# The following algorithm is conducted in ImageJ for the reconstruction stacks.
# Algorithm developed by and presented courtesy of Arttu Miettinen, Ph.D.

Straighten and crop
Save as _straight

Gaussian blur 3D r = 2
Save as _gauss
Otsu threshold from histogram of a slice without gold particle
Save as _bin

RegionRemoval 100000
Invert
RegionRemoval 1000
Invert
Save as _clean

Rotate stack top
Make z-projection of the stack
Select contact area, save selection as _intersection_area
Select area in stack, make inverse and fill with 255.
Rotate stack bottom
Save as _sides_filled

Create mask of contact area (using the saved selection)
Save as _contact_mask

Remove air from the top and the bottom of stack.
Invert
Save as _contact_volume

Blend together _straight and _contact_volume.
Check that contact volume is correct.
17
Save as _contact_volume_visualization.

Take _contact_volume
Rotate stack top
Divide by 255
Calculate sum projection
Save as _opening_thickness