To align specimens and to provide a reference frame for morphologic measures, an anatomic coordinate system was defined. To increase applicability of the coordinate system definition to those with upper extremity amputation or trauma, only proximal humeral landmarks were employed in coordinate system calculation (Fig. 1A). The definition used here was adapted from the humeral coordinate system proposed by DeLude et al. (2007). The origin was established at the center of the humeral head using a sphere fit based on the convex articulating surface. The articulating surface was selected based on 1st principal curvature (PostView, www.febio.org) (Fig. 1B). Next the articulating margin plane (AMP) was established by further refining the selection of the convex region to isolate nodes at the transition from convex to concave at the anatomic neck and creating a best‐fit plane (Fig. 1C). The normal vector to this AMP was the first vector needed for coordinate system generation. The second vector was a humeral shaft axis (HSA) calculated by fitting a line to the centroids of the medullary segmentation from mid‐shaft (median slice) to one humeral head diameter below the origin (Fig. 1C). This range was selected to prevent lateral drift of the HSA due to the proximal metaphyseal flare. Using the AMP normal vector and HSA, the coordinate system was defined as follows (Figs. 1D,E):

Origin: Coincident with the center of the sphere fit to the articulating surface of the humeral head.

Z‐axis: HSA, defined as a best‐fit line through the centroid of the medullary canal from mid‐shaft to one humeral head diameter below the origin.

X‐axis: Cross‐product of AMP normal vector and Z. Positive in anterior direction.

Y‐axis: Cross‐product of Z and X. Positive in medial direction.

Surface reconstructions of left humeri were mirrored prior to coordinate system generation to avoid the use of right‐ and left‐handed coordinate systems.