seattle, WA, USA
| | - Jackie Swapp
- Allen Institute for Brain Science, Seattle, WA, USA
| | | | | | - Thomas Zhou
- Allen Institute for Brain Science, Seattle, WA, USA
| | - Philip R Nicovich
- Allen Institute for Brain Science, Seattle, WA, USA
- Cajal Neuroscience, Seattle, WA, USA
| | | | | | - Medea McGraw
- Allen Institute for Brain Science, Seattle, WA, USA
| | - Lydia Ng
- Allen Institute for Brain Science, Seattle, WA, USA
| | | | | | | | - Julie A Harris
- Allen Institute for Brain Science, Seattle, WA, USA
- Cajal Neuroscience, Seattle, WA, USA
| | - Ali Cetin
- Allen Institute for Brain Science, Seattle, WA, USA
- CNC Program, Stanford University, Palo Alto, CA, USA
| | - Hongkui Zeng
- Allen Institute for Brain Science, Seattle, WA, USA.
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16
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A method to estimate the cellular composition of the mouse brain from heterogeneous datasets. PLoS Comput Biol 2022; 18:e1010739. [PMID: 36542673 PMCID: PMC9838873 DOI: 10.1371/journal.pcbi.1010739] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2022] [Revised: 01/13/2023] [Accepted: 11/15/2022] [Indexed: 12/24/2022] Open
Abstract
The mouse brain contains a rich diversity of inhibitory neuron types that have been characterized by their patterns of gene expression. However, it is still unclear how these cell types are distributed across the mouse brain. We developed a computational method to estimate the densities of different inhibitory neuron types across the mouse brain. Our method allows the unbiased integration of diverse and disparate datasets into one framework to predict inhibitory neuron densities for uncharted brain regions. We constrained our estimates based on previously computed brain-wide neuron densities, gene expression data from in situ hybridization image stacks together with a wide range of values reported in the literature. Using constrained optimization, we derived coherent estimates of cell densities for the different inhibitory neuron types. We estimate that 20.3% of all neurons in the mouse brain are inhibitory. Among all inhibitory neurons, 18% predominantly express parvalbumin (PV), 16% express somatostatin (SST), 3% express vasoactive intestinal peptide (VIP), and the remainder 63% belong to the residual GABAergic population. We find that our density estimations improve as more literature values are integrated. Our pipeline is extensible, allowing new cell types or data to be integrated as they become available. The data, algorithms, software, and results of our pipeline are publicly available and update the Blue Brain Cell Atlas. This work therefore leverages the research community to collectively converge on the numbers of each cell type in each brain region.
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17
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Okoro SU, Goz RU, Njeri BW, Harish M, Ruff CF, Ross SE, Gerfen C, Hooks BM. Organization of Cortical and Thalamic Input to Inhibitory Neurons in Mouse Motor Cortex. J Neurosci 2022; 42:8095-8112. [PMID: 36104281 PMCID: PMC9637002 DOI: 10.1523/jneurosci.0950-22.2022] [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: 05/18/2022] [Revised: 09/01/2022] [Accepted: 09/06/2022] [Indexed: 11/21/2022] Open
Abstract
Intracortical inhibition in motor cortex (M1) regulates movement and motor learning. If cortical and thalamic inputs target different inhibitory cell types in different layers, then these afferents may play different roles in regulating M1 output. Using mice of both sexes, we quantified input to two main classes of M1 interneurons, parvalbumin+ (PV+) cells and somatostatin+ (SOM+) cells, using monosynaptic rabies tracing. We then compared anatomic and functional connectivity based on synaptic strength from sensory cortex and thalamus. Functionally, each input innervated M1 interneurons with a unique laminar profile. Different interneuron types were excited in a distinct, complementary manner, suggesting feedforward inhibition proceeds selectively via distinct circuits. Specifically, somatosensory cortex (S1) inputs primarily targeted PV+ neurons in upper layers (L2/3) but SOM+ neurons in middle layers (L5). Somatosensory thalamus [posterior nucleus (PO)] inputs targeted PV+ neurons in middle layers (L5). In contrast to sensory cortical areas, thalamic input to SOM+ neurons was equivalent to that of PV+ neurons. Thus, long-range excitatory inputs target inhibitory neurons in an area and a cell type-specific manner, which contrasts with input to neighboring pyramidal cells. In contrast to feedforward inhibition providing generic inhibitory tone in cortex, circuits are selectively organized to recruit inhibition matched to incoming excitatory circuits.SIGNIFICANCE STATEMENT M1 integrates sensory information and frontal cortical inputs to plan and control movements. Although inputs to excitatory cells are described, the synaptic circuits by which these inputs drive specific types of M1 interneurons are unknown. Anatomical results with rabies tracing and physiological quantification of synaptic strength shows that two main classes of inhibitory cells (PV+ and SOM+ interneurons) both receive substantial cortical and thalamic input, in contrast to interneurons in sensory areas (where thalamic input strongly prefers PV+ interneurons). Further, each input studied targets PV+ and SOM+ interneurons in a different fashion, suggesting that separate, specific circuits exist for recruitment of feedforward inhibition.
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Affiliation(s)
- Sandra U Okoro
- University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania 15261
| | - Roman U Goz
- University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania 15261
| | - Brigdet W Njeri
- University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania 15261
| | - Madhumita Harish
- University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania 15261
| | - Catherine F Ruff
- University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania 15261
| | - Sarah E Ross
- University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania 15261
| | - Charles Gerfen
- National Institute of Mental Health, Bethesda, Maryland 20892
| | - Bryan M Hooks
- University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania 15261
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18
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Dissection of the long-range projections of specific neurons at the synaptic level in the whole mouse brain. Proc Natl Acad Sci U S A 2022; 119:e2202536119. [PMID: 36161898 PMCID: PMC9546530 DOI: 10.1073/pnas.2202536119] [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] [Indexed: 11/18/2022] Open
Abstract
Through synaptic connections, long-range circuits transmit information among neurons and connect different brain regions to form functional motifs and execute specific functions. Tracing the synaptic distribution of specific neurons requires submicron-level resolution information. However, it is a great challenge to map the synaptic terminals completely because these fine structures span multiple regions, even in the whole brain. Here, we develop a pipeline including viral tracing, sample embedding, fluorescent micro-optical sectional tomography, and big data processing. We mapped the whole-brain distribution and architecture of long projections of the parvalbumin neurons in the basal forebrain at the synaptic level. These neurons send massive projections to multiple downstream regions with subregional preference. With three-dimensional reconstruction in the targeted areas, we found that synaptic degeneration was inconsistent with the accumulation of amyloid-β plaques but was preferred in memory-related circuits, such as hippocampal formation and thalamus, but not in most hypothalamic nuclei in 8-month-old mice with five familial Alzheimer's disease mutations. Our pipeline provides a platform for generating a whole-brain atlas of cell-type-specific synaptic terminals in the physiological and pathological brain, which can provide an important resource for the study of the organizational logic of specific neural circuits and the circuitry changes in pathological conditions.
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19
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Himthani N, Brunn M, Kim JY, Schulte M, Mang A, Biros G. CLAIRE-Parallelized Diffeomorphic Image Registration for Large-Scale Biomedical Imaging Applications. J Imaging 2022; 8:jimaging8090251. [PMID: 36135416 PMCID: PMC9501197 DOI: 10.3390/jimaging8090251] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2022] [Revised: 08/31/2022] [Accepted: 09/06/2022] [Indexed: 11/25/2022] Open
Abstract
We study the performance of CLAIRE—a diffeomorphic multi-node, multi-GPU image-registration algorithm and software—in large-scale biomedical imaging applications with billions of voxels. At such resolutions, most existing software packages for diffeomorphic image registration are prohibitively expensive. As a result, practitioners first significantly downsample the original images and then register them using existing tools. Our main contribution is an extensive analysis of the impact of downsampling on registration performance. We study this impact by comparing full-resolution registrations obtained with CLAIRE to lower resolution registrations for synthetic and real-world imaging datasets. Our results suggest that registration at full resolution can yield a superior registration quality—but not always. For example, downsampling a synthetic image from 10243 to 2563 decreases the Dice coefficient from 92% to 79%. However, the differences are less pronounced for noisy or low contrast high resolution images. CLAIRE allows us not only to register images of clinically relevant size in a few seconds but also to register images at unprecedented resolution in reasonable time. The highest resolution considered are CLARITY images of size 2816×3016×1162. To the best of our knowledge, this is the first study on image registration quality at such resolutions.
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Affiliation(s)
- Naveen Himthani
- Oden Institute, The University of Texas at Austin, Austin, TX 78712, USA
- Correspondence:
| | - Malte Brunn
- Institute for Parallel and Distributed Systems, University of Stuttgart, 70569 Stuttgart, Germany
| | - Jae-Youn Kim
- Department of Mathematics, University of Houston, Houston, TX 77004, USA
| | - Miriam Schulte
- Institute for Parallel and Distributed Systems, University of Stuttgart, 70569 Stuttgart, Germany
| | - Andreas Mang
- Department of Mathematics, University of Houston, Houston, TX 77004, USA
| | - George Biros
- Oden Institute, The University of Texas at Austin, Austin, TX 78712, USA
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20
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Li Y, Wang J, Yan X, Li H. Combined fractional anisotropy and subcortical volumetric deficits in patients with mild-to-moderate depression: Evidence from the treatment of antidepressant traditional Chinese medicine. Front Neurosci 2022; 16:959960. [PMID: 36081664 PMCID: PMC9448251 DOI: 10.3389/fnins.2022.959960] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2022] [Accepted: 07/29/2022] [Indexed: 12/03/2022] Open
Abstract
Numerous neuroimaging studies have demonstrated that diverse brain structural plasticity could occur in a human brain during a depressive episode. However, there is a lack of knowledge regarding the underlying mechanisms of mild-to-moderate depression (MMD), especially the changes of brain structural characteristics after treatment with the Shuganjieyu capsule (SG), a kind of traditional Chinese medicine that has been recommended for the specialized treatment of MMD. In this study, we investigated the structural brain plasticity in MMD that have been undergoing 8 weeks of SG treatment compared with age- and sex-matched healthy controls (HCs) and assessed the relationship between these brain structural alternations and clinical symptoms in MMD. At the baseline, we found that: (1) fractional anisotropy (FA) values in patients with MMD were found to be significantly increased in the regions of anterior limb of internal capsule (ALIC) [MNI coordinates: Peak (x/y/z) = 102, 126, 77; MMD FApeak (Mean ± SD) = 0.621 ± 0.043; HCs FApeak (Mean ± SD) = 0.524 ± 0.052; MMD > HCs, t = 9.625, p < 0.001] and posterior limb of internal capsule (PLIC) [MNI coordinates: Peak (x/y/z) = 109, 117, 87; MMD FApeak (Mean ± SD) = 0.694 ± 0.042; HCs FApeak (Mean ± SD) = 0.581 ± 0.041; MMD > HCs, t = 12.90, p < 0.001], and FA values were significantly positively correlated with HAMD scores in patients with MMD. (2) Patients with MMD showed smaller gray matter volume (GMV) of the dorsolateral prefrontal cortex (DLPFC), frontal cortex, occipital cortex, and precuneus, and the GMV of DLPFC was negatively correlated with HAMD scores. After SG treatment, we found that (1) the HAMD scores decreased; (2) FA values were significantly decreased in the regions of the ALIC and PLIC compared to those at baseline and TBSS revealed no significant differences in FA values between patients with MMD and HCs. (3) The structural characteristics of DLPFC in patients with MMD obtained at the 8th week were improved, e.g., no significant differences in GMV of DLPFC between the two groups. Taken together, our results provided neuroimaging evidence suggesting that SG is an effective treatment for patients with MMD. Moreover, alterations of GMV after 8 weeks of SG treatment indicated a potential modulation mechanism in brain structural plasticity within the DLPFC in patients with MMD.
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Affiliation(s)
- Yuan Li
- Department of Radiology, Heping Hospital Affiliated to Changzhi Medical College, Changzhi, China
| | - Junjie Wang
- Shanxi Key Laboratory of Artificial Intelligence Assisted Diagnosis and Treatment for Mental Disorder, First Hospital of Shanxi Medical University, Taiyuan, China
- Department of Psychiatry, First Hospital/First Clinical Medical College of Shanxi Medical University, Taiyuan, China
| | - Xu Yan
- Department of Medical Imaging, Changzhi Medical College, Changzhi, China
| | - Hong Li
- Shanxi Key Laboratory of Artificial Intelligence Assisted Diagnosis and Treatment for Mental Disorder, First Hospital of Shanxi Medical University, Taiyuan, China
- Department of Psychiatry, First Hospital/First Clinical Medical College of Shanxi Medical University, Taiyuan, China
- Department of Mental Health, Shanxi Medical University, Taiyuan, China
- *Correspondence: Hong Li
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21
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Wang Y, Liu Z, Sun D, Sun L, Cao G, Dai J. The Connectome and Chemo-Connectome Databases for Mice Brain Connection Analysis. Front Neuroanat 2022; 16:886925. [PMID: 35756500 PMCID: PMC9218099 DOI: 10.3389/fnana.2022.886925] [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: 03/01/2022] [Accepted: 05/06/2022] [Indexed: 11/13/2022] Open
Abstract
The various brain functions rely on the intricate connection networks and certain molecular characteristics of neurons in the brain. However, the databases for the mouse brain connectome and chemo-connectome are still inadequate, hindering the brain circuital and functional analysis. Here, we created mice brain connectome and chemo-connectome databases based on mouse brain projection data of 295 non-overlapping brain areas and in situ hybridization (ISH) data of 50 representative neurotransmission-related genes from the Allen Brain Institute. Based on this connectome and chemo-connectome databases, functional connection patterns and detailed chemo-connectome for monoaminergic nuclei were analyzed and visualized. These databases will aid in the comprehensive research of the mouse connectome and chemo-connectome in the whole brain and serve as a convenient resource for systematic analysis of the brain connection and function.
