Please use this identifier to cite or link to this item: http://dx.doi.org/10.14279/depositonce-9195
Main Title: Neo: an object model for handling electrophysiology data in multiple formats
Author(s): Garcia, Samuel
Guarino, Domenico
Jaillet, Florent
Jennings, Todd
Pröpper, Robert
Rautenberg, Philipp L.
Rodgers, Chris C.
Sobolev, Andrey
Wachtler, Thomas
Yger, Pierre
Davison, Andrew P.
Type: Article
Language Code: en
Abstract: Neuroscientists use many different software tools to acquire, analyze and visualize electrophysiological signals. However, incompatible data models and file formats make it difficult to exchange data between these tools. This reduces scientific productivity, renders potentially useful analysis methods inaccessible and impedes collaboration between labs. A common representation of the core data would improve interoperability and facilitate data-sharing. To that end, we propose here a language-independent object model, named “Neo,” suitable for representing data acquired from electroencephalographic, intracellular, or extracellular recordings, or generated from simulations. As a concrete instantiation of this object model we have developed an open source implementation in the Python programming language. In addition to representing electrophysiology data in memory for the purposes of analysis and visualization, the Python implementation provides a set of input/output (IO) modules for reading/writing the data from/to a variety of commonly used file formats. Support is included for formats produced by most of the major manufacturers of electrophysiology recording equipment and also for more generic formats such as MATLAB. Data representation and data analysis are conceptually separate: it is easier to write robust analysis code if it is focused on analysis and relies on an underlying package to handle data representation. For that reason, and also to be as lightweight as possible, the Neo object model and the associated Python package are deliberately limited to representation of data, with no functions for data analysis or visualization. Software for neurophysiology data analysis and visualization built on top of Neo automatically gains the benefits of interoperability, easier data sharing and automatic format conversion; there is already a burgeoning ecosystem of such tools. We intend that Neo should become the standard basis for Python tools in neurophysiology.
URI: https://depositonce.tu-berlin.de/handle/11303/10234
http://dx.doi.org/10.14279/depositonce-9195
Issue Date: 20-Feb-2014
Date Available: 1-Nov-2019
DDC Class: 004 Datenverarbeitung; Informatik
610 Medizin und Gesundheit
Subject(s): electrophysiology
interoperability
Python
software
file formats
Sponsor/Funder: EC/FP7/269921/EU/Brain-inspired multiscale computation in neuromorphic hybrid systems/BrainScaleS
DFG, GRK 1589, Verarbeitung sensorischer Informationen in neuronalen Systemen
BMBF, 01GQ1302, Nationaler Neuroinformatik Knoten
License: https://creativecommons.org/licenses/by/3.0/
Journal Title: Frontiers in Neuroinformatics
Publisher: Frontiers Media S.A.
Publisher Place: Lausanne
Volume: 8
Article Number: 10
Publisher DOI: 10.3389/fninf.2014.00010
EISSN: 1662-5196
Appears in Collections:FG Neuronale Informationsverarbeitung » Publications

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