scholarly journals ShapeRotator: an R tool for standardised rigid rotations of articulated Three-Dimensional structures with application for geometric morphometrics

2017 ◽  
Author(s):  
Marta Vidal-García ◽  
Lashi Bandara ◽  
J. Scott Keogh
Keyword(s):  
Geometric Morphometrics ◽  
Phenotypic Diversity ◽  
Three Dimensional ◽  
R Package ◽  
Morphological Data ◽  
List Type ◽  
Shape Variation ◽  
Data Set ◽  
Articulated Structures ◽  
Shape And Size

SummaryThe quantification of complex morphological patterns typically involves comprehensive shape and size analyses, usually obtained by gathering morphological data from all the structures that capture the phenotypic diversity of an organism or object. Articulated structures are a critical component of overall phenotypic diversity, but data gathered from these structures are difficult to incorporate in to modern analyses because of the complexities associated with jointly quantifying 3D shape in multiple structures.While there are existing methods for analysing shape variation in articulated structures in Two-Dimensional (2D) space, these methods do not work in 3D, a rapidly growing area of capability and research.Here we describe a simple geometric rigid rotation approach that removes the effect of random translation and rotation, enabling the morphological analysis of 3D articulated structures. Our method is based on Cartesian coordinates in 3D space so it can be applied to any morphometric problem that also uses 3D coordinates (e.g. spherical harmonics). We demonstrate the method by applying it to a landmark-based data set for analysing shape variation using geometric morphometrics.We have developed an R tool (ShapeRotator) so that the method can be easily implemented in the commonly used R package geomorph and MorphoJ software. This method will be a valuable tool for 3D morphological analyses in articulated structures by allowing an exhaustive examination of shape and size diversity.

scholarly journals Variation in pelvic shape and size in Eastern European males: a computed tomography comparative study

PeerJ ◽  
2019 ◽  
Vol 7 ◽  
pp. e6433 ◽  
Author(s):  
Bartosz Musielak ◽  
Anna Maria Kubicka ◽  
Michał Rychlik ◽  
Jarosław Czubak ◽  
Adam Czwojdziński ◽  
...  
Keyword(s):  
Geometric Morphometrics ◽  
Body Mass ◽  
Three Dimensional ◽  
Opening Angle ◽  
Control Group ◽  
Human Society ◽  
Eastern European ◽  
Adult Males ◽  
Pelvic Shape ◽  
Shape And Size

Background The significantly accelerated development of human society in the last millennium has brought about changes in human behavior and body mass that may have influenced human bone morphology. Our objective was to analyze the variation in pelvic shape and size in males from modern and medieval populations. Methods We obtained 22 pelvic girdles of adult males from a medieval cemetery located in Cedynia, Poland. The control group comprised 31 contemporary male pelves from individuals inhabiting the same region. The analyzed parameters were: interspinous distance (ISD), intercristal distance (ICD), intertuberous distance (ITD), anatomic conjugate of the pelvis, height of the pelvis (HP), iliac opening angle (IOA), iliac tilt angle (ITA), and ISD/ITD/HP ratio. Geometric morphometrics was used to analyze differences in shape in the pelves. All analyses were carried out on three-dimensional CT reconstructions of pelves. Results ISD, ICD, and IOA were significantly greater in modern pelves than in those from Cedynia, but no significant differences were seen between the two groups in ITD, anatomical conjugate, HP, or ITA. ISD/ITD/HP ratios were significantly lower in the Cedynia group. Geometric morphometrics revealed significant differences in pelvic shape between the analyzed groups. Discussion The pelves of modern males are larger, wider, and flatter than those of medieval males. Changes in the set of daily activities that produce mechanical loading and estimated body mass may constitute the main factors explaining pelvic variability. However, differences in ontogenesis should also be taken into consideration, especially since growth in past populations is often found to be reduced relative to modern populations.

scholarly journals Generation and application of river network analogues for use in ecology and evolution

2020 ◽  
Author(s):  
Luca Carraro ◽  
Enrico Bertuzzo ◽  
Emanuel A. Fronhofer ◽  
Reinhard Furrer ◽  
Isabelle Gounand ◽  
...  
Keyword(s):  
Spatial Ecology ◽  
Spanning Trees ◽  
Random Search ◽  
Three Dimensional ◽  
R Package ◽  
River Network ◽  
River Networks ◽  
List Type ◽  
Freshwater Ecology ◽  
Scaling Features

