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Journal articles on the topic '3D Geometric morphometrics'

Author: Grafiati

Published: 4 June 2021

Last updated: 1 February 2022

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1

Vitkovic, Nikola, Ljiljana Radovic, Miroslav Trajanovic, and Miodrag Manic. "3d point cloud model of human bio form created by the application of geometric morphometrics and method of anatomical features: human tibia example." Filomat 33, no. 4 (2019): 1217–25. http://dx.doi.org/10.2298/fil1904217v.

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Morphometrics refers to the quantitative analysis of a biological form and it can be used to describe its shape. Common types of geometric morphometrics are Landmark-based Geometric Morphometrics which describe shape by using anatomical landmarks (e.g. points), and Outline-based geometric morphometrics which uses envelope curves to describe shape of the biological form (e.g. bone), and they are not absolutely exclusive. Geometric morphometrics can be used for the creation of statistical models which represent shape variation of specific bio form. In this paper, novel application of geometric morphometrics for the creation of personalized models of unique bio-forms, i.e. models which are created for the specific patient is presented. Personalized model is defined as 3D point cloud model of biological form (in this case human tibia). Positions of points in 3D space are determined by using set of parametric functions defined by applying geometrical morphometrics, morphology properties and statistical analysis on the input set of human tibia samples. By using this technique, anatomically correct and geometrically accurate personalized models of bio forms can be created and used in pre, intra, and post-operative procedures in clinical practice.

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Goswami, Anjali, Akinobu Watanabe, Ryan N. Felice, Carla Bardua, Anne-Claire Fabre, and P. David Polly. "High-Density Morphometric Analysis of Shape and Integration: The Good, the Bad, and the Not-Really-a-Problem." Integrative and Comparative Biology 59, no. 3 (June 27, 2019): 669–83. http://dx.doi.org/10.1093/icb/icz120.

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Abstract The field of comparative morphology has entered a new phase with the rapid generation of high-resolution three-dimensional (3D) data. With freely available 3D data of thousands of species, methods for quantifying morphology that harness this rich phenotypic information are quickly emerging. Among these techniques, high-density geometric morphometric approaches provide a powerful and versatile framework to robustly characterize shape and phenotypic integration, the covariances among morphological traits. These methods are particularly useful for analyses of complex structures and across disparate taxa, which may share few landmarks of unambiguous homology. However, high-density geometric morphometrics also brings challenges, for example, with statistical, but not biological, covariances imposed by placement and sliding of semilandmarks and registration methods such as Procrustes superimposition. Here, we present simulations and case studies of high-density datasets for squamates, birds, and caecilians that exemplify the promise and challenges of high-dimensional analyses of phenotypic integration and modularity. We assess: (1) the relative merits of “big” high-density geometric morphometrics data over traditional shape data; (2) the impact of Procrustes superimposition on analyses of integration and modularity; and (3) differences in patterns of integration between analyses using high-density geometric morphometrics and those using discrete landmarks. We demonstrate that for many skull regions, 20–30 landmarks and/or semilandmarks are needed to accurately characterize their shape variation, and landmark-only analyses do a particularly poor job of capturing shape variation in vault and rostrum bones. Procrustes superimposition can mask modularity, especially when landmarks covary in parallel directions, but this effect decreases with more biologically complex covariance patterns. The directional effect of landmark variation on the position of the centroid affects recovery of covariance patterns more than landmark number does. Landmark-only and landmark-plus-sliding-semilandmark analyses of integration are generally congruent in overall pattern of integration, but landmark-only analyses tend to show higher integration between adjacent bones, especially when landmarks placed on the sutures between bones introduces a boundary bias. Allometry may be a stronger influence on patterns of integration in landmark-only analyses, which show stronger integration prior to removal of allometric effects compared to analyses including semilandmarks. High-density geometric morphometrics has its challenges and drawbacks, but our analyses of simulated and empirical datasets demonstrate that these potential issues are unlikely to obscure genuine biological signal. Rather, high-density geometric morphometric data exceed traditional landmark-based methods in characterization of morphology and allow more nuanced comparisons across disparate taxa. Combined with the rapid increases in 3D data availability, high-density morphometric approaches have immense potential to propel a new class of studies of comparative morphology and phenotypic integration.

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Loth, Anthony, Julien Corny, Laure Santini, Laurie Dahan, Patrick Dessi, Pascal Adalian, and Nicolas Fakhry. "Analysis of Hyoid–Larynx Complex Using 3D Geometric Morphometrics." Dysphagia 30, no. 3 (April 3, 2015): 357–64. http://dx.doi.org/10.1007/s00455-015-9609-2.

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4

Dhoop, Thomas, Sarah Stark, Juan‐Pablo Olaberria, and Julian Whitewright. "Quantifying Ship Shape in Archaeology: Evaluating 3D Geometric Morphometrics." International Journal of Nautical Archaeology 49, no. 1 (March 2020): 49–64. http://dx.doi.org/10.1111/1095-9270.12413.

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Hirst, Cara S., Suzanna White, and Sian E. Smith. "Standardisation in 3D Geometric Morphometrics: Ethics, Ownership, and Methods." Archaeologies 14, no. 2 (August 2018): 272–98. http://dx.doi.org/10.1007/s11759-018-9349-7.

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Bastir, Markus, Daniel García-Martínez, Scott A. Williams, Wolfgang Recheis, Isabel Torres-Sánchez, Francisco García Río, Motoharu Oishi, and Naomichi Ogihara. "3D geometric morphometrics of thorax variation and allometry in Hominoidea." Journal of Human Evolution 113 (December 2017): 10–23. http://dx.doi.org/10.1016/j.jhevol.2017.08.002.

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7

Hedrick, Brandon P., and Peter Dodson. "Lujiatun Psittacosaurids: Understanding Individual and Taphonomic Variation Using 3D Geometric Morphometrics." PLoS ONE 8, no. 8 (August 9, 2013): e69265. http://dx.doi.org/10.1371/journal.pone.0069265.

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8

Black, Valda Gail, and Danielle Shawn Kurin. "Reliable classification of intentional cranial vault modification and nonsynostotic deformational plagiocephaly using 3D geometric morphometrics." HOMO 72, no. 2 (June 26, 2021): 99–111. http://dx.doi.org/10.1127/homo/2021/1339.

