594 research outputs found
Comparison of geometric morphometric outline methods in the discrimination of age-related differences in feather shape
BACKGROUND: Geometric morphometric methods of capturing information about curves or outlines of organismal structures may be used in conjunction with canonical variates analysis (CVA) to assign specimens to groups or populations based on their shapes. This methodological paper examines approaches to optimizing the classification of specimens based on their outlines. This study examines the performance of four approaches to the mathematical representation of outlines and two different approaches to curve measurement as applied to a collection of feather outlines. A new approach to the dimension reduction necessary to carry out a CVA on this type of outline data with modest sample sizes is also presented, and its performance is compared to two other approaches to dimension reduction. RESULTS: Two semi-landmark-based methods, bending energy alignment and perpendicular projection, are shown to produce roughly equal rates of classification, as do elliptical Fourier methods and the extended eigenshape method of outline measurement. Rates of classification were not highly dependent on the number of points used to represent a curve or the manner in which those points were acquired. The new approach to dimensionality reduction, which utilizes a variable number of principal component (PC) axes, produced higher cross-validation assignment rates than either the standard approach of using a fixed number of PC axes or a partial least squares method. CONCLUSION: Classification of specimens based on feather shape was not highly dependent of the details of the method used to capture shape information. The choice of dimensionality reduction approach was more of a factor, and the cross validation rate of assignment may be optimized using the variable number of PC axes method presented herein
An Examination of Morphometric Variations in a Neotropical Toad Population (Proceratophrys cristiceps, Amphibia, Anura, Cycloramphidae)
The species Proceratophrys cristiceps belongs to the genus Proceratophrys within the family Cycloramphidae. These amphibians are found exclusively in South America in the morphoclimatic domain of the semi-arid depression zones in northeastern Brazil known as the Caatinga. We examined intrapopulational variation using univariate and multivariate statistics with traditional and geometric morphometrics, which supported the existence of two morphotypes of this species. Our results indicated significant degrees of variation in skeletal characteristics between some natural populations of this species. Careful analyses of variability levels are fundamental to avoid taxonomic errors, principally in populations that demonstrate characteristics intimately associated with their area of occurrence, as is the case of Proceratophrys cristiceps
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Landmark detection in 2D bioimages for geometric morphometrics: a multi-resolution tree-based approach
The detection of anatomical landmarks in bioimages is a necessary but tedious step for geometric morphometrics studies in many research domains. We propose variants of a multi-resolution tree-based approach to speed-up the detection of landmarks in bioimages. We extensively evaluate our method variants on three different datasets (cephalometric, zebrafish, and drosophila images). We identify the key method parameters (notably the multi-resolution) and report results with respect to human ground truths and existing methods. Our method achieves recognition performances competitive with current existing approaches while being generic and fast. The algorithms are integrated in the open-source Cytomine software and we provide parameter configuration guidelines so that they can be easily exploited by end-users. Finally, datasets are readily available through a Cytomine server to foster future research
Do Not Mask What You Do Not Need to Mask: a Parser-Free Virtual Try-On
The 2D virtual try-on task has recently attracted a great interest from the
research community, for its direct potential applications in online shopping as
well as for its inherent and non-addressed scientific challenges. This task
requires fitting an in-shop cloth image on the image of a person, which is
highly challenging because it involves cloth warping, image compositing, and
synthesizing. Casting virtual try-on into a supervised task faces a difficulty:
available datasets are composed of pairs of pictures (cloth, person wearing the
cloth). Thus, we have no access to ground-truth when the cloth on the person
changes. State-of-the-art models solve this by masking the cloth information on
the person with both a human parser and a pose estimator. Then, image synthesis
modules are trained to reconstruct the person image from the masked person
image and the cloth image. This procedure has several caveats: firstly, human
parsers are prone to errors; secondly, it is a costly pre-processing step,
which also has to be applied at inference time; finally, it makes the task
harder than it is since the mask covers information that should be kept such as
hands or accessories. In this paper, we propose a novel student-teacher
paradigm where the teacher is trained in the standard way (reconstruction)
before guiding the student to focus on the initial task (changing the cloth).
