New modular software architecture and APIs to enable users/developers to efficiently interact with the…
With scientists storing data in scores of different ways, Neurodata Without Borders provides a common format or “language” for brain data, beginning with neurophysiology
An alliance of brain researchers and funders has announced a common data format to facilitate the free and open exchange of complex information about the brain—information that scientists can then use to accelerate progress in understanding the brain and developing new treatments for brain disorders.
The new format, known as Neurodata Without Borders (NWB): Neurophysiology, is the first widely available format that allows researchers to capture and share data generated by two of the most widely used methods in brain research: optical and electrical neurophysiology. A description of the format and its potential impact on the field of neuroscience was published online November 18 in the journal Neuron.
“A unified data format is a prerequisite to really achieving breakthroughs in understanding the brain,” said Fritz Sommer, a neuroscientist at the Redwood Center for Theoretical Neuroscience and Helen Wills Neuroscience Institute, University of California, Berkeley (UC Berkeley), and senior author on the paper. “It’s hard to overstate the importance of new tools that will allow neuroscientists to share, search, analyze and integrate the large, complex data sets that are the product of modern neurophysiology experiments. The NWB format enables such tools to be developed.”
New research approaches, developed in the last decade, are profoundly altering the way neuroscientists study the brain, a trend that is accelerating due to President Obama’s Brain Research through Advancing Innovative Neurotechnologies (BRAIN) Initiative. Scientists can now ask questions about how the brain functions at the level of brain circuits and networks by recording the simultaneous activity of hundreds, even thousands, of brain cells in live animals. As a result, neuroscience data sets have become extremely large and complex, and it has become a major challenge to manage those data and extract meaning from them.
“It’s of the utmost importance that neuroscience arrives at a standard, as other fields such as astronomy and genomics have, so that there’s a way to compare and to contrast experimental data,” said Christof Koch, President and Chief Scientific Officer of the Allen Institute for Brain Science in Seattle and one of the researchers who initiated the project. “Our current tools generate an abundance of data in different formats that are not easily transcribed from one into the other, yielding a Tower of Babel situation. Thanks to NWB, we can now easily read and analyze data streaming in from different instruments to understand the underlying logic.”
Read “Identifying the Brain’s Essential Elements,”a roundtable discussion on the Allen Cell Types Database with Christof Koch, Chinh Dang and Kenneth Harris.
As the World Wide Web developed, standards were adopted for web pages so that they could be viewed consistently in different browsers. Similarly, the NWB:Neurophysiology format ensures that neuroscientists around the world can access, share, compare and analyze cellular-based neurophysiology data sets, which are essential to studying the connection between brain function and behavior.
The NWB:Neurophysiology format expands neuroscientists’ toolkit in two ways: First, it encodes both raw data and related metadata, which describe the experimental conditions under which the data were produced, for optical and electrical recordings of the brain in action. That combination is important because existing standards focus on electrical recordings, which limits the ability of neuroscientists to integrate their data. Second, it is extensible, therefore it can be modified to capture other types of neurophysiology data, such as imaging data.
“Currently, there are almost as many data formats as major neurophysiology laboratories. In addition to a common format, NWB also places a strong emphasis on providing sufficient metadata. Oftentimes it is impossible to figure out whether recordings were made from male or female animals, from the right or left hemisphere of the brain, or the time of recording, even in published papers. Information of this kind will be extremely valuable when meta-analyses on many data sets will be performed. Even if the NWB format changes over the years, the desire of an agreed format is made very clear by our effort,” said György Buzsáki of New York University and a scientific partner of the NWB:Neurophysiology project.
The Neurodata Without Borders alliance launched in mid 2014 to break down the obstacles to data sharing. The NWB:Neurophysiology data format is the result of a dedicated, one-year pilot project. It was created by software developers and theoretical and experimental neuroscientists from UC Berkeley and the Allen Institute for Brain Science, György Buzsáki of New York University, Markus Meister of the California Institute of Technology and Karel Svoboda of the Janelia Research Campus of the Howard Hughes Medical Institute (HHMI).
These scientific partners have publicly released multiple large, web-based data sets in the NWB:Neurophysiology format, including the Allen Institute’s Cell Types Database, which contains detailed information about hundreds of individual cells in the mouse brain.
I’m really proud of the fact that we have this format and that it was created in such a way that we can continue to build on it. It’s much more than anything that we had before,” said Chinh Dang, Chief Administrative Officer at the Allen Institute.
The NWB:Neurophysiology team will continue to refine the data format and develop new analysis tools to maximize its usefulness, in partnership with the neuroscience community.
“Would it not be wonderful to have a ‘Neurophysiology DropBox’ into which investigators could simply drop their recordings and share with everyone? We are not there yet but the NWB program is steering us in that direction. Agreeing on a format facilitates this sender-receiver communication,” said Buzsáki.
“Real understanding of the brain and its diseases can only come from the whole world being engaged in the challenge. The NWB format is a key step to enable collaborative research on the brain,” said Linda Lanyon, Executive Director, and Sean Hill, Scientific Director, INCF.
Funding and support for NWB:Neurophysiology was provided by the Allen Institute, GE, the International Neuroinformatics Coordinating Facility (INCF), HHMI and The Kavli Foundation.
“We are delighted by the progress made by these outstanding researchers and we’re confident that this new format will make a significant contribution to better understanding the brain,” said Robert Wells, Executive Director for Strategy, GE Healthymagination. “GE is proud to have been a supporter of this important initiative.”
“This is such an exciting time for brain research. But there are still hurdles to overcome to understand the brain. We hope that neuroscientists will embrace the NWB data standard and improve it so that the full impact of their creativity and ingenuity can be felt,” said Miyoung Chun, Executive Vice President of Science Programs at The Kavli Foundation.
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