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9

Selden, Robert Z., Timothy K. Perttula, and Michael J. O’Brien. "Advances in Documentation, Digital Curation, Virtual Exhibition, and a Test of 3D Geometric Morphometrics." Advances in Archaeological Practice 2, no. 2 (May 2014): 64–79. http://dx.doi.org/10.7183/2326-3768.2.2.64.

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AbstractThree-dimensional (3D) digital scanning of archaeological materials is typically used as a tool for artifact documentation. With the permission of the Caddo Nation of Oklahoma, 3D documentation of Caddo funerary vessels from the Vanderpool site (41SM77) was conducted with the initial goal of ensuring that these data would be publicly available for future research long after the vessels were repatriated. A digital infrastructure was created to archive and disseminate the resultant 3D datasets, ensuring that they would be accessible by both researchers and the general public (CRHR 2014a). However, 3D imagery can be used for much more than documentation. To illustrate this, these data were utilized in a 3D morphometric analysis of the intact and reconstructed vessels to explore the range of variation that occurs in ceramic vessel shape and its potential contribution to the local ceramic taxonomy. Results of the 3D morphometric analysis demonstrate the potential for substantive analytical gains in discussions of temporal resolution and ceramic technological organization in the ancestral Caddo region.

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Mucedero, Manuela, Matteo Rozzi, Alessia Milazzo, and Paola Cozza. "Morphometric analysis of the palatal shape and arch dimension in subjects with palatally displaced canine." European Journal of Orthodontics 41, no. 5 (January 2, 2019): 460–67. http://dx.doi.org/10.1093/ejo/cjy080.

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Summary Objectives The aim of this study is to analyse the morphological variations of the palate shape and maxillary arch dimension in a group of subjects with unilaterally or bilaterally impacted maxillary canines compared with a control group, using three-dimensional (3D) geometric morphometric. Materials The subject of this study consisted of pre-treatment records of 46 (18 males and 28 females) patients with one or both canines palatally displaced. A control group of 26 subjects was selected from a list of orthodontic patients at the same dental hospital. The subjects were divided in two study groups: unilateral palatally displaced canine (UPDC) and bilateral palatally displaced canine (BPDC). Study casts were scanned to analyse the palate’s shape and maxillary arch dimension. The 3D geometric morphometric analysis was used to study the entirety of the shape of the palate. The virtual 3D models were measured with a specific software to analyse the maxillary arch dimension. (VAM, Vectra; Canfield Scientific, Fairfield, New Jersey, USA). Results When comparing the groups with the geometric morphometrics analysis, no significant palatal shape change was found. For the analysis of linear measurements, only a significant reduction of intercanine width was found in the UPDC and BPDC groups when compared with the control subjects. Conclusions Patients with palatally displaced permanent canine showed no maxillary transverse constriction or variation in palatal vault morphology but the absence of permanent teeth was associated with a reduction in the intercanine width.

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Palancar, Carlos A., Nicole Torres-Tamayo, Daniel García-Martínez, Antonio García-Tabernero, Antonio Rosas, and Markus Bastir. "Comparative anatomy and 3D geometric morphometrics of the El Sidrón atlases (C1)." Journal of Human Evolution 149 (December 2020): 102897. http://dx.doi.org/10.1016/j.jhevol.2020.102897.

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Weinberg, Seth M., Trish E. Parsons, Mary L. Marazita, and Brion S. Maher. "Heritability of face shape in twins: a preliminary study using 3D stereophotogrammetry and geometric morphometrics." Dentistry 3000 1, no. 1 (November 25, 2013): 7–11. http://dx.doi.org/10.5195/d3000.2013.14.

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Introduction: Previous research suggests that aspects of facial surface morphology are heritable. Traditionally, heritability studies have used a limited set of linear distances to quantify facial morphology and often employ statistical methods poorly designed to deal with biological shape. In this preliminary report, we use a combination of 3D photogrammetry and landmark-based morphometrics to explore which aspects of face shape show the strongest evidence of heritability in a sample of twins. Methods: 3D surface images were obtained from 21 twin pairs (10 monozygotic, 11 same-sex dizygotic). Thirteen 3D landmarks were collected from each facial surface and their coordinates subjected to geometric morphometric analysis. This involved superimposing the individual landmark configurations and then subjecting the resulting shape coordinates to a principal components analysis. The resulting PC scores were then used to calculate rough narrow-sense heritability estimates. Results: Three principal components displayed evidence of moderate to high heritability and were associated with variation in the breadth of orbital and nasal structures, upper lip height and projection, and the vertical and forward projection of the root of the nose due to variation in the position of nasion. Conclusions: Aspects of facial shape, primarily related to variation in length and breadth of central midfacial structures, were shown to demonstrate evidence of strong heritability. An improved understanding of which facial features are under strong genetic control is an important step in the identification of specific genes that underlie normal facial variation.

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Yravedra, José, Julia Aramendi, Miguel Ángel Maté-González, Lloyd Austin Courtenay, and Diego González-Aguilera. "Differentiating percussion pits and carnivore tooth pits using 3D reconstructions and geometric morphometrics." PLOS ONE 13, no. 3 (March 28, 2018): e0194324. http://dx.doi.org/10.1371/journal.pone.0194324.

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Márquez, Federico, and Andres Averbuj. "Sexual dimorphism in the shell of a nassariid gastropod. A 3D geometric morphometrics approach." Journal of the Marine Biological Association of the United Kingdom 97, no. 2 (March 7, 2016): 249–55. http://dx.doi.org/10.1017/s0025315416000254.