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Affiliation(s)
- Yang Wang
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China.,College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
| | - Zhixiang Liu
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China.,College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China.,Britton Chance Center for Biomedical Photonics, Wuhan National Laboratory for Optoelectronics, Huazhong University of Science and Technology, Wuhan, China
| | - Da Sun
- College of Veterinary Medicine, China Agricultural University, Beijing, China
| | - Leqiang Sun
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China.,College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
| | - Gang Cao
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China.,College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China.,Biomedical Center, Huazhong Agricultural University, Wuhan, China
| | - Jinxia Dai
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China.,College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
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22
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Yan M, Yu W, Lv Q, Lv Q, Bo T, Chen X, Liu Y, Zhan Y, Yan S, Shen X, Yang B, Hu Q, Yu J, Qiu Z, Feng Y, Zhang XY, Wang H, Xu F, Wang Z. Mapping brain-wide excitatory projectome of primate prefrontal cortex at submicron resolution and comparison with diffusion tractography. eLife 2022; 11:72534. [PMID: 35593765 PMCID: PMC9122499 DOI: 10.7554/elife.72534] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2021] [Accepted: 04/07/2022] [Indexed: 11/13/2022] Open
Abstract
Resolving trajectories of axonal pathways in the primate prefrontal cortex remains crucial to gain insights into higher-order processes of cognition and emotion, which requires a comprehensive map of axonal projections linking demarcated subdivisions of prefrontal cortex and the rest of brain. Here, we report a mesoscale excitatory projectome issued from the ventrolateral prefrontal cortex (vlPFC) to the entire macaque brain by using viral-based genetic axonal tracing in tandem with high-throughput serial two-photon tomography, which demonstrated prominent monosynaptic projections to other prefrontal areas, temporal, limbic, and subcortical areas, relatively weak projections to parietal and insular regions but no projections directly to the occipital lobe. In a common 3D space, we quantitatively validated an atlas of diffusion tractography-derived vlPFC connections with correlative green fluorescent protein-labeled axonal tracing, and observed generally good agreement except a major difference in the posterior projections of inferior fronto-occipital fasciculus. These findings raise an intriguing question as to how neural information passes along long-range association fiber bundles in macaque brains, and call for the caution of using diffusion tractography to map the wiring diagram of brain circuits. In the brain is a web of interconnected nerve cells that send messages to one another via spindly projections called axons. These axons join together at junctions called synapses to create circuits of nerve cells which connect neighboring or distant brain regions. Notably, long-range neural connections underpin higher-order cognitive skills (such as planning and emotion regulation) which make humans distinct from our primate relatives. Only by untangling these far-reaching networks can researchers begin to delineate what sets the human brain apart from other species. Researchers deploy a range of imaging techniques to map neural networks: scanning entire brains using MRI machines, or imaging thin slices of fluorescently labelled brain tissue using powerful microscopes. However, tracing long-range axons at a high resolution is challenging, and has stirred up debate about whether some neural tracts, such as the inferior fronto-occipital fasciculus, are present in all primates or only humans. To address these discrepancies, Yan, Yu et al. employed a two-pronged approach to map neural circuits in the brains of macaques. First, two techniques – called viral tracing and two-photon microscopy – were used to create a three-dimensional, fine-grain map showing how the ventrolateral prefrontal cortex (vlPFC), which regulates complex behaviors, connects to the rest of the brain. This revealed prominent axons from the vlPFC projecting via a single synapse to distant brain regions involved in higher-order functions, such as encoding memories and processing emotion. However, there were no direct, monosynaptic connections between the vlPFC and the occipital lobe, the brain’s visual processing center at the back of the head. Next, Yan, Yu et al. used a specialized MRI scanner to create an atlas of neural circuits connected to the vlPFC, and compared these results to a technique tracing axons stained with a fluorescent dye. In general, there was good agreement between the two methods, except for major differences in the rear-end projections that typically form the inferior fronto-occipital fasciculus. This suggests that this long-range neural pathway exists in monkeys, but it connects via multiple synapses instead of a single junction as was previously thought. The findings of Yan, Yu et al. provide new insights on the far-reaching neural pathways connecting distant parts of the macaque brain. It also suggests that atlases of neural circuits from whole brain scans should be taken with caution and validated using neural tracing experiments.
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Affiliation(s)
- Mingchao Yan
- Institute of Neuroscience, State Key Laboratory of Neuroscience, Center for Excellence in Brain Science and Intelligence Technology, Chinese Academy of Sciences, Shanghai, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Wenwen Yu
- Institute of Science and Technology for Brain-inspired Intelligence, Fudan University, Shanghai, China
| | - Qian Lv
- School of Psychological and Cognitive Sciences; Beijing Key Laboratory of Behavior and Mental Health; IDG/McGovern Institute for Brain Research; Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, China
| | - Qiming Lv
- Institute of Neuroscience, State Key Laboratory of Neuroscience, Center for Excellence in Brain Science and Intelligence Technology, Chinese Academy of Sciences, Shanghai, China
| | - Tingting Bo
- Institute of Neuroscience, State Key Laboratory of Neuroscience, Center for Excellence in Brain Science and Intelligence Technology, Chinese Academy of Sciences, Shanghai, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Xiaoyu Chen
- Institute of Neuroscience, State Key Laboratory of Neuroscience, Center for Excellence in Brain Science and Intelligence Technology, Chinese Academy of Sciences, Shanghai, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Yilin Liu
- Institute of Neuroscience, State Key Laboratory of Neuroscience, Center for Excellence in Brain Science and Intelligence Technology, Chinese Academy of Sciences, Shanghai, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Yafeng Zhan
- Institute of Neuroscience, State Key Laboratory of Neuroscience, Center for Excellence in Brain Science and Intelligence Technology, Chinese Academy of Sciences, Shanghai, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Shengyao Yan
- Institute of Neuroscience, State Key Laboratory of Neuroscience, Center for Excellence in Brain Science and Intelligence Technology, Chinese Academy of Sciences, Shanghai, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Xiangyu Shen
- Institute of Neuroscience, State Key Laboratory of Neuroscience, Center for Excellence in Brain Science and Intelligence Technology, Chinese Academy of Sciences, Shanghai, China
| | - Baofeng Yang
- Institute of Science and Technology for Brain-inspired Intelligence, Fudan University, Shanghai, China
| | - Qiming Hu
- College of Information Engineering, Zhejiang University of Technology, Hangzhou, China
| | - Jiangli Yu
- College of Information Engineering, Zhejiang University of Technology, Hangzhou, China
| | - Zilong Qiu
- Institute of Neuroscience, State Key Laboratory of Neuroscience, Center for Excellence in Brain Science and Intelligence Technology, Chinese Academy of Sciences, Shanghai, China
| | - Yuanjing Feng
- College of Information Engineering, Zhejiang University of Technology, Hangzhou, China
| | - Xiao-Yong Zhang
- Institute of Science and Technology for Brain-inspired Intelligence, Fudan University, Shanghai, China
| | - He Wang
- Institute of Science and Technology for Brain-inspired Intelligence, Fudan University, Shanghai, China
| | - Fuqiang Xu
- Shenzhen Key Lab of Neuropsychiatric Modulation and Collaborative Innovation Center for Brain Science, Guangdong Provincial Key Laboratory of Brain Connectome and Behavior, CAS Key Laboratory of Brain Connectome and Manipulation, Brain Cognition and Brain Disease Institute (BCBDI), Shenzhen Institutes of Advanced Technology, Shenzhen-Hong Kong Institute of Brain Science-Shenzhen Fundamental Research Institutions, Shenzhen, China
| | - Zheng Wang
- School of Psychological and Cognitive Sciences; Beijing Key Laboratory of Behavior and Mental Health; IDG/McGovern Institute for Brain Research; Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, China
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23
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The brainstem connectome database. Sci Data 2022; 9:168. [PMID: 35414055 PMCID: PMC9005652 DOI: 10.1038/s41597-022-01219-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2020] [Accepted: 02/25/2022] [Indexed: 11/29/2022] Open
Abstract
Connectivity data of the nervous system and subdivisions, such as the brainstem, cerebral cortex and subcortical nuclei, are necessary to understand connectional structures, predict effects of connectional disorders and simulate network dynamics. For that purpose, a database was built and analyzed which comprises all known directed and weighted connections within the rat brainstem. A longterm metastudy of original research publications describing tract tracing results form the foundation of the brainstem connectome (BC) database which can be analyzed directly in the framework neuroVIISAS. The BC database can be accessed directly by connectivity tables, a web-based tool and the framework. Analysis of global and local network properties, a motif analysis, and a community analysis of the brainstem connectome provides insight into its network organization. For example, we found that BC is a scale-free network with a small-world connectivity. The Louvain modularity and weighted stochastic block matching resulted in partially matching of functions and connectivity. BC modeling was performed to demonstrate signal propagation through the somatosensory pathway which is affected in Multiple sclerosis. Measurement(s) | brainstem | Technology Type(s) | tract tracing metastudy | Factor Type(s) | brain region | Sample Characteristic - Organism | Rattus rattus | Sample Characteristic - Environment | Experimental setup | Sample Characteristic - Location | Germany |
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24
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Im S, Ueta Y, Otsuka T, Morishima M, Youssef M, Hirai Y, Kobayashi K, Kaneko R, Morita K, Kawaguchi Y. Corticocortical innervation subtypes of layer 5 intratelencephalic cells in the murine secondary motor cortex. Cereb Cortex 2022; 33:50-67. [PMID: 35396593 PMCID: PMC9758586 DOI: 10.1093/cercor/bhac052] [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: 03/15/2021] [Revised: 01/25/2022] [Accepted: 01/26/2022] [Indexed: 11/15/2022] Open
Abstract
Feedback projections from the secondary motor cortex (M2) to the primary motor and sensory cortices are essential for behavior selection and sensory perception. Intratelencephalic (IT) cells in layer 5 (L5) contribute feedback projections to diverse cortical areas. Here we show that L5 IT cells participating in feedback connections to layer 1 (L1) exhibit distinct projection patterns, genetic profiles, and electrophysiological properties relative to other L5 IT cells. An analysis of the MouseLight database found that L5 IT cells preferentially targeting L1 project broadly to more cortical regions, including the perirhinal and auditory cortices, and innervate a larger volume of striatum than the other L5 IT cells. We found experimentally that in upper L5 (L5a), ER81 (ETV1) was found more often in L1-preferring IT cells, and in IT cells projecting to perirhinal/auditory regions than those projecting to primary motor or somatosensory regions. The perirhinal region-projecting L5a IT cells were synaptically connected to each other and displayed lower input resistance than contra-M2 projecting IT cells including L1-preferring and nonpreferring cells. Our findings suggest that M2-L5a IT L1-preferring cells exhibit stronger ER81 expression and broader cortical/striatal projection fields than do cells that do not preferentially target L1.
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Affiliation(s)
- Sanghun Im
- National Institute for Physiological Sciences (NIPS), Okazaki 444-8787, Japan,Department of Physiological Sciences, The Graduate University for Advanced Studies (SOKENDAI), Okazaki 444-8787, Japan,Brain Science Institute, Tamagawa University, Machida, Tokyo 194-8610, Japan
| | - Yoshifumi Ueta
- Department of Physiology, Division of Neurophysiology, School of Medicine, Tokyo Women's Medical University, Tokyo 162-8666, Japan
| | - Takeshi Otsuka
- National Institute for Physiological Sciences (NIPS), Okazaki 444-8787, Japan,Department of Physiological Sciences, The Graduate University for Advanced Studies (SOKENDAI), Okazaki 444-8787, Japan
| | - Mieko Morishima
- National Institute for Physiological Sciences (NIPS), Okazaki 444-8787, Japan,Institute of Clinical Medicine and Research, Jikei University School of Medicine, Chiba 277-8567, Japan
| | - Mohammed Youssef
- National Institute for Physiological Sciences (NIPS), Okazaki 444-8787, Japan,Department of Animal Physiology, Faculty of Veterinary Medicine, South Valley University, Qena 83523, Egypt
| | - Yasuharu Hirai
- Laboratory of Histology and Cytology, Faculty of Medicine, Hokkaido University, Sapporo 060-8638, Japan
| | - Kenta Kobayashi
- Section of Viral Vector Development, National Institute for Physiological Sciences, Okazaki 444-8585, Japan
| | - Ryosuke Kaneko
- Bioresource Center, Gunma University Graduate School of Medicine, Gunma 371-8511, Japan,KOKORO-Biology Group, Laboratories for Integrated Biology, Graduate School of Frontier Biosciences, Osaka University, Osaka 565-0871, Japan
| | - Kenji Morita
- Physical and Health Education, Graduate School of Education, The University of Tokyo, Tokyo 113-0033, Japan,International Research Center for Neurointelligence (WPI-IRCN), The University of Tokyo, Tokyo 113-0033, Japan
| | - Yasuo Kawaguchi
- Corresponding author: Brain Science Institute, Tamagawa University Machida, Tokyo 1948610, Japan.
