Nav: Home

International initiative launched to advance state-of-the-art digital tracings of neurons

March 31, 2015

The Allen Institute for Brain Science is spearheading a landmark international effort to define and advance the state-of-the-art digital reconstruction and analysis of single neurons. The project launching today, called BigNeuron, aims to create reliable high-throughput and quantitative 3D reconstructions of the thousands of branches that make up individual neurons: a crucial step to ultimately understanding how the brain encodes information.

"In our quest to learn how the brain works, one of the fundamental steps is to understand how neurons function, and an individual neuron's shape is a major contributor to its role in the brain," says Allan Jones, Ph.D., CEO of the Allen Institute for Brain Science. "There has been much exciting work in the field of digitally reconstructing the shapes of individual neurons, but the community needs standards in order to both make the most of the work we've already done and to make sure that the work we do in the future will be of the greatest possible value."

Advances in technology and imaging of individual brain cells have yielded a large library of three-dimensional images of neurons, as well as dozens of different programs to create digital reconstructions of the neurons' structures. But because no standards exist to compare the algorithms, which are often built on different platforms and use different standards of analysis, these large data sets cannot be analyzed and compared as a whole. BigNeuron is a partnership with some of the leading research and computing centers around the world, including: Janelia Research Campus (HHMI); Oak Ridge National Laboratory; National Energy Research Scientific Computing Center at the Lawrence Berkeley National Laboratory; the Human Brain Project; the University of Cambridge; the Wellcome Trust; and George Mason University; Beijing University of Technology; the International Neuroinformatics Coordinating Facility (INCF);; and Erasmus University Medical Center.

"This is truly a worldwide collaboration to define the best algorithms and methods, with the goal to create the most reliable and robust neural reconstructions possible," says Hanchuan Peng, Ph.D., Associate Investigator at the Allen Institute for Brain Science and lead organizer of BigNeuron. "We are 'bench testing' many different algorithms, comparing how each of them handles very large scale, publicly available 3D neuron image datasets."

The results of BigNeuron will include a large set of open-source, community-based tools for neuroscience studies, standardized protocols for researchers to create their own neuron morphologies, and a rich library of morphological feature definitions and algorithms to provide a foundation of quality metrics and classification organized in an openly available database of single neuron morphology data. "Each of the nearly 100 billion neurons in a human brain is shaped like a miniaturized tree, with thousands of ultra-thin branches that can span from ear to ear, enabling neurons to connect, process information, and learn," says Giorgio Ascoli, Ph.D., Principal Investigator of NeuroMorpho.Org, Director of the Center for Neural Informatics at George Mason University, and author of Trees of the Brain Roots of the Mind.

"These arbors are so diverse that, after three decades of manual reconstructions from microscopic imaging in countless labs worldwide, no one knows yet the number of distinct types or shapes even in the nervous systems of mice or flies. BigNeuron's success will provide the community with much needed reliable, repeatable, high-throughput, quantitative data to begin piecing together the complex neural puzzle."

BigNeuron will encompass a series of international hackathons and workshops, the first of which took place in Beijing, China on March 16-20, 2015. Future workshops are scheduled in Cambridge, UK, at Janelia Research Campus (HHMI), and in Boston and Seattle. Algorithms and data for bench testing are being collected from labs around the world, using different light microscopy techniques in many different species, and supercomputing analysis will be conducted and validated at Oak Ridge National Laboratory and Lawrence Berkeley National Laboratory, among others.

"As data collection for neuron morphologies becomes automated, high-throughput approaches will generate high-resolution images of thousands, perhaps even millions of neurons," says Nelson Spruston, Ph.D., Scientific Program Director at the Janelia Research Campus at HHMI. "As these experimental methods accelerate, it is critical that the methods for analyzing the data keep up. BigNeuron is an effort to make that happen."

The partners of BigNeuron are:
  • Allen Institute for Brain Science, Seattle, Wash., USA
  • Janelia Research Campus, HHMI, Ashburn, Va., USA
  • Oak Ridge National Laboratory, Oak Ridge, Tenn., USA
  • National Energy Research Scientific Computing Center at the Lawrence Berkeley National Laboratory, Berkeley, Calif., USA
  • Human Brain Project, Europe
  • Wellcome Trust, London, UK
  • University of Cambridge, Cambridge, UK
  • Mason University, Fairfax, Va., USA
  • International Neuroinformatics Coordinating Facility (INCF), Stockholm, Sweden
  • Tsing Hua University, Hsinchu, Taiwan
  • Beijing University of Technology, Beijing, China
  • Broad Institute, Cambridge, Mass., USA
  • Erasmus University Medical Center, Rotterdam, Netherlands

For more information about BigNeuron, visit

About the Allen Institute for Brain Science

The Allen Institute for Brain Science is an independent, 501(c)(3) nonprofit medical research organization dedicated to accelerating the understanding of how the human brain works in health and disease. Using a big science approach, the Allen Institute generates useful public resources used by researchers and organizations around the globe, drives technological and analytical advances, and discovers fundamental brain properties through integration of experiments, modeling and theory. Launched in 2003 with a seed contribution from founder and philanthropist Paul G. Allen, the Allen Institute is supported by a diversity of government, foundation and private funds to enable its projects. Given the Institute's achievements, Mr. Allen committed an additional $300 million in 2012 for the first four years of a ten-year plan to further propel and expand the Institute's scientific programs, bringing his total commitment to date to $500 million. The Allen Institute's data and tools are publicly available online at