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Among gastropods, dimorphism is reported in shell size, radular characteristic, and to a lesser extent in shell shape. The relationship of dimorphic characters of the shell with spawning is scarcely studied in literature. Buccinanops globulosus is an interesting model to study sexual dimorphism in shell shape, because the adults attach their egg capsules to the females’ own shells (callus zone). Our hypothesis is that the shell dimorphism is evidenced in the form (size and shape) of callus zones of the females' shells, compared with the males'. In order to test this hypothesis we use a 3D geometric morphometrics (GM) method with several advantages over 2D GM. The relationship between callus shape and size was allometric. During growth, the main callus shape changes are related to the mean size increment, which is more evident in larger females. These callus zones are characteristically slender in males and small females, and more inflated in large females. Our analyses revealed that female shells are different from male ones and those differences are significant on the callus zone where the egg capsules are attached by the female. This finding suggests a relationship of the shell form with spawning. Our findings are not only relevant in terms of the shell dimorphism of the particular spawning substrate area (callus zones) and its reproductive implications, but also provide insights into the evaluation of shell shape variation on areas without type I or II anatomical landmarks in 3D GM.

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Rosas, Antonio, Anabel Ferrando, Markus Bastir, Antonio García-Tabernero, Almudena Estalrrich, Rosa Huguet, Daniel García-Martínez, Juan Francisco Pastor, and Marco de la Rasilla. "Neandertal talus bones from El Sidrón site (Asturias, Spain): A 3D geometric morphometrics analysis." American Journal of Physical Anthropology 164, no. 2 (July 17, 2017): 394–415. http://dx.doi.org/10.1002/ajpa.23280.

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Boschin, Francesco, Erika Moretti, Jacopo Crezzini, and Simona Arrighi. "Geometric morphometrics reveal relationship between cut-mark morphology and cutting tools." ACTA IMEKO 10, no. 1 (March 31, 2021): 109. http://dx.doi.org/10.21014/acta_imeko.v10i1.846.

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The analysis of bone-surface modifications (BSM), such as butchering marks, is necessary to better understand how the exploitation of animal resources by past hominins influenced their biological and cultural evolution. In this paper, we try to quantify to what extent the depth of the cut marks influences the shape of their cross sections. This is of crucial importance for a valid interpretation of the shape data collected on archaeological BSMs. Two groups of slicing cut-mark cross sections were experimentally produced with two flint burins on a defleshed cattle innominate, and a set of butchering marks were produced with an unretouched flint flake. These were analysed by means of 3D microscopy and geometric morphometrics. The resulting sets of striae show different depths and different cross-sectional shapes. Shallower cross sections display less steep walls and, consequently, a wider opening angle. When the characteristics of the burin cutting edges were investigated, it was clear that the difference in shape between the two groups of striations was probably a function of the way in which the tool penetrated the bone. These results are taphonomically relevant since similar differences in cross-sectional shapes have been found in marks produced with different tools.

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Atwood, James W., and Colin D. Sumrall. "Morphometric investigation of the Pentremites fauna from the Glen Dean Formation, Kentucky." Journal of Paleontology 86, no. 5 (September 2012): 813–28. http://dx.doi.org/10.1666/12-003.1.

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New techniques involving three-dimensional (3D) data collection and landmark analysis provide an opportunity to make considerable advances in understanding blastoid morphology. This pilot study examines four species (Pentremites pyriformis, P. tulipaformis, P. fredericki n. sp. and P. meganae n. sp.) using 3D morphological variation and geometric morphometrics to discriminate between species. All specimens were collected from a single shale unit within the Upper Mississippian Glen Dean Formation near Hopkinsville, Kentucky. A 3D laser scanner was used to acquire 3D images for all specimens. Conservative blastoid thecal plating allowed the collection of 3D coordinates for a series of homologous landmarks from these laser images that fully describe specimen morphology. Data were analyzed using the R (language and environment for statistical computing and graphics) packages SHAPES and MCLUST. Mixture modeling identified and separated all four species based on shape alone. In addition, three new species were discovered during this study, including: Pentremites fredericki, P. meganae and Diploblastus fadigai.

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Hennessy, Robin J., Patrizia A. Baldwin, David J. Browne, Anthony Kinsella, and John L. Waddington. "Frontonasal dysmorphology in bipolar disorder by 3D laser surface imaging and geometric morphometrics: Comparisons with schizophrenia." Schizophrenia Research 122, no. 1-3 (September 2010): 63–71. http://dx.doi.org/10.1016/j.schres.2010.05.001.

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Marchal, Antoine F. J., Philippe Lejeune, and P. J. Nico de Bruyn. "Identification of the Anteroposterior and Mediolateral Position of Lion Paws and Tracks Using 3D Geometric Morphometrics." African Journal of Wildlife Research 47, no. 2 (October 2017): 106–13. http://dx.doi.org/10.3957/056.047.0106.

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Vanhoof, Marie J. M., Lorenzo Galletta, Isabelle De Groote, and Evie E. Vereecke. "Functional signals and covariation in triquetrum and hamate shape of extant primates using 3D geometric morphometrics." Journal of Morphology 282, no. 9 (July 20, 2021): 1382–401. http://dx.doi.org/10.1002/jmor.21393.

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Pavoni, Chiara, Valeria Paoloni, Luis Tomas Huanca Ghislanzoni, Giuseppina Laganà, and Paola Cozza. "Geometric morphometric analysis of the palatal morphology in children with impacted incisors: A three-dimensional evaluation." Angle Orthodontist 87, no. 3 (October 20, 2016): 404–8. http://dx.doi.org/10.2319/071716-557.1.

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ABSTRACT Objective: To analyze variations in palatal morphology in subjects presenting unilaterally impacted maxillary permanent central incisors compared with a control group of subjects without eruption anomalies using a three-dimensional (3D) analysis. Materials and Methods: Twenty-six white subjects (10 girls and 16 boys; mean age 9.5 ± 1.5 years) with unilaterally impacted maxillary permanent central incisors (impacted incisor group [IIG]) were compared with a control group (CG) of 26 subjects (14 girls and 12 boys, mean age 8.7 ± 1.6 years) presenting no eruption disorders. For each subject, dental casts were taken and the upper arch was scanned using a 3D laser scanner. To study the entirety of the shape of the palate in any point of the surface, 3D geometric morphometrics was applied. Results: Subjects with impacted maxillary incisors showed skeletal adaptations of the maxilla. In the IIG, both the superior palatal region and lateral palatal surface showed significantly different morphology when compared with CG, with a narrower and higher palatal vault. Conclusion: The absence of maxillary central incisors over the physiological age of eruption influenced the development of the palatal morphology compared with subjects without eruption anomalies.

