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33 results for “3D morphometrics”
An Improved Global Catalog LU1319373 of Lunar Craters (≥1 km) with 3D Morphometric Information of Craters
<p>A global crater catalog LU1319373 that includes approximately 1.32 million lunar craters with diameters ≥ 1 km. The crater catalog also include 3D morphometric data on the craters.</p> <p>This first version of the crater catalog LU1319373 includes the following information for each crater:</p> <ul> <li>Longitude and latitude coordinates of the center;</li> <li>Crater diameter;</li> <li>Crater depth (other morphometric data will be provided in future versions).</li> </ul> <p>Please cite the following reference for using the crater catalog LU1319373.</p> <p>Wang, Y., Wu, B., Xue, H., Li, X., & Ma, J. (2021). An improved global catalog of lunar impact craters (≥1 km) with 3D morphometric information and updates on global crater analysis. Journal of Geophysical Research: Planets, 126, e2020JE006728.</p>
Data from: facial growth and development trajectories based on 3D images: geometric morphometrics with a deformation perspective
<p>Developmental changes of facial shape are commonly investigated through geometric morphometrics. A limitation with this approach is the inability to investigate patterns of morphological changes at local scale. This could be addressed through quantifying the deformation required to deform one shape to another. This study aimed to investigate changes in mean, rate, and variance of facial shape at local scale using geometric morphometrics through deformation perspective. 2112 Europeans 3 to 40 years-old from the 3D Facial Norms project were included. Shape and rate trajectories from partial least-squares regressions revealed that the developmentally protrusive nasal bridge was due to local expansion in surrounding tissues as opposed to shape changes in nasal bridge per-ser. Local expansion of the supraorbital region, in particular the medial part in males, resulted in the sloping forehead and deep-situated eyes with development. Facial shape variation increased non-linearly with age (p < 0.05), with features having larger rate of change becoming more developmentally diversified. In summary, our deformation perspective facilitates unravelling morphogenetic processes underlying shape changes. Our extended analytical scope inspires novel measures worthy of consideration while establishing facial growth charts. The analytical framework in this study is broadly applicable for analysis of shape changes in general.</p>
Research compendium for 'Practical and technical aspects for the 3D scanning of lithic artefacts using micro-computed tomography techniques and laser light scanners for subsequent geometric morphometric analysis. Introducing the StyroStone protocol'
<p><strong>Abstract:</strong></p> <p>Here, we present a new method to scan a large number of lithic artefacts using three-dimensional (3D) scanning technology. Despite the rising use of high-resolution 3D surface scanners in archaeological sciences, no virtual studies have focused on the 3D digitization and analysis of small lithic implements such as bladelets, microblades, and microflakes. This is mostly due to difficulties in creating reliable 3D meshes of these artefacts resulting from several inherent features (i.e., size, translucency, and acute edge angles), which compromise the efficiency of structured light or laser scanners and photogrammetry. Our new protocol <em>StyroStone</em> addresses this problem by proposing a step-by-step procedure relying on the use of micro-computed tomographic technology, which is able to capture the 3D shape of small lithic implements in high detail. We tested a system that enables us to scan hundreds of artefacts together at once within a single scanning session lasting a few hours. As also bigger lithic artefacts (i.e., blades) are present in our sample, this protocol is complemented by a short guide on how to effectively scan such artefacts using a structured light scanner (Artec Space Spider). Furthermore, we estimate the accuracy of our scanning protocol using principal component analysis of 3D Procrustes shape coordinates on a sample of meshes of bladelets obtained with both micro-computed tomography and another scanning device (i.e., Artec Micro). A comprehensive review on the use of 3D geometric morphometrics in lithic analysis and other computer-based approaches is provided in the introductory chapter to show the advantages of improving 3D scanning protocols and increasing the digitization of our prehistoric human heritage.</p> <p><strong>Content List:</strong></p> <ul> <li><strong>S1. </strong>Step-by-step protocol entitled ‘StyroStone: A protocol for scanning and extracting three-dimensional meshes of stone artefacts using Micro-CT scanners’. Also available on protocols.io (dx.doi.org/10.17504/protocols.io.bzbfp2jn);</li> <li><strong>S2. </strong>Dataset with all raw semilandmark coordinate data (in .xlsx format) used in the validation study;</li> <li><strong>S3. </strong>AGMT3D project. The file “Validation Protocol-MorphoProject.mat” can be used to open the project in the software AGMT3D;</li> <li><strong>S4. </strong>Dataset in .csv format of the principal component score data of the validation study;</li> <li><strong>S5.</strong> R script used to create Figure 2 using the R package ggplot2;</li> <li><strong>S6. </strong>3D models of the experimental bladelets obtained with the Micro-CT scanner used in the validation study. Both .ply and .wrl formats are provided;</li> <li><strong>S7. </strong>3D models of the experimental bladelets obtained with the Artec Micro scanner used in the validation study. Both .ply and .wrl formats are provided.</li> </ul>
