# <img src=”docs/spykesim_logo/wtext/spykesim_wtext.svg” width=”320px”> [](https://pypi.org/project/spykesim/) [](LICENSE) [](https://travis-ci.org/KeitaW/spykesim)
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.
https://www.frontiersin.org/articles/10.3389/fninf.2019.00039
This library is re-implementation of the algorithm. The original implementation can be found in [this repo](https://github.com/KeitaW/Chaldea).
# Supported Operating Systems This library tested on Ubuntu and MacOS.
For Windows users: Please consider to use Ubuntu via [Windows Subsystem for Linux](https://docs.microsoft.com/en-us/windows/wsl/install-win10).
# Installation If you do not have Python3.7 on your environment, you may use [Anaconda](https://www.anaconda.com/distribution/).
[Cython](https://github.com/cython/cython) and [Numpy](https://github.com/numpy/numpy) needs to be preinstalled as these will be used in the installation process.
If you have not installed these packages, run the following: `bash pip install numpy cython ` You can install this library via pip as well: `bash pip install spykesim ` or you may clone and build by yourself: `bash git clone https://github.com/KeitaW/spykesim.git cd spykesim python setup.py build_ext --inplace install `
## Dependencies
Python (>= 3.7)
Numpy(Needs to be preinstalled)
Cython(Needs to be preinstalled)
scipy
tqdm
h5py
# Tutorial You can find a tutorial in [doc](https://github.com/KeitaW/spykesim/blob/master/docs/tutorial.ipynb).
# Citation You can use the following bib entry to cite this work: ` @article{Watanabe:2019eq, 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.
https://github.com/kennethreitz/samplemod The original LICENSE file can be found in [here](misc/original_license.md).
1 maintainer
Release files for spykesim 1.2.4
For a detailed explanation of source distributions (sdists) and built distributions (wheels), please see the package formats documentation.
Source distribution (sdist)
| File | Size | Uploaded | |
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| spykesim-1.2.4.tar.gz | 16.5 kB | Details |
Release files / spykesim-1.2.4.tar.gz
| Download URL | spykesim-1.2.4.tar.gz |
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| Size | 16.5 kB |
| Tags | Source |
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