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Messer, Dolores, Michelle S. Svendsen, Anders Galatius, Morten T. Olsen, Vedrana A. Dahl, Knut Conradsen, and Anders B. Dahl. "Measurement error using a SeeMaLab structured light 3D scanner against a Microscribe 3D digitizer." PeerJ 9 (August 20, 2021): e11804. http://dx.doi.org/10.7717/peerj.11804.

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Background Geometric morphometrics is a powerful approach to capture and quantify morphological shape variation. Both 3D digitizer arms and structured light surface scanners are portable, easy to use, and relatively cheap, which makes these two capturing devices obvious choices for geometric morphometrics. While digitizer arms have been the “gold standard”, benefits of having full 3D models are manifold. We assessed the measurement error and investigate bias associated with the use of an open-source, high-resolution structured light scanner called SeeMaLab against the popular Microscribe 3D digitizer arm. Methodology The analyses were based on 22 grey seal (Halichoerus grypus) skulls. 31 fixed anatomical landmarks were annotated both directly using a Microscribe 3D digitizer and on reconstructed 3D digital models created from structured light surface scans. Each skull was scanned twice. Two operators annotated the landmarks, each twice on all the skulls and 3D models, allowing for the investigation of multiple sources of measurement error. We performed multiple Procrustes ANOVAs to compare the two devices in terms of within- and between-operator error, to quantify the measurement error induced by device, to compare between-device error with other sources of variation, and to assess the level of scanning-related error. We investigated the presence of general shape bias due to device and operator. Results Similar precision was obtained with both devices. If landmarks that were identified as less clearly defined and thus harder to place were omitted, the scanner pipeline would achieve higher precision than the digitizer. Between-operator error was biased and seemed to be smaller when using the scanner pipeline. There were systematic differences between devices, which was mainly driven by landmarks less clearly defined. The factors device, operator and landmark replica were all statistically significant and of similar size, but were minor sources of total shape variation, compared to the biological variation among grey seal skulls. The scanning-related error was small compared to all other error sources. Conclusions As the scanner showed precision similar to the digitizer, a scanner should be used if the advantages of obtaining detailed 3D models of a specimen are desired. To obtain high precision, a pre-study should be conducted to identify difficult landmarks. Due to the observed bias, data from different devices and/or operators should not be combined when the expected biological variation is small, without testing the landmarks for repeatability across platforms and operators. For any study necessitating the combination of landmark measurements from different operators, the scanner pipeline will be better suited. The small scanning-related error indicates that by following the same scanning protocol, different operators can be involved in the scanning process without introducing significant error.

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Shin, Ja Young, Aspalilah Alias, Eric Chung, Wei Lin Ng, Yuan Seng Wu, Quan Fu Gan, and Ker Woon Choy. "Identification of Race: A Three-Dimensional Geometric Morphometric and Conventional Analysis of Human Fourth Cervical Vertebrae in Adult Malaysian Population." Journal of Clinical and Health Sciences 6, no. 1(Special) (June 30, 2021): 17. http://dx.doi.org/10.24191/jchs.v6i1(special).13167.

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Introduction: Estimation of race plays a significant role in establishing personal identity in forensic anthropology. A cervical vertebra is one of the bones that is least researched in forensic applications. Our study aims to investigate the morphologic variations of the fourth cervical vertebrae (C4) between the different major races in the adult Malaysian population using a three-dimensional (3D) geometric morphometrics method. Methods: Computer tomography images of C4 vertebra, which consist of 386 subjects (169 Malay, 82 Chinese, and 135 Indian) were collected retrospectively from University of Malaya. Twenty-eight landmarks were placed on the images. Procrustes MANOVA, canonical variates analysis(CVA), discriminant function analysis (DFA), and linear measurement were performed using Planmeca Romexis, Checkpoint Stratovan, Morpho J, and Graphpad Prism software respectively to analyze the morphological variations of C4. Results: Procrustes MANOVA showed significant differences in the shape (p <0.0001) and centroid size (p = 0.0003) of the C4 vertebra between races. Canonical variate analysis showed significant differences for Mahalanobis (p <0.0001) and Procrustes (p <0.0001) distances among races. Besides that, a cross-validation value of 66.5% was demonstrated by discriminant function analysis. The use of linear measurements reveals no significant differences between the races, thesemeasurements are the vertebral body height, anterior-posterior length of the vertebral body, length of superior articular facet, and spinous process length. Both intra- and inter-observational reliabilities showed that acceptable human errors for measurement accuracy. Conclusions: Morphologic variations in the shape of C4 can assist in race estimation of the adult Malaysian population using the 3D geometric morphometric approach.

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Touzé, Romain, Yann Heuzé, Matthieu P. Robert, Dominique Brémond-Gignac, Charles-Joris Roux, Syril James, Giovanna Paternoster, Eric Arnaud, and Roman Hossein Khonsari. "Extraocular muscle positions in anterior plagiocephaly: V-pattern strabismus explained using geometric mophometrics." British Journal of Ophthalmology 104, no. 8 (November 6, 2019): 1156–60. http://dx.doi.org/10.1136/bjophthalmol-2019-314989.

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IntroductionOphthalmological involvement in anterior plagiocephaly (AP) due to unicoronal synostosis (UCS) raises management challenges. Two abnormalities of the extraocular muscles (EOM) are commonly reported in UCS without objective quantification: (1) excyclorotation of the eye and (2) malposition of the trochlea of the superior oblique muscle. Here we aimed to assess the positions of the EOM in AP, using geometric morphometrics based on MRI data.Materials and methodsPatient files were listed using Dr WareHouse, a dedicated big data search engine. We included all patients with AP managed between 2013 and 2018, with an available digital preoperative MRI. MRIs from age-matched controls without craniofacial conditions were also included. We defined 13 orbital and skull base landmarks in order to model the 3D position of the EOM. Cephalometric analyses and geometric morphometrics with Procrustes superimposition and principal component analysis were used with the aim of defining specific EOM anomalies in UCS.ResultsWe included 15 preoperative and 7 postoperative MRIs from patients with UCS and 24 MRIs from age-matched controls. Cephalometric analyses, Procrustes superimposition and distance computations showed a significant shape difference for the position of the trochlea of the superior oblique muscle and an excyclorotation of the EOM.ConclusionsOur results confirm that UCS-associated anomalies of the superior oblique muscle function are associated with malposition of its trochlea in the roof of the orbit. This clinical anomaly supports the importance of MRI imaging in the surgical management of strabismus in patients with UCS.

