Neuronvisio

What is it

Neuronvisio is a Graphical User Interface for NEURON simulator environment with 3D capabilities. Neuronvisio makes easy to select and investigate sections’ properties and it offers easy integration with matplotlib for plotting the results.

The geometry can be saved using NeuroML and the computational results in a customised and extensible HDF5 format; the results can then be reload in the software and analysed in a later stage, without re-running the simulation.

Features

• 3D visualization of the model with the possibility to change it runtime
• Creation of vectors to record any variables present in the section
• Pylab integration to plot directly the result of the simulation
• Exploration of the timecourse of any variable among time using a color coded scale
• Saving the results simulation for later analysis
• Automatic download and running of models in ModelDB

How to use it

Launch it from the terminal:

$ neuronvisio

then check the Getting Started section for more info.

Quick Links

• Install Neuronvisio: Install
• Browse the code: Github Repo
• Subscribe to the Mailing List: Google group
• Read the docs of any versions: Read the docs
• Report an issue: Issues tracker

How to cite Neuronvisio

The paper describing Neuronvisio has been published in Frontiers Neuroinformatics, here the text citation:

Note

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

or get the BibTeX.

Contents

• Install
  • Requirements
  • Package Install
  • Source Code
• Getting Started
  • How does it work
  • How to integrate Neuronvisio with your code
  • Neuronvisio features
  • Plotting the simulation results
  • Investigate the section parameters
  • ModelDB Integration
  • Troubleshooting
• Saving and loading simulations’ reults
  • HDF structure
  • Saving your variables in storage.h5 and use Neuronvisio to plot them
• How to take screenshots and make movies
  • GUI control
  • 3-D rendering
  • Timecourse movie and pylab graphs
  • Network example
  • Making a movie
• Reference
  • neuronvisio.manager – Manage the map between vectors and sections
  • neuronvisio.visio – 3D Visual operations
  • neuronvisio.controls – User Interface module
• Changes in Neuronvisio
  • 0.8.6 – 8 March 2013
  • 0.8.5 – 6 Jul 2012
  • 0.8.4 – 12 Jun 2012
  • 0.8.3 – 18 May 2012
  • 0.8.2 – 23 Apr 2012
  • 0.8.1 – 19 March 2012
  • 0.8.0 – 15 Feb 2012
  • 0.7.3 – 24 Nov 2011
  • 0.7.2 – 8 Nov 2011
  • 0.7.1 – 8 Nov 2011
  • 0.7.0 – 3 Nov 2011
  • 0.6.2 – 16 Jun 2011
  • 0.6.1 – 9 Jun 2011
  • 0.6.0 – 10 May 2011
  • 0.5.2 – 26 Jan 2011
  • 0.5.1 - 23 Nov 2010
  • 0.5.0 - 19 Jun 2010
  • 0.4.4 - 1 Apr 2010
  • 0.4.3 - 2 Mar 2010
  • 0.4.2 - 18 Feb 2010
  • 0.4.1 - 28 Jan 2010
  • 0.4.0 - 19 Jan 2010
  • 0.3.5 - 20 Nov 2009
  • 0.3.4 - 15 Sep 2009
  • 0.3.3 - 3 Sep 2009
  • 0.3.22 - 31 Jul 2009
  • 0.3.21 - 20 Jul 2009
  • 0.3.2 - 20 Jul 2009
  • 0.3.1 - 18 Jul 2009
  • 0.3.0 - 14 Jul 2009
  • 0.2.0 - 6 Jul 2009
  • 0.1.0 - 30 Jun 2009

Indices and tables

• Index
• Module Index
• Search Page