Antonio Profico1, Stefan Schlager2, Veronica Valoriani3, Costantino Buzi1, Marina Melchionna4, Alessio Veneziano5, Pasquale Raia4, Jacopo Moggi-Cecchi3, Giorgio Manzi1
1Dipartimento di Biologia Ambientale, Sapienza Universita di Roma, Rome, Italy 2Department of Biological Anthropology, University of Freiburg, Germany 3Dipartimento di Biologia, Università degli Studi di Firenze, Firenze, Italy
4Dipartimento di Scienze della Terra, dell’Ambiente e delle Risorse, Università di Napoli, Federico II, Naples, Italy 5School of Natural Sciences and Psychology, Faculty of Science, John Moores University, Liverpool L3 3AF, United
Kingdom
Author for Correspondence: Dr. Antonio Profico, Dipartimento di Biologia Ambientale, Sapienza Università di Roma, P.le Aldo Moro 5, 00185 Roma. Email: antonio.profico@uniroma1.it
Abstract
Objectives
We present two new automatic tools, developed under the R environment, to reproduce the internal and external structures of bony elements. The first method, Computer‐Aided Laser Scanner Emulator (CA‐LSE), provides the reconstruction of the external portions of a 3D mesh by simulating the action of a laser scanner. The second method, Automatic Segmentation Tool for 3D objects (AST‐3D), performs the digital reconstruction of anatomical cavities.
Materials and methods
We present the application of CA‐LSE and AST‐3D methods to different anatomical remains, highly variable in terms of shape, size and structure: a modern human skull, a malleus bone, and a Neanderthal deciduous tooth. Both methods are developed in the R environment and embedded in the packages “Arothron” and “Morpho,” where both the codes and the data are fully available.
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Results
The application of CA‐LSE and AST‐3D allows the isolation and manipulation of the internal and external components of the 3D virtual representation of complex bony elements. In particular, we present the output of the four case studies: a complete modern human endocast and the right maxillary sinus, the dental pulp of the Neanderthal tooth and the inner network of blood vessels of the malleus.
Discussion
Both methods demonstrated to be much faster, cheaper, and more accurate than other conventional approaches. The tools we presented are available as add‐ons in existing software within the R platform. Because of ease of application, and unrestrained availability of the methods proposed, these tools can be widely used by paleoanthropologists, paleontologists and anatomists.
1. Introduction
The use of 3D models is revolutionizing the study of the human fossil record, giving rise to the burgeoning field of “Virtual Anthropology” (Weber, 2001). In virtual anthropology applications, a fossil specimen is represented by a 3D object, commonly a surface mesh formed by a net of oriented triangular facets, which are individually defined by the coordinates of their vertices and by their mutual connections. The collection of vertices, coordinates, and connections defines the shape of the virtual surface in the computer language (Weber and Bookstein, 2011). Besides reduced handling of the fossil items, the advantages of using virtual objects over the original fossil specimens are the unrestrained availability, ease of magnification, and unlimited access to inner details. There arises the possibility of digitally “dissecting” the specimen in order to observe its internal structures, which often have significant diagnostic value and are hard to access, measure, and study otherwise.
The attention of paleoanthropologists to the inner cavities of the human skull is longstanding, tracing back at least to Taung child's natural endocast discovered in South Africa, and described by Raymond Dart (1925). In palaeoanthropology, the use of CT‐scans is now becoming very common, also given the ever‐increasing availability of web‐based repositories (e.g., Nespos, Digital Morphology
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Museum, KUPRI, MorphoSource). By using digital specimens, it is possible to reconstruct both inner cavities and outer surfaces, such as cranial endocasts and partially missing, broken or deformed vaults. The CT‐scan allows the application of such procedures to almost every specimen whose preservation is good enough to present quality details. Thanks to this technology, the number of studies dedicated to inner cavity sizes and shapes has increased in the last few years. Such studies include investigations on inner ear structure (Gunz and Mitteroecker, 2013), cranial nerve organization (Ibrahim et al., 2014), trabecular bone geometry (Chirchir et al., 2015; Ryan and Ketcham, 2002), and, of course, the volume and shape of brain endocasts (Beaudet and Bruner, 2017; Diniz‐Filho and Raia, 2017; Falk et al., 2005; Iurino et al., 2015).Similarly, biological symmetry and reference shapes (i.e., integral or better‐preserved specimens available for comparison) are becoming the focus of growing interest, for they can be used as a guide to reconstruct missing, deformed or broken portions, allowing the study of the original external anatomy of incomplete fossil material (Daura et al., 2017; Di Vincenzo et al., 2017; Gunz, Mitteroecker, Neubauer, Weber, & Bookstein, 2009; Gunz et al., 2012; Hublin et al., 2017; Profico, Di Vincenzo, Tafuri, & Manzi, 2016b; Spoor et al., 2015; Zollikofer et al., 2005).
The protocol usually applied to render three‐dimensional fossil remains using computer graphics demands manual segmentation of the CT‐scan data (Weber and Bookstein, 2011). Proceeding through sequential CT slices, the operator defines a mask of the inner cavities in each region of interest. Eventually, the operator performs a triangulation of the segmented slices, thus obtaining a 3D mesh. This procedure is time‐consuming and prone to generating topological artefacts (Profico et al., 2016c; Veneziano et al., 2018), due to the almost unavoidable inaccuracies in the manual processing (closure) of holes and gaps, such as foramina or missing portions (Huotilainen et al., 2014; Nicolielo et al., 2017). On the other hand, the isolation of the external surface could be useful to virtually restore incomplete/damaged specimens. In virtual reconstructions, reference models (e.g., well‐preserved specimens) are used to fill the gaps in a deficient specimen. These portions can be warped by Thin‐Plate‐ Spline (TPS) interpolation (Gunz et al., 2005) or aligned and merged via digital alignment (Profico et al., 2016a).