To install Neuronvisio you need to satisfy the following dependencies

and of course NEURON>=7.2 compiled with python support

Easy Way: Use conda

You can install all the dependencies and everything you need (also NEURON) to run Neuronvisio with one command once you have conda installed. If you do not have, get it from here (

# Create a new environment and install neuronvisio there
conda create -n neuronvisio_env neuronvisio -c mattions

After the installation activate the environment and you good to go:

source activate neuronvisio_env

If the HOC file does not get found, export NEURONHOME variable like

export NEURONHOME=$CONDA_ENV_PATH/share/nrn/

The packages are made only for linux-x64, but we are looking into expanding them to all the supported platforms.

Otherwise you could install by hand following the instructions below.

Ubuntu and friends

On Ubuntu you can easily install all the requirements using apt-get with:

sudo apt-get install python-qt4 python-matplotlib python-setuptools python-tables \

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 available at

Proceed to the Package Install .

Mac OS X

Install the Homebrew package manager:

ruby -e "$(curl -fsSL"

Ensure your homebrew installation is fully updated:

brew update

and “raring to brew” (configured to Homebrew’s liking) by following the instructions given by:

brew doctor

For example, it is critical to ensure sure that you don’t have another python distribution on your path (eg. Enthought), and it is also recommended that you place “/usr/local/bin” before “/usr/bin” in your PATH variable set in your “$HOME/.bash_profile” settings file.

Install all the homebrew packages you need, including the Homebrew version of python. NB: It is recommended by a few internet sources (eg. to install python as a framework (the ‘–framework’ option below) but it is not strictly necessary for the installation of Neuronvisio:

brew install python --framework
brew install qt
brew install homebrew/science/hdf5

At the time of writing, Mayavi (installed by the NeuronVisio package installer) doesn’t work with the latest version of VTK (6.0.0) so you will need to install version 5.10.1 instead. Also, VTK has been moved to the homebrew-science “tap” so you will need to tap that first before installing it, i.e.:

brew tap homebrew/science
cd /usr/local/Library/Taps/homebrew-science
git checkout 27a4327 vtk.rb
brew install vtk --python --qt --pyqt

Install python packages using pip, ensuring that you are using the Homebrew version of pip, /usr/local/bin/pip, which you should be if you put /usr/local/bin before /usr/bin in your PATH variable (this can be checked using the “which pip” command). You may also run into problems if you have setuptools in your system python (‘/Library/Python/2.7/site-packages’), in this case temporarily move the system setuptools to somewhere else for the rest of the installation procedure:

pip install numpy
pip install matplotlib
pip install numexpr
pip install cython
pip install ipython

After installing ipython you will probably want to put a link to it somewhere on your path, eg. /usr/local/bin:

ln -s /usr/local/share/ipython /usr/local/bin/ipython

Next, see the instructions on installation of NEURON with Python available at (again ensuring you are using the Homebrew version of python ‘/usr/local/bin/python’)

Try the Package Install but if that fails use the Source Code instructions (I needed to do this at least)


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 or simply by using:

pip install PyNEURON

Proceed to the Package Install .

Package Install

To install Neuronvisio we suggest to create a virtualenv and install the packages there. Check out virtualenv and virtualenvwrapper

If you have pip installed and all the requirements are already met you can install neuronvisio from PyPi typing:

pip install -U neuronvisio


Mayavi stack and ipython will be installed automatically as Neuronvisio requirements from PyPi.

Running the bleeding edge

If you want to run the latest code, directly from the repo, you can do it using pip:

pip install -e git+

then you need to add the directory (the absolute path) to your PYTHONPATH (in bash):

export PYTHONPATH=$PYTHONPATH:/path-to-neuronvisio-dir

Source Code

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://

and then run:

python install