Neuronvisio: a graphical user interface with 3D capabilities for NEURON
- 1 European Molecular Biology Laboratory-European Bioinformatics Institute, Wellcome Trust Genome Campus, Cambridge, UK
- 2 The Interdisciplinary Center for Neural Computation, The Hebrew University of Jerusalem, Jerusalem, Israel
The NEURON simulation environment is a commonly used tool to perform electrical simulation of neurons and neuronal networks. The NEURON User Interface, based on the now discontinued InterViews library, provides some limited facilities to explore models and to plot their simulation results. Other limitations include the inability to generate a three-dimensional visualization, no standard mean to save the results of simulations, or to store the model geometry within the results. Neuronvisio (http://neuronvisio.org) aims to address these deficiencies through a set of well designed python APIs and provides an improved UI, allowing users to explore and interact with the model. Neuronvisio also facilitates access to previously published models, allowing users to browse, download, and locally run NEURON models stored in ModelDB. Neuronvisio uses the matplotlib library to plot simulation results and uses the HDF standard format to store simulation results. Neuronvisio can be viewed as an extension of NEURON, facilitating typical user workflows such as model browsing, selection, download, compilation, and simulation. The 3D viewer simplifies the exploration of complex model structure, while matplotlib permits the plotting of high-quality graphs. The newly introduced ability of saving numerical results allows users to perform additional analysis on their previous simulations.
Keywords: neuron model, 3D visualization, electrophysiological model, hdf storage, matplotlib integration
Citation: Mattioni M, Cohen U and Le Novère N (2012) Neuronvisio: a graphical user interface with 3D capabilities for NEURON. Front. Neuroinform. 6:20. doi: 10.3389/fninf.2012.00020
Received: 25 November 2011; Accepted: 07 May 2012;
Published online: 06 June 2012.
Copyright: © 2012 Mattioni, Cohen and Le Novère. This is an open-access article distributed under the terms of the Creative Commons Attribution Non Commercial License, which permits non-commercial use, distribution, and reproduction in other forums, provided the original authors and source are credited.
*Correspondence: Michele Mattioni, European Molecular Biology Laboratory-European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK. e-mail: firstname.lastname@example.org