A Proposal for a Coordinated Effort for the Determination of Brainwide Neuroanatomical Connectivity in Model Organisms at a Mesoscopic Scale
Bohland, Jason W., Wu, Caizhi, Barbas, Helen, Bokil, Hemant, Bota, Mihail, Breiter, Hans C., Cline, Hollis T., Doyle, John C., Freed, Peter J., Greenspan, Ralph J., Haber, Suzanne N., Hawrylycz, Michael, Herrera, Daniel G., Hilgetag, Claus C., Huang, Z. Josh, Jones, Allan, Jones, Edward G., Karten, Harvey J., Kleinfeld, David, Kötter, Rolf, Lester, Henry A., Lin, John M., Mensh, Brett D., Mikula, Shawn, Panksepp, Jaak, Price, Joseph L., Safdieh, Joseph, Saper, Clifford B., Schiff, Nicholas D., Schmahmann, Jeremy D., Stillman, Bruce W., Svoboda, Karel, Swanson, Larry W., Toga, Arthur W., Van Essen, David C., Watson, James D., Mitra, Partha P.·2009·PLoS Computational Biology
Cited by (264)
Items 101–200 of 264
- A deep learning-based stripe self-correction method for stitched microscopic imagesShu Wang, Xixiang Liu, Yueying Li, Xinquan Sun, Qi Li, Yinhua She, Yixuan Xu, Xingxin Huang, Ruolan Lin, Deyong Kang et al. · 2023 · Nature Communications
- Visible rodent brain-wide networks at single-neuron resolutionJing Yuan, Hui Gong, Anan Li, Xiangning Li, Shangbin Chen, Shaoqun Zeng, Qingming Luo · 2015 · Frontiers in Neuroanatomy
- The connectome of the basal gangliaOliver Schmitt, Peter Eipert, Richard Kettlitz, Felix Leßmann, Andreas Wree · 2014 · Brain Structure and Function
- Molecular neuroanatomy: a generation of progressPollock, Jonathan D., Wu, Da-Yu, Satterlee, John S. · 2014 · Trends in Neurosciences
- Single‐neuron axonal reconstruction: The search for a wiring diagram of the brainMichael N. Economo, Johan Winnubst, Erhan Bas, Tiago Ferreira, Jayaram Chandrashekar · 2019 · The Journal of Comparative Neurology
- Neuronal network analyses: premises, promises and uncertaintiesDavid Parker · 2010 · Philosophical Transactions of the Royal Society B Biological Sciences
- Recovery of consciousness after severe brain injury: The role of arousal regulation mechanisms and some speculation on the heart-brain interfaceNicholas D. Schiff · 2010 · Cleveland Clinic Journal of Medicine
- A strategy for building neuroanatomy ontologiesDavid Osumi-Sutherland, Simon P. Reeve, Chris Mungall, Fabian Neuhaus, Alan Ruttenberg, Gregory S.X.E. Jefferis, J. Douglas Armstrong · 2012 · Bioinformatics
- Toward a more collaborative research culture: Extending translational science from research to community and back againAubyn C. Stahmer, Aritz Aranbarri, Amy Drahota, Sarah R. Rieth · 2017 · Autism
- Quantitative mouse brain phenotyping based on single and multispectral MR protocolsAlexandra Badea, Sally L. Gewalt, Brian Avants, James J. H. Cook, G. Allan Johnson · 2012 · NeuroImage
- Informing brain connectivity with optogenetic functional magnetic resonance imagingJin Hyung Lee · 2012 · NeuroImage
- Total Number Is Important: Using the Disector Method in Design-Based Stereology to Understand the Structure of the Rodent BrainRuth M. A. Napper · 2018 · Frontiers in Neuroanatomy
- Bi-channel image registration and deep-learning segmentation (BIRDS) for efficient, versatile 3D mapping of mouse brainXuechun Wang, Weilin Zeng, Xiaodan Yang, Yong-Sheng Zhang, Chunyu Fang, Shaoqun Zeng, Yunyun Han, Peng Fei · 2021 · eLife
