The file ‘AnalysisFigS2d.m’ is the program to make the figure files (‘ResultGrayMap_F1.png’, ‘ResultGrayMap_F2.png’ and ‘ResultGrayMap_F3.png’).  The corresponded data are contained in the '../../Fig3_A4/Fig3a/Simulations_3dim_VUW/R1_A_data*seq*’ (* is the index).  The five shown conditions (R1, (1), (2), (3) and (4)) are contained in the folder ‘R1_R1_A_data3seq1’, ‘(1)_R1_A_data13seq1’, ‘(2)_R1_A_data18seq1’, ‘(3)_R1_A_data11seq1’ and ‘(4)_R1_A_data15seq1’, respectively.