Development of the Neurodata Without Borders: Neurophysiology file format
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1
University of California at Berkeley, United States
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2
The Allen Institute for Brain Science, United States
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3
Physion LLC, United States
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4
University College London, United Kingdom
Neurodata Without Borders (NWB): Neurophysiology is the first collaboration launched by The Kavli Foundation’s “Neurodata Without Borders,” (http://nwb.org) a broad initiative with the goal of standardizing neuroscience data on an international scale, making it more easily sharable by researchers worldwide. NWB: Neurophysiology aims to develop a unified data format for cellular-based, neurophysiology data based on representative use cases from four laboratories – the Buzsaki group at NYU, the Svoboda group at Janelia Farm, the Meister group at Caltech, and the Allen Institute for Brain Science in Seattle. The project was sponsored by The Kavli Foundation, General Electric, The Allen Institute for Brain Science, the Howard Hughes Medical Institute and the International Neuroinformatics Coordinating Facility. It started in August 2014 and had a goal to complete an initial format in one year.
During the project, input from the partner labs and the broader neuroscience community was solicited and used to produce an inventory of the information that needs to be included in the storage of data of different experiment modalities. This inventory supplements the more general neurophysiology data types given in the requirements document [1] produced by the Electrophysiology Task Force of the INCF Program on Standards for Data Sharing. Input was also solicited about the “how” to store data, that is, neuroinformatic methods for storing and organizing such data. The main system that were considered were the NIX format [2] and the LBNL Brain Format [3]. Some ideas from these systems were incorporated into the NWB format.
The first version of the format, the NWB alpha version, is now available. It uses HDF5 to store data. Contents are organized into several top-level groups, each storing data of a particular type, and top-level datasets, storing basic information about the NWB file. The layout allows understanding the organization of the data by examining the contents of the HDF5 file without requiring an API. The format is also sufficiently structured to allow software tools to easily access the data. A specification language is used to concisely describe the format in a machine and human readable way. The specification language also allows extending the format to support new use cases in a flexible but structured manner.
The NWB alpha version is already used to share data sets from the NWB collaborators at crcns.org. In addition, the Allen Institute has adopted the NWB format for all physiology experiments, including the electrophysiology characterization of single cells as a part of the publicly released Allen Cell Types Database [4]. Information about the NWB alpha version is at http://neurodatawithoutborders.github.io
1. http://www.incf.org/activities/our-programs/datasharing/requirements-for-storing-electrophysiology-data-version-0.72
2. https://github.com/G-Node/nix
3. https://bitbucket.org/oruebel/brainformat
4. http://celltypes.brain-map.org/
Acknowledgements
Funding provided the Kavli Foundation, General Electric, the Howard Hughes Medical Institute Janelia Research Campus, the Allen Institute for Brain Science, the International Neuroinformatics Coordinating Facility and the National Science Foundation (NSF grant 0855272). Some of this work was conducted within the Electrophysiology Task Force of the INCF Program on Standards for Data Sharing.
Keywords:
data sharing,
standard format,
Electrophysiology,
optophysiology,
HDF5,
File format
Conference:
Neuroinformatics 2015, Cairns, Australia, 20 Aug - 22 Aug, 2015.
Presentation Type:
Poster, not to be considered for oral presentation
Topic:
Electrophysiology
Citation:
Teeters
JL,
Godfrey
KB,
Friedsam
C,
Harris
K,
Young
R,
Dang
C and
Sommer
FT
(2015). Development of the Neurodata Without Borders: Neurophysiology file format.
Front. Neurosci.
Conference Abstract:
Neuroinformatics 2015.
doi: 10.3389/conf.fnins.2015.91.00033
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Received:
01 Jun 2015;
Published Online:
05 Aug 2015.
*
Correspondence:
PhD. Jeffrey L Teeters, University of California at Berkeley, Berkeley, United States, teeters@berkeley.edu