A total of 45 well-preserved humeri from three different populations (G1, G2, and G3) were used for this study, to insure coverage of multiple time periods and geographical locations. Thirty-one humeri were scanned via computed tomography (CT) and 14 humeri were three-dimensional surface scanned. The main difference between the CT and 3D surface scan data was that the 3D surface data does not include the internal structures of the objects which were scanned .
Ten known pairs of humeri (G1) originated from the Ballumbie and St. Andrews medieval Scottish collections (fifteenth to seventeenth century) held by the University of Edinburgh [21, 22]. Eleven humeri (G2), including four pairs and three individual humeri, originated from the archaeological Ibizan cathedral collection (thirteenth to early nineteenth century) in Spain, held by the Ibizan city hall . Seven known pairs of humeri (G3) originated from the Frassetto Collection (Collezione Frassetto) in Italy, a modern collection held by the Anthropology Museum at the University of Bologna. All of these individuals originated from Sassai (Sardinia), died in the first decade of the twentieth century, and were donated to the collection. For a full list of specimens, see Table 1.
CT scans of G1 were taken at the Clinical Research Imaging Centre, University of Edinburgh, using a Toshiba Aquilion ONE 320 Detector Row Computed Tomography system, a multidetector CT scanning system. Data were collected using a slice thickness of 0.5 mm and a matrix of 512 × 512 pixels. CT scans of G2 were taken at the Can Misses Hospital, Ibiza, using a GE Medical System HiSpeed NX/I Computed Tomography Scanner. Data were collected using a slice thickness of 1.5 mm and a matrix of 512 × 512 pixels. All data were saved as a Digital Imaging and Communications in Medicine (DICOM) format.
Three-dimensional surface scans of the humeri in G3 were made using a two camera system, each 1.9 megapixels, with a ScanProbe Standard structured light scanner at the University of Bologna. After the initial data acquisition and aligning phases, the point cloud models were input into XOR2 software to generate the final models and saved as stereolithography (.stl) files.
All scan data were randomized before the pair-matching process was tested to minimize bias.
After randomization, the 31 humeri of G1 and G2 were segmented using AMIRA 5.3.3 to create three-dimensional models using a slightly modified version of Spoor et al.’s Half Maximum Height Value (Online Resource 1) . The 14 humeri from G3 were already three-dimensional surface models and therefore did not need to be segmented. All of the three-dimensional models were then converted from their stereolithography [.stl] format to wavefront [.obj] files.
Mesh-to-mesh value comparison method — manual
The manual MVC method utilized LMI Technologies’ Flexscan 3D to compare all the humeri. The protocol for comparison is as follows:
All right humeri were mirror-imaged using the free software NetFabb basic. All mirror-imaged humeri were then loaded into the Flexscan3D software. One left humerus at a time was then also loaded into the software for comparison against all of the mirrored humeri. All 22 left humeri were subsequently compared to all 23 mirrored-right humeri. To compare any two humeri, both scans were roughly lined up on top of each other using the mouse. Then, the “fine alignment” feature was used in order to obtain a mesh-to-mesh value, which was recorded for comparison (see Fig. 1 for an example).
The mesh-to-mesh values were used as a proxy for pair-matching, where the lowest agreed-upon value indicated the best match. The side of the humeri was initially used to narrow down these values, as a left humerus could not be pair-matched with another left humerus. For the actual test of pair-matching, the three lowest mesh-to-mesh values of each humerus were cross-compared and values were only considered as true matches if both the left and right sides agreed. This was done in order to avoid confusion, for example, if Left Humerus A indicated that it matched best with Right Humerus B, but Right Humerus B indicated that it matched best with Left Humerus C. The standard deviations of mesh-to-mesh values from true pair-matches were calculated to inform a possible cutoff threshold for positive pair matches. In total, comparing all of the humeri to obtain mesh-to-mesh values and recording said values took approximately 45 user-active hours.
Mesh-to-mesh value comparison method — automated
The automated MVC method utilized Viewbox 4 for comparison. The following settings were used, comparing all meshes to each other from a single folder. The estimated overlap for the scans was 100 %, while the initial position for rough alignment was set at 20. The rough alignment used the nearest neighbor search “Approximate (fast)” with a point sampling of 1 %. It matched point to point, with one hundred iterations. The fine alignment used the nearest neighbor search “Exact with normal compatibility” with a point sampling of 100 %. It matched point to plane, with one hundred iterations. The program then automatically generated an Excel spreadsheet of all of the mesh-to-mesh values for analysis. It should be noted that as this program cannot yet handle comparing 3D surface scans to full CT scan data, the 31 CT scan models were internally hollowed before comparison.
Again, the mesh-to-mesh values were used as a proxy for pair-matching, where the lowest agreed-upon value indicated the best match. The side of the humeri was initially used to narrow down these values. For the actual test of pair-matching, the three lowest mesh-to-mesh values of each humerus were cross-compared, and values were only considered as true matches if both the left and right sides agreed. The standard deviations of mesh-to-mesh values from true pair-matches were calculated to inform a possible cutoff threshold for positive pair matches. The process took approximately five minutes to set up and then approximately 45 hours to run. Only the first five minutes of set up required any activity from the user.
Comparison of the methods
To compare the efficacy of the two MVC methods, specificity and sensitivity were calculated using Microsoft Excel 2007 . For this study, the gold standard method for comparison was the known humeri pairs. In other words, the main question for assessment was: is this pair of humeri a correct match?
Three previous, high quality studies on visual pair-matching, osteometric comparison, and geometric morphometric pair-matching were also analyzed using sensitivity and specificity in order to directly compare the results of the two MVC methods.