AbstractSeveral key processes in freshwater ecology and evolution are governed by the connectivity inherent to dendritic river networks. These networks have extensively been analyzed from a geomorphological and hydrological viewpoint, yet network structures classically used in modelling have only been partially representative of the structure of real river basins, and have often failed to capture well known scaling features of real river networks. Pioneering work has identified optimal channel networks (OCNs) as spanning trees that reproduce all scaling features characteristic of real, natural stream networks worldwide. While these networks have been used to generate landscapes for studies on metapopulations, biodiversity and epidemiology, their generation has not been generally accessible.Given the increasing interest in dendritic riverine networks by ecologists and evolutionary biologists, we here present a method to generate OCNs and, to facilitate its application, we also provide the R-package OCNet. Owing to the random search process that generates OCNs, multiple network replicas spanning the same surface can be built, allowing one to perform computational experiments whose results do not depend on the particular shape of a single river network. The OCN construct also enables the generation of elevational gradients derived from the optimal network configuration, which can constitute three-dimensional landscapes for spatial studies in both terrestrial and freshwater realms. Moreover, the OCNet package provides functions that aggregate the OCN into an arbitrary number of nodes, calculate several metrics and descriptors of river networks, and draw relevant features of the network.We describe the main functionalities of the package and present how it can be integrated into other R-packages commonly used in spatial ecology. Moreover, we exemplify the generation of OCNs and discuss an application to a metapopulation model for an invasive riverine species.In conclusion, OCNet provides a powerful tool to generate and use realistic river network analogues for various applications. It thereby allows the design of spatially realistic studies in increasingly impacted ecosystems, and enhances our knowledge on spatial processes in freshwater ecology in general.

scholarly journals Unexpected Morphological Diversity in New Zealand’s Large Diplodactylidae Geckos

2021 ◽  
Author(s):  
Lachie Scarsbrook ◽  
Emma Sherratt ◽  
Rod Hitchmough ◽  
R. Ewan Fordyce ◽  
Nicolas J. Rawlence
Keyword(s):  
New Zealand ◽  
Geometric Morphometrics ◽  
Relative Size ◽  
Three Dimensional ◽  
Morphological Diversity ◽  
Anthropogenic Disturbances ◽  
Species Level ◽  
Global Biodiversity ◽  
The Impact ◽  
Shape And Size

Abstract Prehistoric anthropogenically-mediated extinctions have impacted global biodiversity; however effects on herpetofauna are poorly-documented. New Zealand’s Diplodactylidae geckos exhibit high species-level diversity, largely independent of discernible osteological changes (cryptic). Consequently, taxonomic affinities of isolated skeletal elements (fossils) are primarily determined by relative size, particularly in the identification of Hoplodactylus duvaucelii; New Zealand’s largest extant gecko species. Here, three-dimensional geometric morphometrics of maxillae (a common fossilized element) was used to determine whether consistent shape and size differences exist between genera, and if cryptic extinctions have occurred in ‘Hoplodactylus cf. duvaucelii’. Sampling included 13 Diplodactylidae species from five genera, and 11 Holocene ‘H. cf. duvaucelii’ subfossil individuals. We found phylogenetic history was the most important predictor of maxilla morphology among extant Diplodactylidae genera. Relative size comparisons could only differentiate Hoplodactylus from other genera, with the remaining genera exhibiting variable degrees of overlap. Six subfossils were positively identified as H. duvaucelii, confirming their proposed Holocene distribution throughout New Zealand. Conversely, five subfossils showed no affinities towards any modern Diplodactylidae genera, implying either increased morphological diversity in mainland ‘H. cf. duvaucelii’ or the presence of at least one extinct, large, broad-toed Diplodactylidae species. These results highlight the impact of anthropogenic disturbances on insular reptile diversity.

scholarly journals Three-dimensional geometric morphometrics for studying floral shape variation

