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A library of extended edit similarity measurement for high dimensional discrete-time series signal (e.g., multi-unit spike-train).
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Makefile Initial commit. This repo starts from the template that is provided a… May 28, 2018
requirements.txt remove hdbscan in the mean time Apr 14, 2019

PyPI MIT License Build Status

spykesim is a Python module that offers functions for measuring the similarity between two segmented multi-neuronal spiking activities.

Extended edit similarity measurement is implemented. You can find details in the following paper.

This library is re-implementation of the algorithm. The original implementation can be found in this repo.

Supported Operating Systems

This library tested on Ubuntu and MacOS.

For Windows users: Please consider to use Ubuntu via Windows Subsystem for Linux.


If you do not have Python3.6 on your environment, you may use Anaconda.

Cython and Numpy needs to be preinstalled as these will be used in the installation process.

If you have not installed these packages, run the following:

pip install numpy cython

You can install this library via pip as well:

pip install spykesim

or you may clone and build by yourself:

git clone
cd spykesim
python build_ext --inplace install


  • Python (>= 3.6)
  • Numpy(Needs to be preinstalled)
  • Cython(Needs to be preinstalled)
  • scipy
  • tqdm
  • h5py


You can find a tutorial in doc.


You can use the following bib entry to cite this work:

author = {Watanabe, Keita and Haga, Tatsuya and Tatsuno, Masami and Euston, David R and Fukai, Tomoki},
title = {{Unsupervised Detection of Cell-Assembly Sequences by Similarity-Based Clustering}},
journal = {Frontiers in Neuroinformatics},
year = {2019},
volume = {13},
month = may

This project uses the following repository as a template. The original LICENSE file can be found in here.

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