Supplementary dataset for AutoScan3D: Photogrammetric workflow, 3D cranial models, landmark configurations, and reproducibility analyses for geometric morphometrics

This dataset provides the complete supplementary materials associated with the study “A low-cost automated photogrammetric system (AutoScan3D) for 3D human cranial digitization: metric accuracy, landmark repeatability and geometric morphometric shape-space fidelity.” Current limitations in low-cost photogrammetric systems include insufficient transparency regarding data processing workflows, limited access to raw and processed three-dimensional models, and a lack of standardized resources for evaluating landmark repeatability and morphometric fidelity. To address this gap, the present dataset ensures full reproducibility of the digitization and analysis pipeline implemented for cranial geometric morphometrics. The dataset includes: (i) A detailed photogrammetric workflow implemented in Agisoft Metashape, covering image acquisition, alignment, dense point cloud generation, mesh construction, and texture mapping; ii) One folder for each skull (25 in total), each containing the Agisoft Metashape project file (.psx), a high-resolution three-dimensional cranial model (.obj) together with its associated material file (.mtl) and texture image (.jpg), a dense point cloud (.laz), a confidence-colored dense point cloud (.ply), and the project support files required by Metashape. (iii) A curated set of anatomical cranial landmarks, including identifiers, three-dimensional coordinates, and standardized anatomical definitions based on homology criteria;(iv) landmark coordinate files exported in .fcsv format from 3D Slicer (ALPACA module), structured for direct use in geometric morphometric pipelines; (v) R scripts developed for data processing and statistical analysis, including inter-landmark distance matrix generation, Bland–Altman analysis, coefficient of variation, intraclass correlation coefficient (ICC), and graphical outputs; (vi) Quantitative repeatability analyses, providing precision error metrics (SD, CV), ICC values, and 95% confidence intervals for assessing the reliability and stability of the digitization process; (vii) Confidence-coloured dense point cloud images (.jpg). This appendix contains 150 high-resolution JPEG images showing the dense point clouds colour-coded by point confidence as generated in Agisoft Metashape. Images are organized by skull number and viewing perspective, with six standardized views per skull: frontal (F), inferior (I), left (L), posterior (P), right (R), and superior (S). Thus, filenames such as 1F, 1I, 1L, 1P, 1R, and 1S correspond to the six perspectives of skull 1, and the same naming convention is used for all 25 skulls; (viii) Linear distance measurements (Excel file). This appendix contains an Excel spreadsheet with linear measurements (in millimetres) between the cranial landmarks Nasion and Prosthion for 25 skulls. Each value corresponds to the mean of three independent measurements obtained using a digital sliding caliper. These measurements were used as reference distances to apply scale calibration to the 3D models in Agisoft Metashape, ensuring metric consistency across all reconstructed specimens.