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README.md

README.md

[Re] Spike Synchronization and Rate Modulation Differentially Involved in Motor Cortical Function

Authors: Vahid Rostami, Junji Ito, Michael Denker, Sonja Grün

Corresponding author: Vahid Rostami, v.rostami@fz-juelich.de

A reference implementation of:

Spike synchronization and rate modulation differentially involved in motor cortical function. Alexa Riehle, Sonja Grün, Markus Diesmann, and Ad Aertsen (1997) Science 278:1950-1953. DOI:10.1126/science.278.5345.1950

In this paper we illustrate the successful reproduction of the results shown in Riehle et al (1997) using our new Python implementation of the Unitary Events (UE) method. Our implementation of the UE analysis is available in the unitary_event_analysis module of the the Electrophysiology Analysis Toolbox Elephant.

Dependencies

  • Elephant>=0.4.1
  • neo>=0.4.0
  • quantities>=0.9.0
  • numpy>=1.6.2
  • matplotlib>=1.5.1

Installation

On Ubuntu/Debian:

  • sudo apt-get install python-numpy python-matplotlib python-pip ipython
  • pip install quantities
  • pip install elephant

Run instructions

  • cd code
  • pip install -r requirements.txt
  • python Plotting_Figures.py

Structure of this repository

article

This folder contains the accompanying text in markdown/pdf/tex format and all the reproduced figures (used in our paper).

code

This folder contains all the plotting functions, and the functions for loading and converting (from gdf format to Neo) the data (provided in utils.py).

The source code of our UE implementation is pull requested and accepted after peer-review https://github.com/NeuralEnsemble/elephant/pull/64 in Elephant.

data

This folder contains the preprocessed versions of the spike train data used in the original publication (provided by Dr. Alexa Riehle, CNRS-AMU, Marseille).

notebook

An jupyter notebook is provided here to plot the figures (Figure 1, Figure 2 and Figure 5) of our paper.

how to use the jupyter notebook:

how to install the jupyter notebook:

  • pip install jupyter