Specimen alignment with limited point-based homology: 3D morphometrics of disparate bivalve shells (Mollusca: Bivalvia)
<p>Supplemental data and code for Edie, Collins, and Jablonski, Specimen alignment with limited point-based homology: 3D morphometrics of disparate bivalve shells (Mollusca: Bivalvia).</p>
Data from: Integrating 3D models with morphometric measurements to improve volumetric estimates in marine mammals
<p>1. Studies of body condition are key to understanding the health, bioenergetics, and ecological roles of marine mammals. Due to challenges in studying marine mammals at sea, body condition is often approximated using metrics representing the size of the dorsal surface visible from aerial imagery, but quantifying variability in body volume would enable a more holistic understanding of bioenergetics. Further, the number and location of measurements needed to accurately quantify body condition has received little attention. Three-dimensional (3D) models provide a promising tool for representing morphology and providing holistic estimates of marine mammal body condition when combined with field-based morphometric measurements.</p> <p>2. We use humpback whales (Megaptera novaeangliae) to demonstrate the utility of 3D models for estimating body condition in marine mammals. We integrate morphometric measurements taken from Unoccupied Aerial Vehicles (UAVs) with scalable 3D models to generate estimates of humpback whale body volume. We assess which and how many morphometric measurements are required to accurately estimate body volume and compare the error between volume estimates derived from 3D models and previously developed models representing volume as a series of ellipses. Using UAV measurements, we assess the contribution of each morphometric measurement to volumetric estimates, and quantify the error produced by all combinations and numbers of morphometric measurements (131,072 combinations).</p> <p>3. Error in volume estimates from 3D models generated with as few as five width measurements was <5% compared to the full models and was lower than the error produced when using five width measurements with the elliptical approach. We suggest that by conserving the external morphology of marine mammals, 3D models allow body volume and body condition to be estimated accurately with few measurements.</p> <p>4. We provide code and guidelines for creating 3D models using the open-source software Blender and for assessing which measurements are needed to accurately capture the morphology of cetaceans. The 3D modeling approach we present will facilitate studies of intra- and interannual changes in body volume in marine mammals, which is vital to providing a more holistic understanding of bioenergetics and to assessing responses to environmental change and anthropogenic stressors.</p>
Data from: A 3D geometric morphometric analysis of the bovid distal humerus, with special reference to Rusingoryx atopocranion (Pleistocene, Eastern Africa)
<p>The family Bovidae [Mammalia: Artiodactyla] is speciose and has extant representatives on every continent, forming key components of mammal communities. For these reasons, bovids are ideal candidates for studies of ecomorphology. In particular, the morphology of the bovid humerus has been identified as highly related to functional variables such as body mass and habitat. This study investigates the functional morphology of the bovid distal humerus in isolation due to its increased likelihood of preservation in the fossil record, and the resulting opportunity for better understanding the ecomorphology of extinct bovids. A landmark scheme of 30 landmarks was used to capture the 3D distal humerus morphology in 111 extant bovid specimens. We find that the distal humerus has identifiable morphologies associated with body mass, habitat preference, and tribe affiliation, and that some characteristics are shared between high body mass bovids and those living on hard, flat terrain which is likely due to the high stress on the bone in both cases. We directly apply our findings regarding extant bovids to the extinct alcelaphine bovid, <em>Rusingoryx</em> <em>atopocranion</em> from the mid to late Pleistocene (>33-45 ka) Lake Victoria region of Kenya. This species is known for some peculiar morphologies including a domed cranium with hollow nasal crests, and having small hooves for a bovid of its size. Another interesting aspect of <em>Rusingoryx</em>'s skeletal morphology which has not been addressed is an unusual protrusion on the lateral epicondyle of the distal humerus. Despite considerable individual variation in the <em>Rusingoryx</em> specimens, we find evidence to support its historical assignment to the tribe Alcelaphini, and that it likely preferred open grassland habitats, which is consistent with independent reconstructions of the paleoenvironment. We also provide the most accurate body mass estimate for <em>Rusingoryx</em> to date, based on distal humerus centroid size. Overall, we are able to conclude that the distal humerus in extant bovids is highly informative regarding body mass, habitat preference and tribe, and that this can be applied directly to a fossil taxon with promising results.</p>
Reshaping Foramen Magnum Research. Analyzing foramen magnum variation in modern humans using 2D osteometry and 3D geometric morphometrics – A master thesis summary and research review. Supplementary Materials.
