The NEURON simulation environment is one of the most popular options for simulating multi-compartment neuron models. Hines et al. (2009) developed a module that allowed users to execute simulations from python. This option appears to be very popular with users.
However, much of the data analysis capabilities of NEURON (e.g. shape plots) are still limited to the traditional InterViews plotting environment. This toolbox provides some functions to do data analysis and visualization in matplotlib. One of the advantages of this approach is that plots and animations can be easily shared with other researchers in iPython notebooks.
Disclaimer: This code is only a side project at the moment. Use with caution and let me know if you find any unexpected behaviors. Feature requests are also welcome.
Download or clone this repository, then run:
python setup.py install
I am updating this repository on a semi-regular basis, so check back for updates and contact me if you have questions.
At the moment, only a few basic functions are included in the toolbox. These mostly relate to visualizing the morphology of model cells. Click here for a tutorial on the morphology toolbox - the animations seem to work best when viewed in Chrome.
I would like to add functions to support:
Alex H Williams. (2014). PyNeuron-Toolbox. GitHub Repository. https://github.com/ahwillia/PyNeuron-Toolbox DOI:10.5281/zenodo.12576