TABLE 1.
Summary of procedures
| Procedure | Purpose | Parameter | |
|---|---|---|---|
| Pixel processing | binary filtering | remove background noise while retaining salient structural features | *pixel intensity cutoff |
| pixel noise removal: area-based | remove holes and debris that are distinctly smaller than feature areas | *pixel area cutoff (20 pixels) | |
| pixel noise removal: rank-based | remove larger holes | *cluster rank order cutoff (three to four clusters) | |
| contiguous region extraction | remove irregular and narrow pixel protrusions and segment contiguous areas | *reference position (anywhere in the region to be extracted) *running window size (two to three pixels) |
|
| 2D BOC | assign beads and bonds smoothen BOC | generate BOC along structure boundaries reduce jagged outline | *bond length cutoff b0 (three to five pixels) number of beads used for local linear fit (four beads) |
| equalize bond length | evenly space beads within a BOC | none | |
| 3D mesh | assign z-bonds | connect beads between slices | b 0 |
| close mesh holes | add beads and z-bonds to reduce number and size of holes | none | |
| depress mesh protrusions | smoothen irregular regions missing z-bonds | number of slices to propagate (two slices) |
Distance-based 2D and 3D parameters are scaled based on the distance cutoff b0 for contour tracing. Typical values for parameters are in parentheses. Six parameters require manual adjustment between sets (marked by *). “None” indicates no user input value is needed.