The programs included in this folder are helpful for understanding the outputs at each step. They are primarily ways of viewing the matched model data atop the real image data. bc_new_residual_plot and bc_sk_plot_model can be used during the orientation-finding, bc_sk_find_frame_colors can be run using the final file from the orientation-finding, and bc_degenerateorientations_plots produces figures with all of the equivalent orientations for each of the four particle types.
bc_new_residual_plot, bc_sk_plot_model, and bc_sk_find_frame_colors all tend to work best using MATLAB 2012 instead of MATLAB 2015.