mattions / neuronvisio
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A Graphical User Interface with 3D Visualization features for NEURON simulation enviroment
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NeuronVisio
What is it
NeuronVisio is a Graphical User Interface for NEURON simulator enviroment. NeuronVisio connect with NEURON using the new python NEURON interface.
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 - the GUI runs in its own thread so it's possible to use the console (strongly suggested to run through ipython)
Installation
To install NeuronVisio you need to satisfy the following dependencies
- pygtk: http://www.pygtk.org/
- visual: http://vpython.org/
- matplotlib: http://matplotlib.sourceforge.net/
and of course NEURON
Easy Install
The easiest way to get neuronvisio is if you have setuptools installed:
easy_install neuronvisio
Without setuptools, it's still pretty easy. Download the neuronvisio.tgz file from neuronvisio's Cheeseshop page, untar it and run:
python setup.py install
Documentation
The documentation is available in the doc folder or online or in pdf format in the docs direcotry
Quickstart
This code is just to give an idea in how to use nrnvisio module:
fire up an ipython console with pylab switch.:
ipython -pylab # If you don't use the switch you will not see any graph.
Import the module:
from neuronvisio.controls import Controls controls = Controls()
When nrnvisio is started the thread is launched. In this thread all the process of nrnvisio will happen without blocking the console.
As a quick example the following code:
- Creates a single section called soma
- Insert an Hodgkey-Huxley channel and a passive conductance
- Insert an alphaSynapse to provide a stimul.
A quick example can be the following::
from nrnvisio.controls import Controls
controls = Controls() # Starting the GUI
from neuron import h # Getting the HocInterpreter
soma = h.Section() # Creating a section
soma.insert('hh') # Inserting a HH channel
soma.insert('pas') # inserting a passive conductance
syn = h.AlphaSynapse(0.5, sec=soma) # synaptic input
syn.onset = 0.5 # when to fire
syn.gmax = 0.05 # the conductance of the synapse
syn.e = 0 # the reversal potential
More example in the example directory show how to use Neuronvisio with more complex model.
Contacts
Homepage: http://mattions.github.com/neuronvisio/ Mailing List: http://groups.google.com/group/neuronvisio
Help and development
If you'd like to help out, you can fork the project at http://github.com/mattions/neuronvisio and report any bugs at http://github.com/mattions/neuronvisio/issues.
