Find research datasets worth reusing
Search datasets from major research repositories and use ShareScore to quickly assess how well each record supports discovery, access, and reuse.
21
datasets available to search
ShareScore release 0.9.0
Dataset results
21 results for “3D geometric morphometrics”
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>
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
Open the record for dataset details and reuse information.
Data from: A 3D geometric morphometric analysis of the bovid distal humerus, with special reference to Rusingoryx atopocranion (Pleistocene, Eastern Africa)
Open the record for dataset details and reuse information.
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).
Figure 2. A in Using 3D geometric morphometrics to aid taxonomic and ecological understanding of a recent speciation event within a small Australian marsupial (Antechinus: Dasyuridae)
Figure 2. A, box plot and dot plot of centroid size labelling each clade as per Figure 1. Centroid size differences were clear only between the larger Antechinus subtropicus and the smaller A. stuartii (both mean comparisons between A. subtropicus and the two clades of A. stuartii were significant; P = 0.003), but not between A. stuartii south and A. stuartii north (P = 0.282). B, allometry plot consisting of centroid sizes versus shape scores obtained from the regression of shape on size (Drake & Klingenberg, 2008).
Figure 3. 3D in Cranial variation between coastal and offshore boưlenose dolphins, Tursiops truncatus (Cetacea: Delphinidae) in Ecuador and the Mediterranean: a three-dimensional geometric morphometric study
Figure 3. 3D LMs points generated from the automatic landmarking from the boưlenose dolphin skull reference template.
Data from: 2D or Not 2D? Testing the utility of 2D vs. 3D landmark data in geometric morphometrics of the sculpin subfamily Oligocottinae (Pisces; Cottoidea)
Open the record for dataset details and reuse information.
Functional and ecomorphological evolution of orbit shape in Mesozoic archosaurs is driven by body size and diet: Geometric morphometric data, 3D models (stl files), FEA models (Hypermesh, Abaqus files)
<p class="MsoNormal">The orbit is one of several skull openings in the archosauromorph skull. Intuitively, it could be assumed that orbit shape would closely approximate the shape and size of the eyeball resulting in a predominantly circular morphology. However, a quantification of orbit shape across Archosauromorpha using a geometric morphometric approach demonstrates a large morphological diversity despite the fact that the majority of species retained a circular orbit. This morphological diversity is nearly exclusively driven by large (skull length > 1000 mm) and carnivorous species in all studied archosauromorph groups, but particularly prominently in theropod dinosaurs. While circular orbit shapes are retained in most herbivores and smaller species, as well as in juveniles and early ontogenetic stages, large carnivores adopted elliptical and keyhole-shaped orbits. Biomechanical modeling using finite element analysis reveals that these morphologies are beneficial in mitigating and dissipating feeding-induced stresses without additional reinforcement of the bony structure of the skull.</p>
Functional and ecomorphological evolution of orbit shape in Mesozoic archosaurs is driven by body size and diet: Geometric morphometric data, 3D models (stl files), FEA models (Hypermesh, Abaqus files)
Open the record for dataset details and reuse information.
Fig. 1 in Functional morphology of the cave bear (Ursus spelaeus) mandible: a 3D geometric morphometric analysis
Fig. 1 Phylogenetic tree of the family Ursidae as used in the present study, based on BinindaEmonds et al. (1999), Hofreiter et al. (2002) and Krause et al. (2008)
ScienceDex guides
Understand access before you commit
These curated guides explain access requirements, typical timelines, costs, and reuse considerations for widely used research datasets.
Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.