To install NeuronVisio you need to satisfy the following dependencies
and of course NEURON>=7.2 compiled with python support
On Ubuntu you can easily install all the requirements using apt-get with:
sudo apt-get install python-qt4 ipython python-matplotlib \
python-setuptools python-tables python-mayavi
If you are running a different flavour of GNU/Linux, like Fedora for example, just install the requirements with your package manager.
Next, see the instructions on installation of NEURON with Python availabe at http://www.davison.webfactional.com/notes/installation-neuron-python/.
Proceed to the Package Install .
Under Mac it is recommended to get a prepackaged scientific python distribution which contains most of neuronvisio’s dependencies, such as:
Alternatively, if you want to do it yourself, you should look at the following:
Next, see the instructions on installation of NEURON with Python availabe at http://www.davison.webfactional.com/notes/installation-neuron-python/.
Proceed to the Package Install .
Under Windows it is recommended to get a prepackaged scientific python distribution which contains most of neuronvisio’s dependencies, such as:
Alternatively, if you want to do it yourself, you will need to manually install and configure the dependencies listed in Requirements
A portable and already compiled version of NEURON for Python is available from https://bitbucket.org/uric/pyneuron/ or simply by using:
pip install PyNEURON
Proceed to the Package Install .
To install neuronvisio we suggest to create a virtualenv and install the packages there. Check out virtualenv and virtualenvwrapper
Note
Neuronvisio 0.8.0 depends on a development version of Mayavi, until this is integrated in Mayavi master. You still have to fullfill the Mayavi’s requirements listed on Mayavi website.
If you have pip installed and all the requirements are already met you can install neuronvisio typing:
pip install -U --extra-index-url=http://www.ebi.ac.uk/~mattioni/snapshots/ neuronvisio
If you want to run the latest code you can clone the git repo and run the software from there:
git clone git://github.com/mattions/neuronvisio.git neuronvisio
then you need to add the directory (the absolute path) to your PYTHONPATH (in bash):
export PYTHONPATH=$PYTHONPATH:/path-to-neuronvisio-dir
The source code is on github at this address and git is used as software management tool
To install from the git just clone the repo:
git clone git://github.com/mattions/neuronvisio.git
and then run:
python setup.py install