NeuronVisio connects with NEURON using the new Python NEURON interface.
Installation:
To install NeuronVisio you need to satisfy the following dependencies
* pygtk
* visual
* matplotlib
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.
Quickstart
This code is just to give an idea in how to use nrnvisio module:
1. fire up an ipython console with pylab switch.:
ipython -pylab # If you don't use the switch you will not see any graph.
2. 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:
1. Creates a single section called soma
2. Insert an Hodgkey-Huxley channel and a passive conductance
3. 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.
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 ipython)
Requirements:
- Python
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