37,227 research outputs found
Application of the morphological alpha shape method to the extraction of topographical features from engineering surfaces
In contrast to the mean-line based filters, morphological filters are function oriented and more suitable for the functional prediction of component performance. This paper presents a novel morphological method based on the alpha shape for the extraction of topographical features from engineering surfaces. Compared to the traditional implementation of morphological filters, the alpha shape method is more efficient in performance for large structuring element. The resulting envelope follows the form of the surface all over such that the distortions caused the end effects are avoided. A series of measured surfaces from the automotive cylinder liner and the bioengineering femoral heads are analyzed using the morphological alpha shape method. The topographical features are successfully extracted, enabling further analysis to the components
Visual Quality Enhancement in Optoacoustic Tomography using Active Contour Segmentation Priors
Segmentation of biomedical images is essential for studying and
characterizing anatomical structures, detection and evaluation of pathological
tissues. Segmentation has been further shown to enhance the reconstruction
performance in many tomographic imaging modalities by accounting for
heterogeneities of the excitation field and tissue properties in the imaged
region. This is particularly relevant in optoacoustic tomography, where
discontinuities in the optical and acoustic tissue properties, if not properly
accounted for, may result in deterioration of the imaging performance.
Efficient segmentation of optoacoustic images is often hampered by the
relatively low intrinsic contrast of large anatomical structures, which is
further impaired by the limited angular coverage of some commonly employed
tomographic imaging configurations. Herein, we analyze the performance of
active contour models for boundary segmentation in cross-sectional optoacoustic
tomography. The segmented mask is employed to construct a two compartment model
for the acoustic and optical parameters of the imaged tissues, which is
subsequently used to improve accuracy of the image reconstruction routines. The
performance of the suggested segmentation and modeling approach are showcased
in tissue-mimicking phantoms and small animal imaging experiments.Comment: Accepted for publication in IEEE Transactions on Medical Imagin
Morphological analysis of cells by means of an elastic metric in the shape space
Shape analysis is of great importance in many fields, such as computer vision, medical imaging, and computational biology. This analysis can be performed considering shapes as closed planar curves in the shape space. This approach has been used for the first time to obtain the morphological classification of erythrocytes in digital images of sickle cell disease considering the shape space S1, which has the property of being isometric to an infinite-dimensional Grassmann manifold of two-dimensional subspaces (Younes et al., 2008), without taking advantage of all the features offered by the elastic metric related to the possibility of stretching and bending of the curves. In this paper, we study this deformation in the shape space, S2, which is based on the representation of closed planar curves by means of the square-root velocity function (SRVF) (Srivastava et al., 2011), using the elastic metric of this space to obtain more efficient geodesics and geodesic lengths between planar curves. Supervised classification with this approach achieved an accuracy of 94.3%, classification using templates achieved 94.2% and unsupervised clustering in three groups achieved 94.7%, considering three classes of erythrocytes: normal, sickle, and with other deformations. These results are better than those previously achieved in the morphological analysis of erythrocytes and the method can be used in different applications related to the treatment of sickle cell disease, even in cases where it is necessary to study the process of evolution of the deformation, something that can not be done in a natural way in the feature space
Methods for Analysing Endothelial Cell Shape and Behaviour in Relation to the Focal Nature of Atherosclerosis
The aim of this thesis is to develop automated methods for the analysis of the
spatial patterns, and the functional behaviour of endothelial cells, viewed under
microscopy, with applications to the understanding of atherosclerosis.
Initially, a radial search approach to segmentation was attempted in order to
trace the cell and nuclei boundaries using a maximum likelihood algorithm; it
was found inadequate to detect the weak cell boundaries present in the available
data. A parametric cell shape model was then introduced to fit an equivalent
ellipse to the cell boundary by matching phase-invariant orientation fields of the
image and a candidate cell shape. This approach succeeded on good quality
images, but failed on images with weak cell boundaries. Finally, a support
vector machines based method, relying on a rich set of visual features, and a
small but high quality training dataset, was found to work well on large numbers
of cells even in the presence of strong intensity variations and imaging noise.
Using the segmentation results, several standard shear-stress dependent parameters
of cell morphology were studied, and evidence for similar behaviour
in some cell shape parameters was obtained in in-vivo cells and their nuclei.
Nuclear and cell orientations around immature and mature aortas were broadly
similar, suggesting that the pattern of flow direction near the wall stayed approximately
constant with age. The relation was less strong for the cell and
nuclear length-to-width ratios.
Two novel shape analysis approaches were attempted to find other properties
of cell shape which could be used to annotate or characterise patterns, since a
wide variability in cell and nuclear shapes was observed which did not appear
to fit the standard parameterisations. Although no firm conclusions can yet be
drawn, the work lays the foundation for future studies of cell morphology.
