1,721,274 research outputs found
Arothron: an R package for virtual anthropology to build endocast and to perform digital reconstruction
No full textArothron is an R package [1] containing brand new tools for geometric morphometric analysis. The package comes with examples
pertaining to the field of virtual anthropology, yet it is addressed to the entire audience of geometric morphometricians. The functions
embedded in the package allow aligning disarticulated parts belonging to a single specimen (i.e. broken skull fragments), to
build internal cavities such as endocasts, and to reproduce and analyse the shapes of three-dimensional objects. Arothron functions
import and export landmark coordinates and 3D paths into ’landmarkAscii’ and ’am’ format files. The Digital Tool for Alignment
(DTA) is a landmark-based methodology which allows aligning two or more portions of a 3D mesh (i.e. a disarticulated model,
DM) by using a reference sample or model (RM) for comparison. To run DTA, a set of anatomical landmarks is defined on two
separated portions of the DM. Each point of the landmark sets is moved to the nearest vertex of the triangles. This way, each landmark
is identified by a number corresponding to a row of the vertex matrix of the mesh and its position is tracked on the 3D models
moved in the Cartesian coordinate system.The second step is the alignment via Generalized Procrustes Analysis (GPA) of each part
of the DM on each RM of the comparative sample, where the same landmark configuration as with the DM has been previously
defined. The items of the reference sample are previously scaled to the mean of the single scale factors calculated for each half of
the DM, separately, and symmetrized via reflection and relabelling, thereby producing a perfectly symmetrical, bilateral, and scaled
landmark configurations (to avoid alignment error as introduced by asymmetry). The last step consists in the quantification of the
morphological (Euclidean) distances between each part of the DM and the corresponding landmark configurations on each item in
the RM set. Computer-Aided Laser Scanner Emulator (CA-LSE) and Automatic Segmentation Tool for 3D objects (AST-3D) are
two new tools designed for the reconstruction of virtual cavities and external shapes [2]. CA-LSE provides the reconstruction of the
external portions of a 3D mesh by simulating the action of a laser scanner. AST-3D performs the digital reconstruction of anatomical
cavities as endocasts. Both tools use the definition of points of views that can be placed externally to the object (CA-LSE) or
inside the object (AST-3D). By applying these tools is possible in few minutes to build virtual cavities as endocast, maxillary sinuses
and trabecular bone. In the Arothron R package, we supplied three examples of reconstructing: the dental pulp cavity within a deciduous
Neanderthal tooth, the network of blood vessels within a human malleus bone, and an endocast of a human skull.The tools
could be used in virtual anthropology application.The digital alignment tool is efficient in find ideal alignments of broken pieces. It
could be applied as the first step in virtual reconstruction on human fossil specimens that often consist of a disarticulated fragments
such as BOU-VP12/130 (Australopithecus garhi), AL-442 (Australopithecus afarensis), OH5 (Paranthropus boisei), ATD6-15 and
ATD6-69 (Homo antecessor), Amud 1 (Homo neanderthalensis), Le Moustier 1 (Homo neanderthalensis). The easily and quickly
use of the Arothron R package to build virtual cavities may provide a new means largely applicable in virtual Anthropology.
References:[1] Profico A., Veneziano A., Melchionna M., Piras P. & Raia P., 2018. Arothron: Geometric Morphometrics Analyses. R package version 1.0.1, developer version available at
https://github/Arothron DOI:10.5281/zenodo.1218712.[2] Profico A., Schlager S., Valoriani V., Buzi C., Melchionna M., Veneziano A., Raia P., MoggifiCecchi J. & Manzi G., 2018. Reproducing the
internal and external anatomy of fossil bones: Two new automatic digital tools. American Journal of Physical Anthropology
Old and new methods in geometric morphometrics applied to the study of human evolution: case studies
No full textThe main aim of this thesis is the application of Geometric Morphometric methods on different case-studies for the study of human evolution. When combined with techniques of acquisition of 3D models, Geometric Morphometrics allows us: - to investigate different experimental designs;
- to analyse the interaction of several aspects on morphological adaptations detected within taxon-specific studies (e.g., allometry, phylogenetic signal, functional factors);
- to study fragmentary fossils and incomplete specimens, through estimation of missing data and 3D virtual restoration (e.g., surface and curve slid semilandmark);
- to plan, code and test new algorithms and/or methodological approaches.
The first part deals with the use of smoothing filters applied to 3D model for Geometric Morphometric studies. These algorithms are used to remove the background noise deriving from digital acquisition (e.g., photogrammetry, laser scan and computerized tomography scan). The effects of the different smoothing filters have been assessed. In particular have been defined guidelines for a correct use of these algorithms, besides the developing of an automatized tool, in R environment, to find the best combination between algorithm type, settings and number of iterations.
The second part consists of a protocol developed, with the collaboration of the University of Freiburg, for the digital retrodeformation of fossil specimens showing evidence of shearing, bending and compressing alterations due to taphonomic processes. Traditional methods of retrodeformation only use a sparse set of bilateral landmarks; the number of points appears to affects the success of retrodeformation. On the contrary, this method uses, in addition to the landmark configurations, the curve and surface semilandmarks, which allow us to capture
morphological information more accurately. This protocol was applied here to the neanderthalian cranium of Saccopastore 1.
The third part reports the results of the first analysis on the specimen nicknamed "Pàus” (St.n.166623), recently discovered near Spinadesco in the Po Valley (Northern Italy). A set of 100 semilandmarks was built on the specimen and slid, using a set of 6 landmark, on a comparative sample including specimens dated to the Middle-to-Late Pleistocene. The results show how the morphology of “Pàus” is consistent with the variability observed in the Neanderthal lineage.
