Downlad stable versions of LFPy here:
Or, download the development version of LFPy using subversion into a local folder:
svn checkout http://bebiservice.umb.no/svn-public/LFPy-release
The development code is then found under “trunk/”, and different numbered releases under “tags/”.
To browse the source codes online, see http://bebiservice.umb.no/projects-public/LFPy-release/browser.
To install LFPy you will need the following:
Python, seems to work fine with recent python since 2.6.x (2.6.6 or newer recommended), 2.7.x works fine. Not tested with Python 3.x.
Python modules numpy, scipy, matplotlib
NEURON compiled as a Python module, so the following should execute without error in Python console:
import neuron
neuron.test()
If this step fails, see the next section.
LFPy was tested to work with NEURON 7.2 and the 7.3 development branch, we had some issues with a precompiled version of NEURON 7.1.
Cython (C-extensions for python) to speed up simulations of extracellular fields. Tested with version > 1.4., and known to fail with version 1.1.
Download the LFPy source distribution (LFPy-x.x.tar.gz) and unpack.
In “LFPy-x.x/” run
sudo python setup.py install
or
python setup.py install --user
in case you want to install in your home directory (e.g. if you do not have root access).
If you only want to have LFPy in one place, you can add this working folder to your $PYTHONPATH, and just compile the Cython extensions;
python setup.py build_ext -i
In a fresh python-session you should now be able to
import LFPy
There are some basic usage examples provided in
LFPy-x.x/examples/
We suggest you start with example1.py
cd examples
python example1.py
or
cd examples
ipython
>>> run "example1.py"
For the example2.py and example3.py, the NEURON mechanisms (.mod-files) must be compiled using “nrnivmodl” from your NEURON installation first.
HTML documentation is available at:
LFPy-x.x/html/index.html
Some users have difficulties install NEURON as a Python module, depending on their platform. We will provide some explanations here, and otherwise direct to the NEURON download pages; http://www.neuron.yale.edu/neuron/download and http://www.neuron.yale.edu/neuron/download/getstd. The NEURON forums are also a useful resource for installation problems.
The instructions below show how to meet all the requirements starting from a clean Ubuntu 10.4 for the installation of NEURON from the development branch.
Start by installing the required packages
sudo apt-get install mercurial autoconf libtool
sudo apt-get install libxext-dev libncurses-dev
sudo apt-get install bison flex
sudo apt-get install python-dev python-numpy python-scipy python-matplotlib
sudo apt-get install ipython
The cython version provided in Ubuntu 10.4LTS is out of date, compile a more recent version yourself. Download Cython (Cython-0.15.1.tar.gz, or newer) from Cython.org, unpack and install;
sudo python setup.py install
Now get the source code of NEURON using mercurial
cd $HOME
mkdir neuron
cd neuron
hg clone http://www.neuron.yale.edu/hg/neuron/iv
hg clone http://www.neuron.yale.edu/hg/neuron/nrn
Compile and install InterViews
cd iv
sh build.sh
./configure --prefix=`pwd`
make
make install
Compile and install NEURON
cd ../nrn
sh build.sh
./configure --prefix=`pwd` --with-iv=$HOME/neuron/iv --with-nrnpython=/usr/bin/python
make
make install
Install NEURON as a Python module
cd src/nrnpython/
sudo python setup.py install
(or python setup.py install --user if you want to install the Python package in your home folder).
Now you should be able to import neuron from Python console and run a small test with success;
cd $HOME
ipython
import neuron
neuron.test()
You might want to add the folder with NEURON executables to your PATH, so that you can easily compile NEURON mechanisms using nrnivmodl
export PATH=$PATH:$HOME/neuron/nrn/x86_64/bin
Most of the development work and testing of LFPy has been done on Max OS X 10.6.* Snow Leopard and 10.7.* Lion. Our preferred way of building Python has been through MacPorts; http://www.macports.org. Here is an step-by-step explanation on how to compile NEURON agains that installation of Python.
To start using MacPorts, follow the instructions on http://www.macports.org/install.php.
Building a python 2.7 environment using MacPorts issue in Terminal:
sudo port install python27 py27-ipython py27-numpy py27-matplotlib py27-scipy py27-cython
Make the installed Python and IPython default:
sudo port select --set python python27
sudo port select --set ipython ipython27
Install the necessary packages for cloning into repository and compiling NEURON:
sudo port install automake autoconf libtool libxext xorg-libXext ncurses mercurial bison flex
Install NEURON from the bleeding edge source code. The following recipe assumes a 64 bit build of NEURON and Python on OSX 10.7 Lion, so change “x86_64-apple-darwin10.7.0” throughout to facilitate your system accordingly;
#create a directory in home directory
cd $HOME
mkdir nrn64
cd nrn64
#creating directories
sudo mkdir /Applications/NEURON-7.2
sudo mkdir /Applications/NEURON-7.2/iv
sudo mkdir /Applications/NEURON-7.2/nrn
#Downloading bleeding edge source code
hg clone http://www.neuron.yale.edu/hg/neuron/iv
hg clone http://www.neuron.yale.edu/hg/neuron/nrn
cd iv
hg up
cd ../nrn
hg up
cd ..
#compiling and installing IV under folder /Applications/nrn7.2
cd iv
sh build.sh
./configure --prefix=/Applications/NEURON-7.2/iv \
--build=x86_64-apple-darwin10.7.0 --host=x86_64-apple-darwin10.7.0
make
sudo make install
#Building NEURON with InterViews, you may have to alter the path --with-nrnpython=/python-path
cd $HOME/nrn64/nrn
sh build.sh
./configure --prefix=/Applications/NEURON-7.2/nrn --with-iv=/Applications/NEURON-7.2/iv \
--with-x --x-includes=/usr/X11/include/ --x-libraries=/usr/X11/lib/ \
--with-nrnpython=/opt/local/Library/Frameworks/Python.framework/Versions/2.7/Resources/Python.app/Contents/MacOS/Python \
--host=x86_64-apple-darwin10.7.0 --build=x86_64-apple-darwin10.7.0
make
sudo make install
sudo make install after_install
#You should now have a working NEURON application under Applications. Small test;
#sudo /Applications/NEURON-7.2/nrn/x86_64/bin/neurondemo
#Final step is to install neuron as a python module
cd src/nrnpython
sudo python setup.py install
If you prefer to use Enthough Python distribution, see this forum post: https://www.neuron.yale.edu/phpBB/viewtopic.php?f=2&t=2191
We have not tested this, but there is probably some way or another to compile NEURON as a Python module on the Windows platform. If so, LFPy should work as well.