scholarly journals Three-dimensional morphological variability of Recent rhynchonellide brachiopod crura

Paleobiology ◽  
10.1666/13042 ◽  
2014 ◽  
Vol 40 (4) ◽  
pp. 640-658 ◽  
Author(s):  
Holly A. Schreiber ◽  
Peter D. Roopnarine ◽  
Sandra J. Carlson
Keyword(s):  
Imaging Techniques ◽  
Morphological Variability ◽  
Three Dimensional ◽  
Principal Component ◽  
Shape Space ◽  
Ontogenetic Changes ◽  
Cross Sectional ◽  
Evolutionary Transitions ◽  
Geometric Morphometric ◽  
Computed Microtomography

Crura, the calcareous support structures of the lophophore in rhynchonellide brachiopods, have historically been used to justify higher-level rhynchonellide classification and reveal major evolutionary lineages within rhynchonellides. Seventeen crural types have been described and categorized into four groups based on variation in overall structure and cross-sectional shape, but not evaluated in a quantitative or comprehensive manner. Heterochrony has been hypothesized to play a role in the evolutionary transitions among some types, but the structural, developmental, and phylogenetic context for testing these hypotheses has not yet been established. In this study, we use three-dimensional geometric morphometric techniques to quantify morphological disparity among all six crural morphs in Recent adult rhynchonellides, with the goal of delineating more objective criteria for identifying and comparing crural morphs, ultimately to test hypotheses explaining morphological transformations in ontogeny and phylogeny. We imaged the crura of seven Recent rhynchonellide species, using X-ray computed microtomography. We used landmarks and semi-landmarks to define the dimensions and curvature of the crura and the surrounding hinge area. Procrustes-standardized landmark coordinates were analyzed using a principal component analysis to test the discreteness of the individual crural morphs and named groups of morphs, and to identify features that vary most among the crural configurations.Our results demonstrate that microCT imaging techniques provide novel ways to investigate the morphology of small features that may be otherwise impossible to quantify using more conventional imaging techniques. Although we predicted overlap among crural morphs in the 3-D shape space, the principal component analyses suggest that five of the six crural morphs differ distinctly from one another. Some but not all previously designated crural groups appear to exhibit morphological cohesion. This study establishes a quantitative morphological foundation necessary to begin an investigation of the phylogenetic significance of ontogenetic changes in crura, which will allow hypotheses of heterochrony to be tested.

Statistical Approach to Shape from Shading: Reconstruction of Three-Dimensional Face Surfaces from Single Two-Dimensional Images

1996 ◽  
Vol 8 (6) ◽  
pp. 1321-1340 ◽  
Author(s):  
Joseph J. Atick ◽  
Paul A. Griffin ◽  
A. Norman Redlich
Keyword(s):  
Dimensional Space ◽  
Three Dimensional ◽  
Practical Interest ◽  
Principal Component ◽  
Shape From Shading ◽  
Shape Space ◽  
Two Dimensional ◽  
Two Dimensional Image ◽  
Low Dimensional ◽  
Dimensional Object

The human visual system is proficient in perceiving three-dimensional shape from the shading patterns in a two-dimensional image. How it does this is not well understood and continues to be a question of fundamental and practical interest. In this paper we present a new quantitative approach to shape-from-shading that may provide some answers. We suggest that the brain, through evolution or prior experience, has discovered that objects can be classified into lower-dimensional object-classes as to their shape. Extraction of shape from shading is then equivalent to the much simpler problem of parameter estimation in a low-dimensional space. We carry out this proposal for an important class of three-dimensional (3D) objects: human heads. From an ensemble of several hundred laser-scanned 3D heads, we use principal component analysis to derive a low-dimensional parameterization of head shape space. An algorithm for solving shape-from-shading using this representation is presented. It works well even on real images where it is able to recover the 3D surface for a given person, maintaining facial detail and identity, from a single 2D image of his face. This algorithm has applications in face recognition and animation.

scholarly journals Characterising 3D spherical packings by principal component analysis

