Advances in computational modelling offer unprecedented potential for obtaining insights into the mechanics of cell-cell interactions. With the aid of such models, cell-level phenomena such as cell sorting and tissue self-organization are now being understood in terms of forces generated by specific sub-cellular structural components. Three-dimensional systems can behave differently from two-dimensional ones and since models cannot be validated without corresponding data, it is crucial to build accurate three-dimensional models of real cell aggregates. The lack of automated methods to determine which cell outlines in successive images of a confocal stack or time-lapse image set belong to the same cell is an important unsolved problem in the reconstruction process. This thesis addresses this problem through a contour grouping algorithm (CGA) designed to lead to unsupervised three-dimensional reconstructions of biological cells. The CGA associates contours obtained from fluorescently-labeled cell membranes in individual confocal slices using concepts from the fields of machine learning and combinatorics. The feature extraction step results in a set of association metrics. The algorithm then uses a probabilistic grouping step and a greedy-cost optimization step to produce grouped sets of contours. Groupings are representative of imaged cells and are manually evaluated for accuracy. The CGA presented here is able to produce accuracies greater than 96% when properly tuned. Parameter studies show that the algorithm is robust. That is, acceptable results are obtained under moderately varied probabilistic constraints and reasonable cost weightings. Image properties – such as slicing distance, image quality – affect the results. Sources of error are identified and enhancements based on fuzzy-logic and other optimization methods are considered. The successful grouping of cell contours, as realized here, is an important step toward the development of realistic, three-dimensional, cell-based finite element models.

Object tracking is an important problem with wide ranging applications. The purpose is to detect object contours and track their motion in a video. Issues of concern are to be able to map objects correctly between two frames, and to be able to track through occlusion. This thesis discusses a novel framework for the purpose of object tracking which is inspired from image registration and segmentation models. Occlusion of objects is also detected and handled in this framework in an appropriate manner. The main idea of our tracking framework is to reconstruct the sequence of images in the video. The process involves deforming all the objects in a given image frame, called the initial frame. Regularization terms are used to govern the deformation of the shape of the objects. We use elastic and viscous fluid model as the regularizer. The reconstructed frame is formed by combining the deformed objects with respect to the depth ordering. The correct reconstruction is selected by parameters that minimize the difference between the reconstruction and the consecutive frame, called the target frame. These parameters provide the required tracking information, such as the contour of the objects in the target frame including the occluded regions. The regularization term restricts the deformation of the object shape in the occluded region and thus gives an estimate of the object shape in this region. The other idea is to use a segmentation model as a measure in place of the frame difference measure. This is separate from image segmentation procedure, since we use the segmentation model in a tracking framework to capture object deformation. Numerical examples are presented to demonstrate tracking in simple and complex scenes, alongwith occlusion handling capability of our model. Segmentation measure is shown to be more robust with regard to accumulation of tracking error.

This report presents an algorithm for locating the cut points for and separatingvertically attached traffic signs in Sweden. This algorithm provides severaladvanced digital image processing features: binary image which representsvisual object and its complex rectangle background with number one and zerorespectively, improved cross correlation which shows the similarity of 2Dobjects and filters traffic sign candidates, simplified shape decompositionwhich smoothes contour of visual object iteratively in order to reduce whitenoises, flipping point detection which locates black noises candidates, chasmfilling algorithm which eliminates black noises, determines the final cut pointsand separates originally attached traffic signs into individual ones. At each step,the mediate results as well as the efficiency in practice would be presented toshow the advantages and disadvantages of the developed algorithm. Thisreport concentrates on contour-based recognition of Swedish traffic signs. Thegeneral shapes cover upward triangle, downward triangle, circle, rectangle andoctagon. At last, a demonstration program would be presented to show howthe algorithm works in real-time environment.

This thesis develops an algorithm for tracking the boundary of an airbag throughout an image sequence. The algorithm is designed to work even if various problematic features, e.g. objects in the background, are present in the image. The work is built on an existing commercially available image processing and analysis suite targeted at the automotive industry. The software suite runs on standard PC hardware. Firstly, improvements to the airbag tracking algorithm already available in the suite are considered. Testing reveals that these measures are not sufficient to overcome the problems posed by the problematic image sequences. A new tracking algorithmis then proposed. It consists of a Canny edge detector, optional steps to enhance feature detection by removing edges in the background and edges interior to the boundary of the airbag and finally an active contour. The role of the active contour is to produce a closed curve while imposing smoothness constraints on the detected boundary. The active contour is in each frame initialized by linearly extrapolating the contour from previous frames. The algorithm works very well and it is fast enough to run on slower machines than was initially targeted.