- On Optical Detection of Densely Labeled Synapses in Neuropil and Mapping Connectivity with Combinatorially Multiplexed Fluorescent Synaptic MarkersYuriy Mishchenko · 2010 · Nature Precedings
- Computational genetic neuroanatomy of the developing mouse brain: dimensionality reduction, visualization, and clusteringShuiwang Ji · 2013 · BMC Bioinformatics
- Shifting the paradigm: new approaches for characterizing and classifying neuronsBernard, Amy, Sorensen, Staci A, Lein, Ed S · 2009 · Current Opinion in Neurobiology
- New and emerging imaging techniques for mapping brain circuitryHong Pan, Jane Epstein, David Silbersweig, Emily R. Stern · 2011 · Brain Research Reviews
- White Matter: Beyond Focal DisconnectionChristopher Mark Filley · 2010 · Neurologic Clinics
- ADVANCED OPTICAL TECHNIQUES TO EXPLORE BRAIN STRUCTURE AND FUNCTIONLudovico Silvestri, Anna Letizia Allegra Mascaro, Jacopo Lotti, Leonardo Sacconi, Francesco Saverio Pavone · 2012 · Journal of Innovative Optical Health Sciences
- The Complexity of Dynamics in Small Neural CircuitsDiego Fasoli, Anna Cattani, Stefano Panzeri · 2016 · PLoS Computational Biology
- Workflow and Atlas System for Brain-Wide Mapping of Axonal Connectivity in RatIzabela M. Zakiewicz, Yvette C. van Dongen, Trygve Brauns Leergaard, Jan Gunnar Bjaalie · 2011 · PLoS ONE
- Following the genes: a framework for animal modeling of psychiatric disordersKevin J. Mitchell, Z. Josh Huang, Bita Moghaddam, Akira Sawa · 2011 · BMC Biology
- Graph Theoretic Analysis of Human Brain NetworksAlex Fornito · 2016 · Neuromethods
- Comparative Principles for Next-Generation NeuroscienceCory Thomas Miller, Melina E. Hale, Hideyuki Okano, Shigeo Okabe, Partha P. Mitra · 2019 · Frontiers in Behavioral Neuroscience
- Rosetta Brains: A Strategy for Molecularly-Annotated ConnectomicsAdam Henry Marblestone, Evan R Daugharthy, Reza Kalhor, Ian D. Peikon, Justus M. Kebschull, Seth L. Shipman, Yuriy Mishchenko, Je Hyuk Lee, Konrad Paul Kording, Edward S. Boyden et al. · 2014 · arXiv (Cornell University)
- Integrating multimodal data to understand cortical circuit architecture and functionAnton S. Arkhipov, Nuno Maçarico da Costa, Saskia E. J. de Vries, Trygve E. Bakken, Corbett Bennett, Amy Bernard, Jim Berg, Michael A. Buice, Forrest Collman, Tanya L. Daigle et al. · 2025 · Nature Neuroscience
- Three-dimensional brain reconstruction of in vivo electrode tracks for neuroscience and neural prosthetic applicationsCraig D. Markovitz, Tien T. Tang, David P. Edge, Hubert H. Lim · 2012 · Frontiers in Neural Circuits
- The whole brain architecture approach: Accelerating the development of artificial general intelligence by referring to the brainHiroshi Yamakawa · 2021 · Neural Networks
- Neural systems language: A formal modeling language for the systematic description, unambiguous communication, and automated digital curation of neural connectivityRamsay A. Brown, Larry W. Swanson · 2013 · The Journal of Comparative Neurology
- Brain-Wide Mapping of Axonal Connections: Workflow for Automated Detection and Spatial Analysis of Labeling in Microscopic SectionsEszter A. Papp, Trygve Brauns Leergaard, Gergely Csucs, Jan Gunnar Bjaalie · 2016 · Frontiers in Neuroinformatics