2019 ◽  
Vol 37 (3) ◽  
pp. 1023-1041 ◽  
Author(s):  
Tingting Zhao ◽  
Y.T. Feng ◽  
Yuanqiang Tan
Keyword(s):  
Principal Component Analysis ◽  
Gaussian Quadrature ◽  
Three Dimensional ◽  
Principal Component ◽  
Component Analysis ◽  
Particle Packing ◽  
Cross Sectional ◽  
Content Type ◽  
Computer Methods ◽  
Novel Approach

Purpose The purpose of this paper is to extend the previous study [Computer Methods in Applied Mechanics and Engineering 340: 70-89, 2018] on the development of a novel packing characterising system based on principal component analysis (PCA) to quantitatively reveal some fundamental features of spherical particle packings in three-dimensional. Design/methodology/approach Gaussian quadrature is adopted to obtain the volume matrix representation of a particle packing. Then, the digitalised image of the packing is obtained by converting cross-sectional images along one direction to column vectors of the packing image. Both a principal variance (PV) function and a dissimilarity coefficient (DC) are proposed to characterise differences between different packings (or images). Findings Differences between two packings with different packing features can be revealed by the PVs and DC. Furthermore, the values of PV and DC can indicate different levels of effects on packing caused by configuration randomness, particle distribution, packing density and particle size distribution. The uniformity and isotropy of a packing can also be investigated by this PCA based approach. Originality/value Develop an alternative novel approach to quantitatively characterise sphere packings, particularly their differences.

scholarly journals Subspecies and sexual craniofacial size and shape variations in Japanese macaques (Macaca fuscata)

2018 ◽  
Author(s):  
Wataru Yano ◽  
Naoko Egi ◽  
Tomo Takano ◽  
Naomichi Ogihara
Keyword(s):  
Macaca Fuscata ◽  
Japanese Macaque ◽  
Three Dimensional ◽  
Principal Component ◽  
Shape Space ◽  
Size Difference ◽  
Shape Variation ◽  
Three Dimensional Model ◽  
Temporal Fossa ◽  
Size And Shape

AbstractIn order to investigate craniofacial size and three-dimensional shape variations independently in the Japanese macaque (Macaca fuscata) we used a geometric morphometries technique. A total of 55 specimens were CT scanned to generate a three-dimensional model of each cranium, and 57 landmarks were digitized to analyze the craniofacial shape variation in the Japanese macaque. The results showed that four intra-specific groups, consisting of two subspecies and the two sexes, differed in both size and shape space. In size, the cranium of the Macaca fuscata yakui (MFY) was smaller than that of Macaca fuscata fuscata (MFF) in both sexes, and female crania were smaller than male crania in both subspecies. Shape sexual dimorphisms in both subspecies were detected in the first axis of principal component analysis and were related to a relatively broad orbit, smaller neurocranium, enlarged snout, and broader temporal fossa in males. The shape differences between subspecies showed different features than those between sexes. Male subspecies shape differences were detected in the first and third axes, while those for females were in the first and second axes. Subspecies shape differences common to both sexes were a narrower orbit, relatively small neurocranium, longer snout, and postorbital constriction in MFY. Male MFY was specifically characterized by a more anterior and superior direction of snout protrusion. In contrast, female MFY showed an inferior direction of snout protrusion. Female MFY also had a taller orbit. With regard to the relationship between size and shape differences, shape sexual dimorphism for each subspecies was positively associated with size difference, but there was no such association between subspecies in either sex. Size does not seem to play an important role in subspeciation of Macaca fuscata.

scholarly journals Rapid and objective characterization of channel morphology in a small, forested stream

2020 ◽  
Author(s):  
Carina Helm ◽  
Marwan A. Hassan ◽  
David Reid
Keyword(s):  
Spatial Scale ◽  
Forest Canopy ◽  
Morphological Variability ◽  
Principal Component ◽  
Morphological Diversity ◽  
Channel Morphology ◽  
Classification Rate ◽  
Cross Sectional ◽  
Small Width ◽  
Gravel Bed Streams