The student additionally learns from an adversarial loss, which pushes it to
follow the distribution of the real images. Consequently, the student exploits
information that is masked to the teacher. A student trained without the
adversarial loss would not use this information. Also, getting rid of both
human parser and pose estimator at inference time allows obtaining a real-time
virtual try-on.Comment: Accepted at ECCV 2020. arXiv admin note: text overlap with
arXiv:1906.0134
New quantitative approaches reveal the spatial preference of nuclear compartments in mammalian fibroblasts
The nuclei of higher eukaryotic cells display compartmentalization and certain nuclear compartments have been shown to follow a degree of spatial organization. To date, the study of nuclear organization has often involved simple quantitative procedures that struggle with both the irregularity of the nuclear boundary and the problem of handling replicate images. Such studies typically focus on inter-object distance, rather than spatial location within the nucleus. The concern of this paper is the spatial preference of nuclear compartments, for which we have developed statistical tools to quantitatively study and explore nuclear organization. These tools combine replicate images to generate ‘aggregate maps' which represent the spatial preferences of nuclear compartments. We present two examples of different compartments in mammalian fibroblasts (WI-38 and MRC-5) that demonstrate new knowledge of spatial preference within the cell nucleus. Specifically, the spatial preference of RNA polymerase II is preserved across normal and immortalized cells, whereas PML nuclear bodies exhibit a change in spatial preference from avoiding the centre in normal cells to exhibiting a preference for the centre in immortalized cells. In addition, we show that SC35 splicing speckles are excluded from the nuclear boundary and localize throughout the nucleoplasm and in the interchromatin space in non-transformed WI-38 cells. This new methodology is thus able to reveal the effect of large-scale perturbation on spatial architecture and preferences that would not be obvious from single cell imaging
Automated Analysis of Craniofacial Morphology Using Magnetic Resonance Images
Quantitative analysis of craniofacial morphology is of interest to scholars
working in a wide variety of disciplines, such as anthropology, developmental
biology, and medicine. T1-weighted (anatomical) magnetic resonance images (MRI)
provide excellent contrast between soft tissues. Given its three-dimensional
nature, MRI represents an ideal imaging modality for the analysis of
craniofacial structure in living individuals. Here we describe how T1-weighted
MR images, acquired to examine brain anatomy, can also be used to analyze facial
features. Using a sample of typically developing adolescents from the Saguenay
Youth Study (N = 597; 292 male, 305 female, ages: 12 to 18
years), we quantified inter-individual variations in craniofacial structure in
two ways. First, we adapted existing nonlinear registration-based morphological
techniques to generate iteratively a group-wise population average of
craniofacial features. The nonlinear transformations were used to map the
craniofacial structure of each individual to the population average. Using
voxel-wise measures of expansion and contraction, we then examined the effects
of sex and age on inter-individual variations in facial features. Second, we
employed a landmark-based approach to quantify variations in face surfaces. This
approach involves: (a) placing 56 landmarks (forehead, nose, lips, jaw-line,
cheekbones, and eyes) on a surface representation of the MRI-based group
average; (b) warping the landmarks to the individual faces using the inverse
nonlinear transformation estimated for each person; and (3) using a principal
components analysis (PCA) of the warped landmarks to identify facial features
(i.e. clusters of landmarks) that vary in our sample in a correlated fashion. As
with the voxel-wise analysis of the deformation fields, we examined the effects
of sex and age on the PCA-derived spatial relationships between facial features.
Both methods demonstrated significant sexual dimorphism in craniofacial
structure in areas such as the chin, mandible, lips, and nose
Anisotropic Radial Layout for Visualizing Centrality and Structure in Graphs
This paper presents a novel method for layout of undirected graphs, where
nodes (vertices) are constrained to lie on a set of nested, simple, closed
curves. Such a layout is useful to simultaneously display the structural
centrality and vertex distance information for graphs in many domains,
including social networks. Closed curves are a more general constraint than the
previously proposed circles, and afford our method more flexibility to preserve
vertex relationships compared to existing radial layout methods. The proposed
approach modifies the multidimensional scaling (MDS) stress to include the
estimation of a vertex depth or centrality field as well as a term that
penalizes discord between structural centrality of vertices and their alignment
with this carefully estimated field. We also propose a visualization strategy
for the proposed layout and demonstrate its effectiveness using three social
network datasets.Comment: Appears in the Proceedings of the 25th International Symposium on
Graph Drawing and Network Visualization (GD 2017
Convergence and divergence in the evolution of cat skulls: temporal and spatial patterns of morphological diversity
Background: Studies of biological shape evolution are greatly enhanced when framed in a phylogenetic perspective.
Inclusion of fossils amplifies the scope of macroevolutionary research, offers a deep-time perspective on tempo and mode
of radiations, and elucidates life-trait changes. We explore the evolution of skull shape in felids (cats) through morphometric
analyses of linear variables, phylogenetic comparative methods, and a new cladistic study of saber-toothed cats.
Methodology/Principal Findings: A new phylogenetic analysis supports the monophyly of saber-toothed cats
(Machairodontinae) exclusive of Felinae and some basal felids, but does not support the monophyly of various sabertoothed
tribes and genera. We quantified skull shape variation in 34 extant and 18 extinct species using size-adjusted linear
variables. These distinguish taxonomic group membership with high accuracy. Patterns of morphospace occupation are
consistent with previous analyses, for example, in showing a size gradient along the primary axis of shape variation and a
separation between large and small-medium cats. By combining the new phylogeny with a molecular tree of extant Felinae,
we built a chronophylomorphospace (a phylogeny superimposed onto a two-dimensional morphospace through time). The
evolutionary history of cats was characterized by two major episodes of morphological divergence, one marking the
separation between saber-toothed and modern cats, the other marking the split between large and small-medium cats.
Conclusions/Significance: Ancestors of large cats in the ‘Panthera’ lineage tend to occupy, at a much later stage,
morphospace regions previously occupied by saber-toothed cats. The latter radiated out into new morphospace regions
peripheral to those of extant large cats. The separation between large and small-medium cats was marked by considerable
morphologically divergent trajectories early in feline evolution. A chronophylomorphospace has wider applications in
reconstructing temporal transitions across two-dimensional trait spaces, can be used in ecophenotypical and functional
diversity studies, and may reveal novel patterns of morphospace occupation
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