You can try this step by step, it handles everything from extracting contours to displaying the aligned regions. // Extract contours from both the source and reference regions get_region_contour(RegionSource, RowSource, ColumnSource); get_region_contour(RegionReference, RowReference, ColumnReference); // Create a shape model from the reference region s contour gen_contour_polygon_xld(ContourReference, RowReference, ColumnReference); create_shape_model_xld(ContourReference, auto , rad(-360), rad(360), auto , auto , ignore_global_polarity , 5, auto , ShapeModelID); // Match the model to the source region to find necessary transformations find_shape_model(ContourSource, ShapeModelID, rad(-360), rad(360), 0.5, 1, 0.5, least_squares , 0, 0.9, RowCheck, ColumnCheck, Angle, Scale, Score); // Generate a transformation matrix using the match results vector_angle_to_rigid(RowReference, ColumnReference, 0, RowCheck, ColumnCheck, Angle, HomMat2D); // Apply the transformation to fit the source region into the reference region affine_trans_region(RegionSource, RegionTrans, HomMat2D, nearest_neighbor ); // Display both regions for visual verification of alignment disp_obj(RegionReference, WindowHandle); set_colored(WindowHandle, 12); disp_obj(RegionTrans, WindowHandle);