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25
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Taniguchi T, Yamakawa H, Nagai T, Doya K, Sakagami M, Suzuki M, Nakamura T, Taniguchi A. A whole brain probabilistic generative model: Toward realizing cognitive architectures for developmental robots. Neural Netw 2022; 150:293-312. [PMID: 35339010 DOI: 10.1016/j.neunet.2022.02.026] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2021] [Revised: 02/25/2022] [Accepted: 02/28/2022] [Indexed: 01/08/2023]
Abstract
Building a human-like integrative artificial cognitive system, that is, an artificial general intelligence (AGI), is the holy grail of the artificial intelligence (AI) field. Furthermore, a computational model that enables an artificial system to achieve cognitive development will be an excellent reference for brain and cognitive science. This paper describes an approach to develop a cognitive architecture by integrating elemental cognitive modules to enable the training of the modules as a whole. This approach is based on two ideas: (1) brain-inspired AI, learning human brain architecture to build human-level intelligence, and (2) a probabilistic generative model (PGM)-based cognitive architecture to develop a cognitive system for developmental robots by integrating PGMs. The proposed development framework is called a whole brain PGM (WB-PGM), which differs fundamentally from existing cognitive architectures in that it can learn continuously through a system based on sensory-motor information. In this paper, we describe the rationale for WB-PGM, the current status of PGM-based elemental cognitive modules, their relationship with the human brain, the approach to the integration of the cognitive modules, and future challenges. Our findings can serve as a reference for brain studies. As PGMs describe explicit informational relationships between variables, WB-PGM provides interpretable guidance from computational sciences to brain science. By providing such information, researchers in neuroscience can provide feedback to researchers in AI and robotics on what the current models lack with reference to the brain. Further, it can facilitate collaboration among researchers in neuro-cognitive sciences as well as AI and robotics.
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Affiliation(s)
| | - Hiroshi Yamakawa
- The University of Tokyo, 7-3-1, Hongo, Bunkyo-ku, Tokyo, Japan; The Whole Brain Architecture Initiative, 2-19-21 Nishikoiwa , Edogawa-ku, Tokyo, Japan; RIKEN, 6-2-3 Furuedai, Suita, Osaka, Japan
| | - Takayuki Nagai
- Osaka University, 1-3 Machikane-yama, Toyonaka, Osaka, Japan
| | - Kenji Doya
- Okinawa Institute of Science and Technology Graduate University, 1919-1 Tancha, Onna-son, Kunigami, Okinawa, Japan
| | | | - Masahiro Suzuki
- The University of Tokyo, 7-3-1, Hongo, Bunkyo-ku, Tokyo, Japan
| | - Tomoaki Nakamura
- The University of Electro-Communications, 1-5-1 Chofugaoka, Chofu, Tokyo, Japan
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26
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Jeon H, Lee H, Kwon DH, Kim J, Tanaka-Yamamoto K, Yook JS, Feng L, Park HR, Lim YH, Cho ZH, Paek SH, Kim J. Topographic connectivity and cellular profiling reveal detailed input pathways and functionally distinct cell types in the subthalamic nucleus. Cell Rep 2022; 38:110439. [PMID: 35235786 DOI: 10.1016/j.celrep.2022.110439] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2021] [Revised: 12/02/2021] [Accepted: 02/03/2022] [Indexed: 11/27/2022] Open
Abstract
The subthalamic nucleus (STN) controls psychomotor activity and is an efficient therapeutic deep brain stimulation target in individuals with Parkinson's disease. Despite evidence indicating position-dependent therapeutic effects and distinct functions within the STN, the input circuit and cellular profile in the STN remain largely unclear. Using neuroanatomical techniques, we construct a comprehensive connectivity map of the indirect and hyperdirect pathways in the mouse STN. Our circuit- and cellular-level connectivities reveal a topographically graded organization with three types of indirect and hyperdirect pathways (external globus pallidus only, STN only, and collateral). We confirm consistent pathways into the human STN by 7 T MRI-based tractography. We identify two functional types of topographically distinct glutamatergic STN neurons (parvalbumin [PV+/-]) with synaptic connectivity from indirect and hyperdirect pathways. Glutamatergic PV+ STN neurons contribute to burst firing. These data suggest a complex interplay of information integration within the basal ganglia underlying coordinated movement control and therapeutic effects.
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Affiliation(s)
- Hyungju Jeon
- Brain Science Institute, Korea Institute of Science and Technology (KIST), 39-1 Hawolgokdong, Seongbukgu, Seoul 02792 Korea
| | - Hojin Lee
- Brain Science Institute, Korea Institute of Science and Technology (KIST), 39-1 Hawolgokdong, Seongbukgu, Seoul 02792 Korea; Division of Bio-Medical Science & Technology, KIST School, University of Science and Technology, Seoul 02792, Korea
| | - Dae-Hyuk Kwon
- Neuroscience Convergence Center, Korea University, Seoul 02841, Korea
| | - Jiwon Kim
- Brain Science Institute, Korea Institute of Science and Technology (KIST), 39-1 Hawolgokdong, Seongbukgu, Seoul 02792 Korea; Division of Bio-Medical Science & Technology, KIST School, University of Science and Technology, Seoul 02792, Korea
| | - Keiko Tanaka-Yamamoto
- Brain Science Institute, Korea Institute of Science and Technology (KIST), 39-1 Hawolgokdong, Seongbukgu, Seoul 02792 Korea; Division of Bio-Medical Science & Technology, KIST School, University of Science and Technology, Seoul 02792, Korea
| | - Jang Soo Yook
- Brain Science Institute, Korea Institute of Science and Technology (KIST), 39-1 Hawolgokdong, Seongbukgu, Seoul 02792 Korea
| | - Linqing Feng
- Brain Science Institute, Korea Institute of Science and Technology (KIST), 39-1 Hawolgokdong, Seongbukgu, Seoul 02792 Korea
| | - Hye Ran Park
- Soonchunhyang University Seoul Hospital, Seoul 04401, Korea
| | - Yong Hoon Lim
- Neurosurgery, Movement Disorder Center, Seoul National University College of Medicine, Advanced Institute of Convergence Technology (AICT), Seoul National University, Seoul 03080, Korea
| | - Zang-Hee Cho
- Neuroscience Convergence Center, Korea University, Seoul 02841, Korea
| | - Sun Ha Paek
- Neurosurgery, Movement Disorder Center, Seoul National University College of Medicine, Advanced Institute of Convergence Technology (AICT), Seoul National University, Seoul 03080, Korea
| | - Jinhyun Kim
- Brain Science Institute, Korea Institute of Science and Technology (KIST), 39-1 Hawolgokdong, Seongbukgu, Seoul 02792 Korea; Division of Bio-Medical Science & Technology, KIST School, University of Science and Technology, Seoul 02792, Korea.
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27
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Richardson DS, Guan W, Matsumoto K, Pan C, Chung K, Ertürk A, Ueda HR, Lichtman JW. TISSUE CLEARING. NATURE REVIEWS. METHODS PRIMERS 2022; 1. [PMID: 35128463 DOI: 10.1038/s43586-021-00080-9] [Citation(s) in RCA: 51] [Impact Index Per Article: 25.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Tissue clearing of gross anatomical samples was first described over a century ago and has only recently found widespread use in the field of microscopy. This renaissance has been driven by the application of modern knowledge of optical physics and chemical engineering to the development of robust and reproducible clearing techniques, the arrival of new microscopes that can image large samples at cellular resolution and computing infrastructure able to store and analyze large data volumes. Many biological relationships between structure and function require investigation in three dimensions and tissue clearing therefore has the potential to enable broad discoveries in the biological sciences. Unfortunately, the current literature is complex and could confuse researchers looking to begin a clearing project. The goal of this Primer is to outline a modular approach to tissue clearing that allows a novice researcher to develop a customized clearing pipeline tailored to their tissue of interest. Further, the Primer outlines the required imaging and computational infrastructure needed to perform tissue clearing at scale, gives an overview of current applications, discusses limitations and provides an outlook on future advances in the field.
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Affiliation(s)
- Douglas S Richardson
- Harvard Center for Biological Imaging, Harvard University, Cambridge, MA, USA.,Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA, USA
| | - Webster Guan
- Department of Chemical Engineering, MIT, Cambridge, MA, USA
| | - Katsuhiko Matsumoto
- Department of Systems Pharmacology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan.,Laboratory for Synthetic Biology, RIKEN Center for Biosystems Dynamics Research, Osaka, Japan
| | - Chenchen Pan
- Institute for Stroke and Dementia Research, Klinikum der Universität München, Ludwig Maximilians University of Munich, Munich, Germany.,Graduate School of Systemic Neurosciences (GSN), Munich, Germany.,Munich Cluster for Systems Neurology (SyNergy), Munich, Germany
| | - Kwanghun Chung
- Department of Systems Pharmacology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan.,Picower Institute for Learning and Memory, MIT, Cambridge, MA, USA.,Institute for Medical Engineering and Science, Massachusetts Institute of Technology, Cambridge, MA, USA.,Department of Brain and Cognitive Sciences, MIT, Cambridge, MA, USA.,Broad Institute of Harvard University and MIT, Cambridge, MA, USA.,Center for Nanomedicine, Institute for Basic Science (IBS), Seoul, Republic of Korea.,Nano Biomedical Engineering (Nano BME) Graduate Program, Yonsei-IBS Institute, Yonsei University, Seoul, Republic of Korea
| | - Ali Ertürk
- Institute for Stroke and Dementia Research, Klinikum der Universität München, Ludwig Maximilians University of Munich, Munich, Germany.,Graduate School of Systemic Neurosciences (GSN), Munich, Germany.,Munich Cluster for Systems Neurology (SyNergy), Munich, Germany
| | - Hiroki R Ueda
- Department of Systems Pharmacology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan.,Laboratory for Synthetic Biology, RIKEN Center for Biosystems Dynamics Research, Osaka, Japan
| | - Jeff W Lichtman
- Harvard Center for Biological Imaging, Harvard University, Cambridge, MA, USA.,Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA, USA.,Center for Brain Science, Harvard University, Cambridge, MA, USA
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28
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Ose T, Autio JA, Ohno M, Frey S, Uematsu A, Kawasaki A, Takeda C, Hori Y, Nishigori K, Nakako T, Yokoyama C, Nagata H, Yamamori T, Van Essen DC, Glasser MF, Watabe H, Hayashi T. Anatomical variability, multi-modal coordinate systems, and precision targeting in the marmoset brain. Neuroimage 2022; 250:118965. [PMID: 35122965 PMCID: PMC8948178 DOI: 10.1016/j.neuroimage.2022.118965] [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] [Received: 09/13/2021] [Revised: 01/31/2022] [Accepted: 02/01/2022] [Indexed: 01/02/2023] Open
Abstract
Localising accurate brain regions needs careful evaluation in each experimental species due to their individual variability. However, the function and connectivity of brain areas is commonly studied using a single-subject cranial landmark-based stereotactic atlas in animal neuroscience. Here, we address this issue in a small primate, the common marmoset, which is increasingly widely used in systems neuroscience. We developed a non-invasive multi-modal neuroimaging-based targeting pipeline, which accounts for intersubject anatomical variability in cranial and cortical landmarks in marmosets. This methodology allowed creation of multi-modal templates (MarmosetRIKEN20) including head CT and brain MR images, embedded in coordinate systems of anterior and posterior commissures (AC-PC) and CIFTI grayordinates. We found that the horizontal plane of the stereotactic coordinate was significantly rotated in pitch relative to the AC-PC coordinate system (10 degrees, frontal downwards), and had a significant bias and uncertainty due to positioning procedures. We also found that many common cranial and brain landmarks (e.g., bregma, intraparietal sulcus) vary in location across subjects and are substantial relative to average marmoset cortical area dimensions. Combining the neuroimaging-based targeting pipeline with robot-guided surgery enabled proof-of-concept targeting of deep brain structures with an accuracy of 0.2 mm. Altogether, our findings demonstrate substantial intersubject variability in marmoset brain and cranial landmarks, implying that subject-specific neuroimaging-based localization is needed for precision targeting in marmosets. The population-based templates and atlases in grayordinates, created for the first time in marmoset monkeys, should help bridging between macroscale and microscale analyses.