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Attard, Marie R. G., Emma Sherratt, Paul McDonald, Iain Young, Marta Vidal-García, and Stephen Wroe. "A new, three-dimensional geometric morphometric approach to assess egg shape." PeerJ 6 (June 27, 2018): e5052. http://dx.doi.org/10.7717/peerj.5052.

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This paper proposes a new methodology to quantify patterns of egg shape variation using geometric morphometrics of three-dimensional landmarks captured on digitally reconstructed eggshells and demonstrates its performance in capturing shape variation at multiple biological levels. This methodology offers unique benefits to complement established linear measurement or two-dimensional (2D) contour profiling techniques by (i) providing a more precise representation of eggshell curvature by accounting for variation across the entire surface of the egg; (ii) avoids the occurrence of correlations from combining multiple egg shape features; (iii) avoids error stemming from projecting a highly-curved three-dimensional (3D) object into 2D space; and (iv) enables integration into 3D workflows such as finite elements analysis. To demonstrate, we quantify patterns of egg shape variation and estimate morphological disparity at multiple biological levels, within and between clutches and among species of four passerine species of different lineages, using volumetric dataset obtained from micro computed tomography. The results indicate that species broadly have differently shaped eggs, but with extensive within-species variation so that all four-focal species occupy a range of shapes. Within-species variation is attributed to between-clutch differences in egg shape; within-clutch variation is surprisingly substantial. Recent comparative analyses that aim to explain shape variation among avian taxa have largely ignored potential biases due to within-species variation, or use methods limited to a narrow range of egg shapes. Through our approach, we suggest that there is appreciable variation in egg shape across clutches and that this variation needs to be accounted for in future research. The approach developed in this study to assess variation in shape is freely accessible and can be applied to any spherical-to-conical shaped object, including eggs of non-avian dinosaurs and reptiles through to other extant taxa such as poultry.

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Fakhry, Nicolas, Laurent Puymerail, Justin Michel, Laure Santini, Catherine Lebreton-Chakour, Danielle Robert, Antoine Giovanni, Pascal Adalian, and Patrick Dessi. "Analysis of Hyoid Bone Using 3D Geometric Morphometrics: An Anatomical Study and Discussion of Potential Clinical Implications." Dysphagia 28, no. 3 (February 28, 2013): 435–45. http://dx.doi.org/10.1007/s00455-013-9457-x.

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Sztencel-Jabłonka, Anna, Gareth Jones, and Wiesław BogdanowicZ. "Skull Morphology of Two Cryptic Bat Species:Pipistrellus pipistrellusandP. pygmaeus— A 3D Geometric Morphometrics Approach with Landmark Reconstruction." Acta Chiropterologica 11, no. 1 (June 2009): 113–26. http://dx.doi.org/10.3161/150811009x465730.

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Claes, Peter, Mark Walters, Mark D. Shriver, David Puts, Greg Gibson, John Clement, Gareth Baynam, Geert Verbeke, Dirk Vandermeulen, and Paul Suetens. "Sexual dimorphism in multiple aspects of 3D facial symmetry and asymmetry defined by spatially dense geometric morphometrics." Journal of Anatomy 221, no. 2 (June 18, 2012): 97–114. http://dx.doi.org/10.1111/j.1469-7580.2012.01528.x.

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Couette, Sébastien, and Jess White. "3D geometric morphometrics and missing-data. Can extant taxa give clues for the analysis of fossil primates?" Comptes Rendus Palevol 9, no. 6-7 (September 2010): 423–33. http://dx.doi.org/10.1016/j.crpv.2010.07.002.

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Forrest, Frances L., Thomas W. Plummer, and Ryan L. Raaum. "Ecomorphological analysis of bovid mandibles from Laetoli Tanzania using 3D geometric morphometrics: Implications for hominin paleoenvironmental reconstruction." Journal of Human Evolution 114 (January 2018): 20–34. http://dx.doi.org/10.1016/j.jhevol.2017.09.010.

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Marcy, Ariel E., Carmelo Fruciano, Matthew J. Phillips, Karine Mardon, and Vera Weisbecker. "Low resolution scans can provide a sufficiently accurate, cost- and time-effective alternative to high resolution scans for 3D shape analyses." PeerJ 6 (June 22, 2018): e5032. http://dx.doi.org/10.7717/peerj.5032.

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BackgroundAdvances in 3D shape capture technology have made powerful shape analyses, such as geometric morphometrics, more feasible. While the highly accurate micro-computed tomography (µCT) scanners have been the “gold standard,” recent improvements in 3D surface scanners may make this technology a faster, portable, and cost-effective alternative. Several studies have already compared the two devices but all use relatively large specimens such as human crania. Here we perform shape analyses on Australia’s smallest rodent to test whether a 3D scanner produces similar results to a µCT scanner.MethodsWe captured 19 delicate mouse (Pseudomys delicatulus) crania with a µCT scanner and a 3D scanner for geometric morphometrics. We ran multiple Procrustes ANOVAs to test how variation due to scan device compared to other sources such as biologically relevant variation and operator error. We quantified operator error as levels of variation and repeatability. Further, we tested if the two devices performed differently at classifying individuals based on sexual dimorphism. Finally, we inspected scatterplots of principal component analysis (PCA) scores for non-random patterns.ResultsIn all Procrustes ANOVAs, regardless of factors included, differences between individuals contributed the most to total variation. The PCA plots reflect this in how the individuals are dispersed. Including only the symmetric component of shape increased the biological signal relative to variation due to device and due to error. 3D scans showed a higher level of operator error as evidenced by a greater spread of their replicates on the PCA, a higher level of multivariate variation, and a lower repeatability score. However, the 3D scan and µCT scan datasets performed identically in classifying individuals based on intra-specific patterns of sexual dimorphism.DiscussionCompared to µCT scans, we find that even low resolution 3D scans of very small specimens are sufficiently accurate to classify intra-specific differences. We also make three recommendations for best use of low resolution data. First, we recommend that extreme caution should be taken when analyzing the asymmetric component of shape variation. Second, using 3D scans generates more random error due to increased landmarking difficulty, therefore users should be conservative in landmark choice and avoid multiple operators. Third, using 3D scans introduces a source of systematic error relative to µCT scans, therefore we recommend not combining them when possible, especially in studies expecting little biological variation. Our findings support increased use of low resolution 3D scans for most morphological studies; they are likely also applicable to low resolution scans of large specimens made in a medical CT scanner. As most vertebrates are relatively small, we anticipate our results will bolster more researchers in designing affordable large scale studies on small specimens with 3D surface scanners.