The fourth part concerns a Geometric Morphometric investigation performed on two human cranial fossil remains from Melka Kunture, dated to about 850 ka. The two cranial fragments consist in a partial left parietal (MK73/GOM II- 6769; formally Melka Kunture 1, or MK1) and a right portion of the frontal bone (MK76/GOM II - 576, or MK2). Specifically, evenly-spaced semilandmark sets were used acquired along the sagittal suture and the inferior temporal line on MK1 and MK2 respectively. The results of the analyses, in agreement with the chronology of the fossils, represent at present, evidence of one of the best candidates to be the most ancient example of H. heidelbergensis.
The fifth part treats with the external morphology of the cranial base in extant and living Hominoids in relation to ontogenetic, allometric, locomotor and phylogenetic factors. The sample selected consists of 3D landmark configurations acquired on specimens (male and female) including infant, sub-adult and adult individuals. The centroid size of the landmark set configuration was used as indicator of size while the pattern of dental eruption (at death) was used to define six age groups. The relation between morphology and locomotion was explored through the estimation of the position of the foramen magnum along the Frankfurt plane.
Finally, a phylogenetic tree was build using molecular and paleontological data, with the phylogenetic signal investigated through centroid size and shape
Three-dimensional visualisation of skeletal cavities
No full textBones contain spaces within them. The extraction and the analysis of those cavities are crucial in the study of bone tissue function and can inform about pathologies or past traumatic events. The use of medical imaging techniques allows a non-invasive visualisation of skeletal cavities opening a new frontier in medical inspection and diagnosis. Here, we report the application of a new mesh-based approach for the isolation of skeletal cavities of different size and geometrical structure. We apply a mesh-based approach to extract (i) the main virtual cavities inside the human skull, (ii) a complete human endocast, (iii) the inner vas-culature of the malleus bone and (iv) the medullary of a human femur. The detailed description of the mesh-based isolation method and its pioneristic application to four different case-studies show the potential of this approach in medical visualisation
Arothron: R Functions for Geometric Morphometrics Analyses
No full text<p>Tools for Geometric Morphometrics</p>
Arothron: R Functions for Geometric Morphometrics Analyses
No full text<p>Tools for Geometric Morphometrics</p>
Maxillary sinus growth and development in Neanderthals and H. sapiens
No full textWe investigate and compare facial and maxillary sinus ontogeny among Neanderthals and H. sapiens to understand the extent of any differences and to investigate if these might arise through differences in developmental interactions. 3D facial and sinus landmarks were acquired from virtual reconstructions of H. sapiens and Neanderthals (H. sapiens N=60, Neanderthals=5). Geometric morphometric analyses compared ontogenetic trajectories of size and shape as well as patterns of covariation among the maxillary sinuses, facial skeleton and its sub-regions. Our results show that facial ontogeny diverges and that maxillary sinuses develop divergently among Neanderthals and modern humans. In both, maxillary sinus, facial and maxillary form are strongly associated. Further, PLS analyses indicate that the ontogeny of maxillary sinus form is strongly associated with that of several facial regions in infancy but becomes most closely associated with the form of the maxilla and nasal cavity in older individuals. In part, this is because the great changes in size that occur in the first few years of life dominate the analyses. However when shape alone is considered a similar shift in patterns of association is observed, albeit with lower correlations indicating that ontogenetic size changes alone do not explain the observed interactions. These findings suggest that despite differences in facial form and ontogenetic trajectories between modern humans and Neanderthals, their maxillary sinuses develop similarly, showing similar patterns of interaction with other facial components, but attaining larger sizes, consistent with the greater space available or expansion provided by the larger maxilla of Neanderthals
A Comparison of Semilandmarking Approaches in the Analysis of Size and Shape
No full textOften, few landmarks can be reliably identified in analyses of form variation and covariation. Thus, ‘semilandmarking’ algorithms have increasingly been applied to surfaces and curves. However, the locations of semilandmarks depend on the investigator’s choice of algorithm and their density. In consequence, to the extent that different semilandmarking approaches and densities result in different locations of semilandmarks, they can be expected to yield different results concerning patterns of variation and co-variation. The extent of such differences due to methodology is, as yet, unclear and often ignored. In this study, the performance of three landmark-driven semilandmarking approaches is assessed, using two different surface mesh datasets (ape crania and human heads) with different degrees of variation and complexity, by comparing the results of morphometric analyses. These approaches produce different semilandmark locations, which, in turn, lead to differences in statistical results, although the non-rigid semilandmarking approaches are consistent. Morphometric analyses using semilandmarks must be interpreted with due caution, recognising that error is inevitable and that results are approximations. Further work is needed to investigate the effects of using different landmark and semilandmark templates and to understand the limitations and advantages of different semilandmarking approaches
Surface smoothing, decimation, and their effects on 3D biological specimens
No full textObjective
Smoothing and decimation filters are commonly used to restore the realistic appearance of virtual biological specimens, but they can cause a loss of topological information of unknown extent. In this study, we analyzed the effect of smoothing and decimation on a 3D mesh to highlight the consequences of an inappropriate use of these filters.
Materials and methods
Topological noise was simulated on four anatomical regions of the virtual reconstruction of an orangutan cranium. Sequential levels of smoothing and decimation were applied, and their effects were analyzed on the overall topology of the 3D mesh and on linear and volumetric measurements.
Results
Different smoothing algorithms affected mesh topology and measurements differently, although the influence on the latter was generally low. Decimation always produced detrimental effects on both topology and measurements. The application of smoothing and decimation, both separate and combined, is capable of recovering topological information.
Conclusion
Based on the results, objective guidelines are provided to minimize information loss when using smoothing and decimation on 3D meshes
Arothron: R Functions for Geometric Morphometrics Analyses
No full textTools for Geometric Morphometric
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