2010 ◽  
Vol 15 (8) ◽  
pp. 423-426 ◽  
Author(s):  
Timotheüs van der Niet ◽  
Christoph P.E. Zollikofer ◽  
Marcia S. Ponce de León ◽  
Steven D. Johnson ◽  
H. Peter Linder
Keyword(s):  
Geometric Morphometrics ◽  
Three Dimensional ◽  
Shape Variation

scholarly journals A Registration and Deep Learning Approach to Automated Landmark Detection for Geometric Morphometrics

2019 ◽  
Author(s):  
Jay Devine ◽  
Jose D. Aponte ◽  
David C. Katz ◽  
Wei Liu ◽  
Lucas D. Lo Vercio ◽  
...  
Keyword(s):  
Image Registration ◽  
Geometric Morphometrics ◽  
Small Scale ◽  
List Type ◽  
Shape Variation ◽  
Landmark Detection ◽  
Sample Mean ◽  
Computed Tomography Images ◽  
Mean Shape ◽  
Landmark Data

ABSTRACTGeometric morphometrics is the statistical analysis of landmark-based shape variation and its covariation with other variables. Over the past two decades, the gold standard of landmark data acquisition has been manual detection by a single observer. This approach has proven accurate and reliable in small-scale investigations. However, big data initiatives are increasingly common in biology and morphometrics. This requires fast, automated, and standardized data collection. Image registration, or the spatial alignment of images, is a fundamental technique in automatic image analysis that is well-poised for such purposes. Yet, in the few studies that have explored the utility of registration-based landmarks for geometric morphometrics, relatively high or catastrophic labelling errors around anatomical extrema are common. Such errors can result in misleading representations of the mean shape, an underestimation of biological signal, and altered variance-covariance patterns.We combine image registration with a deep and domain-specific neural network to automate and optimize anatomical landmark detection for geometric morphometrics. Using micro-computed tomography images of genetically and morphologically variable mouse skulls, we test our landmarking approach under a variety of registration conditions, including different non-linear deformation frameworks (small vs. large) and atlas strategies (single vs. multi).Compared to landmarks derived from conventional image registration workflows, our optimized landmark data show significant reductions in error at problematic locations (up to 0.63 mm), a 36.4% reduction in average landmark coordinate error, and up to a 45.1% reduction in total landmark distribution error. We achieve significant improvements in estimates of the sample mean shape and variance-covariance structure.For biological imaging datasets and morphometric research questions, our method can eliminate the time and subjectivity of manual landmark detection whilst retaining the biological integrity of these expert annotations.

New Three-Dimensional Algebraic Reconstruction Techniques (Art)

1971 ◽  
Vol 29 ◽  
pp. 82-83 ◽  
Author(s):  
Richard Gordon ◽  
Robert Bender
Keyword(s):  
Three Dimensional ◽  
Fourier Method ◽  
List Type ◽  
Type Number ◽  
Data Set ◽  
3 Dimensional ◽  
Dimensional Reconstruction ◽  
Algebraic Reconstruction Techniques ◽  
Electron Microscope Data ◽  
Algebraic Reconstruction

Algebraic reconstruction techniques (ART) for 3-dimensional reconstruction from electron microscope data have been developed and implemented in this laboratory. These methods are an alternitive to the Fourier method of de Rosier and Klug and have several advantages over it, such as:relatively few views are required (about 6-12)limited angular ranges give useful reconstructions (+/-30°)no presumption of symmetry is necessary for facile implementingcomputation is fasterthe computation is stable in the presence of noiseThe dimensionality of the problem may be reduced from three to two by tilts about a single axis, so that planes perpendicular to the axis of tilt are independent of each other. This is not absolutely necessary, but is by far the most tractable mode computationally. A typical input data set, then, consists of m≥6 photos of the same region of the specimen at several known angles of tilt about the same axis. In general the direction of the tilt axis is not known.

scholarly journals Three-Dimensional Reconstruction of Thoracic Structures: Based on Chinese Visible Human

2013 ◽  
Vol 2013 ◽  
pp. 1-7
Author(s):  
Yi Wu ◽  
Na Luo ◽  
Liwen Tan ◽  
Binji Fang ◽  
Ying Li ◽  
...  
Keyword(s):  
Volume Rendering ◽  
Cardiovascular Surgery ◽  
Three Dimensional ◽  
Vena Cava ◽  
Morphological Data ◽  
Surface Rendering ◽  
Data Set ◽  
Chinese Visible Human ◽  
Reconstructed Model ◽  
Visible Human

