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Neuronvisio: A Graphical User Interface with 3D Capabilities for NEURON.

Mattioni M, Cohen U, Le Novère N - Front Neuroinform (2012)

Bottom Line: 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.The newly introduced ability of saving numerical results allows users to perform additional analysis on their previous simulations.

View Article: PubMed Central - PubMed

Affiliation: European Molecular Biology Laboratory-European Bioinformatics Institute, Wellcome Trust Genome Campus Cambridge, UK.

ABSTRACT
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.

No MeSH data available.


Related in: MedlinePlus

Matplotlib integration in Neuronvisio. The graph shows the time courses of the depolarization of the pyramidal Neuron, using the model from Mainen et al. (1995). The voltage of soma is plotted in blue, while two dendrites are plotted in red and green. The voltage (y-axis) is in millivolts and the time (x-axis) is in milliseconds.
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Figure 3: Matplotlib integration in Neuronvisio. The graph shows the time courses of the depolarization of the pyramidal Neuron, using the model from Mainen et al. (1995). The voltage of soma is plotted in blue, while two dendrites are plotted in red and green. The voltage (y-axis) is in millivolts and the time (x-axis) is in milliseconds.

Mentions: The recorded vectors are visible in the “Plot” tab, where the user can decide to plot any recorded variable within any section. Existing figures can be modified to include new points or lines, or new figures can be created. The Neuronvisio Qt4 main thread is integrated with the Qt matplotlib back-end, allowing interactive user-directed figure customization with the standard matplotlib commands. Figure 3 shows how to use to plot the vectors.


Neuronvisio: A Graphical User Interface with 3D Capabilities for NEURON.

Mattioni M, Cohen U, Le Novère N - Front Neuroinform (2012)

Matplotlib integration in Neuronvisio. The graph shows the time courses of the depolarization of the pyramidal Neuron, using the model from Mainen et al. (1995). The voltage of soma is plotted in blue, while two dendrites are plotted in red and green. The voltage (y-axis) is in millivolts and the time (x-axis) is in milliseconds.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC3368231&req=5

Figure 3: Matplotlib integration in Neuronvisio. The graph shows the time courses of the depolarization of the pyramidal Neuron, using the model from Mainen et al. (1995). The voltage of soma is plotted in blue, while two dendrites are plotted in red and green. The voltage (y-axis) is in millivolts and the time (x-axis) is in milliseconds.
Mentions: The recorded vectors are visible in the “Plot” tab, where the user can decide to plot any recorded variable within any section. Existing figures can be modified to include new points or lines, or new figures can be created. The Neuronvisio Qt4 main thread is integrated with the Qt matplotlib back-end, allowing interactive user-directed figure customization with the standard matplotlib commands. Figure 3 shows how to use to plot the vectors.

Bottom Line: 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.The newly introduced ability of saving numerical results allows users to perform additional analysis on their previous simulations.

View Article: PubMed Central - PubMed

Affiliation: European Molecular Biology Laboratory-European Bioinformatics Institute, Wellcome Trust Genome Campus Cambridge, UK.

ABSTRACT
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.

No MeSH data available.


Related in: MedlinePlus