Within-cycle instantaneous frequency profiles report oscillatory waveform dynamics.

This repository contains the scripts to run the simulations and analysis from:

Quinn, A. J., Lopes-dos-Santos, V., Huang, N., Liang, W.-K., Juan, C., Yeh, J.-R., Nobre, A. C., Dupret, D., & Woolrich, M. W. (2021). Within-cycle instantaneous frequency profiles report oscillatory waveform dynamics. Journal of Neurophysiology. https://doi.org/10.1152/jn.00201.2021

and the preprint:

Quinn, A. J., Lopes-dos-Santos, V., Huang, N., Liang, W.-K., Juan, C.-H., Yeh, J.-R., Nobre, A. C., Dupret, D., & Woolrich, M. W. (2021). Within-cycle instantaneous frequency profiles report oscillatory waveform dynamics. Cold Spring Harbor Laboratory. https://doi.org/10.1101/2021.04.12.439547

Requirements

The LFP data used in this analysis can be freely downloaded from the MRC BNDU data portal (requires free registration).

The original analysis used Python 3.7.6 but should run ok in more recent versions. The package requirements to exactly reproduce the the original analysis are detailed in the requirements.txt file in the repository. These can be installed using pip:

pip install -r requirements.txt

or by creating a specific anaconda environment:

conda create --name emd_waveform --python 3.7.6 --file requirements.txt

Getting started

Once you have downloaded the data and have a Python environment with the required dependencies installed, you can begin the analyses.

1. Open emd_waveform_utils.py and specify the filepaths at the top. basedir must be specified but the rest are optional - see the script for more details.
2. Ensure that the right python environment is active.
3. Run emd_waveform_0_analysis.py. This will run the EMD analysis on the six datafiles and save the output in the analysisdir specifed in emd_waveform_utils.py
4. Work through the emd_waveform_fig*py scripts in any order. Each script reproduces one or more of the figures in the paper.