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Otárola-Castillo, Erik, Melissa G. Torquato, Hannah C. Hawkins, Emma James, Jacob A. Harris, Curtis W. Marean, Shannon P. McPherron, and Jessica C. Thompson. "Differentiating between cutting actions on bone using 3D geometric morphometrics and Bayesian analyses with implications to human evolution." Journal of Archaeological Science 89 (January 2018): 56–67. http://dx.doi.org/10.1016/j.jas.2017.10.004.

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Hedrick, B. P., P. Antalek‐Schrag, A. J. Conith, L. J. Natanson, and P. L. R. Brennan. "Variability and asymmetry in the shape of the spiny dogfish vagina revealed by 2D and 3D geometric morphometrics." Journal of Zoology 308, no. 1 (February 8, 2019): 16–27. http://dx.doi.org/10.1111/jzo.12653.

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Menéndez, Lumila Paula. "Comparing Methods to Assess Intraobserver Measurement Error of 3D Craniofacial Landmarks Using Geometric Morphometrics Through a Digitizer Arm." Journal of Forensic Sciences 62, no. 3 (November 22, 2016): 741–46. http://dx.doi.org/10.1111/1556-4029.13301.

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Braga, José, Veronika Zimmer, Jean Dumoncel, Chafik Samir, Frikkie de Beer, Clément Zanolli, Deborah Pinto, F. James Rohlf, and Frederick E. Grine. "Efficacy of diffeomorphic surface matching and 3D geometric morphometrics for taxonomic discrimination of Early Pleistocene hominin mandibular molars." Journal of Human Evolution 130 (May 2019): 21–35. http://dx.doi.org/10.1016/j.jhevol.2019.01.009.

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Zhang, Yameng, and Lynne A. Schepartz. "Three-dimensional geometric morphometric studies of modern human occipital variation." PLOS ONE 16, no. 1 (January 14, 2021): e0245445. http://dx.doi.org/10.1371/journal.pone.0245445.

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Objectives To investigate three-dimensional morphological variation of the occipital bone between sexes and among populations, to determine how ancestry, sex and size account for occipital shape variation and to describe the exact forms by which the differences are expressed. Methods CT data for 214 modern crania of Asian, African and European ancestry were compared using 3D geometric morphometrics and multivariate statistics, including principal component analysis, Hotelling’s T2 test, multivariate regression, ANOVA, and MANCOVA. Results Sex differences in average occipital morphology are only observed in Europeans, with males exhibiting a pronounced inion. Significant ancestral differences are observed among all samples and are shared by males and females. Asian and African crania have smaller biasterionic breadths and flatter clivus angles compared to Europeans. Asian and European crania are similar in their nuchal and occipital plane proportions, nuchal and occipital angles, and lower inion positions compared to Africans. Centroid size significantly differs between sexes and among populations. The overall allometry, while significant, explains little of the shape variation. Larger occipital bones were associated with a more curved occipital plane, a pronounced inion, a narrower biasterionic breadth, a more flexed clivus, and a lower and relatively smaller foramen magnum. Conclusions Although significant shape differences were observed among populations, it is not recommended to use occipital morphology in sex or population estimation as both factors explained little of the observed variance. Other factors, relating to function and the environment, are suggested to be greater contributors to occipital variation. For the same reason, it is also not recommended to use the occiput in phylogenetic studies.

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Ruiz, Sthepanie, Anderson Silva, Mayra Celis, Rocio Ruales, Francined Pardo, Sofia Moreno, Juan Bermeo, David Gutierrez, and Itzjak Kadar. "Description of facial symmetry in patients with unilateral cleft lip and palate using geometric morphometry and computerized tomography." Revista Estomatología 22, no. 1 (September 29, 2017): 20–25. http://dx.doi.org/10.25100/re.v22i1.5770.

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Objective: To describe the maxillary asymmetry in patients with single cleft lip and palate by using morphometrics geometric methods. Materials and Methods: Applied morphometrics geometric methods to analyze images captured from 3D reconstructions of CT scans of 9 patients with unilateral cleft lip and palate, mean age of 13.7 years was used. Tps Dig2 software was used to digitalize 6 maxillary landmarks shaping both the affected and the sides unaffected. TpsPower and TpsPLS to a small sample for relative warps and consensus for superimposition. Thin plate function and asymmetry was used applying ASI-CLIC® package, and the principal component analysis was performed with the PAST software version 2.17.0. Results: There is a statistically significant difference (p<0.05) between the conformation of the maxilla on the affected side compared to unaffected. The study of asymmetry indicated different degrees and differences in the nature of the asymmetry that characterizes different deformities of unilateral cleft lip and palate. The principal component analysis demonstrates both inter-group variability and recognizes two principal components, 39.4%, to the first component and 27.5% to the second component. There is a high correlation between the formation of the unaffected side and affected side conformation r= 0.93847. The thin plate deformation is uniform. The allometry study indicated that there is no association between the shape and size. Conclusions: Morphometry Geometric method is a useful tool for assessing preoperative maxillary conformations in patients with unilateral cleft lip and palate. The side without the cleft is also affected, and is associated with the formation on the side of the cleft. The frontonasal suture is also affected, in a greater proportion than the fronto zigomatic.