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Affiliation(s)
- Takayuki Ose
- Laboratory for Brain Connectomics Imaging, RIKEN Center for Biosystems Dynamics Research, Kobe, Japan; Graduate School of Biomedical Engineering, Tohoku University, Sendai, Japan.
| | - Joonas A Autio
- Laboratory for Brain Connectomics Imaging, RIKEN Center for Biosystems Dynamics Research, Kobe, Japan.
| | - Masahiro Ohno
- Laboratory for Brain Connectomics Imaging, RIKEN Center for Biosystems Dynamics Research, Kobe, Japan.
| | | | - Akiko Uematsu
- Laboratory for Brain Connectomics Imaging, RIKEN Center for Biosystems Dynamics Research, Kobe, Japan.
| | - Akihiro Kawasaki
- Laboratory for Brain Connectomics Imaging, RIKEN Center for Biosystems Dynamics Research, Kobe, Japan.
| | - Chiho Takeda
- Laboratory for Brain Connectomics Imaging, RIKEN Center for Biosystems Dynamics Research, Kobe, Japan.
| | - Yuki Hori
- Laboratory for Brain Connectomics Imaging, RIKEN Center for Biosystems Dynamics Research, Kobe, Japan; Department of Functional Brain Imaging, National Institutes for Quantum and Radiological Science and Technology, Chiba, Japan.
| | - Kantaro Nishigori
- Laboratory for Brain Connectomics Imaging, RIKEN Center for Biosystems Dynamics Research, Kobe, Japan; Sumitomo Dainippon Pharma Co., Ltd., Osaka, Japan.
| | - Tomokazu Nakako
- Laboratory for Brain Connectomics Imaging, RIKEN Center for Biosystems Dynamics Research, Kobe, Japan; Sumitomo Dainippon Pharma Co., Ltd., Osaka, Japan.
| | - Chihiro Yokoyama
- Laboratory for Brain Connectomics Imaging, RIKEN Center for Biosystems Dynamics Research, Kobe, Japan; Faculty of Human life and Environmental Science, Nara women's University, Nara, Japan.
| | | | - Tetsuo Yamamori
- Laboratory for Molecular Analysis of Higher Brain Function, RIKEN Center for Brain Science, Wako, Japan.
| | - David C Van Essen
- Department of Neuroscience, Washington University Medical School, St Louis, MO USA.
| | - Matthew F Glasser
- Department of Neuroscience, Washington University Medical School, St Louis, MO USA; Department of Radiology, Washington University Medical School, St Louis, MO USA.
| | - Hiroshi Watabe
- Graduate School of Biomedical Engineering, Tohoku University, Sendai, Japan.
| | - Takuya Hayashi
- Laboratory for Brain Connectomics Imaging, RIKEN Center for Biosystems Dynamics Research, Kobe, Japan; Department of Brain Connectomics, Kyoto University Graduate School of Medicine, Kyoto, Japan.
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29
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Liang Z, Lee CH, Arefin TM, Dong Z, Walczak P, Hai Shi S, Knoll F, Ge Y, Ying L, Zhang J. Virtual mouse brain histology from multi-contrast MRI via deep learning. eLife 2022; 11:72331. [PMID: 35088711 PMCID: PMC8837198 DOI: 10.7554/elife.72331] [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: 07/20/2021] [Accepted: 01/27/2022] [Indexed: 11/16/2022] Open
Abstract
1H MRI maps brain structure and function non-invasively through versatile contrasts that exploit inhomogeneity in tissue micro-environments. Inferring histopathological information from magnetic resonance imaging (MRI) findings, however, remains challenging due to absence of direct links between MRI signals and cellular structures. Here, we show that deep convolutional neural networks, developed using co-registered multi-contrast MRI and histological data of the mouse brain, can estimate histological staining intensity directly from MRI signals at each voxel. The results provide three-dimensional maps of axons and myelin with tissue contrasts that closely mimic target histology and enhanced sensitivity and specificity compared to conventional MRI markers. Furthermore, the relative contribution of each MRI contrast within the networks can be used to optimize multi-contrast MRI acquisition. We anticipate our method to be a starting point for translation of MRI results into easy-to-understand virtual histology for neurobiologists and provide resources for validating novel MRI techniques.
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Affiliation(s)
- Zifei Liang
- Department of Radiology, New York University School of Medicine, New York, United States
| | - Choong H Lee
- Department of Radiology, New York University School of Medicine, New York, United States
| | - Tanzil M Arefin
- Department of Radiology, New York University School of Medicine, New York, United States
| | - Zijun Dong
- Department of Radiology, New York University School of Medicine, New York, United States
| | - Piotr Walczak
- Department of Diagnostic Radiology and Nuclear Medicine, University of Maryland, Baltimore, United States
| | - Song Hai Shi
- Developmental Biology Program, Memorial Sloan Kettering Cancer Center
| | - Florian Knoll
- Department of Radiology, New York University School of Medicine, New York, United States
| | - Yulin Ge
- Department of Radiology, New York University School of Medicine, New York, United States
| | - Leslie Ying
- Departments of Biomedical Engineering, University at Buffalo, State University of New York, Buffalo, United States
| | - Jiangyang Zhang
- Department of Radiology, New York University School of Medicine, New York, United States
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30
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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: 8] [Impact Index Per Article: 4.0] [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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31
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van Albada SJ, Morales-Gregorio A, Dickscheid T, Goulas A, Bakker R, Bludau S, Palm G, Hilgetag CC, Diesmann M. Bringing Anatomical Information into Neuronal Network Models. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2022; 1359:201-234. [DOI: 10.1007/978-3-030-89439-9_9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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32
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Tyson AL, Margrie TW. Mesoscale microscopy and image analysis tools for understanding the brain. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2022; 168:81-93. [PMID: 34216639 PMCID: PMC8786668 DOI: 10.1016/j.pbiomolbio.2021.06.013] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/22/2021] [Revised: 06/09/2021] [Accepted: 06/29/2021] [Indexed: 12/12/2022]
Abstract
Over the last ten years, developments in whole-brain microscopy now allow for high-resolution imaging of intact brains of small animals such as mice. These complex images contain a wealth of information, but many neuroscience laboratories do not have all of the computational knowledge and tools needed to process these data. We review recent open source tools for registration of images to atlases, and the segmentation, visualisation and analysis of brain regions and labelled structures such as neurons. Since the field lacks fully integrated analysis pipelines for all types of whole-brain microscopy analysis, we propose a pathway for tool developers to work together to meet this challenge.
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Affiliation(s)
- Adam L Tyson
- Sainsbury Wellcome Centre, University College London, 25 Howland Street, London, W1T 4JG, United Kingdom
| | - Troy W Margrie
- Sainsbury Wellcome Centre, University College London, 25 Howland Street, London, W1T 4JG, United Kingdom.
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33
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Sanchez-Arias JC, Carrier M, Frederiksen SD, Shevtsova O, McKee C, van der Slagt E, Gonçalves de Andrade E, Nguyen HL, Young PA, Tremblay MÈ, Swayne LA. A Systematic, Open-Science Framework for Quantification of Cell-Types in Mouse Brain Sections Using Fluorescence Microscopy. Front Neuroanat 2021; 15:722443. [PMID: 34949993 PMCID: PMC8691181 DOI: 10.3389/fnana.2021.722443] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2021] [Accepted: 10/28/2021] [Indexed: 02/03/2023] Open
Abstract
The ever-expanding availability and evolution of microscopy tools has enabled ground-breaking discoveries in neurobiology, particularly with respect to the analysis of cell-type density and distribution. Widespread implementation of many of the elegant image processing tools available continues to be impeded by the lack of complete workflows that span from experimental design, labeling techniques, and analysis workflows, to statistical methods and data presentation. Additionally, it is important to consider open science principles (e.g., open-source software and tools, user-friendliness, simplicity, and accessibility). In the present methodological article, we provide a compendium of resources and a FIJI-ImageJ-based workflow aimed at improving the quantification of cell density in mouse brain samples using semi-automated open-science-based methods. Our proposed framework spans from principles and best practices of experimental design, histological and immunofluorescence staining, and microscopy imaging to recommendations for statistical analysis and data presentation. To validate our approach, we quantified neuronal density in the mouse barrel cortex using antibodies against pan-neuronal and interneuron markers. This framework is intended to be simple and yet flexible, such that it can be adapted to suit distinct project needs. The guidelines, tips, and proposed methodology outlined here, will support researchers of wide-ranging experience levels and areas of focus in neuroscience research.
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Affiliation(s)
| | - Micaël Carrier
- Division of Medical Sciences, University of Victoria, Victoria, BC, Canada.,Axe Neurosciences, Centre de Recherche du CHU de Québec, Université de Laval, Québec City, QC, Canada
| | | | - Olga Shevtsova
- Division of Medical Sciences, University of Victoria, Victoria, BC, Canada
| | - Chloe McKee
- Division of Medical Sciences, University of Victoria, Victoria, BC, Canada
| | - Emma van der Slagt
- Division of Medical Sciences, University of Victoria, Victoria, BC, Canada
| | | | - Hai Lam Nguyen
- Division of Medical Sciences, University of Victoria, Victoria, BC, Canada
| | - Penelope A Young
- Division of Medical Sciences, University of Victoria, Victoria, BC, Canada
| | - Marie-Ève Tremblay
- Division of Medical Sciences, University of Victoria, Victoria, BC, Canada.,Axe Neurosciences, Centre de Recherche du CHU de Québec, Université de Laval, Québec City, QC, Canada.,Department of Neurology and Neurosurgery, McGill University, Montréal, QC, Canada.,Department of Molecular Medicine, Université de Laval, Québec City, QC, Canada.,Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, BC, Canada.,Djavad Mowafaghian Centre for Brain Health, University of British Columbia, Vancouver, BC, Canada
| | - Leigh Anne Swayne
- Division of Medical Sciences, University of Victoria, Victoria, BC, Canada.,Djavad Mowafaghian Centre for Brain Health, University of British Columbia, Vancouver, BC, Canada.,Department of Cellular and Physiological Sciences, University of British Columbia, Vancouver, BC, Canada.,Department of Neurology and Neurosurgery, Centre for Research in Neuroscience, Brain Repair and Integrative Neuroscience Program, Research Institute of the McGill University Health Centre, Montreal General Hospital, Montreal, QC, Canada
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34
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Towards an Architecture of a Multi-purpose, User-Extendable Reference Human Brain Atlas. Neuroinformatics 2021; 20:405-426. [PMID: 34825350 PMCID: PMC9546954 DOI: 10.1007/s12021-021-09555-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/09/2021] [Indexed: 11/29/2022]
Abstract
Human brain atlas development is predominantly research-oriented and the use of atlases in clinical practice is limited. Here I introduce a new definition of a reference human brain atlas that serves education, research and clinical applications, and is extendable by its user. Subsequently, an architecture of a multi-purpose, user-extendable reference human brain atlas is proposed and its implementation discussed. The human brain atlas is defined as a vehicle to gather, present, use, share, and discover knowledge about the human brain with highly organized content, tools enabling a wide range of its applications, massive and heterogeneous knowledge database, and means for content and knowledge growing by its users. The proposed architecture determines major components of the atlas, their mutual relationships, and functional roles. It contains four functional units, core cerebral models, knowledge database, research and clinical data input and conversion, and toolkit (supporting processing, content extension, atlas individualization, navigation, exploration, and display), all united by a user interface. Each unit is described in terms of its function, component modules and sub-modules, data handling, and implementation aspects. This novel architecture supports brain knowledge gathering, presentation, use, sharing, and discovery and is broadly applicable and useful in student- and educator-oriented neuroeducation for knowledge presentation and communication, research for knowledge acquisition, aggregation and discovery, and clinical applications in decision making support for prevention, diagnosis, treatment, monitoring, and prediction. It establishes a backbone for designing and developing new, multi-purpose and user-extendable brain atlas platforms, serving as a potential standard across labs, hospitals, and medical schools.
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35
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Accurate Localization of Linear Probe Electrode Arrays across Multiple Brains. eNeuro 2021; 8:ENEURO.0241-21.2021. [PMID: 34697075 PMCID: PMC8597948 DOI: 10.1523/eneuro.0241-21.2021] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2021] [Revised: 07/02/2021] [Accepted: 10/14/2021] [Indexed: 11/21/2022] Open
Abstract
Recently developed probes for extracellular electrophysiological recordings have large numbers of electrodes on long linear shanks. Linear electrode arrays, such as Neuropixels probes, have hundreds of recording electrodes distributed over linear shanks that span several millimeters. Because of the length of the probes, linear probe recordings in rodents usually cover multiple brain areas. Typical studies collate recordings across several recording sessions and animals. Neurons recorded in different sessions and animals thus have to be aligned to each other and to a standardized brain coordinate system. Here, we evaluate two typical workflows for localization of individual electrodes in standardized coordinates. These workflows rely on imaging brains with fluorescent probe tracks and warping 3D image stacks to standardized brain atlases. One workflow is based on tissue clearing and selective plane illumination microscopy (SPIM), whereas the other workflow is based on serial block-face two-photon (SBF2P) microscopy. In both cases electrophysiological features are then used to anchor particular electrodes along the reconstructed tracks to specific locations in the brain atlas and therefore to specific brain structures. We performed groundtruth experiments, in which motor cortex outputs are labeled with ChR2 and a fluorescence protein. Light-evoked electrical activity and fluorescence can be independently localized. Recordings from brain regions targeted by the motor cortex reveal better than 0.1-mm accuracy for electrode localization, independent of workflow used.
