Installation

Neo is a pure Python package, so it should be easy to get it running on any system.

Dependencies

For Debian/Ubuntu, you can install these using:

$ apt-get install python-numpy python-pip
$ pip install quantities

You may need to run these as root. For other operating systems, you can download installers from the links above, or use a scientific Python distribution such as Anaconda.

Certain IO modules have additional dependencies. If these are not satisfied, Neo will still install but the IO module that uses them will fail on loading:

  • scipy >= 0.12.0 for NeoMatlabIO
  • h5py >= 2.5 for Hdf5IO, KwikIO
  • igor >= 0.2 for IgorIO
  • nixio >= 1.2 for NixIO
  • stfio for StimfitIO

Installing from the Python Package Index

Warning

alpha and beta releases cannot be installed from PyPI.

If you have pip installed:

$ pip install https://github.com/NeuralEnsemble/python-neo/archive/neo-0.5.0alpha1.zip

This will automatically download and install the latest release (again you may need to have administrator privileges on the machine you are installing on).

To download and install manually, download:

Then:

$ unzip neo-0.5.0alpha1.zip
$ cd neo-0.5.0alpha1
$ python setup.py install

or:

$ python3 setup.py install

depending on which version of Python you are using.

Installing from source

To install the latest version of Neo from the Git repository:

$ git clone git://github.com/NeuralEnsemble/python-neo.git
$ cd python-neo
$ python setup.py install

Python 3 support

neo.core is fully compatible with Python 3, but only some of the IO modules support it, as shown in the table below:

Module Python 2 Python 3
AlphaOmegaIO Yes No
AsciiSignalIO Yes Yes
AsciiSpikeTrainIO Yes Yes
AxonIO Yes Yes
BlackrockIO Yes No
BrainwareDamIO Yes Yes
BrainwareF32IO Yes Yes
BrainwareSrcIO Yes Yes
ElanIO Yes No
IgorIO Yes Yes
NeoHdf5IO Yes Yes
KlustakwikIO Yes No
KwikIO Yes Yes
MicromedIO Yes No
NeoMatlabIO Yes Yes
NeuroExplorerIO Yes No
NeuroscopeIO Yes Yes
NixIO Yes Yes
PickleIO Yes Yes
PlexonIO Yes No
PyNNIO Yes Yes
RawBinarySignalIO Yes Yes
Spike2IO Yes Yes
TdtIO Yes No
WinEdrIO Yes Yes
WinWcpIO Yes Yes