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Baynam, Gareth, Peter Claes, Jeffrey M. Craig, Jack Goldblatt, Stefanie Kung, Peter Le Souef, and Mark Walters. "Intersections of Epigenetics, Twinning and Developmental Asymmetries: Insights Into Monogenic and Complex Diseases and a Role for 3D Facial Analysis." Twin Research and Human Genetics 14, no. 4 (August 1, 2011): 305–15. http://dx.doi.org/10.1375/twin.14.4.305.

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For decades the relationships of twinning and alterations in body patterning, such as laterality and asymmetry, have been investigated. However, the tools to define and quantify these relationships have been limited and the majority of these studies have relied on associations with subjectively defined phenotypes. The emerging technologies of 3-dimensional (3D) facial scanning and geometric morphometrics are providing the means to establish objective criteria, including measures of asymmetry, which can be used for phenotypic classification and investigations. Additionally, advances in molecular epigenetics provide new opportunities for novel investigations of mechanisms central to early developmental processes, twinning and related phenotypes. We review the evidence for overlapping etiologies of twinning, asymmetry and selected monogenic and complex diseases, and we suggest that the combination of epigenetic investigations with detailed and objective phenotyping, utilizing 3D facial analysis tools, can reveal insights into the genesis of these phenomena.

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Caro, Amaia, Benjamín Juan Gómez-Moliner, and María José Madeira. "Integrating multilocus DNA data and 3D geometric morphometrics to elucidate species boundaries in the case of Pyrenaearia (Pulmonata: Hygromiidae)." Molecular Phylogenetics and Evolution 132 (March 2019): 194–206. http://dx.doi.org/10.1016/j.ympev.2018.12.007.

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de Bonnecaze, G., N. Telmon, S. Vergez, P. Chaynes, E. Serrano, and F. Savall. "Analyses of the inferior turbinate using 3D geometric morphometrics: an anatomical study and discussion of the potential clinical implications." Rhinology Online 1, no. 1 (May 1, 2018): 38–44. http://dx.doi.org/10.4193/rhinol/18.010.

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Kraatz, Brian, and Emma Sherratt. "Evolutionary morphology of the rabbit skull." PeerJ 4 (September 22, 2016): e2453. http://dx.doi.org/10.7717/peerj.2453.

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The skull of leporids (rabbits and hares) is highly transformed, typified by pronounced arching of the dorsal skull and ventral flexion of the facial region (i.e., facial tilt). Previous studies show that locomotor behavior influences aspects of cranial shape in leporids, and here we use an extensive 3D geometric morphometrics dataset to further explore what influences leporid cranial diversity. Facial tilt angle, a trait that strongly correlates with locomotor mode, significantly predicts the cranial shape variation captured by the primary axis of cranial shape space, and describes a small proportion (13.2%) of overall cranial shape variation in the clade. However, locomotor mode does not correlate with overall cranial shape variation in the clade, because there are two district morphologies of generalist species, and saltators and cursorial species have similar morphologies. Cranial shape changes due to phyletic size change (evolutionary allometry) also describes a small proportion (12.5%) of cranial shape variation in the clade, but this is largely driven by the smallest living leporid, the pygmy rabbit (Brachylagus idahoensis). By integrating phylogenetic history with our geometric morphometric data, we show that the leporid cranium exhibits weak phylogenetic signal and substantial homoplasy. Though these results make it difficult to reconstruct what the ‘ancestral’ leporid skull looked like, the fossil records suggest that dorsal arching and facial tilt could have occurred before the origin of the crown group. Lastly, our study highlights the diversity of cranial variation in crown leporids, and highlights a need for additional phylogenetic work that includes stem (fossil) leporids and includes morphological data that captures the transformed morphology of rabbits and hares.

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Černá Bolfíková, Barbora, Allowen Evin, Markéta Rozkošná Knitlová, Miroslava Loudová, Anna Sztencel-Jabłonka, Wiesław Bogdanowicz, and Pavel Hulva. "3D Geometric Morphometrics Reveals Convergent Character Displacement in the Central European Contact Zone between Two Species of Hedgehogs (Genus Erinaceus)." Animals 10, no. 10 (October 4, 2020): 1803. http://dx.doi.org/10.3390/ani10101803.

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Hedgehogs, as medium-sized plantigrade insectivores with low basal metabolic rates and related defensive anti-predator strategies, are quite sensitive to temperature and ecosystem productivity. Their ranges therefore changed dramatically due to Pleistocene climate oscillations, resulting in allopatric speciation and the subsequent formation of secondary contact zones. Such interactions between closely related species are known to generate strong evolutionary forces responsible for niche differentiation. In this connection, here, we detail the results of research on the phenotypic evolution in the two species of hedgehog present in central Europe, as based on genetics and geometric morphometrics in samples along a longitudinal transect that includes the contact zone between the species. While in allopatry, Erinaceus europaeus is found to have a larger skull than E. roumanicus and distinct cranial and mandibular shapes; the members of the two species in sympatry are smaller and more similar to each other, with a convergent shape of the mandible. The relevant data fail to reveal any major role for either hybridisation or clinal variation. We, therefore, hypothesise that competitive pressure exerted on the studied species does not generate divergent selection sufficient for divergent character displacement to evolve, instead giving rise to convergent selection in the face of resource limitation in the direction of smaller skull size. Considering the multi-factorial constraints present in the relevant adaptive landscape, reduction in size could also be facilitated by predator pressure in ecosystems characterised by mesopredator release and other anthropogenic factors. As the function of the animals’ lower jaw is mainly connected with feeding (in contrast to the cranium whose functions are obviously more complex), we interpret the similarity in shape as reflecting local adaptations to overlapping dietary resources in the two species and hence as convergent character displacement.

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Owen, Joseph, Keith Dobney, Allowen Evin, Thomas Cucchi, Greger Larson, and Una Strand Vidarsdottir. "The zooarchaeological application of quantifying cranial shape differences in wild boar and domestic pigs (Sus scrofa) using 3D geometric morphometrics." Journal of Archaeological Science 43 (March 2014): 159–67. http://dx.doi.org/10.1016/j.jas.2013.12.010.

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Schmidt, Dominik, and Katrin Kahlen. "Towards More Realistic Leaf Shapes in Functional-Structural Plant Models." Symmetry 10, no. 7 (July 12, 2018): 278. http://dx.doi.org/10.3390/sym10070278.

