Five teams will compete in the final round of an international scientific challenge designed to speed development of new computational tools to accurately and automatically reconstruct the shape of brain cells.
The Allen Institute for Brain Science, the Howard Hughes Medical Institute (HHMI), and the Krasnow Institute for Advanced Study at George Mason University are announcing the names of five teams of finalists in an international scientific challenge designed to speed development of new computational tools to accurately and automatically reconstruct the shape of brain cells.
Later this summer, the finalists will travel to HHMI’s Janelia Farm Research Campus in Ashburn, Virginia, where their algorithms will be tested to see which one performs best in analyses using real-world data supplied by neuroscientists. The organizers will award a $75,000 cash prize to the winning individual or team. Funding for the prize is provided by HHMI and the Allen Institute.
This is not a problem with an answer in the back of the book.
The DIADEM Challenge—short for Digital Reconstruction of Axonal and Dendritic Morphology—was created in the hope that it would lead to innovative solutions to a frustrating problem that has slowed efforts to create a functional atlas of the brain. Neuroscientists agree that a systematic characterization of neurons with their dendrites and axons is essential, since these tree-like structures are highly correlated with the electric activity of, and precise connections between, neurons and are thus linked to the functions of specific brain circuits. But scientists currently spend weeks—and, in some cases, months—tracing the intricate neuronal processes by hand, using data supplied by imaging studies.
“Optimizing the tools for automated reconstruction is very, very important if we are serious about mapping neural circuitry. We believe the competition format of DIADEM has already fostered greater development than we could have gotten had we simply told people what to do,” said Giorgio A. Ascoli, University Professor and Director of the Center for Neural Informatics, Structures, and Plasticity at the Krasnow Institute for Advanced Study.
The DIADEM Challenge was launched in April 2009, and was open to individuals and teams from the private sector and academic laboratories. More than one hundred teams registered for the qualifier stage. Ascoli says the organizers were pleased to receive submissions both from researchers who had already been working on the problem of digital reconstruction and from teams for whom DIADEM presented an entirely new challenge. The five teams of finalists, he says, are reflective of that mix.
Competitors were given a year to implement an algorithm for digital reconstruction of neuronal morphology and to test it against manual reconstruction, which is the current “gold standard.” An international panel of experts evaluated the submissions using a comprehensive battery of quantitative metrics and qualitative evaluations. The five finalists were selected based on the panel’s recommendations.
While researchers worked independently during the qualifier phase, the final round, to be held at Janelia Farm from August 29-September 1, 2010, will bring competitors together with neuroscientists, who will provide real data to put the reconstruction algorithms to the test. Each competitor will have an opportunity to work with each of five data sets and their owners.
The final round will mimic real lab dynamics, with algorithm providers and data owners working together to achieve the most satisfactory solution to each problem. Ascoli notes that the competitors who advanced to the final round all recognize the challenges of analyzing real data, and bring a sense of pragmatism to the problem that will be essential to success. “This is not a problem with an answer in the back of the book,” he says. “You’re not going to get it perfect, but you’ve got to take your best shot.”
At the end of the final round, the organizers will award a $75,000 cash prize to the winning individual or team whose algorithm is judged to perform the best.
The National Institutes of Health is providing partial support to a scientific conference that is independent of—but held in conjunction with—the final round of the DIADEM Challenge. The goal of the conference is to bring neuroscientists and computational scientists together to discuss potential solutions to the scientific challenges in the field of digital reconstruction and identify future research directions and opportunities. Yuan Liu, program director for Computational Neuroscience and Neuroinformatics at the National Institute of Neurological Disorders and Stroke, is co-organizing the scientific conference with Ascoli and Janelia Farm group leader Karel Svoboda.
The idea for the DIADEM Challenge was originally discussed in 2007 at a scientific workshop at Janelia Farm. Scientists at the meeting noted that progress in understanding neural circuits was being slowed by the tedious task of tracing the structure of individual nerve cells by hand.
Even with the advent of computer technology that enables mapping in three dimensions, the full reconstruction of single neurons may take months. The vast majority of axons (the long neuronal projections that transmit information to neighboring cells) and dendrites (the branches on nerve cells that receive information from neighboring cells) must be traced manually. Researchers trace axons and dendrites that have been labeled with markers, such as green fluorescent protein, and imaged using a variety of microscopy techniques.
Full details about the DIADEM Challenge can be found at www.diademchallenge.org.
