Spike and Spike-Field Analysis for Rat EE/Stroke Data

Las edited by Zachary Ip (ip.zachary.t@gmail.com) 3/7/23.

This repository is expected to be used in conjunction with spectral-analysis-tools, and utils-toolbox. Code will not run without those repositories on path. This repository was developed in MATLAB, and requires a license with Signal processing toolbox among others. This code was developed to process a dataset collected by Jialing Liu (Jialing.liu@ucsf.edu). Data was collected using 16-site and occasionally 32-site linear depth electrodes bilaterally in rats after distal middle cerebral artery stroke (dMCAO) in the ipsilesional (left) hemisphere.

Code was developed independently by by Zachary Ip (ip.zachary.t@gmail.com) and Ilse Dippenaar (ilsedipp@uw.edu). There is some overlap in analysis done, but the most up to date code was performed by Ilse.

For Zach's code:

Code is run from the main script Analysis_Data_Loader, which saves outputs to file in /Documents\MATLAB\output\Spike Sorting Scripts/. From there, Analysis_Statistics takes over and runs statistical comparisons between groups. Subfunctions are called for both scripts using the naming scheme calculate_variable.

For Ilse's code:

1. Create an untracked config.m file in the root directory of the project which defines the following variables: root_dir, cache_dir, and plot_dir. root_dir should be the location of the Z drive, so on the lab Windows computers, it should be "Z:". cache_dir will be where data copies from the file server are stored for faster access, and so it should be local to the computer and user-specific. plot_dir is where plots are saved. Finally, this file should add Fieldtrip to the Matlab path if it isn't already. An example file might look like this:

   root_dir = "Z:";
   cache_dir = "~/Documents/cache/Stroke-Spike-Analysis";
   plot_dir = "~/Documents/plots/Stroke-Spike-Analysis";
   addpath(fullfile(matlabroot, 'toolbox/fieldtrip'));

2. Run the init script
3. Run the data caching function, cacheData as cacheData(data_dir, cache_dir) (only necessary to do this once).
4. You should be able to run any notebook in the notebooks directory now.