- Meeting the brain on its own termsPhilipp Haueis · 2014 · Frontiers in Human Neuroscience
- Building the FerretomeDmitrii I. Sukhinin, Andreas Karl Engel, Paul R. Manger, Claus Christian Hilgetag · 2016 · Frontiers in Neuroinformatics
- Label-free volumetric optical imaging of intact murine brainsJian Ren, Heejin Choi, Kwanghun Chung, Brett E. Bouma · 2017 · Scientific Reports
- Big data in nanoscale connectomics, and the greed for training labelsAlessandro Motta, Meike Sievers, Benedikt Staffler, Moritz N. Helmstaedter · 2019 · Current Opinion in Neurobiology
- Imaging Studies in Focal Dystonias: A Systems Level Approach to Studying a Systems Level DisorderAnne J. Blood · 2013 · Current Neuropharmacology
- A Bayesian compressed-sensing approach for reconstructing neural connectivity from subsampled anatomical dataYuriy Mishchenko, Liam Paninski · 2012 · Journal of Computational Neuroscience
- Efficient methods for sampling spike trains in networks of coupled neuronsYuriy Mishchenko, Liam Paninski · 2011 · The Annals of Applied Statistics
- Review of quantitative multiscale imaging of breast cancerMichael A. Pinkert, Lonie R. Salkowski, Patricia J. Keely, Timothy J. Hall, Walter F. Block, Kevin W. Eliceiri · 2018 · Journal of medical imaging
- MRI-based Parcellation and Morphometry of the Individual Rhesus Monkey Brain: the macaque Harvard-Oxford Atlas (mHOA), a translational system referencing a standardized ontologyJarrett Rushmore, Sylvain Bouix A, Marek R. Kubicki, Yogesh Rathi A, Douglas L. Rosene, Edward H. Yeterian, Nikos Makris · 2020 · Brain Imaging and Behavior
- Between neurons and networks: investigating mesoscale brain connectivity in neurological and psychiatric disordersAna Clara Caznok Silveira, André Saraiva Leão Marcelo Antunes, Maria Carolina Pedro Athié, Bárbara Filomena da Silva, João Victor Ribeiro dos Santos, Camila Canateli, Marina Alves Fontoura, Allan da Silva Pinto, Luciana Ramalho Pimentel‐Silva, Simoni Helena Avansini et al. · 2024 · Frontiers in Neuroscience
- Population neuroscienceTomáš Paus · 2016 · Handbook of clinical neurology
- A Mutual Information Approach to Automate Identification of Neuronal Clusters in Drosophila Brain ImagesNicolas Y. Masse, Sebastian Cachero, Aaron D. Ostrovsky, Gregory S.X.E. Jefferis · 2012 · Frontiers in Neuroinformatics
- Highlights from the Era of Open Source Web-Based ToolsKristin R. Anderson, Julie A. Harris, Lydia Ng, Pjotr Prins, Sara Memar, Bengt Ljungquist, Daniel Fürth, Robert W. Williams, Giorgio A. Ascoli, Dani Dumitriu · 2021 · Journal of Neuroscience
- Revealing Dynamics, Communities, and Criticality from DataDeniz Eroglu, Matteo Tanzi, Sebastian J. van Strien, Tiago Pereira · 2020 · Physical Review X
- Toward Community-Driven Big Open Brain Science: Open Big Data and Tools for Structure, Function, and GeneticsAdam S. Charles, Benjamin Falk, Nicholas L. Turner, Talmo Pereira, Daniel Jacob Tward, Benjamin D. Pedigo, Jaewon Chung, Randal C. Burns, Satrajit Ghosh, Justus M. Kebschull et al. · 2020 · Annual Review of Neuroscience
- Pursuit of precision medicine: Systems biology approaches in Alzheimer's disease mouse modelsBrianna Gurdon, Catherine Cook Kaczorowski · 2021 · Neurobiology of Disease
