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.

Detection of 3′-End RNA Uridylation with a Protein Nanopore

“…44–46 The analysis was based on threshold searches. For the calculation of kinetic values the traces were divided into open and blocked levels.…”

Why sharing matters for electrophysiological data analysis

“…NEO, http://neo.readthedocs. org/en/0.3.1/index.html, Garcia et al (2014), is an object-oriented Python toolbox using Neuroshare, intended to make re-use easier. It has the added advantage of being open source.…”

MEArec: a fast and customizable testbench simulator for ground-truth extracellular spiking activity

“…spiketrains contains the spike trains -list of (n_neurons) neo.Spiketrain objects [15] templates contains the selected templates -array with shape (n_neurons, n_jitters, n_electrodes, n_templates samples) templates for non-drifting recordings -or (n_neurons, n_drift_steps, n_jitters, n_electrodes, n_neurons) for drifting ones templates_celltypes contains the cell type of the selected templates -array of strings with length (n_neurons)…”