<p>This supplementary materials document refers to: <em>Göldner, D., 2024. Reshaping Foramen Magnum Research. Analyzing foramen magnum variation in modern humans using 2D osteometry and 3D geometric morphometrics – A master thesis summary and research review. Mitteilungen der Berliner Gesellschaft für Anthropologie, Ethnologie und Urgeschichte 44 (2023).</em></p> <p> </p> <p> </p>
Raw coordinates of 3D landmarks related to the article 'A new zooarchaeological application for geometric morphometric methods: Distinguishing Ovis aries morphotypes to address connectivity and mobility of prehistoric Central Asian pastoralists' by Haruda et al.
<p>Raw coordinates from 3D landmarks of <em>Ovis aries </em>astragali. These bones originate from Final Bronze Age archaeological contexts from central and southeastern Kazakhstan. These relate to the article 'A new zooarchaeological application for geometric morphometric methods: Distinguishing <em>Ovis aries</em> morphotypes to address connectivity and mobility of prehistoric Central Asian pastoralists' by Haruda et al. </p>
Data from: facial growth and development trajectories based on 3D images: geometric morphometrics with a deformation perspective
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Data from: Integrating 3D models with morphometric measurements to improve volumetric estimates in marine mammals
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Data from: Diurnal moths have larger hearing organs: Evidence from comparative 3D morphometric study on geometrid moths
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Data from: A 3D geometric morphometric analysis of the bovid distal humerus, with special reference to Rusingoryx atopocranion (Pleistocene, Eastern Africa)
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Data from: The evolution of skull and body shape in Triturus newts reconstructed from 3D morphometric data and phylogeny
To explore the relationship between morphological change and species diversification, we reconstructed the evolutionary changes in skull size, skull shape, and body elongation in a monophyletic group of eight species that make up salamander genus Triturus. Their well-studied phylogenetic relationships and the marked difference in ecological preferences among five species groups makes this genus an excellent model system for the study of morphological evolution. The study involved three-dimensional imagery of the skull and the number of trunk vertebrae, in material that represents the morphological, spatial, and molecular diversity of the genus. Morphological change largely followed the pattern of descent. The reconstruction of ancestral skull shape indicated that morphological change was mostly confined to two episodes, corresponding to the ancestral lineage that all crested newts have in common and the Triturus dobrogicus lineage. When corrected for common descent, evolution of skull shape was correlated to change in skull size. Also, skull size and shape, as well as body shape, as inferred from the number of trunk vertebrae, were correlated, indicating a marked impact of species' ecological preferences on morphological evolution, accompanied by a series of niche shifts, with the most pronounced one in the T. dobrogicus lineage. The presence of phylogenetic signal and correlated evolutionary changes in skull and body shape suggested complex interplay of niche shifts, natural selection, and constraints by a common developmental system
Comparability of skeletal fibulae surfaces generated by different source scanning (dual-energy CT scan vs. high resolution laser scanning) and 3D geometric morphometric validation
<p><strong>SI_Appendix 1.</strong> Matrix of Cartesian coordinates of analyzed specimens.</p> <p><strong>SI_Appendix 2</strong>. Sample list and acquisition methods. </p>
Fig. 4 in Functional morphology of the cave bear (Ursus spelaeus) mandible: a 3D geometric morphometric analysis