- From a meso- to micro-scale connectome: array tomography and mGRASPJong‐Cheol Rah, Linqing Feng, Shaul Druckmann, Hojin Lee, Jinhyun Kim · 2015 · Frontiers in Neuroanatomy
- Exploration and visualization of connectivity in the adult mouse brainDavid H. Feng, Chris Lau, Lydia Ng, Yang Li, Leonard Kuan, Susan M. Sunkin, Chinh Dang, Michael Hawrylycz · 2015 · Methods
- What would a synthetic connectome look like?Ithai Rabinowitch · 2019 · Physics of Life Reviews
- Challenges of Processing and Analyzing Big Data in Mesoscopic Whole-Brain ImagingAnan Li, Yue Guan, Hui Gong, Qingming Luo · 2019 · Genomics Proteomics & Bioinformatics
- Network analysis of mesoscale optical recordings to assess regional, functional connectivityDiana H. Lim, Jeffrey M. LeDue, Timothy H. Murphy · 2015 · Neurophotonics
- Putting neurons on the mapMichael S. Eisenstein · 2009 · Nature
- The Coming of Age of the HippocampomeGiorgio A. Ascoli · 2010 · Neuroinformatics
- Correction: Digital Atlasing and Standardization in the Mouse BrainMichael Hawrylycz, Richard Baldock, Albert Burger, Tsutomu Hashikawa, G. Allan Johnson, Maryann Elizabeth Martone, Lydia Ng, Chris Lau, Stephen D. Larsen, Jonathan Nissanov et al. · 2011 · PLoS Computational Biology
- The connectomics challenge.Ludovico Silvestri, Leonardo Sacconi, Francesco Saverio Pavone · 2013 · Europe PMC (PubMed Central)
- Comparing the Expression of Genes Related to Serotonin (5-HT) in C57BL/6J Mice and Humans Based on Data Available at the Allen Mouse Brain Atlas and Allen Human Brain AtlasCésar Andrés Acevedo-Triana, Laura Andrea León, Fernando P. Cárdenas · 2017 · Neurology Research International
- An Introduction to Brain Networks2016 · Elsevier eBooks
- Fos‐expressing neuronal ensembles in rat infralimbic cortex encode initial and maintained oxycodone seeking in ratsChristina M. Gobin, Bo W. Sortman, Samantha Rakela, Richard Quintana‐Feliciano, Brandon L. Warren · 2022 · Addiction Biology
- Moral conduct and social behaviorRicardo de Oliveira‐Souza, Jorge Moll · 2019 · Handbook of clinical neurology
- Automatedin situbrain imaging for mapping theDrosophilaconnectomeChi–Wen Lin, Hsuan-Wen Lin, Mei-Tzu Chiu, Yung-Hsin Shih, Ting-Yuan Wang, Hsiu-Ming Chang, Ann‐Shyn Chiang · 2015 · Journal of Neurogenetics
- Deep learning in mesoscale brain image analysis: A reviewRunze Chen, Min Liu, Weixun Chen, Yaonan Wang, Erik H. W. Meijering · 2023 · Computers in Biology and Medicine
- An automated method for removal of striping artifacts in fluorescent whole-slide microscopyAngeliki Pollatou · 2020 · Journal of Neuroscience Methods
- Fitting elephants in modern machine learning by statistically consistent interpolationPartha P. Mitra · 2021 · Nature Machine Intelligence
- Brain connectomes come of ageXiao‐Jing Wang, Ulises Pereira, Marcello G. P. Rosa, Henry Kennedy · 2020 · Current Opinion in Neurobiology
- Algorithmic choice of coordinates for injections into the brain: encoding a neuroanatomical atlas on a gridGrange, Pascal, Partha P. Mitra · 2011 · Cold Spring Harbor Laboratory Institutional Repository (Cold Spring Harbor Laboratory)
- Differential Levels of Glutamate Dehydrogenase 1 (GLUD1) in Balb/c and C57BL/6 Mice and the Effects of Overexpression of the Glud1 Gene on Glutamate Release in StriatumKevin N. Hascup, Xiaodong Bao, Erin R. Hascup, Dongwei Hui, Wenhao Xu, François Pomerleau, Peter F. Huettl, Mary Lou Michaelis, Elias K. Michaelis, Greg A. Gerhardt · 2011 · ASN NEURO