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36
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Chen H, Huang T, Yang Y, Yao X, Huo Y, Wang Y, Zhao W, Ji R, Yang H, Guo ZV. Sparse imaging and reconstruction tomography for high-speed high-resolution whole-brain imaging. CELL REPORTS METHODS 2021; 1:100089. [PMID: 35474896 PMCID: PMC9017159 DOI: 10.1016/j.crmeth.2021.100089] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/26/2021] [Revised: 08/12/2021] [Accepted: 09/03/2021] [Indexed: 01/05/2023]
Abstract
Understanding brain functions requires detailed knowledge of long-range connectivity through which different areas communicate. A key step toward illuminating the long-range structures is to image the whole brain at synaptic resolution to trace axonal arbors of individual neurons to their termini. However, high-resolution brain-wide imaging requires continuous imaging for many days to sample over 10 trillion voxels, even in the mouse brain. Here, we have developed a sparse imaging and reconstruction tomography (SMART) system that allows brain-wide imaging of cortical projection neurons at synaptic resolution in about 20 h, an order of magnitude faster than previous methods. Analyses of morphological features reveal that single cortical neurons show remarkable diversity in local and long-range projections, with prefrontal, premotor, and visual neurons having distinct distribution of dendritic and axonal features. The fast imaging system and diverse projection patterns of individual neurons highlight the importance of high-resolution brain-wide imaging in revealing full neuronal morphology.
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Affiliation(s)
- Han Chen
- School of Medicine, Tsinghua University, Beijing 100084, China
- IDG/McGovern Institute for Brain Research, Tsinghua University, Beijing 100084, China
| | - Tianyi Huang
- School of Medicine, Tsinghua University, Beijing 100084, China
- IDG/McGovern Institute for Brain Research, Tsinghua University, Beijing 100084, China
| | - Yuexin Yang
- School of Medicine, Tsinghua University, Beijing 100084, China
- IDG/McGovern Institute for Brain Research, Tsinghua University, Beijing 100084, China
| | - Xiao Yao
- Tsinghua-Peking Joint Center for Life Sciences, Beijing 100084, China
- IDG/McGovern Institute for Brain Research, Tsinghua University, Beijing 100084, China
| | - Yan Huo
- School of Medicine, Tsinghua University, Beijing 100084, China
- IDG/McGovern Institute for Brain Research, Tsinghua University, Beijing 100084, China
| | - Yu Wang
- Tsinghua-Peking Joint Center for Life Sciences, Beijing 100084, China
- IDG/McGovern Institute for Brain Research, Tsinghua University, Beijing 100084, China
| | - Wenyu Zhao
- Tsinghua-Peking Joint Center for Life Sciences, Beijing 100084, China
- IDG/McGovern Institute for Brain Research, Tsinghua University, Beijing 100084, China
| | - Runan Ji
- School of Medicine, Tsinghua University, Beijing 100084, China
- IDG/McGovern Institute for Brain Research, Tsinghua University, Beijing 100084, China
| | - Hongjiang Yang
- School of Medicine, Tsinghua University, Beijing 100084, China
- IDG/McGovern Institute for Brain Research, Tsinghua University, Beijing 100084, China
| | - Zengcai V. Guo
- School of Medicine, Tsinghua University, Beijing 100084, China
- Tsinghua-Peking Joint Center for Life Sciences, Beijing 100084, China
- IDG/McGovern Institute for Brain Research, Tsinghua University, Beijing 100084, China
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37
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Yamakawa H. The whole brain architecture approach: Accelerating the development of artificial general intelligence by referring to the brain. Neural Netw 2021; 144:478-495. [PMID: 34600220 DOI: 10.1016/j.neunet.2021.09.004] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2021] [Revised: 07/27/2021] [Accepted: 09/01/2021] [Indexed: 11/19/2022]
Abstract
The vastness of the design space that is created by the combination of numerous computational mechanisms, including machine learning, is an obstacle to creating artificial general intelligence (AGI). Brain-inspired AGI development; that is, the reduction of the design space to resemble a biological brain more closely, is a promising approach for solving this problem. However, it is difficult for an individual to design a software program that corresponds to the entire brain as the neuroscientific data that are required to understand the architecture of the brain are extensive and complicated. The whole-brain architecture approach divides the brain-inspired AGI development process into the task of designing the brain reference architecture (BRA), which provides the flow of information and a diagram of the corresponding components, and the task of developing each component using the BRA. This is known as BRA-driven development. Another difficulty lies in the extraction of the operating principles that are necessary for reproducing the cognitive-behavioral function of the brain from neuroscience data. Therefore, this study proposes structure-constrained interface decomposition (SCID), which is a hypothesis-building method for creating a hypothetical component diagram that is consistent with neuroscientific findings. The application of this approach has been initiated for constructing various regions of the brain. In the future, we will examine methods for evaluating the biological plausibility of brain-inspired software. This evaluation will also be used to prioritize different computational mechanisms, which should be integrated and associated with the same regions of the brain.
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Affiliation(s)
- Hiroshi Yamakawa
- The Whole Brain Architecture Initiative, Nishikoiwa 2-19-21, Edogawa-ku, Tokyo 133-0057, Japan; The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan; RIKEN, 6-2-3, Furuedai, Suita, Osaka 565-0874, Japan.
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38
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Muñoz-Castañeda R, Zingg B, Matho KS, Chen X, Wang Q, Foster NN, Li A, Narasimhan A, Hirokawa KE, Huo B, Bannerjee S, Korobkova L, Park CS, Park YG, Bienkowski MS, Chon U, Wheeler DW, Li X, Wang Y, Naeemi M, Xie P, Liu L, Kelly K, An X, Attili SM, Bowman I, Bludova A, Cetin A, Ding L, Drewes R, D'Orazi F, Elowsky C, Fischer S, Galbavy W, Gao L, Gillis J, Groblewski PA, Gou L, Hahn JD, Hatfield JT, Hintiryan H, Huang JJ, Kondo H, Kuang X, Lesnar P, Li X, Li Y, Lin M, Lo D, Mizrachi J, Mok S, Nicovich PR, Palaniswamy R, Palmer J, Qi X, Shen E, Sun YC, Tao HW, Wakemen W, Wang Y, Yao S, Yuan J, Zhan H, Zhu M, Ng L, Zhang LI, Lim BK, Hawrylycz M, Gong H, Gee JC, Kim Y, Chung K, Yang XW, Peng H, Luo Q, Mitra PP, Zador AM, Zeng H, Ascoli GA, Josh Huang Z, Osten P, Harris JA, Dong HW. Cellular anatomy of the mouse primary motor cortex. Nature 2021; 598:159-166. [PMID: 34616071 PMCID: PMC8494646 DOI: 10.1038/s41586-021-03970-w] [Citation(s) in RCA: 94] [Impact Index Per Article: 31.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2020] [Accepted: 08/27/2021] [Indexed: 12/24/2022]
Abstract
An essential step toward understanding brain function is to establish a structural framework with cellular resolution on which multi-scale datasets spanning molecules, cells, circuits and systems can be integrated and interpreted1. Here, as part of the collaborative Brain Initiative Cell Census Network (BICCN), we derive a comprehensive cell type-based anatomical description of one exemplar brain structure, the mouse primary motor cortex, upper limb area (MOp-ul). Using genetic and viral labelling, barcoded anatomy resolved by sequencing, single-neuron reconstruction, whole-brain imaging and cloud-based neuroinformatics tools, we delineated the MOp-ul in 3D and refined its sublaminar organization. We defined around two dozen projection neuron types in the MOp-ul and derived an input-output wiring diagram, which will facilitate future analyses of motor control circuitry across molecular, cellular and system levels. This work provides a roadmap towards a comprehensive cellular-resolution description of mammalian brain architecture.
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Affiliation(s)
| | - Brian Zingg
- UCLA Brain Research and Artificial Intelligence Nexus, Department of Neurobiology, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, USA
- USC Stevens Neuroimaging and Informatics Institute (INI), Keck School of Medicine of USC, University of Southern California, Los Angeles, CA, USA
| | | | - Xiaoyin Chen
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
- Allen Institute for Brain Science, Seattle, WA, USA
| | - Quanxin Wang
- Allen Institute for Brain Science, Seattle, WA, USA
| | - Nicholas N Foster
- UCLA Brain Research and Artificial Intelligence Nexus, Department of Neurobiology, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, USA
- USC Stevens Neuroimaging and Informatics Institute (INI), Keck School of Medicine of USC, University of Southern California, Los Angeles, CA, USA
| | - 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
- HUST-Suzhou Institute for Brainsmatics, JITRI, Suzhou, China
| | | | - Karla E Hirokawa
- Allen Institute for Brain Science, Seattle, WA, USA
- Cajal Neuroscience, Seattle, WA, USA
| | - Bingxing Huo
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
| | | | - Laura Korobkova
- USC Stevens Neuroimaging and Informatics Institute (INI), Keck School of Medicine of USC, University of Southern California, Los Angeles, CA, USA
| | - Chris Sin Park
- Center for Neurobehavioral Genetics, Jane and Terry Semel Institute for Neuroscience and Human Behavior, Department of Psychiatry and Biobehavioral Sciences, David Geffen School of Medicine at UCLA, Los Angeles, CA, USA
| | - Young-Gyun Park
- Institute for Medical Engineering and Science, Department of Chemical Engineering, Picower Institute for Learning and Memory, Massachusetts Institute of Technology (MIT), Cambridge, MA, USA
| | - Michael S Bienkowski
- USC Stevens Neuroimaging and Informatics Institute (INI), Keck School of Medicine of USC, University of Southern California, Los Angeles, CA, USA
- Department of Physiology and Neuroscience, Zilkha Neurogenetic Institute, Keck School of Medicine of USC, University of Southern California, Los Angeles, California, USA
| | - Uree Chon
- Department of Neural and Behavioral Sciences, College of Medicine, Penn State University, Hershey, PA, USA
| | - Diek W Wheeler
- Center for Neural Informatics, Structures and Plasticity, Bioengineering Department and Krasnow Institute for Advanced Study, George Mason University, Fairfax, VA, USA
| | - Xiangning 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
- HUST-Suzhou Institute for Brainsmatics, JITRI, Suzhou, China
| | - Yun Wang
- Allen Institute for Brain Science, Seattle, WA, USA
| | | | - 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
| | - Kathleen Kelly
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
| | - Xu An
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
- Department of Neurobiology, Duke University School of Medicine, Durham, NC, USA
| | - Sarojini M Attili
- Center for Neural Informatics, Structures and Plasticity, Bioengineering Department and Krasnow Institute for Advanced Study, George Mason University, Fairfax, VA, USA
| | - Ian Bowman
- UCLA Brain Research and Artificial Intelligence Nexus, Department of Neurobiology, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, USA
- USC Stevens Neuroimaging and Informatics Institute (INI), Keck School of Medicine of USC, University of Southern California, Los Angeles, CA, USA
| | | | - Ali Cetin
- Allen Institute for Brain Science, Seattle, WA, USA
| | - Liya Ding
- SEU-ALLEN Joint Center, Institute for Brain and Intelligence, Southeast University, Nanjing, China
| | - Rhonda Drewes
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
| | | | - Corey Elowsky
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
| | | | | | - Lei Gao
- UCLA Brain Research and Artificial Intelligence Nexus, Department of Neurobiology, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, USA
- USC Stevens Neuroimaging and Informatics Institute (INI), Keck School of Medicine of USC, University of Southern California, Los Angeles, CA, USA
| | - Jesse Gillis
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
| | | | - Lin Gou
- UCLA Brain Research and Artificial Intelligence Nexus, Department of Neurobiology, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, USA
- USC Stevens Neuroimaging and Informatics Institute (INI), Keck School of Medicine of USC, University of Southern California, Los Angeles, CA, USA
| | - Joel D Hahn
- Department of Biological Sciences, University of Southern California, Los Angeles, CA, USA
| | - Joshua T Hatfield
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
- Department of Neurobiology, Duke University School of Medicine, Durham, NC, USA
| | - Houri Hintiryan
- UCLA Brain Research and Artificial Intelligence Nexus, Department of Neurobiology, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, USA
- USC Stevens Neuroimaging and Informatics Institute (INI), Keck School of Medicine of USC, University of Southern California, Los Angeles, CA, USA
| | - Junxiang Jason Huang
- Center for Neural Circuits and Sensory Processing Disorders, Zilkha Neurogenetics Institute (ZNI), Department of Physiology and Neuroscience, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Hideki Kondo
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
| | - Xiuli Kuang
- School of Optometry and Ophthalmology, Wenzhou Medical University, Wenzhou, China
| | | | - Xu Li
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
| | - Yaoyao Li
- School of Optometry and Ophthalmology, Wenzhou Medical University, Wenzhou, China
| | - Mengkuan Lin
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
| | - Darrick Lo
- UCLA Brain Research and Artificial Intelligence Nexus, Department of Neurobiology, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, USA
- USC Stevens Neuroimaging and Informatics Institute (INI), Keck School of Medicine of USC, University of Southern California, Los Angeles, CA, USA
| | | | | | - Philip R Nicovich
- Allen Institute for Brain Science, Seattle, WA, USA
- Cajal Neuroscience, Seattle, WA, USA
| | | | - Jason Palmer
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
| | - Xiaoli Qi
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
| | - Elise Shen
- Allen Institute for Brain Science, Seattle, WA, USA
| | - Yu-Chi Sun
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
| | - Huizhong W Tao
- Center for Neural Circuits and Sensory Processing Disorders, Zilkha Neurogenetics Institute (ZNI), Department of Physiology and Neuroscience, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | | | - 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
| | - Shenqin Yao
- Allen Institute for Brain Science, Seattle, WA, USA
| | - Jing Yuan
- 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, Suzhou, China
| | - Huiqing Zhan
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
| | - Muye Zhu
- UCLA Brain Research and Artificial Intelligence Nexus, Department of Neurobiology, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, USA
- USC Stevens Neuroimaging and Informatics Institute (INI), Keck School of Medicine of USC, University of Southern California, Los Angeles, CA, USA
| | - Lydia Ng
- Allen Institute for Brain Science, Seattle, WA, USA
| | - Li I Zhang
- Center for Neural Circuits and Sensory Processing Disorders, Zilkha Neurogenetics Institute (ZNI), Department of Physiology and Neuroscience, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Byung Kook Lim
- HUST-Suzhou Institute for Brainsmatics, JITRI, Suzhou, China
- Division of Biological Science, Neurobiology section, University of California San Diego, San Diego, CA, USA
| | | | - 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, Suzhou, China
| | - James C Gee
- Department of Radiology, University of Pennsylvania, Philadelphia, PA, USA
| | - Yongsoo Kim
- Department of Neural and Behavioral Sciences, College of Medicine, Penn State University, Hershey, PA, USA
| | - Kwanghun Chung
- Institute for Medical Engineering and Science, Department of Chemical Engineering, Picower Institute for Learning and Memory, Massachusetts Institute of Technology (MIT), Cambridge, MA, USA
| | - X William Yang
- Center for Neurobehavioral Genetics, Jane and Terry Semel Institute for Neuroscience and Human Behavior, Department of Psychiatry and Biobehavioral Sciences, David Geffen School of Medicine at UCLA, Los Angeles, CA, USA
| | - Hanchuan Peng
- SEU-ALLEN Joint Center, Institute for Brain and Intelligence, Southeast University, Nanjing, 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, Suzhou, China
| | - Partha P Mitra
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
| | | | - Hongkui Zeng
- Allen Institute for Brain Science, Seattle, WA, USA
| | - Giorgio A Ascoli
- Center for Neural Informatics, Structures and Plasticity, Bioengineering Department and Krasnow Institute for Advanced Study, George Mason University, Fairfax, VA, USA.