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Fluctuating asymmetry in plant leaves is a widely used measure in geometric morphometrics for assessing random deviations from perfect symmetry. In this study, we considered the concept of fluctuating asymmetry to improve the prototype leaf shape of the functional-structural plant model L-Cucumber. The overall objective was to provide a realistic geometric representation of the leaves for the light sensitive plant reactions in the virtual plant model. Based on three-dimensional data from several hundred in situ digitized cucumber leaves comparisons of model leaves and measurements were conducted. Robust Bayesian comparison of groups was used to assess statistical differences between leaf halves while respecting fluctuating asymmetries. Results indicated almost no directional asymmetry in leaves comparing different distances from the prototype while detecting systematic deviations shared by both halves. This information was successfully included in an improved leaf prototype and implemented in the virtual plant model L-Cucumber. Comparative virtual plant simulations revealed a slight improvement in plant internode development against experimental data using the novel leaf shape. Further studies can now focus on analyses of stress on the 3D-deformation of the leaf and the development of a dynamic leaf shape model.

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Lewton, Kristi L., Ryan Brankovic, William A. Byrd, Daniela Cruz, Jocelyn Morales, and Serin Shin. "The effects of phylogeny, body size, and locomotor behavior on the three-dimensional shape of the pelvis in extant carnivorans." PeerJ 8 (February 20, 2020): e8574. http://dx.doi.org/10.7717/peerj.8574.

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The mammalian pelvis is thought to exhibit adaptations to the functional demands of locomotor behaviors. Previous work in primates has identified form-function relationships between pelvic shape and locomotor behavior; few studies have documented such relationships in carnivorans, instead focusing on long bones. Most work on the functional morphology of the carnivoran pelvis, in particular, has used univariate measures, with only a few previous studies incorporating a three-dimensional (3D) analysis. Here we test the hypothesis that carnivoran taxa that are characterized by different locomotor modes also differ in 3D shape of the os coxae. Using 3D geometric morphometrics and phylogenetic comparative methods, we evaluate the phylogenetic, functional, and size-related effects on 3D pelvis shape in a sample of 33 species of carnivorans. Using surface models derived from laser scans, we collected a suite of landmarks (N = 24) and curve semilandmarks (N = 147). Principal component analysis on Procrustes coordinates demonstrates patterns of shape change in the ischiopubis and ilium likely related to allometry. Phylogenetic generalized least squares analysis on principal component scores demonstrates that phylogeny and body size have greater effects on pelvic shape than locomotor function. Our results corroborate recent research finding little evidence of locomotor specialization in the pelvis of carnivorans. More research on pelvic morphological integration and evolvability is necessary to understand the factors driving pelvic evolution in carnivorans.

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Nakamura, Yuki, Charles Romans, and Ravi Ashwath. "Patient-Specific Patch for an Intra-Atrial Rerouting Procedure Developed Through Surgical Simulation." World Journal for Pediatric and Congenital Heart Surgery 12, no. 2 (March 2021): 234–43. http://dx.doi.org/10.1177/2150135120985469.

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Background: In pediatric cardiac surgery, an application of three-dimensional (3D) modeling to develop custom-made prostheses is limited, and currently surgeons use their intraoperative visual estimation to develop 3D complex structures from 2D patch materials. Contemporary 3D designers are developing complex surfaces using surface modeling in other industries, which can be applied to pediatric cardiac surgery. However, its free-form nature may lead to intradesigner variability. Methods: A patient with a body weight of 4 kg with partial anomalous pulmonary venous connection and preoperative computed tomography data was selected, and a patient-specific 3D heart model was obtained. Through collaboration with a pediatric cardiologist and a pediatric cardiac surgeon, a 3D designer developed two patient-specific 3D patches for an intra-atrial rerouting procedure (IAR) for the patient using different methods of surface modeling. The shape and size of two flattened patches were analyzed using a geometric morphometrics (GM) approach. Computational fluid dynamics (CFD) analysis was also performed to calculate pressure drop across streamlines and flow energy loss in the right atrium for both patches. Results: The GM analysis showed that the size and shape of the two patches around the systemic vein orifice, crucial to prevent systemic venous obstruction, were almost equivalent. However, the CFD analysis showed that the pressure drop and flow energy loss were almost twice for one patch compared with the other. Conclusions: Our platform of developing a patient-specific 3D patch for an IAR procedure using surface modeling seemed promising, although intradesigner patch variability was not neglectable in our small-sized patient.

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Parr, W. C. H., S. Wroe, U. Chamoli, H. S. Richards, M. R. McCurry, P. D. Clausen, and C. McHenry. "Toward integration of geometric morphometrics and computational biomechanics: New methods for 3D virtual reconstruction and quantitative analysis of Finite Element Models." Journal of Theoretical Biology 301 (May 2012): 1–14. http://dx.doi.org/10.1016/j.jtbi.2012.01.030.

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Rochman, Dina, and Efraín De Luna. "Prototyping the complex biological form of the beetle Deltochilum Lobipes via 2D geometric morphometrics landmarks and descriptive geometry for 3D printing." Computer-Aided Design and Applications 14, no. 1 (June 20, 2016): 107–16. http://dx.doi.org/10.1080/16864360.2016.1199761.

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Kuzminsky, Susan C., Tiffiny A. Tung, Mark Hubbe, and Antonio Villaseñor-Marchal. "The application of 3D geometric morphometrics and laser surface scanning to investigate the standardization of cranial vault modification in the Andes." Journal of Archaeological Science: Reports 10 (December 2016): 507–13. http://dx.doi.org/10.1016/j.jasrep.2016.11.007.

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Arias-Martorell, Julia, David M. Alba, Josep M. Potau, Gaëlle Bello-Hellegouarch, and Alejandro Pérez-Pérez. "Morphological affinities of the proximal humerus of Epipliopithecus vindobonensis and Pliopithecus antiquus: Suspensory inferences based on a 3D geometric morphometrics approach." Journal of Human Evolution 80 (March 2015): 83–95. http://dx.doi.org/10.1016/j.jhevol.2014.08.012.

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