To run the program, you need to have all the .m files in the same folder, after that simply run ISMB3D.m . The .ct files are the standard input for this code, but you can reshape any other files with the same information to be used here. The main functions are ISMB3D , ComputeP, and ComputeBStar. Minksum and p_poly_dist are also required.
With the name of input file, Plot_Analysis_Results function gives you the 3D or 2D plot of the final polytope, whichever is applicable.
Analysis code provides you with the statistics of the result. Using the output of main code and the original data files, it computes the distance and generates some helpful histograms. count_3Dpoly_sides computes the number of faces in the final polytope.