| | - Z Josh Huang
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA.
- Department of Neurobiology, Duke University School of Medicine, Durham, NC, USA.
| | - Pavel Osten
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA.
| | - Julie A Harris
- Allen Institute for Brain Science, Seattle, WA, USA.
- Cajal Neuroscience, Seattle, WA, USA.
| | - Hong-Wei Dong
- UCLA Brain Research and Artificial Intelligence Nexus, Department of Neurobiology, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, USA.
- USC Stevens Neuroimaging and Informatics Institute (INI), Keck School of Medicine of USC, University of Southern California, Los Angeles, CA, USA.
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39
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Aggleton JP, Yanakieva S, Sengpiel F, Nelson AJ. The separate and combined properties of the granular (area 29) and dysgranular (area 30) retrosplenial cortex. Neurobiol Learn Mem 2021; 185:107516. [PMID: 34481970 DOI: 10.1016/j.nlm.2021.107516] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2021] [Revised: 07/27/2021] [Accepted: 08/30/2021] [Indexed: 12/31/2022]
Abstract
Retrosplenial cortex contains two principal subdivisions, area 29 (granular) and area 30 (dysgranular). Their respective anatomical connections in the rat brain reveal that area 29 is the primary recipient of hippocampal and parahippocampal spatial and contextual information while area 30 is the primary interactor with current visual information. Lesion studies and measures of neuronal activity in rodents indicate that retrosplenial cortex helps to integrate space from different perspectives, e.g., egocentric and allocentric, providing landmark and heading cues for navigation and spatial learning. It provides a repository of scene information that, over time, becomes increasingly independent of the hippocampus. These processes, reflect the interactive actions between areas 29 and 30, along with their convergent influences on cortical and thalamic targets. Consequently, despite their differences, both areas 29 and 30 are necessary for an array of spatial and learning problems.
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Affiliation(s)
- John P Aggleton
- School of Psychology, Cardiff University, Tower Building, Park Place, Cardiff, Wales CF10 3AT, UK.
| | - Steliana Yanakieva
- School of Psychology, Cardiff University, Tower Building, Park Place, Cardiff, Wales CF10 3AT, UK
| | - Frank Sengpiel
- School of Biosciences, Cardiff University, Sir Martin Evans Building, Museum Avenue, Cardiff, Wales CF10 3AX, UK
| | - Andrew J Nelson
- School of Psychology, Cardiff University, Tower Building, Park Place, Cardiff, Wales CF10 3AT, UK
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40
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Perens J, Salinas CG, Skytte JL, Roostalu U, Dahl AB, Dyrby TB, Wichern F, Barkholt P, Vrang N, Jelsing J, Hecksher-Sørensen J. An Optimized Mouse Brain Atlas for Automated Mapping and Quantification of Neuronal Activity Using iDISCO+ and Light Sheet Fluorescence Microscopy. Neuroinformatics 2021; 19:433-446. [PMID: 33063286 PMCID: PMC8233272 DOI: 10.1007/s12021-020-09490-8] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
In recent years, the combination of whole-brain immunolabelling, light sheet fluorescence microscopy (LSFM) and subsequent registration of data with a common reference atlas, has enabled 3D visualization and quantification of fluorescent markers or tracers in the adult mouse brain. Today, the common coordinate framework version 3 developed by the Allen’s Institute of Brain Science (AIBS CCFv3), is widely used as the standard brain atlas for registration of LSFM data. However, the AIBS CCFv3 is based on histological processing and imaging modalities different from those used for LSFM imaging and consequently, the data differ in both tissue contrast and morphology. To improve the accuracy and speed by which LSFM-imaged whole-brain data can be registered and quantified, we have created an optimized digital mouse brain atlas based on immunolabelled and solvent-cleared brains. Compared to the AIBS CCFv3 atlas, our atlas resulted in faster and more accurate mapping of neuronal activity as measured by c-Fos expression, especially in the hindbrain. We further demonstrated utility of the LSFM atlas by comparing whole-brain quantitative changes in c-Fos expression following acute administration of semaglutide in lean and diet-induced obese mice. In combination with an improved algorithm for c-Fos detection, the LSFM atlas enables unbiased and computationally efficient characterization of drug effects on whole-brain neuronal activity patterns. In conclusion, we established an optimized reference atlas for more precise mapping of fluorescent markers, including c-Fos, in mouse brains processed for LSFM.
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Affiliation(s)
- Johanna Perens
- Gubra ApS, 2970, Hørsholm, Denmark.,Department of Applied Mathematics and Computer Science, Technical University Denmark, 2800, Kongens Lyngby, Denmark
| | | | | | | | - Anders Bjorholm Dahl
- Department of Applied Mathematics and Computer Science, Technical University Denmark, 2800, Kongens Lyngby, Denmark
| | - Tim B Dyrby
- Department of Applied Mathematics and Computer Science, Technical University Denmark, 2800, Kongens Lyngby, Denmark.,Danish Research Centre for Magnetic Resonance, Centre for Functional and Diagnostic Imaging and Research, Copenhagen University Hospital Hvidovre, 2650, Hvidovre, Denmark
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41
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Oblak AL, Lin PB, Kotredes KP, Pandey RS, Garceau D, Williams HM, Uyar A, O'Rourke R, O'Rourke S, Ingraham C, Bednarczyk D, Belanger M, Cope ZA, Little GJ, Williams SPG, Ash C, Bleckert A, Ragan T, Logsdon BA, Mangravite LM, Sukoff Rizzo SJ, Territo PR, Carter GW, Howell GR, Sasner M, Lamb BT. Comprehensive Evaluation of the 5XFAD Mouse Model for Preclinical Testing Applications: A MODEL-AD Study. Front Aging Neurosci 2021; 13:713726. [PMID: 34366832 DOI: 10.3389/fnagi.2021.71372] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2021] [Accepted: 06/23/2021] [Indexed: 05/23/2023] Open
Abstract
The ability to investigate therapeutic interventions in animal models of neurodegenerative diseases depends on extensive characterization of the model(s) being used. There are numerous models that have been generated to study Alzheimer's disease (AD) and the underlying pathogenesis of the disease. While transgenic models have been instrumental in understanding AD mechanisms and risk factors, they are limited in the degree of characteristics displayed in comparison with AD in humans, and the full spectrum of AD effects has yet to be recapitulated in a single mouse model. The Model Organism Development and Evaluation for Late-Onset Alzheimer's Disease (MODEL-AD) consortium was assembled by the National Institute on Aging (NIA) to develop more robust animal models of AD with increased relevance to human disease, standardize the characterization of AD mouse models, improve preclinical testing in animals, and establish clinically relevant AD biomarkers, among other aims toward enhancing the translational value of AD models in clinical drug design and treatment development. Here we have conducted a detailed characterization of the 5XFAD mouse, including transcriptomics, electroencephalogram, in vivo imaging, biochemical characterization, and behavioral assessments. The data from this study is publicly available through the AD Knowledge Portal.
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Affiliation(s)
- Adrian L Oblak
- Department of Radiology and Imaging Sciences, Indiana University School of Medicine, Indianapolis, IN, United States
- Stark Neurosciences Research Institute, Indiana University School of Medicine, Indianapolis, IN, United States
| | - Peter B Lin
- Stark Neurosciences Research Institute, Indiana University School of Medicine, Indianapolis, IN, United States
| | | | - Ravi S Pandey
- The Jackson Laboratory, Bar Harbor, ME, United States
| | - Dylan Garceau
- The Jackson Laboratory, Bar Harbor, ME, United States
| | | | - Asli Uyar
- The Jackson Laboratory, Bar Harbor, ME, United States
| | - Rita O'Rourke
- The Jackson Laboratory, Bar Harbor, ME, United States
| | | | - Cynthia Ingraham
- Stark Neurosciences Research Institute, Indiana University School of Medicine, Indianapolis, IN, United States
| | | | - Melisa Belanger
- Department of Medicine, University of Pittsburgh, Pittsburgh, PA, United States
| | - Zackary A Cope
- Department of Medicine, University of Pittsburgh, Pittsburgh, PA, United States
| | - Gabriela J Little
- Department of Medicine, University of Pittsburgh, Pittsburgh, PA, United States
| | | | - Carl Ash
- Stark Neurosciences Research Institute, Indiana University School of Medicine, Indianapolis, IN, United States
| | - Adam Bleckert
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, United States
| | - Tim Ragan
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, United States
| | | | | | | | - Paul R Territo
- Stark Neurosciences Research Institute, Indiana University School of Medicine, Indianapolis, IN, United States
- Department of Medicine, Indiana University School of Medicine, Indianapolis, IN, United States
| | | | | | | | - Bruce T Lamb
- Stark Neurosciences Research Institute, Indiana University School of Medicine, Indianapolis, IN, United States
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN, United States
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42
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Oblak AL, Lin PB, Kotredes KP, Pandey RS, Garceau D, Williams HM, Uyar A, O'Rourke R, O'Rourke S, Ingraham C, Bednarczyk D, Belanger M, Cope ZA, Little GJ, Williams SPG, Ash C, Bleckert A, Ragan T, Logsdon BA, Mangravite LM, Sukoff Rizzo SJ, Territo PR, Carter GW, Howell GR, Sasner M, Lamb BT. Comprehensive Evaluation of the 5XFAD Mouse Model for Preclinical Testing Applications: A MODEL-AD Study. Front Aging Neurosci 2021; 13:713726. [PMID: 34366832 PMCID: PMC8346252 DOI: 10.3389/fnagi.2021.713726] [Citation(s) in RCA: 128] [Impact Index Per Article: 42.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2021] [Accepted: 06/23/2021] [Indexed: 12/14/2022] Open
Abstract
The ability to investigate therapeutic interventions in animal models of neurodegenerative diseases depends on extensive characterization of the model(s) being used. There are numerous models that have been generated to study Alzheimer's disease (AD) and the underlying pathogenesis of the disease. While transgenic models have been instrumental in understanding AD mechanisms and risk factors, they are limited in the degree of characteristics displayed in comparison with AD in humans, and the full spectrum of AD effects has yet to be recapitulated in a single mouse model. The Model Organism Development and Evaluation for Late-Onset Alzheimer's Disease (MODEL-AD) consortium was assembled by the National Institute on Aging (NIA) to develop more robust animal models of AD with increased relevance to human disease, standardize the characterization of AD mouse models, improve preclinical testing in animals, and establish clinically relevant AD biomarkers, among other aims toward enhancing the translational value of AD models in clinical drug design and treatment development. Here we have conducted a detailed characterization of the 5XFAD mouse, including transcriptomics, electroencephalogram, in vivo imaging, biochemical characterization, and behavioral assessments. The data from this study is publicly available through the AD Knowledge Portal.