Image segmentation is an important step in image processing, with many applications such as pattern recognition, object detection, and medical image analysis. It is a technique that separates objects of interests from the background in an image. Geometric active contour is a recent image segmentation method that overcomes previous problems with snakes. It is an attractive method for medical image segmentation as it is able to capture the object of interest in one continuous curve. The theory and implementation details of geometric active contours are discussed in this work. The robustness of the algorithm is tested through a series of tests, involving both synthetic images and medical images. Curve leaking past boundaries is a common problem in cases of non-ideal edges. Noise is also problematic for the advancement of the curve. Smoothing and parameters selection are discussed as ways to help solve these problems. This work also explores the incorporation of the multi-resolution method of Gaussian pyramids into the algorithm. Multi-resolution methods, used extensively in the areas of denoising and edge-selection, can help capture the spatial structure of an image. Results show that similar to the multi-resolution methods applied to parametric active contours, the multi-resolution can greatly increase the computation without sacrificing performance. In fact, results show that with successive smoothing and sub-sampling, performance often improves. Although smoothing and parameter adjustment help improve the performance of geometric active contours, the edge-based approach is still localized and the improvement is limited. Region-based approaches are recommended for further work on active contours.

Advances in computational modelling offer unprecedented potential for obtaining insights into the mechanics of cell-cell interactions. With the aid of such models, cell-level phenomena such as cell sorting and tissue self-organization are now being understood in terms of forces generated by specific sub-cellular structural components. Three-dimensional systems can behave differently from two-dimensional ones and since models cannot be validated without corresponding data, it is crucial to build accurate three-dimensional models of real cell aggregates. The lack of automated methods to determine which cell outlines in successive images of a confocal stack or time-lapse image set belong to the same cell is an important unsolved problem in the reconstruction process. This thesis addresses this problem through a contour grouping algorithm (CGA) designed to lead to unsupervised three-dimensional reconstructions of biological cells. The CGA associates contours obtained from fluorescently-labeled cell membranes in individual confocal slices using concepts from the fields of machine learning and combinatorics. The feature extraction step results in a set of association metrics. The algorithm then uses a probabilistic grouping step and a greedy-cost optimization step to produce grouped sets of contours. Groupings are representative of imaged cells and are manually evaluated for accuracy. The CGA presented here is able to produce accuracies greater than 96% when properly tuned. Parameter studies show that the algorithm is robust. That is, acceptable results are obtained under moderately varied probabilistic constraints and reasonable cost weightings. Image properties – such as slicing distance, image quality – affect the results. Sources of error are identified and enhancements based on fuzzy-logic and other optimization methods are considered. The successful grouping of cell contours, as realized here, is an important step toward the development of realistic, three-dimensional, cell-based finite element models.

Object tracking is an important problem with wide ranging applications. The purpose is to detect object contours and track their motion in a video. Issues of concern are to be able to map objects correctly between two frames, and to be able to track through occlusion. This thesis discusses a novel framework for the purpose of object tracking which is inspired from image registration and segmentation models. Occlusion of objects is also detected and handled in this framework in an appropriate manner. The main idea of our tracking framework is to reconstruct the sequence of images in the video. The process involves deforming all the objects in a given image frame, called the initial frame. Regularization terms are used to govern the deformation of the shape of the objects. We use elastic and viscous fluid model as the regularizer. The reconstructed frame is formed by combining the deformed objects with respect to the depth ordering. The correct reconstruction is selected by parameters that minimize the difference between the reconstruction and the consecutive frame, called the target frame. These parameters provide the required tracking information, such as the contour of the objects in the target frame including the occluded regions. The regularization term restricts the deformation of the object shape in the occluded region and thus gives an estimate of the object shape in this region. The other idea is to use a segmentation model as a measure in place of the frame difference measure. This is separate from image segmentation procedure, since we use the segmentation model in a tracking framework to capture object deformation. Numerical examples are presented to demonstrate tracking in simple and complex scenes, alongwith occlusion handling capability of our model. Segmentation measure is shown to be more robust with regard to accumulation of tracking error.

