Mask Smoothing Tests

Tom Goddard and Greg Pintilie
September 28, 2012

Look at the effects of smoothing the boundary of a masked volume. Each voxel outside the boundary is replaced by the average of its 6 nearest neighbors. That is repeated for a given number of iterations. To completely hide the staircase artifacts requires a boundary falloff layer half height thickness of 2 to 3 voxels.

Volume masked to sphere of radius 10, with border padding 2, grid size 100, constant density value 1, created with commands:

shape sphere
mask ones #0 border 2
Original sphere surface. Masked volume at contour level 1.

Volume appearance with different numbers of boundary smoothing iterations and contour level 0.5. At contour level 1 the appearance is the same as with no smoothing. The vop falloff command only modifies grid points having value 0.

vop falloff #1 iterations 20
0 10 20 50 100
Layer thickness (voxels):
0 0.7 1.2 2.0 3.0

Boundary layer images made by showing volume mesh superimposed with original sphere surface. and layer thickness judged by eye.

set projection orthographic
transp 80 #0
vol #2 level 0.5 style mesh region 0,0,49,99,99,51 showOutline true

Below is an image using the Segger implementation of this same type of mask boundary smoothing. It shows a masked monomer of GroEL EMDB map 1080 with 10 iterations of smoothing (left) and without any smoothing (right).