Abstract. Forested, gravel bed streams possess complex channel morphologies which are difficult to objectively characterise. The spatial scale necessary to adequately capture variability in these streams is often unclear, as channels are governed by irregularly spaced features and episodic processes. This issue is compounded by the high cost and time-consuming nature of field surveys in this type of environment. In larger stream systems, remotely piloted aircraft (RPAs) have proven to be effective tools for characterizing channels at high resolutions over large spatial extents, but to date their use in small, forested streams with closed forest canopies has been limited. This paper seeks to demonstrate an objective method for characterizing channel attributes over large areas, using easily extractable data from RPA imagery collected under the forest canopy in a small (width = 10 to 15 m) stream, and to provide information on the spatial scale necessary to capture the dominant spatial morphological variability of these channels. First, the accuracy and coverage of RPAs for extracting channel data was investigated through a sub-canopy survey. From this survey data, relevant cross-sectional variables were extracted and used to characterize channel unit morphology using a principal component analysis-clustering (PCA-clustering) technique. Finally, the length scale required to capture dominant morphological variability was investigated from analysis of morphological diversity along nearly 3 km of channel. The results demonstrate that sub-canopy RPA surveys provide a viable alternative to traditional survey approaches for characterizing these systems, with 87 % coverage of the main channel stream bed. The PCA-clustering analysis provided a more objective means of classifying channel morphology with a correct classification rate of 85 %. Analysis of morphological diversity suggests that reaches of at least 15 bankfull width equivalents are required to capture the channel's dominant heterogeneity. Altogether, the results provide a precedent for using RPAs to characterize the morphology and diversity of forested streams under dense canopies.

scholarly journals Frontal Cryosectioning: An Improved Protocol for Sectioning Large Areas of Fibrous Scaffolds

2015 ◽  
Vol 2015 ◽  
pp. 1-7
Author(s):  
Casey P. Grey ◽  
David G. Simpson
Keyword(s):  
Cross Sections ◽  
Imaging Techniques ◽  
Fibrous Tissue ◽  
Three Dimensional ◽  
3D Models ◽  
Spatial Cues ◽  
Tissue Engineering Scaffolds ◽  
Cross Sectional ◽  
Fibrous Scaffolds ◽  
Scaffold Properties

Fibrous tissue engineering scaffolds, such as those produced by electrospinning, cannot achieve their clinical potential until deep cell-scaffold interactions are understood. Even the most advanced imaging techniques are limited to capturing data at depths of 100 µm due to light scatter associated with the fibers that compose these scaffolds. Conventional cross-sectional analysis provides information on relatively small volumes of space and frontal sections are difficult to generate. Current understanding of cellular penetration into fibrous scaffolds is limited predominantly to the scaffold surface. Although some information is available from cross-sections, sections vary in quality, can distort spatial scaffold properties, and offer virtually no spatial cues as to what scaffold properties instigate specific cellular responses. Without the definitive ability to understand how cells interact with the architecture of an entire scaffold it is difficult to justify scaffold modifications or in-depth cell penetration analyses until appropriate techniques are developed. To address this limitation we have developed a cryosectioning protocol that makes it possible to obtain serial frontal sections from electrospun scaffolds. Microscopic images assembled into montage images from serial sections were then used to create three-dimensional (3D) models of cellular infiltration throughout the entire scaffold.

scholarly journals Centric Allometry: Studying Growth Using Landmark Data

2021 ◽  
Author(s):  
Fred L. Bookstein
Keyword(s):  
Principal Component ◽  
Shape Space ◽  
Allometric Growth ◽  
Differential Growth ◽  
Data Set ◽  
Geometric Morphometric ◽  
Franz Boas ◽  
Landmark Data ◽  
Per Se ◽  
Algebraic Constraints