- Communication Structure of Cortical NetworksLuciano da Fontoura Costa, João Luiz Bunoro Batista, Giorgio A. Ascoli · 2011 · Frontiers in Computational Neuroscience
- Darkfield Adapter for Whole Slide Imaging: Adapting a Darkfield Internal Reflection Illumination System to Extend WSI ApplicationsYoshihiro Kawano, Christopher D. Higgins, Yasuhito Yamamoto, Julie K. Nyhus, Amy Bernard, Hong‐Wei Dong, Harvey J. Karten, Tobias Schilling · 2013 · PLoS ONE
- Exploring Brain Connectivity in Insect Model Systems of Learning and MemoryJürgen Rybak · 2013 · Handbook of behavioral neuroscience
- Bridging the Brain and Data SciencesJohn D. Van Horn · 2020 · Big Data
- Reconstruction of complete connectivity matrix for connectomics by sampling neural connectivity with fluorescent synaptic markersYuriy Mishchenko · 2011 · Journal of Neuroscience Methods
- Progress With Optogenetic Functional Mri and Its Translational ImplicationsAndrew J. Weitz, Jin Hyung Lee · 2013 · Future Neurology
- Multiscale imaging informs translational mouse modeling of neurological diseaseYundi Wang, Jeffrey M. LeDue, Timothy H. Murphy · 2022 · Neuron
- Large-Scale Neuroinformatics for In Situ Hybridization Data in the Mouse BrainLydia Ng, Susan M. Sunkin, David H. Feng, Chris Lau, Chinh Dang, Michael Hawrylycz · 2012 · International review of neurobiology
- The efferent connections of the orbitofrontal, posterior parietal, and insular cortex of the rat brainIngrid Reiten, Grethe M. Olsen, Jan Gunnar Bjaalie, Menno P. Witter, Trygve Brauns Leergaard · 2023 · Scientific Data
- Keypress-Based Musical Preference Is Both Individual and LawfulSherri L. Livengood, John Patrick Sheppard, Byoung Woo Kim, Edward Carl Malthouse, Janet E. Bourne, Anne E. Barlow, Myung Joo Lee, Veronica Marin, Kailyn P. O’Connor, John G. Csernansky et al. · 2017 · Frontiers in Neuroscience
- Structural covariation between cerebellum and neocortex intrinsic structural covariation links cerebellum subregions to the cerebral cortexZilong Wang, Jörn Diedrichsen, Karin Saltoun, Christopher J. Steele, Sheeba Arnold Anteraper, B.T. Thomas Yeo, Jeremy Dan Schmahmann, Danilo Bzdok · 2024 · Journal of Neurophysiology
- Automatic target validation based on neuroscientific literature mining for tractographyXavier Vasques, Renaud Richardet, Sean Hill, David A. Slater, Jean-Cédric Chappelier, Étienne Pralong, Jocelyne Bloch, Bogdan Draganski, Laura Cif · 2015 · Frontiers in Neuroanatomy
- Text-Mining and NeuroscienceKyle H. Ambert, Aaron Michael Cohen · 2012 · International review of neurobiology
- Serial Multiphoton Tomography and Analysis of Volumetric Images of the Mouse BrainDenise M. O. Ramirez, Apoorva D. Ajay, Mark P. Goldberg, Julian P. Meeks · 2019 · Neuromethods
- FNS allows efficient event-driven spiking neural network simulations based on a neuron model supporting spike latencyGianluca Susi, Pilar Garcés, Emanuele Paracone, Alessandro Cristini, Mário Sérgio Salerno, Fernando Maestú, Ernesto Pereda · 2021 · Scientific Reports
- Dense reconstruction of brain-wide neuronal population close to the ground truthZhou Hang, Li Shiwei, Anan Li, Feng Xiong, Li Ning, Han Jiacheng, Kang Hongtao, Chen Yijun, Yun Li, Fang Wenqian et al. · 2017 · bioRxiv (Cold Spring Harbor Laboratory)
