Spike sorters installation

Installing the spike sorters used by SpikeToolkit

Here is quick introduction and installation guide for the available spike sorters

Klusta is a Python package and it can be installed with pip:

pip install numpy scipy h5py six cython tqdm click
pip install klusta klustakwik2

Mountainsort4 is a Python package and can be installed with pip

pip install ml_ms4alg

note: Mountainsort4 at the moment can only be installed on UNIX systems

Herding spikes 2 is a Python package and can be installed with pip

pip install herdingspikes

Tridesclous is a Python package and can be installed with pip

pip install tridesclous

SpyKING-CIRCUS is a Python package and can be installed with pip

pip install spyking-circus --no-binary=mpi4py

note: SpyKING-CIRCUS requires an MPI installation. On UNIX machines you can install MPICH:

sudo apt-get install mpich libmpich-dev

On Windows machines you can install the Windows MPI

Kilosort is a MATLAB package and can be installed as follows:

git clone https://github.com/cortex-lab/KiloSort.git
git clone https://github.com/kwikteam/npy-matlab.git

Set the KILOSORT_PATH and NPY_MATLAB_PATH environment path in your .bashrc (UNIX) or in the system variables (Windows)

export KILOSORT_PATH="path-to-kilosort-repo"
export NPY_MATLAB_PATH="path-to-npy-matlab-repo"

Kilosort2 is a MATLAB package and can be installed as follows:

git clone https://github.com/MouseLand/Kilosort2.git
git clone https://github.com/kwikteam/npy-matlab.git

Set the KILOSORT2_PATH and NPY_MATLAB_PATH environment path in your .bashrc (UNIX) or in the system variables (Windows)

export KILOSORT2_PATH="path-to-kilosort2-repo"
export NPY_MATLAB_PATH="path-to-npy-matlab-repo"

IronClust is a MATLAB package and can be installed as follows:

git clone https://github.com/jamesjun/ironclust.git

Set the IRONCLUST_PATH environment path in your .bashrc (UNIX) or in the system variables (Windows)

export IRONCLUST_PATH="path-to-ironclust-repo"