About the Howard Hughes Medical Institute

The Howard Hughes Medical Institute plays an influential role in advancing scientific research and education in the United States. Its scientists, located across the country and around the world, have made important discoveries that advance both human health and our fundamental understanding of biology. The Institute also aims to transform science education into a creative, interdisciplinary endeavor that reflects the excitement of real research. For more information, visit

About the Oak Ridge National Laboratory

Oak Ridge National Laboratory is the largest US Department of Energy science and energy laboratory, conducting basic and applied research to deliver transformative solutions to compelling problems in energy and security. Visit for more information. UT-Battelle manages ORNL for the DOE's Office of Science. The Office of Science is the single largest supporter of basic research in the physical sciences in the United States, and is working to address some of the most pressing challenges of our time. For more information, please visit

About NERSC and Berkeley Lab

The National Energy Research Scientific Computing Center (NERSC) is the primary high-performance computing facility for scientific research sponsored by the U.S. Department of Energy's Office of Science. Located at Lawrence Berkeley National Laboratory, the NERSC Center serves more than 6,000 scientists at national laboratories and universities researching a wide range of problems in combustion, climate modeling, fusion energy, materials science, physics, chemistry, computational biology, and other disciplines. Berkeley Lab is a U.S. Department of Energy national laboratory located in Berkeley, California. It conducts unclassified scientific research and is managed by the University of California for the U.S. DOE Office of Science. Learn more about computing sciences at:

About The Wellcome Trust

The Wellcome Trust is a global charitable foundation dedicated to improving health. We support bright minds in science, the humanities and the social sciences, as well as education, public engagement and the application of research to medicine. Our investment portfolio gives us the independence to support such transformative work as the sequencing and understanding of the human genome, research that established front-line drugs for malaria, and Wellcome Collection, our free venue for the incurably curious that explores medicine, life and art.

About George Mason University

The George Mason University Center for Neural Informatics, Structures, and Plasticity (CN3) pursues fundamental breakthroughs in neuroscience by fostering data-driven computational approaches to neuroanatomy, learning, and memory. By bringing together faculty expertise in multiple disciplines, the Center provides opportunities for graduate and postdoctoral cross-training in neuroscience, cognitive science, and engineering. CN3 researchers investigate the relationship between brain structure, activity, and function from the subcellular to the network level, with a specific focus on axonal and dendritic morphology (NeuroMorpho.Org) and the hippocampal formation.

Allen Institute

Related Neurons Articles:

How do we get so many different types of neurons in our brain?
SMU (Southern Methodist University) researchers have discovered another layer of complexity in gene expression, which could help explain how we're able to have so many billions of neurons in our brain.
These neurons affect how much you do, or don't, want to eat
University of Arizona researchers have identified a network of neurons that coordinate with other brain regions to influence eating behaviors.
Mood neurons mature during adolescence
Researchers have discovered a mysterious group of neurons in the amygdala -- a key center for emotional processing in the brain -- that stay in an immature, prenatal developmental state throughout childhood.
Astrocytes protect neurons from toxic buildup
Neurons off-load toxic by-products to astrocytes, which process and recycle them.
Connecting neurons in the brain
Leuven researchers uncover new mechanisms of brain development that determine when, where and how strongly distinct brain cells interconnect.
The salt-craving neurons
Pass the potato chips, please! New research discovers neural circuits that regulate craving and satiation for salty tastes.
When neurons are out of shape, antidepressants may not work
Selective serotonin reuptake inhibitors (SSRIs) are the most commonly prescribed medication for major depressive disorder (MDD), yet scientists still do not understand why the treatment does not work in nearly thirty percent of patients with MDD.
Losing neurons can sometimes not be that bad
Current thinking about Alzheimer's disease is that neuronal cell death in the brain is to blame for the cognitive havoc caused by the disease.
Neurons that fire together, don't always wire together
As the adage goes 'neurons that fire together, wire together,' but a new paper published today in Neuron demonstrates that, in addition to response similarity, projection target also constrains local connectivity.
Scientists accidentally reprogram mature mouse GABA neurons into dopaminergic-like neurons
Attempting to make dopamine-producing neurons out of glial cells in mouse brains, a group of researchers instead converted mature inhibitory neurons into dopaminergic cells.
More Neurons News and Neurons Current Events

Best Science Podcasts 2019

We have hand picked the best science podcasts for 2019. Sit back and enjoy new science podcasts updated daily from your favorite science news services and scientists.
Now Playing: TED Radio Hour

Rethinking Anger
Anger is universal and complex: it can be quiet, festering, justified, vengeful, and destructive. This hour, TED speakers explore the many sides of anger, why we need it, and who's allowed to feel it. Guests include psychologists Ryan Martin and Russell Kolts, writer Soraya Chemaly, former talk radio host Lisa Fritsch, and business professor Dan Moshavi.
Now Playing: Science for the People

#538 Nobels and Astrophysics
This week we start with this year's physics Nobel Prize awarded to Jim Peebles, Michel Mayor, and Didier Queloz and finish with a discussion of the Nobel Prizes as a way to award and highlight important science. Are they still relevant? When science breakthroughs are built on the backs of hundreds -- and sometimes thousands -- of people's hard work, how do you pick just three to highlight? Join host Rachelle Saunders and astrophysicist, author, and science communicator Ethan Siegel for their chat about astrophysics and Nobel Prizes.