title: Neo: an object model for handling electrophysiology data in multiple formats.
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.
authors.affiliation: Centre de Recherche en Neuroscience de Lyon, CNRS UMR5292-INSERM U1028-Université Claude Bernard Lyon 1 Lyon, France.
authors.forename: Samuel
authors.initials: S
authors.lastname: Garcia
authors.affiliation: Unité de Neurosciences, Information et Complexité, Neuroinformatics group, CNRS UPR 3293 Gif-sur-Yvette, France.
authors.forename: Domenico
authors.initials: D
authors.lastname: Guarino
authors.affiliation: Institut de Neurosciences de la Timone UMR 7289, Aix Marseille Université, CNRS Marseille, France.
authors.forename: Florent
authors.initials: F
authors.lastname: Jaillet
authors.affiliation: Division of Neurobiology, Department Biology II, Ludwig-Maximilians-Universität München Planegg-Martinsried, Germany.
authors.forename: Todd
authors.initials: T
authors.lastname: Jennings
authors.affiliation: Neural Information Processing Group, TU Berlin Berlin, Germany.
authors.forename: Robert
authors.initials: R
authors.lastname: Pröpper
authors.affiliation: G-Node, Department Biology II, Ludwig-Maximilians-Universität München Planegg-Martinsried, Germany.
authors.forename: Philipp L
authors.initials: PL
authors.lastname: Rautenberg
authors.affiliation: Helen Wills Neuroscience Institute, University of California Berkeley, CA, USA.
authors.forename: Chris C
authors.initials: CC
authors.lastname: Rodgers
authors.affiliation: G-Node, Department Biology II, Ludwig-Maximilians-Universität München Planegg-Martinsried, Germany.
authors.forename: Andrey
authors.initials: A
authors.lastname: Sobolev
authors.affiliation: G-Node, Department Biology II, Ludwig-Maximilians-Universität München Planegg-Martinsried, Germany.
authors.forename: Thomas
authors.initials: T
authors.lastname: Wachtler
authors.affiliation: Unité de Neurosciences, Information et Complexité, Neuroinformatics group, CNRS UPR 3293 Gif-sur-Yvette, France.
authors.forename: Pierre
authors.initials: P
authors.lastname: Yger
authors.affiliation: Unité de Neurosciences, Information et Complexité, Neuroinformatics group, CNRS UPR 3293 Gif-sur-Yvette, France.
authors.forename: Andrew P
authors.initials: AP
authors.lastname: Davison
keywords: Python; electrophysiology; file formats; interoperability; software