The leaders of the five teams of finalists that will compete in the Diadem Tournament are:
- Erhan Bas, Northeastern University
- German Gonzalez, École Polytechnique Fédérale de Lausanne
- Eugene Myers, Janelia Farm Research Campus
- Badri Roysam, Rensselaer Polytechnic Institute
- Armen Stepanyants, Northeastern University
Allen Institute for Brain Science
Launched in 2003, the Seattle-based Allen Institute for Brain Science is an independent, 501(c)(3) nonprofit medical research organization dedicated to advancing brain research. Started with $100 million in seed money from philanthropist Paul G. Allen, the Institute takes on projects at the leading edge of science—far-reaching projects at the intersection of biology and technology. The resulting data create publicly available resources that fuel discovery for countless other researchers worldwide. The Institute’s data, tools and resources are publicly available on the Web at www.alleninstitute.org.
Howard Hughes Medical Institute
The Howard Hughes Medical Institute, a nonprofit medical research organization that ranks as one of the nation's largest philanthropies, plays a powerful role in advancing biomedical research and science education in the United States. HHMI's principal mission is conducting basic biomedical research, which it carries out in collaboration with more than 60 universities, medical centers, and other research institutions throughout the United States. Approximately 350 HHMI investigators, along with a scientific staff of more than 2,000, work at these institutions in Hughes laboratories. In a complementary program at HHMI's Janelia Farm Research Campus in Loudoun County, Virginia, leading scientists are pursuing long-term, high-risk, high-reward research in a campus specially designed to bring together researchers from disparate disciplines. HHMI researchers are widely recognized for their creativity and productivity: 124 HHMI investigators are members of the National Academy of Sciences, and there are currently 13 Nobel laureates within the investigator community. The Institute also has a philanthropic grants program that emphasizes initiatives with the power to transform graduate and undergraduate education in the life sciences. To learn more about the Howard Hughes Medical Institute and the Janelia Farm Research Campus, visit www.hhmi.org.
Krasnow Institute for Advanced Study at George Mason University
The Krasnow Institute seeks to expand understanding of mind, brain, and intelligence by conducting research at the intersection of the separate fields of cognitive psychology, neurobiology, and the computer-driven study of artificial intelligence and complex adaptive systems. These separate disciplines increasingly overlap and promise progressively deeper insight into human thought processes. The Institute also examines how new insights from cognitive science research can be applied for human benefit in the areas of mental health, neurological disease, education, and computer design.
Named the number one national university to watch by U.S. News & World Report, George Mason University is an innovative, entrepreneurial institution with global distinction in a range of academic fields. Located in the heart of Northern Virginia’s technology corridor near Washington, D.C., Mason prepares its students to succeed in the work force and meet the needs of the region and the world. With strong undergraduate and graduate degree programs in engineering and information technology, dance, organization psychology and health care, Mason students are routinely recognized with national and international scholarships. Mason professors conduct ground-breaking research in such areas as climate change, information technology, and the biosciences, and Mason’s Center for the Arts brings world-renowned artists, musicians, and actors to its stage.
To learn more about the Krasnow Institute for Advanced Study and George Mason University, visit http://www.gmu.edu.
National Institutes of Health
The National Institutes of Health (NIH), a part of the U.S. Department of Health and Human Services, is the primary Federal agency for conducting and supporting medical research. Helping to lead the way toward important medical discoveries that improve people's health and save lives, NIH scientists investigate ways to prevent disease as well as the causes, treatments, and even cures for common and rare diseases. Composed of 27 Institutes and Centers, the NIH provides leadership and financial support to researchers in every state and throughout the world.
For over a century, the National Institutes of Health has played an important role in improving the health of the nation. The NIH traces its roots to 1887 with the creation of the Laboratory of Hygiene at the Marine Hospital in Staten Island, NY. The NIH is an agency of the U.S. Department of Health and Human Services. With the headquarters in Bethesda, Maryland, the NIH has more than 18,000 employees on the main campus and at satellite sites across the country. With the support of the American people, the NIH annually invests over $30.6 billion in medical research. More than 83 percent of the NIH's funding is awarded through almost 50,000 competitive grants to more than 325,000 researchers at over 3,000 universities, medical schools, and other research institutions in every state and around the world. About 10 percent of the NIH's budget supports projects conducted by nearly 6,000 scientists in its own laboratories, most of which are on the NIH campus in Bethesda, Maryland. To learn more about the NIH, visit www.nih.gov.