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.

View Github Site

BigNeuron Launch

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


  • 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)
  • Mason University, USA
  • 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), Shuiwang Ji (WSU), 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.


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