AbstractThe geometric morphometric (GMM) construction of Procrustes shape coordinates from a data set of homologous landmark configurations puts exact algebraic constraints on position, orientation, and geometric scale. While position as digitized is not ordinarily a biologically meaningful quantity, and orientation is relevant mainly when some organismal function interacts with a Cartesian positional gradient such as horizontality, size per se is a crucially important biometric concept, especially in contexts like growth, biomechanics, or bioenergetics. “Normalizing” or “standardizing” size (usually by dividing the square root of the summed squared distances from the centroid out of all the Cartesian coordinates specimen by specimen), while associated with the elegant symmetries of the Mardia–Dryden distribution in shape space, nevertheless can substantially impeach the validity of any organismal inferences that ensue. This paper adapts two variants of standard morphometric least-squares, principal components and uniform strains, to circumvent size standardization while still accommodating an analytic toolkit for studies of differential growth that supports landmark-by-landmark graphics and thin-plate splines. Standardization of position and orientation but not size yields the coordinates Franz Boas first discussed in 1905. In studies of growth, a first principal component of these coordinates often appears to involve most landmarks shifting almost directly away from their centroid, hence the proposed model’s name, “centric allometry.” There is also a joint standardization of shear and dilation resulting in a variant of standard GMM’s “nonaffine shape coordinates” where scale information is subsumed in the affine term. Studies of growth allometry should go better in the Boas system than in the Procrustes shape space that is the current conventional workbench for GMM analyses. I demonstrate two examples of this revised approach (one developmental, one phylogenetic) that retrieve all the findings of a conventional shape-space-based approach while focusing much more closely on the phenomenon of allometric growth per se. A three-part Appendix provides an overview of the algebra, highlighting both similarities to the Procrustes approach and contrasts with it.

scholarly journals Research on Measurement Method of Leaf Length and Width Based on Point Cloud

Agriculture ◽  
2021 ◽  
Vol 11 (1) ◽  
pp. 63
Author(s):  
Yawei Wang ◽  
Yifei Chen ◽  
Xiangnan Zhang ◽  
Wenwen Gong
Keyword(s):  
Point Cloud ◽  
Geodesic Distance ◽  
Three Dimensional ◽  
Principal Component ◽  
Leaf Length ◽  
Depth Sensor ◽  
Cross Sectional ◽  
Distance Method ◽  
Shape Information ◽  
Leaf Phenotype

Leaf is an important organ for photosynthesis and transpiration associated with the plants’ growth. Through the study of leaf phenotype, it the physiological characteristics produced by the interaction of the morphological parameters with the environment can be understood. In order to realize the assessment of the spatial morphology of leaves, a method based on three-dimensional stereo vision was introduced to extract the shape information, including the length and width of the leaves. Firstly, a depth sensor was used to collect the point cloud of plant leaves. Then, the leaf coordinate system was adjusted by principal component analysis to extract the region of interest; and compared with a cross-sectional method, the geodesic distance method, we proposed a method based on the cutting plane to obtain the intersecting line of the three-dimensional leaf model. Eggplant leaves were used to compare the accuracy of these methods in the measurement of a single leaf.

Are headforms a poor surrogate for helmet fit?

2019 ◽  
Vol 234 (2) ◽  
pp. 109-124 ◽  
Author(s):  
Kristie Liu ◽  
Daniel I Aponte ◽  
David J Greencorn ◽  
Shawn M Robbins ◽  
David J Pearsall
Keyword(s):  
Adult Male ◽  
Three Dimensional ◽  
Principal Component ◽  
Human Head ◽  
Ice Hockey ◽  
International Standards ◽  
Head Shape ◽  
Critical Determinant ◽  
Cross Sectional ◽  
Three Dimensional Modeling

International standards organizations require ice hockey helmets to be impact tested while mounted to a surrogate headform, with anthropometrics of a 50th percentile male. However, human head shapes are not identical, nor are there consistent guidelines for fitting a helmet to the ordinary user. The interaction between head shape and helmet fit impacts helmet safety: the contact area between a headform and helmet interior has been identified as a critical determinant of protection afforded by a helmet. The objective of this study was to compare quantitative measures of helmet fit between an adult male sample and three 50th percentile male headforms. This study recruited 42 adult male participants who wore a medium-sized ice hockey helmet (560–600 mm interior circumference) in an attempt to compare their quantitative helmet fit to those of three 50th percentile adult male headforms. Through three-dimensional modeling, fit was quantified by assessing dimensional differences in two transverse cross-sectional planes of the head and using principal component analysis to determine the largest components of fit. Significant differences were found between the headforms and the participants’ heads in anthropometrics and dimensional differences. The headforms were smaller than the participants’ heads, demonstrating average gapping with the interior of the helmet. The principal components of fit extracted included mediolateral deformation, gapping/compression at the rear aspect of the head-helmet interface, and general congruence of the head shape to the helmet liner. These findings demonstrated a vast discrepancy between helmet fit on the 50th percentile headforms and the ordinary helmet user.

