1. Run obstruction_detection.m 
   Intermediate results will be displayed as figures and final results will be written to the output folder.

2. Run median_filter.m
   Note that this script is fairly slow. There is a progress counter that prints to the matlab console to indicate how much processing is left, and results from one run have already been saved into the output folder.
   
3. Run stack_propagation.m
   This algorithm wasn't used in the final pipeline but I've included discussion and images from it in the paper, so if you would like to see the results from this attempt, run this script. 