Fig. 4 PCAs on the regression residuals of all extant Ursidae and U. spelaeus after a regression analysis of the Procrustes coordinates onto log centroid size pooled per species (a, b) and on the regression residuals of the regression taking phylogeny into account (c, d). The colors indicate the
Fig. 6 in Functional morphology of the cave bear (Ursus spelaeus) mandible: a 3D geometric morphometric analysis
Fig. 6 Scatterplot of the PC1 scores versus the logarithm of the percentage of foliage in the diet. Linear regression lines were fitted with the 95 % confidence interval of the group mean and the mean scores of U. spelaeus (vertical line)
Fig. 2 in Functional morphology of the cave bear (Ursus spelaeus) mandible: a 3D geometric morphometric analysis
Fig. 2 Mandibles of Ursus spelaeus (a, b) and Tremarctos ornatus (c) and showing the position of the masseteric fossa (MF) and the premasseteric fossa (PMF). Positions of the landmarks on a mandible of Ursus spelaeus on the lingual side (a) and the labial side (b). The landmarks are described in Table 3. Not to scale. Part A of the figure also displays the biomechanics. The resistance (Fout) at the carnassial of the lower jaw depends on the muscular input force (Fin), the angle of insertion of the muscle onto the jaw (α) and the ratio of in-lever arm or moment arm (Li) to out-lever arm (Lo). Angle of insertion of jaw muscles changes during jaw closing and determines the moment arm of the muscular input force (Mi). Mass pertaining to the masseter, Temp pertaining to the temporalis. Li Mass and Mi Mass happen to be the same in this diagram
Fig. 5 2B in Functional morphology of the cave bear (Ursus spelaeus) mandible: a 3D geometric morphometric analysis
Fig. 5 2B-PLS on the regression residuals of all extant Ursidae and U. spelaeus after a regression analysis of the Procrustes coordinates onto log centroid size pooled per species. A phylogenetic overlay is shown in gray
Figure 3 in Using 3D geometric morphometrics to aid taxonomic and ecological understanding of a recent speciation event within a small Australian marsupial (Antechinus: Dasyuridae)
Figure 3. Pairwise comparisons between mean shapes of each clade (Antechinus stuartii south vs. A. stuartii north, P = 0.003; A. stuartii north vs. A. subtropicus, P = 0.003; A. stuartii south vs. A. subtropicus, P = 0.003; all p-values were adjusted with following the Bonferroni method). The 3D images are the specimen closest to the overall mean warped correspondingly to the mean shapes of each clade. Tukey post-hoc analyses of linear measurements after size correction were performed; significance levels (*P <0.05, **P <0.01, ***P <0.001) are shown in the boxplots. For each comparison, we have labelled the best differentiator diagnostic; i.e. the size of the major palatine foramina (mapf) for differentiating A. stuartii south and A. stuartii north, the size of the incisive foramina (inf) for differentiating A. stuartii north and A. subtropicus, and the interpalatal distance (intp) for differentiating between the three clades. Clades are consistently labelled as per Figure 1.
Figure 1 in Using 3D geometric morphometrics to aid taxonomic and ecological understanding of a recent speciation event within a small Australian marsupial (Antechinus: Dasyuridae)
Figure 1. Distribution map of the specimens used for this study. Labelled are Antechinus stuartii south, A. stuartii north, A. subtropicus, specimens of unknown identity within the A. stuartii–A. subtropicus species complex, the holotype of A. subtropicus and the neotype of A. stuartii. All figures in this paper are labelled: A. stuartii south in orange, A. stuartii north in pink and A. subtropicus in green. The phylogeny is adapted from Mutton et al. (2019).
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Allen Brain Atlas
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Annotated Behaviour and Observability Dataset (ABODe)
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