Configuration

Reference Mark Options

The behaviour of reference mark generation can be tuned via the following configuration options or the equivalent CLI arguments:

• tolerance – distance used when matching an existing mark.
• min_distance – minimum distance a mark must maintain from contours and other marks.
• available_shapes – list of shapes that will be cycled through when creating new marks.
• angle – default orientation angle for generated marks in degrees.
• color – outline color used when drawing marks.

These correspond to the CLI flags --mark-tolerance, --mark-min-distance, --available-shapes, --mark-angle and --mark-color respectively.

Workflow

1. Candidate points are sampled within each contour and ranked using the stability metric implemented in ReferenceMarkCalculator.
2. Marks inherited from neighbouring slices keep their original shape so layers remain easy to align.
3. Newly created marks cycle through available_shapes and are filtered by ReferenceMarkAdjuster to ensure a minimum distance from contours and other marks.

By adjusting tolerance and min_distance you can control how closely marks match between slices and how near they may appear to each other.