### Core Alignment Pipeline (Lin 2024)

Select specimen:

▪ Blue = Flaking scars | Pink = Longest scar | Red arrow = Plane normal | Gray plane = Best fitting plane

Compute unit direction vectors from scar endpoints.
The morphological plane normal (Norm_X/Y/Z) is measured
externally via Geomagic as the reference orientation.

Construct rotation matrix R₁ via Rodrigues' formula.
Rotate all coordinates so the morphological normal aligns with Z-axis.
The best-fit plane now lies on the XY plane.

Identify the longest scar and extract its rotated start-point.
Subtract its XY coordinates from all points to anchor the origin.
Preserves absolute spatial relationships between scars.