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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

3D rendering of the depolarization through the Pyramidal Neuron. The figure illustrates the depolarization state of the pyramidal neuron, at time 16.975 ms. The depolarization is initiated at the soma (yellow at +20 mV), and transmitted toward the dendrites (blue at −70 mv). The left color scale ranges from −70 mV (blue) through to +40 mV (red).
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Figure 4: 3D rendering of the depolarization through the Pyramidal Neuron. The figure illustrates the depolarization state of the pyramidal neuron, at time 16.975 ms. The depolarization is initiated at the soma (yellow at +20 mV), and transmitted toward the dendrites (blue at −70 mv). The left color scale ranges from −70 mV (blue) through to +40 mV (red).

Mentions: The 3D representation can be used to investigate the evolution of any of the variables of the model. Figure 4 shows the depolarization of the pyramidal neuron. Using the time-slider in the “Model” tab under the “3D control” (Figure 1), it is possible to follow the depolarization of the sections through time. In this case the depolarization is initiated in the soma, and it is transmitted toward the dendrites.


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

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

3D rendering of the depolarization through the Pyramidal Neuron. The figure illustrates the depolarization state of the pyramidal neuron, at time 16.975 ms. The depolarization is initiated at the soma (yellow at +20 mV), and transmitted toward the dendrites (blue at −70 mv). The left color scale ranges from −70 mV (blue) through to +40 mV (red).
© Copyright Policy - open-access
Related In: Results  -  Collection

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

Figure 4: 3D rendering of the depolarization through the Pyramidal Neuron. The figure illustrates the depolarization state of the pyramidal neuron, at time 16.975 ms. The depolarization is initiated at the soma (yellow at +20 mV), and transmitted toward the dendrites (blue at −70 mv). The left color scale ranges from −70 mV (blue) through to +40 mV (red).
Mentions: The 3D representation can be used to investigate the evolution of any of the variables of the model. Figure 4 shows the depolarization of the pyramidal neuron. Using the time-slider in the “Model” tab under the “3D control” (Figure 1), it is possible to follow the depolarization of the sections through time. In this case the depolarization is initiated in the soma, and it is transmitted toward the dendrites.

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