Towards a common format for storing electrophysiology data

Abstract

Event Abstract Back to Event Towards a common format for storing electrophysiology data Jeffrey L. Teeters1* and Friedrich T. Sommer1 1 University of California at Berkeley, Redwood Center for Theoretical Neuroscience, United States The need for common data formats for neuroscience data is becoming increasingly important because new projects and technologies are greatly enlarging the volume of data to be shared among laboratories and researchers. The focus here is a unified data format for cellular-based, neurophysiology data, including intra- and extra-cellular voltage recordings as well as optical physiology data (i.e., cellular imaging) and include complex metadata related to stimuli and behavior. To define basic requirements for a common data format, use cases from a multitude of laboratories must be considered. This has been done over the last few years by the Electrophysiology Task Force (Teeters et. al. 2013) of the INCF Program on Standards for Data Sharing. The first part of this poster will summarize the comprehensive document worked out by the Task Force. Specifically, the document describes the different types of data and metadata that must be stored at a minimum to represent electrophysiology data, including relationships between the data types, etc. To meet the urgent need of storing existing and currently produced data, the Kavli foundation has organized the initiative “Neurodata without Borders – Cellular Neurophysiology (NWB-CN)” (Reardon, S., 2014), an ambitious one-year project to produce a common data format accommodating use cases of four large experimental labs/institutions: the Allen Brain Institute, Janelia Farm and two big labs at NYU and Caltech. Although focusing on a limited set of use cases, the project’s goal is to use best existing practices, like the Task Force recommendations, and develop products that will serve the broader community. The NWB-CN project started in May 2014 and has three stages, each scheduled to last four months. The first stage, to be completed by the time of the 2014 INCF Congress, is to gather example data sets and make them available at CRCNS.org. Stage 2, starting at the time of the 2014 INCF Congress, will invite proposals from data model designers, vendors of data formats, and developers to propose formats for storing data based on the example data sets; and to select a common format. Stage 3 is to develop software to implement and use the common format. The second part of this poster will describe the particular use cases in the NWB-CN project and provide information on how to propose data models and data formats to the project. Acknowledgements This work was conducted within the Electrophysiology Task Force of the INCF Program on Standards for Data Sharing. Funding for J.L. Teeters and F.T. Sommer provided through NSF grant 0855272 and the Kavli Foundation. References Reardon, Sara (2014). Brain-mapping projects to join forces. Nature, 18 March 2014. doi:10.1038/nature.2014.14871 Teeters JL, Benda J, Davison AP, Eglen S, Gerhard S, Gerkin RC, Grewe J, Harris K, Jackson T, Mouček R, Pröpper R, Sessions HL, Smith LS, Sobolev A, Sommer FT, Stoewer A and Wachtler T (2013). Considerations for developing a standard for storing electrophysiology data in HDF5. Front. Neuroinform. Conference Abstract: Neuroinformatics 2013. doi: 10.3389/conf.fninf.2013.09.00069 Keywords: data sharing, Standards, data format, metadata, HDF5, data model Conference: Neuroinformatics 2014, Leiden, Netherlands, 25 Aug - 27 Aug, 2014. Presentation Type: Poster, not to be considered for oral presentation Topic: Electrophysiology Citation: Teeters JL and Sommer FT (2014). Towards a common format for storing electrophysiology data. Front. Neuroinform. Conference Abstract: Neuroinformatics 2014. doi: 10.3389/conf.fninf.2014.18.00074 Copyright: The abstracts in this collection have not been subject to any Frontiers peer review or checks, and are not endorsed by Frontiers. They are made available through the Frontiers publishing platform as a service to conference organizers and presenters. The copyright in the individual abstracts is owned by the author of each abstract or his/her employer unless otherwise stated. Each abstract, as well as the collection of abstracts, are published under a Creative Commons CC-BY 4.0 (attribution) licence (https://creativecommons.org/licenses/by/4.0/) and may thus be reproduced, translated, adapted and be the subject of derivative works provided the authors and Frontiers are attributed. For Frontiers’ terms and conditions please see https://www.frontiersin.org/legal/terms-and-conditions. Received: 28 Apr 2014; Published Online: 04 Jun 2014. * Correspondence: Dr. Jeffrey L Teeters, University of California at Berkeley, Redwood Center for Theoretical Neuroscience, Berkeley, CA, United States, teeters@berkeley.edu Login Required This action requires you to be registered with Frontiers and logged in. To register or login click here. Abstract Info Abstract The Authors in Frontiers Jeffrey L Teeters Friedrich T Sommer Google Jeffrey L Teeters Friedrich T Sommer Google Scholar Jeffrey L Teeters Friedrich T Sommer PubMed Jeffrey L Teeters Friedrich T Sommer Related Article in Frontiers Google Scholar PubMed Abstract Close Back to top Javascript is disabled. Please enable Javascript in your browser settings in order to see all the content on this page.