We managed to establish three-dimensional digitized visible model of human thoracic structures and to provide morphological data for imaging diagnosis and thoracic and cardiovascular surgery. With Photoshop software, the contour line of lungs and mediastinal structures including heart, aorta and its ramus, azygos vein, superior vena cava, inferior vena cava, thymus, esophagus, diaphragm, phrenic nerve, vagus nerve, sympathetic trunk, thoracic vertebrae, sternum, thoracic duct, and so forth were segmented from the Chinese Visible Human (CVH)-1 data set. The contour data set of segmented thoracic structures was imported to Amira software and 3D thorax models were reconstructed via surface rendering and volume rendering. With Amira software, surface rendering reconstructed model of thoracic organs and its volume rendering reconstructed model were 3D reconstructed and can be displayed together clearly and accurately. It provides a learning tool of interpreting human thoracic anatomy and virtual thoracic and cardiovascular surgery for medical students and junior surgeons.

scholarly journals Morphological variation under domestication: how variable are chickens?

2018 ◽  
Vol 5 (8) ◽  
pp. 180993 ◽  
Author(s):  
Madlen Stange ◽  
Daniel Núñez-León ◽  
Marcelo R. Sánchez-Villagra ◽  
Per Jensen ◽  
Laura A. B. Wilson
Keyword(s):  
Neural Crest ◽  
Geometric Morphometrics ◽  
Multivariate Statistics ◽  
Morphological Variation ◽  
Three Dimensional ◽  
Cranial Vault ◽  
Shape Variation ◽  
Skull Morphology ◽  
Variable Part ◽  
Brain Shape

The process of domestication has long fascinated evolutionary biologists, yielding insights into the rapidity with which selection can alter behaviour and morphology. Previous studies on dogs, cattle and pigeons have demonstrated that domesticated forms show greater magnitudes of morphological variation than their wild ancestors. Here, we quantify variation in skull morphology, modularity and integration in chickens and compare those to the wild fowl using three-dimensional geometric morphometrics and multivariate statistics. Similar to other domesticated species, chickens exhibit a greater magnitude of variation in shape compared with their ancestors. The most variable part of the chicken skull is the cranial vault, being formed by dermal and neural crest-derived bones, its form possibly related to brain shape variation in chickens, especially in crested breeds. Neural crest-derived portions of the skull exhibit a higher amount of variation. Further, we find that the chicken skull is strongly integrated, confirming previous studies in birds, in contrast to the presence of modularity and decreased integration in mammals.

scholarly journals Evolution of hyperossification expands skull diversity in frogs

2020 ◽  
Vol 117 (15) ◽  
pp. 8554-8562 ◽  
Author(s):  
Daniel J. Paluh ◽  
Edward L. Stanley ◽  
David C. Blackburn
Keyword(s):  
Defense Mechanism ◽  
Three Dimensional ◽  
Morphological Data ◽  
Shape Variation ◽  
Skull Shape ◽  
Worldwide Distribution ◽  
History Of ◽  
Wide Scale ◽  
Head Morphology ◽  
Specialized Diet

Frogs (Anura) are one of the most diverse vertebrate orders, comprising more than 7,000 species with a worldwide distribution and extensive ecological diversity. In contrast to other tetrapods, frogs have a highly derived body plan and simplified skull. In many lineages of anurans, increased mineralization has led to hyperossified skulls, but the function of this trait and its relationship with other aspects of head morphology are largely unexplored. Using three-dimensional morphological data from 158 species representing all frog families, we assessed wide-scale patterns of shape variation across all major lineages, reconstructed the evolutionary history of cranial hyperossification across the anuran phylogeny, and tested for relationships between ecology, skull shape, and hyperossification. Although many frogs share a conserved skull shape, several extreme forms have repeatedly evolved that commonly are associated with hyperossification, which has evolved independently more than 25 times. Variation in cranial shape is not explained by phylogenetic relatedness but is correlated with shifts in body size and ecology. The species with highly divergent, hyperossified skulls often have a specialized diet or a unique predator defense mechanism. Thus, the evolution of hyperossification has repeatedly facilitated the expansion of the head into multiple new shapes and functions.

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