1,721,044 research outputs found
Arothron: an R package for virtual anthropology to build endocast and to perform digital reconstruction
Full text linkArothron 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
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
Old and new methods in geometric morphometrics applied to the study of human evolution: case studies
Full text linkThe 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
morphomap: An R package for long bone landmarking, cortical thickness, and cross-sectional geometry mapping
Full text linkObjectives: This study describes and demonstrates the functionalities and application of a new R package, morphomap, designed to extract shape information as semilandmarks in multiple sections, build cortical thickness maps, and calculate biomechanical parameters on long bones. Methods: morphomap creates, from a single input (an oriented 3D mesh representing the long bone surface), multiple evenly spaced virtual sections. morphomap then directly and rapidly computes morphometric and biomechanical parameters on each of these sections. The R package comprises three modules: (a) to place semilandmarks on the inner and outer outlines of each section, (b) to extract cortical thicknesses for 2D and 3D morphometric mapping, and (c) to compute cross-sectional geometry. Results: In this article, we apply morphomap to femora from Homo sapiens and Pan troglodytes to demonstrate its utility and show its typical outputs. morphomap greatly facilitates rapid analysis and functional interpretation of long bone form and should prove a valuable addition to the osteoarcheological analysis software toolkit. Conclusions: Long bone loading history is commonly retrodicted by calculating biomechanical parameters such as area moments of inertia, analyzing external shape and measuring cortical thickness. morphomap is a software written in the open source R environment, it integrates the main methodological approaches (geometric morphometrics, cortical morphometric maps, and cross-sectional geometry) used to parametrize long bones
Digital alignment: an automatized protocol for virtual reconstruction of incomplete fossil specimens
No full textEndomaker, a new algorithm for fully automatic extraction of cranial endocasts and the calculation of their volumes
No full textObjectives: Reproducing cranial endocasts is a major goal of researchers interested in vertebrate brain evolution. We present a new R software, named endomaker, which allows the automatic extraction of endocasts from skull meshes along with the calculation of its volume. Materials and methods: We applied endomaker on non-primate and primate skulls including the Australopithecus africanus specimen Sts-5. Results: We proved endomaker is faster, more feature-rich and possibly more accurate than competing software. Discussion: Endomaker is the only available program endowed with the possibility to process an entire mesh directory straight away, promising to expand the scope and phylogenetic breadth of comparative studies of brain evolution
An ontogenetic perspective on cranial base variations in extant Hominoidea and fossil Hominins
No full text
Going Beyond Counting First Authors in Author Co-citation Analysis
Full text linkThe present study examines one of the fundamental aspects of author co-citation analysis (ACA) - the way co-citation
counts are defined. Co-citation counting provides the data on which all subsequent statistical analyses and mappings
are based, and we compare ACA results based on two different types of co-citation counting - the traditional type that
only counts the first one among a cited work's authors on the one hand and a non-traditional type that takes into
account the first 5 authors of a cited work on the other hand. Results indicate that the picture produced through this non-traditional author co-citation counting contains more coherent author groups and is therefore considerably clearer. However, this picture represents fewer specialties in the research field being studied than that produced through the traditional first-author co-citation counting when the same number of top-ranked authors is selected and analyzed. Reasons for these effects are discussed
Variations on the Author
Full text link“Variations on the Author” discusses two of Eduardo Coutinho’s recent films (Um Dia na Vida, from 2010, and Últimas Conversas, posthumously released in 2015) and their contribution to the general question of documentary authorship. The director’s filmography is characterized by a consistent yet self-effacing form of authorial self-inscription: Coutinho often features as an interviewer that rather than express opinions propels discourses; an interviewer that is good at listening. This mode of self-inscription characterizes him as an author who is not expressive but who is nonetheless markedly present on the screen. In Um Dia na Vida, however, Coutinho is completely absent form the image, while Últimas Conversas, on the contrary, includes a confessional prologue that moves the director from the margins to the center of his films. This article examines the ways in which these works stand out in the filmography of a director who offers new insights into the notion of cinematic authorship
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