Installation

spikeinterface is a Python package.

From PyPi

To install the current release version, you can use:

pip install spikeinterface[full]

The [full] option installs all the extra dependencies for all the different sub-modules.

Note that if using Z shell (zsh - the default shell on mac), you will need to use quotes (pip install "spikeinterface[full]").

To install all interactive widget backends, you can use:

pip install spikeinterface[full, widgets]

Note that the [widgets] option also installs jupyter (and relative dependencies).

If you wish to only install the core module, without optional dependencies, you can use:

pip install spikeinterface

From source

As spikeinterface is undergoing a heavy development phase, it is sometimes convenient to install from source to get latest bug fixes and improvements.

It is also recommended in that case to also install neo and probeinterface from source, as spikeinterface strongly relies on these packages to interface with various formats and handle probes.

git clone https://github.com/NeuralEnsemble/python-neo.git
cd python-neo
python setup.py install (or develop)
cd ..

git clone https://github.com/SpikeInterface/probeinterface.git
cd probeinterface
python setup.py install (or develop)
cd ..

git clone https://github.com/SpikeInterface/spikeinterface.git
cd spikeinterface
python setup.py install (or develop)
cd ..

For beginners

We provide here some installation tips for beginners in Python here:

https://github.com/SpikeInterface/spikeinterface/tree/master/installation_tips

Requirements

spikeinterface.core itself has only a few dependencies:

• numpy

• neo>=0.9.0

• joblib

• probeinterface

• tqdm

Sub-modules have more dependencies, so you should also install:

• scipy

• h5py

• pandas

• sklearn

• matplotlib

• networkx

• datalad

• MEArec

All sorters must installed independently.