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#Key Concept BigNeuron is a community effort to define and advance state-of-the-art of single neuron reconstruction: an essential unsolved challenge in brain science.
The project will both standardize the methods to generate high quality and consistent data, and mobilize the reconstruction community to generate interest in solving these complex and interesting algorithmic problems.
#How It Works BigNeuron will bench-test on a common open platform as many open-source, automated neuron reconstruction algorithms as possible, using very large scale, publicly available single 3D neuron image data sets acquired by several light microscopy methods.
The bench-test results will be produced using some of the fastest supercomputers in the world and then compared and validated using multiple criteria carefully defined by the computational neuroscience community.
#Major Results The major results of BigNeuron will include:
a worldwide community-oriented and large single neuron morphology database, a large set of open-source, community-based novel tools for neuroscience studies, a standardized protocol and resource for any future scientists to study and reconstruct neuron morphology, and a rich library of morphology feature definitions and algorithms to provide the basis of quality metrics and classification.
#Sponsors Allen Institute for Brain Science, USA Janelia Research Campus, HHMI, USA Oak Ridge National Laboratory, USA Lawrence Berkeley National Laboratory, USA Human Brain Project, Europe Wellcome Trust, UK University of Cambridge, UK International Neuroinformatics Coordinating Facility (INCF) NeuroMorpho.org/George Mason University, USA FlyCircuit.org/National Tsing Hua University, Taiwan Beijing University of Technology, China Broad Institute, USA Erasmus University Medical Center, Netherlands Columbia University, USA Imperial College London, UK
About | Overview | Data | Algorithms | Hackathons & Workshops | SuperComputing | How to Participate | FAQ | Terms | Contact Key Concept Sponsors Major Participants & Contributors Timeline
About BigNeuron Key Concept BigNeuron is a community effort to define and advance state-of-the-art of single neuron reconstruction: an essential unsolved challenge in brain science.
The project will both standardize the methods to generate high quality and consistent data, and mobilize the reconstruction community to generate interest in solving these complex and interesting algorithmic problems.
How It Works BigNeuron will bench-test on a common open platform as many open-source, automated neuron reconstruction algorithms as possible, using very large scale, publicly available single 3D neuron image data sets acquired by several light microscopy methods.
The bench-test results will be produced using some of the fastest supercomputers in the world and then compared and validated using multiple criteria carefully defined by the computational neuroscience community.
Major Results The major results of BigNeuron will include:
a worldwide community-oriented and large single neuron morphology database, a large set of open-source, community-based novel tools for neuroscience studies, a standardized protocol and resource for any future scientists to study and reconstruct neuron morphology, and a rich library of morphology feature definitions and algorithms to provide the basis of quality metrics and classification. LEARN MORE AND GET INVOLVED Sponsors Allen Institute for Brain Science, USA Janelia Research Campus, HHMI, USA Oak Ridge National Laboratory, USA Lawrence Berkeley National Laboratory, USA Human Brain Project, Europe Wellcome Trust, UK University of Cambridge, UK International Neuroinformatics Coordinating Facility (INCF) NeuroMorpho.org/George Mason University, USA FlyCircuit.org/National Tsing Hua University, Taiwan Beijing University of Technology, China Broad Institute, USA Erasmus University Medical Center, Netherlands Columbia University, USA Imperial College London, UK Major Participants and Contributors To Date Hanchuan Peng (Allen Institute), Giorgio Ascoli (GMU), Erik Meijering (Erasmus, Netherlands), Michael Hawrylycz (Allen Institute), Arvind Ramanathan (ORNL), Zhi Zhou (Allen Institute), Fuhui Long (Allen Institute), Ting Zhao (Janelia), Giorgia Tourassi (ORNL), Jack Wells (ORNL), Prabhat (LBNL), Kristofer Bouchard (LBNL), Ning Zhong (Maebashi Tech, Japan; WICI/BJUT, China), Jian Yang (WICI/BJUT, China), Zhijiang Wan (Maebashi Tech, Japan; WICI/BJUT, China), Tianming Liu (UGA), Tom W. Cai (University of Sydney, Australia), Li Cheng (A*Star, Singapore), Jie Zhou (NIU), Badri Roysam (University of Houston), Shaoqun Zeng (Huazhong Tech, China), Paloma T. Gonzalez-Bellido (University of Cambridge), Leila Muresan (Cambridge, CAIC), Rachel Wong (University of Washington), Bing Ye (University of Michigan), Kei Ito (University of Tokyo, Japan), Jinhyun Kim (Korea), Greg Jefferies (Cambridge), Edwin Rubel (University of Washington), Hollis Cline (Scripps), Anne Carpenter (Broad), Jane Roskams (Allen Institute), Chinh Dang (Allen Institute), Stefan Mihalas (Allen Institute), Hongkui Zeng (Allen Institute), Ed Lein (Allen Institute), Rafael Yuste (Columbia University), Ann-Shyn Chiang (Taiwan), John Isaac (Wellcome Trust), Nelson Spruston (Janelia), Sean Hill (HBP), Christof Koch (Allen Institute), Gerry Rubin (Janelia), Allan Jones (Allen Institute), and the BigNeuron Consortium.
#Timeline February 1, 2015 BigNeuron White Paper Draft Distribution Organizer: BigNeuron Consortium
March 16, 2015 Beijing Algorithm Porting Hackathon Host: Beijing University of Technology
May 4, 2015 Cambridge Algorithm Porting Hackathon Host: University of Cambridge
June 1, 2015 Janelia Algorithm Porting Hackathon Host: Janelia Research Campus, HHMI
June 15, 2015 Seattle Image Data Annotation Workshop Host: Allen Institute for Brain Science
July 1 - October 31, 2015 Bench testing at supercomputing centers Host: Oak Ridge National Laboratory, Lawrence Berkeley National Laboratory, Human Brain Project
October 31, 2015 Data freezing at all supercomputing sites Host: All supercomputing centers
November 16, 2015 Open Analysis Hackathon Host: Oak Ridge National Laboratory
January 18, 2016 Open Analysis Hackathon Host: Imperial College London
March 2016 Initial Data Release Organizer: Big Neuron consortium