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Affiliation(s)
- Adrian L Oblak
- Department of Radiology and Imaging Sciences, Indiana University School of Medicine, Indianapolis, IN, United States.,Stark Neurosciences Research Institute, Indiana University School of Medicine, Indianapolis, IN, United States
| | - Peter B Lin
- Stark Neurosciences Research Institute, Indiana University School of Medicine, Indianapolis, IN, United States
| | | | - Ravi S Pandey
- The Jackson Laboratory, Bar Harbor, ME, United States
| | - Dylan Garceau
- The Jackson Laboratory, Bar Harbor, ME, United States
| | | | - Asli Uyar
- The Jackson Laboratory, Bar Harbor, ME, United States
| | - Rita O'Rourke
- The Jackson Laboratory, Bar Harbor, ME, United States
| | | | - Cynthia Ingraham
- Stark Neurosciences Research Institute, Indiana University School of Medicine, Indianapolis, IN, United States
| | | | - Melisa Belanger
- Department of Medicine, University of Pittsburgh, Pittsburgh, PA, United States
| | - Zackary A Cope
- Department of Medicine, University of Pittsburgh, Pittsburgh, PA, United States
| | - Gabriela J Little
- Department of Medicine, University of Pittsburgh, Pittsburgh, PA, United States
| | | | - Carl Ash
- Stark Neurosciences Research Institute, Indiana University School of Medicine, Indianapolis, IN, United States
| | - Adam Bleckert
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, United States
| | - Tim Ragan
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, United States
| | | | | | | | - Paul R Territo
- Stark Neurosciences Research Institute, Indiana University School of Medicine, Indianapolis, IN, United States.,Department of Medicine, Indiana University School of Medicine, Indianapolis, IN, United States
| | | | | | | | - Bruce T Lamb
- Stark Neurosciences Research Institute, Indiana University School of Medicine, Indianapolis, IN, United States.,Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN, United States
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43
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Perens J, Salinas CG, Skytte JL, Roostalu U, Dahl AB, Dyrby TB, Wichern F, Barkholt P, Vrang N, Jelsing J, Hecksher-Sørensen J. An Optimized Mouse Brain Atlas for Automated Mapping and Quantification of Neuronal Activity Using iDISCO+ and Light Sheet Fluorescence Microscopy. Neuroinformatics 2021. [PMID: 33063286 DOI: 10.1007/s12021-020-09490-8/figures/5] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/23/2023]
Abstract
In recent years, the combination of whole-brain immunolabelling, light sheet fluorescence microscopy (LSFM) and subsequent registration of data with a common reference atlas, has enabled 3D visualization and quantification of fluorescent markers or tracers in the adult mouse brain. Today, the common coordinate framework version 3 developed by the Allen's Institute of Brain Science (AIBS CCFv3), is widely used as the standard brain atlas for registration of LSFM data. However, the AIBS CCFv3 is based on histological processing and imaging modalities different from those used for LSFM imaging and consequently, the data differ in both tissue contrast and morphology. To improve the accuracy and speed by which LSFM-imaged whole-brain data can be registered and quantified, we have created an optimized digital mouse brain atlas based on immunolabelled and solvent-cleared brains. Compared to the AIBS CCFv3 atlas, our atlas resulted in faster and more accurate mapping of neuronal activity as measured by c-Fos expression, especially in the hindbrain. We further demonstrated utility of the LSFM atlas by comparing whole-brain quantitative changes in c-Fos expression following acute administration of semaglutide in lean and diet-induced obese mice. In combination with an improved algorithm for c-Fos detection, the LSFM atlas enables unbiased and computationally efficient characterization of drug effects on whole-brain neuronal activity patterns. In conclusion, we established an optimized reference atlas for more precise mapping of fluorescent markers, including c-Fos, in mouse brains processed for LSFM.
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Affiliation(s)
- Johanna Perens
- Gubra ApS, 2970, Hørsholm, Denmark
- Department of Applied Mathematics and Computer Science, Technical University Denmark, 2800, Kongens Lyngby, Denmark
| | | | | | | | - Anders Bjorholm Dahl
- Department of Applied Mathematics and Computer Science, Technical University Denmark, 2800, Kongens Lyngby, Denmark
| | - Tim B Dyrby
- Department of Applied Mathematics and Computer Science, Technical University Denmark, 2800, Kongens Lyngby, Denmark
- Danish Research Centre for Magnetic Resonance, Centre for Functional and Diagnostic Imaging and Research, Copenhagen University Hospital Hvidovre, 2650, Hvidovre, Denmark
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44
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Yook JS, Kim J, Kim J. Convergence Circuit Mapping: Genetic Approaches From Structure to Function. Front Syst Neurosci 2021; 15:688673. [PMID: 34234652 PMCID: PMC8255632 DOI: 10.3389/fnsys.2021.688673] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Accepted: 05/28/2021] [Indexed: 12/22/2022] Open
Abstract
Understanding the complex neural circuits that underpin brain function and behavior has been a long-standing goal of neuroscience. Yet this is no small feat considering the interconnectedness of neurons and other cell types, both within and across brain regions. In this review, we describe recent advances in mouse molecular genetic engineering that can be used to integrate information on brain activity and structure at regional, cellular, and subcellular levels. The convergence of structural inputs can be mapped throughout the brain in a cell type-specific manner by antero- and retrograde viral systems expressing various fluorescent proteins and genetic switches. Furthermore, neural activity can be manipulated using opto- and chemo-genetic tools to interrogate the functional significance of this input convergence. Monitoring neuronal activity is obtained with precise spatiotemporal resolution using genetically encoded sensors for calcium changes and specific neurotransmitters. Combining these genetically engineered mapping tools is a compelling approach for unraveling the structural and functional brain architecture of complex behaviors and malfunctioned states of neurological disorders.
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Affiliation(s)
- Jang Soo Yook
- Center for Functional Connectomics, Korea Institute of Science and Technology (KIST), Seoul, South Korea
| | - Jihyun Kim
- Center for Functional Connectomics, Korea Institute of Science and Technology (KIST), Seoul, South Korea.,Department of Integrated Biomedical and Life Sciences, Graduate School, Korea University, Seoul, South Korea
| | - Jinhyun Kim
- Center for Functional Connectomics, Korea Institute of Science and Technology (KIST), Seoul, South Korea.,Department of Integrated Biomedical and Life Sciences, Graduate School, Korea University, Seoul, South Korea
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45
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Ding SL, Yao Z, Hirokawa KE, Nguyen TN, Graybuck LT, Fong O, Bohn P, Ngo K, Smith KA, Koch C, Phillips JW, Lein ES, Harris JA, Tasic B, Zeng H. Distinct Transcriptomic Cell Types and Neural Circuits of the Subiculum and Prosubiculum along the Dorsal-Ventral Axis. Cell Rep 2021; 31:107648. [PMID: 32433957 DOI: 10.1016/j.celrep.2020.107648] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2019] [Revised: 02/23/2020] [Accepted: 04/22/2020] [Indexed: 01/02/2023] Open
Abstract
Subicular regions play important roles in spatial processing and many cognitive functions, and these are mainly attributed to the subiculum (Sub) rather than the prosubiculum (PS). Using single-cell RNA sequencing, we identify 27 transcriptomic cell types residing in sub-domains of the Sub and PS. Based on in situ expression of reliable transcriptomic markers, the precise boundaries of the Sub and PS are consistently defined along the dorsoventral axis. Using these borders to evaluate Cre-line specificity and tracer injections, we find bona fide Sub projections topographically to structures important for spatial processing and navigation. In contrast, the PS sends its outputs to widespread brain regions crucial for motivation, emotion, reward, stress, anxiety, and fear. The Sub and PS, respectively, dominate dorsal and ventral subicular regions and receive different afferents. These results reveal two molecularly and anatomically distinct circuits centered in the Sub and PS, respectively, providing a consistent explanation for historical data and a clearer foundation for future studies.
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Affiliation(s)
- Song-Lin Ding
- Allen Institute for Brain Science, Seattle, WA 98109, USA.
| | - Zizhen Yao
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | | | | | | | - Olivia Fong
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | - Phillip Bohn
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | - Kiet Ngo
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | | | - Christof Koch
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | | | - Ed S Lein
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | - Julie A Harris
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | - Bosiljka Tasic
- Allen Institute for Brain Science, Seattle, WA 98109, USA
| | - Hongkui Zeng
- Allen Institute for Brain Science, Seattle, WA 98109, USA
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46
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Durens M, Soliman M, Millonig J, DiCicco-Bloom E. Engrailed-2 is a cell autonomous regulator of neurogenesis in cultured hippocampal neural stem cells. Dev Neurobiol 2021; 81:724-735. [PMID: 33852756 DOI: 10.1002/dneu.22824] [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: 09/21/2020] [Revised: 04/01/2021] [Accepted: 04/02/2021] [Indexed: 11/07/2022]
Abstract
Abnormalities in genes that regulate early brain development are known risk factors for neurodevelopmental disorders. Engrailed-2 (En2) is a homeodomain transcription factor with established roles in cerebellar patterning. En2 is highly expressed in the developing mid-hindbrain region, and En2 knockout (KO) mice exhibit major deficits in mid-hindbrain structures. However, En2 is also expressed in forebrain regions including the hippocampus, but its function is unknown. Previous studies have shown that the hippocampus of En2-KO mice exhibits reductions in its volume and cell numbers due to aberrant neurogenesis. Aberrant neurogenesis is due, in part, to noncell autonomous effects, specifically, reductions of innervating norepinephrine fibers from the locus coeruleus. In this study, we investigate possible cell autonomous roles of En2 in hippocampal neurogenesis. We examine proliferation, survival, and differentiation using cultures of hippocampal neurospheres of P7 wild-type (WT) and En2-KO hippocampal neural progenitor cells (NPCs). At 7 days, En2-KO neurospheres were larger on average than WT spheres and exhibited 2.5-fold greater proliferation and 2-fold increase in apoptotic cells, similar to in vivo KO phenotype. Further, En2-KO cultures exhibited 40% less cells with neurite projections, suggesting decreased differentiation. Lastly, reestablishing En2 expression in En2-KO NPCs rescued excess proliferation. These results indicate that En2 functions in hippocampal NPCs by inhibiting proliferation and promoting survival and differentiation in a cell autonomous manner. More broadly, this study suggests that En2 impacts brain structure and function in diverse regions outside of the mid-hindbrain.
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Affiliation(s)
- Madel Durens
- School of Graduate Studies, Rutgers, The State University of New Jersey, Piscataway, NJ, USA.,Department of Neuroscience and Cell Biology, Rutgers Robert Wood Johnson Medical School, Rutgers, The State University of New Jersey, Piscataway, NJ, USA
| | - Mai Soliman
- School of Graduate Studies, Rutgers, The State University of New Jersey, Piscataway, NJ, USA.,Center for Advanced Biotechnology and Medicine, Rutgers, The State University of New Jersey, Piscataway, NJ, USA
| | - James Millonig
- Department of Neuroscience and Cell Biology, Rutgers Robert Wood Johnson Medical School, Rutgers, The State University of New Jersey, Piscataway, NJ, USA.,Center for Advanced Biotechnology and Medicine, Rutgers, The State University of New Jersey, Piscataway, NJ, USA
| | - Emanuel DiCicco-Bloom
- School of Graduate Studies, Rutgers, The State University of New Jersey, Piscataway, NJ, USA.,Department of Neuroscience and Cell Biology, Rutgers Robert Wood Johnson Medical School, Rutgers, The State University of New Jersey, Piscataway, NJ, USA.,Department of Pediatrics, Rutgers Robert Wood Johnson Medical School, Rutgers, The State University of New Jersey, New Brunswick, NJ, USA
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47
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Ma G, Liu Y, Wang L, Xiao Z, Song K, Wang Y, Peng W, Liu X, Wang Z, Jin S, Tao Z, Li CT, Xu T, Xu F, Xu M, Zhang S. Hierarchy in sensory processing reflected by innervation balance on cortical interneurons. SCIENCE ADVANCES 2021; 7:7/20/eabf5676. [PMID: 33990327 PMCID: PMC8121429 DOI: 10.1126/sciadv.abf5676] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/04/2020] [Accepted: 03/26/2021] [Indexed: 06/12/2023]
Abstract
Sensory processing is subjected to modulation by behavioral contexts that are often mediated by long-range inputs to cortical interneurons, but their selectivity to different types of interneurons remains largely unknown. Using rabies-virus tracing and optogenetics-assisted recording, we analyzed the long-range connections to various brain regions along the hierarchy of visual processing, including primary visual cortex, medial association cortices, and frontal cortices. We found that hierarchical corticocortical and thalamocortical connectivity is reflected by the relative weights of inputs to parvalbumin-positive (PV+) and vasoactive intestinal peptide-positive (VIP+) neurons within the conserved local circuit motif, with bottom-up and top-down inputs preferring PV+ and VIP+ neurons, respectively. Our algorithms based on innervation weights for these two types of local interneurons generated testable predictions of the hierarchical position of many brain areas. These results support the notion that preferential long-range inputs to specific local interneurons are essential for the hierarchical information flow in the brain.