The accurate detection of static object boundaries such as contours or surfaces and dynamic tunnels of moving objects via deformable models is an ongoing research topic in computer vision. Most deformable models attempt to converge towards a desired solution by minimizing the sum of internal (prior) and external (measurement) energy terms. Such an approach is elegant, but frequently mis-converges in the presence of noise or complex boundaries and typically requires careful semi-dependent parameter tuning and initialization. Furthermore, current deformable model based approaches are computationally demanding which precludes real-time use. To address these limitations, a decoupled deformable model (DDM) is developed which optimizes the two energy terms separately. Essentially, the DDM consists of a measurement update step, employing a Hidden Markov Model (HMM) and Maximum Likelihood (ML) estimator, followed by a separate prior step, which modifies the updated deformable model based on the relative strengths of the measurement uncertainty and the non-stationary prior. The non-stationary prior is generated by using a curvature guided importance sampling method to capture high curvature regions. By separating the measurement and prior steps, the algorithm is less likely to mis-converge; furthermore, the use of a non-iterative ML estimator allows the method to converge more rapidly than energy-based iterative solvers. The full functionality of the DDM is developed in three phases. First, a DDM in 2D called the decoupled active contour (DAC) is developed to accurately identify the boundary of a 2D object in the presence of noise and background clutter. To carry out this task, the DAC employs the Viterbi algorithm as a truncated ML estimator, curvature guided importance sampling as a non-stationary prior generator, and a linear Bayesian estimator to fuse the non-stationary prior with the measurements. Experimental results clearly demonstrate that the DAC is robust to noise, can capture regions of very high curvature, and exhibits limited dependence on contour initialization or parameter settings. Compared to three other published methods and across many images, the DAC is found to be faster and to offer consistently accurate boundary identification. Second, a fast decoupled active contour (FDAC) is proposed to accelerate the convergence rate and the scalability of the DAC without sacrificing the accuracy by employing computationally efficient and scalable techniques to solve the three primary steps of DAC. The computational advantage of the FDAC is demonstrated both experimentally and analytically compared to three computationally efficient methods using illustrative examples. Finally, an extension of the FDAC from 2D to 3D called a decoupled active surface (DAS) is developed to precisely identify the surface of a volumetric 3D image and the tunnel of a moving 2D object. To achieve the objectives of the DAS, the concepts of the FDAC are extended to 3D by using a specialized 3D deformable model representation scheme and a computationally and storage efficient estimation scheme. The performance of the DAS is demonstrated using several natural and synthetic volumetric images and a sequence of moving objects.

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Using a high-resolution deep-towed seismic system, we have discovered a series of contour-current bedforms at the base of the Sigsbee Escarpment in the Bryant Canyon region of the northern Gulf of Mexico. We identify a continuum of bedforms that include furrows, meandering furrows, flutes and fully eroded seafloor. These contourcurrent bedforms are linked to current velocities ranging from 20 to upwards of 60 cm/s based on nearby current meter measurements and similar flume generated bedforms (Allen, 1969). We identify erosion and non-deposition of up to 25 meters of surface sediment at the base of Sigsbee Escarpment. Using 3-D and high-resolution seismic data, sediment samples, and submersible observations from the Green Knoll area, we further define contour-current bedforms along the Sigsbee Escarpment. The study area is divided into eleven zones based on bedform morphology, distribution, and formation processes. We identify a contourcurrent bedform continuum similar to that of the Bryant Canyon region, while the data reveals additional features that result from the interaction between topography and contour-currents. Three regional seismic marker horizons are identified, and we establish an age of ~19 kyr on the deepest horizon. The seismic horizons are correlated with very subtle changes in sediment properties, which in turn define the maximum depth of erosion for each of the individual bedforms. Finally, we show for the first time that furrowed horizons can be acoustically imaged in three dimensions below seafloor. Analysis of imagery of several horizons obtained from 3-D seismic data from the Green Knoll region establishes the existence of multiple paleo-furrow events. The contour current pattern preserved by the paleofurrows is similar to the presently active seafloor furrows. And, based on the morphology and development that we establish for the active seafloor furrows, we show that paleo-furrows are likely formed by currents that are in the same range as those measured today (20-60 cm/s), that erode into sediments with similar physical properties to the fine-grained hemipelagic sediments of the present-day seafloor. We further suggest the possibility that furrows are formed during inter-glacial highstands and buried during glacial lowstands.