OT-2 image analysis is where I put together the template that exists within full data set. This folder is also what I used to practice with any functions I didn't understand. Some of the folders are just attempts to analyze a full video. 

again - attempt to analyze full video

benchMarking - this directory contains all of the bench marking photos, scripts, and goniometer files

csvPractice - figure out how to incorporate csv into our code and use a master csv

graphics - I made images for my graphical abstract and presentation and such

newBackground - a directory containing images of the normalized new paper background and scripts to detect contours

retry - attempt to analyze full video

scripts - the home of my original scripts. If the template or complete Processing module is not making sense it may be helpful to visit this folder. new5.py, chopVideo.py and binaryreference.py all contributed to the full module

Set2 - attempt to analyze full video\

shapeMatch - this directories original use was to find and save a reference contour to compare contours in our images to. Also the original home of the processing module and its first incorporation into the scripts is in trial1. trial2 is essentially trial1 without the processing module imported