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Affiliation(s)
- Guofen Ma
- Center for Brain Science of Shanghai Children's Medical Center, Department of Anatomy and Physiology, Key Laboratory of Cell Differentiation and Apoptosis of the Chinese Ministry of Education, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Yanmei Liu
- Center for Brain Science of Shanghai Children's Medical Center, Department of Anatomy and Physiology, Key Laboratory of Cell Differentiation and Apoptosis of the Chinese Ministry of Education, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Lizhao Wang
- Center for Brain Science of Shanghai Children's Medical Center, Department of Anatomy and Physiology, Key Laboratory of Cell Differentiation and Apoptosis of the Chinese Ministry of Education, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Zhongyi Xiao
- Institute of Neuroscience, CAS Center for Excellence in Brain Science and Intelligence Technology, State Key Laboratory of Neuroscience, Chinese Academy of Sciences, Shanghai 200031, China
| | - Kun Song
- Institute of Neuroscience, CAS Center for Excellence in Brain Science and Intelligence Technology, State Key Laboratory of Neuroscience, Chinese Academy of Sciences, Shanghai 200031, China
| | - Yanjie Wang
- Center for Brain Science of Shanghai Children's Medical Center, Department of Anatomy and Physiology, Key Laboratory of Cell Differentiation and Apoptosis of the Chinese Ministry of Education, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Wanling Peng
- Institute of Neuroscience, CAS Center for Excellence in Brain Science and Intelligence Technology, State Key Laboratory of Neuroscience, Chinese Academy of Sciences, Shanghai 200031, China
| | - Xiaotong Liu
- Institute of Neuroscience, CAS Center for Excellence in Brain Science and Intelligence Technology, State Key Laboratory of Neuroscience, Chinese Academy of Sciences, Shanghai 200031, China
| | - Ziyue Wang
- Center for Brain Science of Shanghai Children's Medical Center, Department of Anatomy and Physiology, Key Laboratory of Cell Differentiation and Apoptosis of the Chinese Ministry of Education, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Sen Jin
- Brain Cognition and Brain Disease Institute (BCBDI), Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen-Hong Kong Institute of Brain Science-Shenzhen Fundamental Research Institutions, Shenzhen 518055, China
| | - Zi Tao
- Institute of Neuroscience, CAS Center for Excellence in Brain Science and Intelligence Technology, State Key Laboratory of Neuroscience, Chinese Academy of Sciences, Shanghai 200031, China
| | - Chengyu T Li
- Institute of Neuroscience, CAS Center for Excellence in Brain Science and Intelligence Technology, State Key Laboratory of Neuroscience, Chinese Academy of Sciences, Shanghai 200031, China
- Shanghai Research Center for Brain Science and Brain-Inspired Intelligence, Shanghai 201210, China
| | - Tianle Xu
- Center for Brain Science of Shanghai Children's Medical Center, Department of Anatomy and Physiology, Key Laboratory of Cell Differentiation and Apoptosis of the Chinese Ministry of Education, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
- Shanghai Research Center for Brain Science and Brain-Inspired Intelligence, Shanghai 201210, China
| | - Fuqiang Xu
- Brain Cognition and Brain Disease Institute (BCBDI), Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen-Hong Kong Institute of Brain Science-Shenzhen Fundamental Research Institutions, Shenzhen 518055, China
| | - Min Xu
- Institute of Neuroscience, CAS Center for Excellence in Brain Science and Intelligence Technology, State Key Laboratory of Neuroscience, Chinese Academy of Sciences, Shanghai 200031, China.
- Shanghai Research Center for Brain Science and Brain-Inspired Intelligence, Shanghai 201210, China
| | - Siyu Zhang
- Center for Brain Science of Shanghai Children's Medical Center, Department of Anatomy and Physiology, Key Laboratory of Cell Differentiation and Apoptosis of the Chinese Ministry of Education, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China.
- Shanghai Research Center for Brain Science and Brain-Inspired Intelligence, Shanghai 201210, China
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48
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Constructing the rodent stereotaxic brain atlas: a survey. SCIENCE CHINA-LIFE SCIENCES 2021; 65:93-106. [PMID: 33860452 DOI: 10.1007/s11427-020-1911-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Accepted: 02/03/2021] [Indexed: 12/22/2022]
Abstract
The stereotaxic brain atlas is a fundamental reference tool commonly used in the field of neuroscience. Here we provide a brief history of brain atlas development and clarify three key conceptual elements of stereotaxic brain atlasing: brain image, atlas, and stereotaxis. We also refine four technical indices for evaluating the construction of atlases: the quality of staining and labeling, the granularity of delineation, spatial resolution, and the precision of spatial location and orientation. Additionally, we discuss state-of-the-art technologies and their trends in the fields of image acquisition, stereotaxic coordinate construction, image processing, anatomical structure recognition, and publishing: the procedures of brain atlas illustration. We believe that the use of single-cell resolution and micron-level location precision will become a future trend in the study of the stereotaxic brain atlas, which will greatly benefit the development of neuroscience.
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Ni H, Feng Z, Guan Y, Jia X, Chen W, Jiang T, Zhong Q, Yuan J, Ren M, Li X, Gong H, Luo Q, Li A. DeepMapi: a Fully Automatic Registration Method for Mesoscopic Optical Brain Images Using Convolutional Neural Networks. Neuroinformatics 2021; 19:267-284. [PMID: 32754778 PMCID: PMC8004526 DOI: 10.1007/s12021-020-09483-7] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
The extreme complexity of mammalian brains requires a comprehensive deconstruction of neuroanatomical structures. Scientists normally use a brain stereotactic atlas to determine the locations of neurons and neuronal circuits. However, different brain images are normally not naturally aligned even when they are imaged with the same setup, let alone under the differing resolutions and dataset sizes used in mesoscopic imaging. As a result, it is difficult to achieve high-throughput automatic registration without manual intervention. Here, we propose a deep learning-based registration method called DeepMapi to predict a deformation field used to register mesoscopic optical images to an atlas. We use a self-feedback strategy to address the problem of imbalanced training sets (sampling at a fixed step size in nonuniform brains of structures and deformations) and use a dual-hierarchical network to capture the large and small deformations. By comparing DeepMapi with other registration methods, we demonstrate its superiority over a set of ground truth images, including both optical and MRI images. DeepMapi achieves fully automatic registration of mesoscopic micro-optical images, even macroscopic MRI datasets, in minutes, with an accuracy comparable to those of manual annotations by anatomists.
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Affiliation(s)
- Hong Ni
- Britton Chance Center for Biomedical Photonics, Wuhan National Laboratory for Optoelectronics, MoE Key Laboratory for Biomedical Photonics, School of Engineering Sciences, Huazhong University of Science and Technology, Wuhan, China
| | - Zhao Feng
- Britton Chance Center for Biomedical Photonics, Wuhan National Laboratory for Optoelectronics, MoE Key Laboratory for Biomedical Photonics, School of Engineering Sciences, Huazhong University of Science and Technology, Wuhan, China
| | - Yue Guan
- Britton Chance Center for Biomedical Photonics, Wuhan National Laboratory for Optoelectronics, MoE Key Laboratory for Biomedical Photonics, School of Engineering Sciences, Huazhong University of Science and Technology, Wuhan, China
| | - Xueyan Jia
- HUST-Suzhou Institute for Brainsmatics, JITRI Institute for Brainsmatics, Suzhou, China
| | - Wu Chen
- Britton Chance Center for Biomedical Photonics, Wuhan National Laboratory for Optoelectronics, MoE Key Laboratory for Biomedical Photonics, School of Engineering Sciences, Huazhong University of Science and Technology, Wuhan, China
| | - Tao Jiang
- HUST-Suzhou Institute for Brainsmatics, JITRI Institute for Brainsmatics, Suzhou, China
| | - Qiuyuan Zhong
- Britton Chance Center for Biomedical Photonics, Wuhan National Laboratory for Optoelectronics, MoE Key Laboratory for Biomedical Photonics, School of Engineering Sciences, Huazhong University of Science and Technology, Wuhan, China
| | - Jing Yuan
- Britton Chance Center for Biomedical Photonics, Wuhan National Laboratory for Optoelectronics, MoE Key Laboratory for Biomedical Photonics, School of Engineering Sciences, Huazhong University of Science and Technology, Wuhan, China
- HUST-Suzhou Institute for Brainsmatics, JITRI Institute for Brainsmatics, Suzhou, China
| | - Miao Ren
- HUST-Suzhou Institute for Brainsmatics, JITRI Institute for Brainsmatics, Suzhou, China
- School of Biomedical Engineering, Hainan University, Haikou, China
| | - Xiangning Li
- Britton Chance Center for Biomedical Photonics, Wuhan National Laboratory for Optoelectronics, MoE Key Laboratory for Biomedical Photonics, School of Engineering Sciences, Huazhong University of Science and Technology, Wuhan, China
- HUST-Suzhou Institute for Brainsmatics, JITRI Institute for Brainsmatics, Suzhou, China
| | - Hui Gong
- Britton Chance Center for Biomedical Photonics, Wuhan National Laboratory for Optoelectronics, MoE Key Laboratory for Biomedical Photonics, School of Engineering Sciences, 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, School of Engineering Sciences, Huazhong University of Science and Technology, Wuhan, China
- HUST-Suzhou Institute for Brainsmatics, JITRI Institute for Brainsmatics, Suzhou, China
- School of Biomedical Engineering, Hainan University, Haikou, China
| | - Anan Li
- Britton Chance Center for Biomedical Photonics, Wuhan National Laboratory for Optoelectronics, MoE Key Laboratory for Biomedical Photonics, School of Engineering Sciences, 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.
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Takata N, Sato N, Komaki Y, Okano H, Tanaka KF. Flexible annotation atlas of the mouse brain: combining and dividing brain structures of the Allen Brain Atlas while maintaining anatomical hierarchy. Sci Rep 2021; 11:6234. [PMID: 33737651 PMCID: PMC7973786 DOI: 10.1038/s41598-021-85807-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2020] [Accepted: 03/04/2021] [Indexed: 11/13/2022] Open
Abstract
A brain atlas is necessary for analyzing structure and function in neuroimaging research. Although various annotation volumes (AVs) for the mouse brain have been proposed, it is common in magnetic resonance imaging (MRI) of the mouse brain that regions-of-interest (ROIs) for brain structures (nodes) are created arbitrarily according to each researcher's necessity, leading to inconsistent ROIs among studies. One reason for such a situation is the fact that earlier AVs were fixed, i.e. combination and division of nodes were not implemented. This report presents a pipeline for constructing a flexible annotation atlas (FAA) of the mouse brain by leveraging public resources of the Allen Institute for Brain Science on brain structure, gene expression, and axonal projection. A mere two-step procedure with user-specified, text-based information and Python codes constructs FAA with nodes which can be combined or divided objectively while maintaining anatomical hierarchy of brain structures. Four FAAs with total node count of 4, 101, 866, and 1381 were demonstrated. Unique characteristics of FAA realized analysis of resting-state functional connectivity (FC) across the anatomical hierarchy and among cortical layers, which were thin but large brain structures. FAA can improve the consistency of whole brain ROI definition among laboratories by fulfilling various requests from researchers with its flexibility and reproducibility.
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Affiliation(s)
- Norio Takata
- Department of Neuropsychiatry, Keio University School of Medicine, 35 Shinanomachi, Shinjuku, Tokyo, 160-8582, Japan.
- Central Institute for Experimental Animals (CIEA), 3-25-12, Tonomachi, Kawasaki, Kanagawa, 210-0821, Japan.
| | - Nobuhiko Sato
- Department of Neuropsychiatry, Keio University School of Medicine, 35 Shinanomachi, Shinjuku, Tokyo, 160-8582, Japan
| | - Yuji Komaki
- Central Institute for Experimental Animals (CIEA), 3-25-12, Tonomachi, Kawasaki, Kanagawa, 210-0821, Japan
| | - Hideyuki Okano
- Department of Physiology, Keio University School of Medicine, 35 Shinanomachi, Shinjuku, Tokyo, 160-8582, Japan
| | - Kenji F Tanaka
- Department of Neuropsychiatry, Keio University School of Medicine, 35 Shinanomachi, Shinjuku, Tokyo, 160-8582, Japan
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