Three-Dimensional Computed Tomography Cephalometry of Plagiocephaly: Asymmetry and Shape Analysis

2006 ◽  
Vol 43 (2) ◽  
pp. 201-210 ◽  
Author(s):  
D. J. Netherway ◽  
A. H. Abbott ◽  
N. Gulamhuseinwala ◽  
K. L. McGlaughlin ◽  
P. J. Anderson ◽  
...  
Keyword(s):  
Computed Tomography ◽  
Small Sample Size ◽  
Three Dimensional ◽  
Principal Component ◽  
Facial Asymmetry ◽  
Cranial Base ◽  
Parietal Bone ◽  
Small Sample ◽  
Deformational Plagiocephaly ◽  
Cross Sectional

Objective To investigate facial asymmetry associated with both deformational and synostotic plagiocephaly and to identify variables based on skeletal landmarks that distinguish the conditions and quantify severity. Design Retrospective, cross sectional. Setting Australian Craniofacial Unit, Adelaide. Main Outcome Measures Proportional differences between bilateral distances and principal component (PC) analysis of the skeletal landmarks. Patients The three-dimensional positions of 78 osseous landmarks were determined from computed tomography (CT) scans of 21 patients with deformational plagiocephaly (DP), 20 patients with unilateral coronal synostosis (UCS), and 2 patients with unilateral lambdoid synostosis (ULS). Results For both DP and UCS, significant asymmetry was found for the orbital depths, mandibular lengths, maxillary depths, zygomatic arch lengths, lateral base of the parietal bone, and the angle between the anterior and the posterior cranial base projected onto the axial plane. The small sample size for ULS precluded definitive statistical statements but allowed some useful comparisons with the other conditions. The first three PC scores were able to distinguish among the three conditions and which side was affected. Conclusions The asymmetry of the cranial base and facial structures, arising from localized abnormality or deformational forces in either the frontal or the occipital regions, can be quantified by a plethora of bilateral features or summarized by PC analysis.

Evaluation of the perforators of the anterior communicating artery (AComA) using routine cerebral 3D rotational angiography

2015 ◽  
Vol 8 (10) ◽  
pp. 1061-1066 ◽  
Author(s):  
Stephanie Lescher ◽  
Maja Zimmermann ◽  
Jürgen Konczalla ◽  
Thomas Deller ◽  
Luciana Porto ◽  
...  
Keyword(s):  
Imaging Techniques ◽  
Three Dimensional ◽  
Therapeutic Interventions ◽  
Anterior Communicating Artery ◽  
Interventional Treatment ◽  
Rotational Angiography ◽  
Cross Sectional ◽  
Therapy Assessment ◽  
Neurologic Deficits

BackgroundDamage to perforating branches of the anterior communicating artery (AComA) is a known complication of surgical or interventional treatment procedures for AComA aneurysm leading to neurologic deficits. In spite of the clinical relevance of these AComA branches, they have not been systematically analyzed using imaging techniques and most of our knowledge is based on post-mortem injection studies or neurosurgical reports. We therefore analyzed three-dimensional rotational angiography (3DRA) images of the AComA, and propose a first imaging definition of the microvascular structures surrounding the AComA.MethodsReconstructed 3D data derived from standard-of-care rotational angiography acquisitions (5 s DSA) were retrospectively analyzed. 20 patients undergoing selective cerebral angiography and 3DRA for therapy assessment were included in our study. 3DRA datasets were reconstructed and displayed using the volume rendering technique (VRT). Additionally, multiplanar reformatted CT-like cross-sectional images (MPR) were used to evaluate the number, size, and origin of the perforators of the AComA.ResultsPerforating branches of the AComA could be demonstrated in all cases with large interindividual variations in vessel visibility. MPRs appeared to be superior to total VRT volumes in the visualization of the perforating branches of the AComA.Conclusions3DRA can be used to visualize perforating branches of the AComA in vivo. Since damage to these perforators may result in neurologic deficits, visualization of these vessels prior to surgery or endovascular aneurysm treatment could help in the planning of therapeutic interventions. Further refinement of current imaging techniques will be necessary, however, to increase the reliability of small vessel angiography.

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