- A computational approach towards the microscale mouse brain connectome from the mesoscaleTielin Zhang, Yi Zeng, Bo Xu · 2017 · Journal of Integrative Neuroscience
- Computational neuroanatomy and gene expression: Optimal sets of marker genes for brain regionsPascal Grange, Partha P. Mitra · 2012 · Conference on Information Sciences and Systems
- How do you wire a brain?Julian M. L. Budd, Zoltán F. Kisvárday · 2013 · Frontiers in Neuroanatomy
- Integrative understanding of emergent brain properties, quantum brain hypotheses and connectome alterations in dementia are key challenges to conquer Alzheimer's diseaseRodrigo Orlando Kuljiš · 2010 · Frontiers in Neurology
- Quantitative study on the hygroscopic expansion of spurr resin to obtain a high-resolution atlas of the mouse brainQingdi Wang, Anan Li, Hui Gong, Dongli Xu, Qingming Luo · 2012 · Experimental Biology and Medicine
- Linking connectomics and dynamics in the human brainLeon Stefanovski, Amna Ghani, Anthony Randal McIntosh, Petra Ritter · 2016 · e-Neuroforum
- The Mind-Brain Relationship as a Mathematical ProblemGiorgio A. Ascoli · 2013 · ISRN Neuroscience
- Golgi: Interactive Online Brain MappingRamsay A. Brown, Larry W. Swanson · 2015 · Frontiers in Neuroinformatics
- Super-resolution Segmentation Network for Reconstruction of Packed NeuritesHang Zhou, Tingting Cao, Tian Liu, Shijie Liu, Lu Chen, Yijun Chen, Qing Huang, Wei Ye, Shaoqun Zeng, Tingwei Quan · 2022 · Neuroinformatics
- The Fractal Geometry of the Human Brain: An Evolutionary PerspectiveMichel A. Hofman · 2016 · Springer series in computational neuroscience
- Marker Genes for Anatomical Regions in the Brain: Insights from the Allen Gene Expression AtlasPascal Grange, Partha P. Mitra · 2011 · Cold Spring Harbor Laboratory Institutional Repository (Cold Spring Harbor Laboratory)
- Tracing evolution of spatio-temporal dynamics of the cerebral cortex: cortico-cortical communication dynamicsP. Roland, C. Hilgetag, G. Deco · 2014 · Frontiers in Systems Neuroscience
- Transitions between asynchronous and synchronous states: a theory of correlations in small neural circuitsDiego Fasoli, Anna Cattani, Stefano Panzeri · 2017 · Journal of Computational Neuroscience
- Contributions of Lorente de Nó to the Nonlinear Circuitry of the BrainLuis Carrillo‐Reid, Jorge A. Larriva-Sahd · 2019 · The Anatomical Record
- FNS: an event-driven spiking neural network simulator based on the LIFL neuron modelGianluca Susi, Pilar Garcés, Cristini, Alessandro, Emanuele Paracone, Mário Sérgio Salerno, Fernando Maestú, Ernesto Pereda · 2018 · arXiv (Cornell University)
- Statistical analysis of co-expression properties of sets of genes in the mouse brainGrange, Pascal, Mitra, Partha P. · 2011 · Cold Spring Harbor Laboratory Institutional Repository (Cold Spring Harbor Laboratory)
- Panoptic Neuroanatomy: Digital Microscopy of Whole Brains and Brain-Wide Circuit MappingPartha P. Mitra, Marcello G. P. Rosa, Harvey J. Karten · 2013 · Brain Behavior and Evolution
- Photonics meets connectomics: case of diffuse, long-range horizontal projections in rat cortexBrett A. Johnson, Ron D. Frostig · 2015 · Neurophotonics