Electro-Physiology analysis

The purpose of this code is to analyze electro-physiology signals and identify features of biological significance.

Requirements

• MATLAB (tested with 2014b)
• MATLAB Curve Fitting

Installation

Dowload and unzip into directory of choice, then add that path to MATLAB.

For example, if you unzipped into C:\ep-analysis-matlab then:

>> addpath('C:\ep-analysis-matlab');

Running

Run AutomaticEPanalysis.m to analyze a single file. It will prompt for a tab-separated file (by default it expects a file with the .atf extension) containing timestamps in the first column and measurements for different sweeps in the remaining columns.

>> AutomaticEPanalysis

Run AutomaticEPanalysis_multipleFiles.m to analyze multiple files in a directory. All files are expected be .atf files.

>> AutomaticEPanalysis_multipleFiles

Outputs

The scripts generate an HTML report for each analyzed file. The report will be in the same directory if using the single-file version, or in the output directory if using the multiple-file version.

Structure

Here is a short summary of the relationship between the different files. See the Running section.

Both scripts write to the global variable infile and then call the publish function in MATLAB passing the name of the EPanalysis.m script. The global variable is the simplest way I am aware of to pass parameters to a script that will be published.

Acknowledgment and authorship

This code was developed by Thomas Pengo (U of Minnesota Informatics Institute, tpengo@umn.edu) for Prof. Susan Keirstead (U of Minnesota Stem Cell Institute).