To draw inferences about patterns in the functional response of cells to flow,
which may play a role in the progression of disease, single-cell analysis was performed
using calcium sensitive florescence probes. Calcium transient rates were
found to change with flow, but more importantly, local patterns of synchronisation
in multi-cellular groups were discernable and appear to change with flow.
The patterns suggest a new functional mechanism in flow-mediation of cell-cell
calcium signalling
Characterizing neuromorphologic alterations with additive shape functionals
The complexity of a neuronal cell shape is known to be related to its
function. Specifically, among other indicators, a decreased complexity in the
dendritic trees of cortical pyramidal neurons has been associated with mental
retardation. In this paper we develop a procedure to address the
characterization of morphological changes induced in cultured neurons by
over-expressing a gene involved in mental retardation. Measures associated with
the multiscale connectivity, an additive image functional, are found to give a
reasonable separation criterion between two categories of cells. One category
consists of a control group and two transfected groups of neurons, and the
other, a class of cat ganglionary cells. The reported framework also identified
a trend towards lower complexity in one of the transfected groups. Such results
establish the suggested measures as an effective descriptors of cell shape
Shape mode analysis exposes movement patterns in biology: flagella and flatworms as case studies
We illustrate shape mode analysis as a simple, yet powerful technique to
concisely describe complex biological shapes and their dynamics. We
characterize undulatory bending waves of beating flagella and reconstruct a
limit cycle of flagellar oscillations, paying particular attention to the
periodicity of angular data. As a second example, we analyze non-convex
boundary outlines of gliding flatworms, which allows us to expose stereotypic
body postures that can be related to two different locomotion mechanisms.
Further, shape mode analysis based on principal component analysis allows to
discriminate different flatworm species, despite large motion-associated shape
variability. Thus, complex shape dynamics is characterized by a small number of
shape scores that change in time. We present this method using descriptive
examples, explaining abstract mathematics in a graphic way.Comment: 20 pages, 6 figures, accepted for publication in PLoS On
Parametrising arbitrary galaxy morphologies: potentials and pitfalls
We demonstrate that morphological observables (e.g. steepness of the radial
light profile, ellipticity, asymmetry) are intertwined and cannot be measured
independently of each other. We present strong arguments in favour of
model-based parametrisation schemes, namely reliability assessment,
disentanglement of morphological observables, and PSF modelling. Furthermore,
we demonstrate that estimates of the concentration and Sersic index obtained
from the Zurich Structure & Morphology catalogue are in excellent agreement
with theoretical predictions. We also demonstrate that the incautious use of
the concentration index for classification purposes can cause a severe loss of
the discriminative information contained in a given data sample. Moreover, we
show that, for poorly resolved galaxies, concentration index and M_20 suffer
from strong discontinuities, i.e. similar morphologies are not necessarily
mapped to neighbouring points in the parameter space. This limits the
reliability of these parameters for classification purposes. Two-dimensional
Sersic profiles accounting for centroid and ellipticity are identified as the
currently most reliable parametrisation scheme in the regime of intermediate
signal-to-noise ratios and resolutions, where asymmetries and substructures do
not play an important role. We argue that basis functions provide good
parametrisation schemes in the regimes of high signal-to-noise ratios and
resolutions. Concerning Sersic profiles, we show that scale radii cannot be
compared directly for profiles of different Sersic indices. Furthermore, we
show that parameter spaces are typically highly nonlinear. This implies that
significant caution is required when distance-based classificaton methods are
used.Comment: 18 pages, 13 figure
A computational framework for the morpho-elastic development of molluskan shells by surface and volume growth
Mollusk shells are an ideal model system for understanding the morpho-elastic
basis of morphological evolution of invertebrates' exoskeletons. During the
formation of the shell, the mantle tissue secretes proteins and minerals that
calcify to form a new incremental layer of the exoskeleton. Most of the
existing literature on the morphology of mollusks is descriptive. The
mathematical understanding of the underlying coupling between pre-existing
shell morphology, de novo surface deposition and morpho-elastic volume growth
is at a nascent stage, primarily limited to reduced geometric representations.
Here, we propose a general, three-dimensional computational framework coupling
pre-existing morphology, incremental surface growth by accretion, and
morpho-elastic volume growth. We exercise this framework by applying it to
explain the stepwise morphogenesis of seashells during growth: new material
surfaces are laid down by accretive growth on the mantle whose form is
determined by its morpho-elastic growth. Calcification of the newest surfaces
extends the shell as well as creates a new scaffold that constrains the next
growth step. We study the effects of surface and volumetric growth rates, and
of previously deposited shell geometries on the resulting modes of mantle
deformation, and therefore of the developing shell's morphology. Connections
are made to a range of complex shells ornamentations.Comment: Main article is 20 pages long with 15 figures. Supplementary material
is 4 pages long with 6 figures and 6 attached movies. To be published in PLOS
Computational Biolog
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