40,952 research outputs found
Efficient Decomposition of Image and Mesh Graphs by Lifted Multicuts
Formulations of the Image Decomposition Problem as a Multicut Problem (MP)
w.r.t. a superpixel graph have received considerable attention. In contrast,
instances of the MP w.r.t. a pixel grid graph have received little attention,
firstly, because the MP is NP-hard and instances w.r.t. a pixel grid graph are
hard to solve in practice, and, secondly, due to the lack of long-range terms
in the objective function of the MP. We propose a generalization of the MP with
long-range terms (LMP). We design and implement two efficient algorithms
(primal feasible heuristics) for the MP and LMP which allow us to study
instances of both problems w.r.t. the pixel grid graphs of the images in the
BSDS-500 benchmark. The decompositions we obtain do not differ significantly
from the state of the art, suggesting that the LMP is a competitive formulation
of the Image Decomposition Problem. To demonstrate the generality of the LMP,
we apply it also to the Mesh Decomposition Problem posed by the Princeton
benchmark, obtaining state-of-the-art decompositions
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
Joint co-clustering: co-clustering of genomic and clinical bioimaging data
AbstractFor better understanding the genetic mechanisms underlying clinical observations, and better defining a group of potential candidates for protein-family-inhibiting therapy, it is interesting to determine the correlations between genomic, clinical data and data coming from high resolution and fluorescent microscopy. We introduce a computational method, called joint co-clustering, that can find co-clusters or groups of genes, bioimaging parameters and clinical traits that are believed to be closely related to each other based on the given empirical information. As bioimaging parameters, we quantify the expression of growth factor receptor EGFR/erb-B family in non-small cell lung carcinoma (NSCLC) through a fully-automated computer-aided analysis approach. This immunohistochemical analysis is usually performed by pathologists via visual inspection of tissue samples images. Our fully-automated techniques streamlines this error-prone and time-consuming process, thereby facilitating analysis and diagnosis. Experimental results for several real-life datasets demonstrate the high quantitative precision of our approach. The joint co-clustering method was tested with the receptor EGFR/erb-B family data on non-small cell lung carcinoma (NSCLC) tissue and identified statistically significant co-clusters of genes, receptor protein expression and clinical traits. The validation of our results with the literature suggest that the proposed method can provide biologically meaningful co-clusters of genes and traits and that it is a very promising approach to analyse large-scale biological data and to study multi-factorial genetic pathologies through their genetic alterations
Superpixels: An Evaluation of the State-of-the-Art
Superpixels group perceptually similar pixels to create visually meaningful
entities while heavily reducing the number of primitives for subsequent
processing steps. As of these properties, superpixel algorithms have received
much attention since their naming in 2003. By today, publicly available
superpixel algorithms have turned into standard tools in low-level vision. As
such, and due to their quick adoption in a wide range of applications,
appropriate benchmarks are crucial for algorithm selection and comparison.
Until now, the rapidly growing number of algorithms as well as varying
experimental setups hindered the development of a unifying benchmark. We
present a comprehensive evaluation of 28 state-of-the-art superpixel algorithms
utilizing a benchmark focussing on fair comparison and designed to provide new
insights relevant for applications. To this end, we explicitly discuss
parameter optimization and the importance of strictly enforcing connectivity.
Furthermore, by extending well-known metrics, we are able to summarize
algorithm performance independent of the number of generated superpixels,
thereby overcoming a major limitation of available benchmarks. Furthermore, we
discuss runtime, robustness against noise, blur and affine transformations,
implementation details as well as aspects of visual quality. Finally, we
present an overall ranking of superpixel algorithms which redefines the
state-of-the-art and enables researchers to easily select appropriate
algorithms and the corresponding implementations which themselves are made
publicly available as part of our benchmark at
davidstutz.de/projects/superpixel-benchmark/
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