28,745 research outputs found
DoctorEye: A clinically driven multifunctional platform, for accurate processing of tumors in medical images
Copyright @ Skounakis et al.This paper presents a novel, open access interactive platform for 3D medical image analysis, simulation and visualization, focusing in oncology images. The platform was developed through constant interaction and feedback from expert clinicians integrating a thorough analysis of their requirements while having an ultimate goal of assisting in accurately delineating tumors. It allows clinicians not only to work with a large number of 3D tomographic datasets but also to efficiently annotate multiple regions of interest in the same session. Manual and semi-automatic segmentation techniques combined with integrated correction tools assist in the quick and refined delineation of tumors while different users can add different components related to oncology such as tumor growth and simulation algorithms for improving therapy planning. The platform has been tested by different users and over large number of heterogeneous tomographic datasets to ensure stability, usability, extensibility and robustness with promising results. AVAILABILITY: THE PLATFORM, A MANUAL AND TUTORIAL VIDEOS ARE AVAILABLE AT: http://biomodeling.ics.forth.gr. It is free to use under the GNU General Public License
A Framework for Symmetric Part Detection in Cluttered Scenes
The role of symmetry in computer vision has waxed and waned in importance
during the evolution of the field from its earliest days. At first figuring
prominently in support of bottom-up indexing, it fell out of favor as shape
gave way to appearance and recognition gave way to detection. With a strong
prior in the form of a target object, the role of the weaker priors offered by
perceptual grouping was greatly diminished. However, as the field returns to
the problem of recognition from a large database, the bottom-up recovery of the
parts that make up the objects in a cluttered scene is critical for their
recognition. The medial axis community has long exploited the ubiquitous
regularity of symmetry as a basis for the decomposition of a closed contour
into medial parts. However, today's recognition systems are faced with
cluttered scenes, and the assumption that a closed contour exists, i.e. that
figure-ground segmentation has been solved, renders much of the medial axis
community's work inapplicable. In this article, we review a computational
framework, previously reported in Lee et al. (2013), Levinshtein et al. (2009,
2013), that bridges the representation power of the medial axis and the need to
recover and group an object's parts in a cluttered scene. Our framework is
rooted in the idea that a maximally inscribed disc, the building block of a
medial axis, can be modeled as a compact superpixel in the image. We evaluate
the method on images of cluttered scenes.Comment: 10 pages, 8 figure
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
Image Segmentation Using Weak Shape Priors
The problem of image segmentation is known to become particularly challenging
in the case of partial occlusion of the object(s) of interest, background
clutter, and the presence of strong noise. To overcome this problem, the
present paper introduces a novel approach segmentation through the use of
"weak" shape priors. Specifically, in the proposed method, an segmenting active
contour is constrained to converge to a configuration at which its geometric
parameters attain their empirical probability densities closely matching the
corresponding model densities that are learned based on training samples. It is
shown through numerical experiments that the proposed shape modeling can be
regarded as "weak" in the sense that it minimally influences the segmentation,
which is allowed to be dominated by data-related forces. On the other hand, the
priors provide sufficient constraints to regularize the convergence of
segmentation, while requiring substantially smaller training sets to yield less
biased results as compared to the case of PCA-based regularization methods. The
main advantages of the proposed technique over some existing alternatives is
demonstrated in a series of experiments.Comment: 27 pages, 8 figure
Optic nerve head segmentation
Reliable and efficient optic disk localization and segmentation are important tasks in automated retinal screening. General-purpose edge detection algorithms often fail to segment the optic disk due to fuzzy boundaries, inconsistent image contrast or missing edge features. This paper presents an algorithm for the localization and segmentation of the optic nerve head boundary in low-resolution images (about 20 /spl mu//pixel). Optic disk localization is achieved using specialized template matching, and segmentation by a deformable contour model. The latter uses a global elliptical model and a local deformable model with variable edge-strength dependent stiffness. The algorithm is evaluated against a randomly selected database of 100 images from a diabetic screening programme. Ten images were classified as unusable; the others were of variable quality. The localization algorithm succeeded on all bar one usable image; the contour estimation algorithm was qualitatively assessed by an ophthalmologist as having Excellent-Fair performance in 83% of cases, and performs well even on blurred image
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