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Cancer is one of the leading causes of death in the world, but advances in research and development of treatment methods is constantly ongoing to reduce the number of deaths and the amount of suffering. One of many approaches is radiation therapy, which uses high doses of radiation to kill tumors. Radiation therapy requires advanced software in image analysis to create careful treatment plans, evaluate treatment responses and to perform dose accumulation, among other things. One important tool for this is deformable image registration (DIR) which is used to find a correspondence between the images. The aim with this master thesis is to improve the DIR method ANACONDA by automatically provide additional information to the algorithm before the registration is performed.This work focuses on the registration of internal tubular structures in lung and liver images (bronchial and vascular tree, respectively). Two challenges in registering lung images are the sliding motion of lung surfaces and large motion of small internal structures. Several DIR methods have been proposed for solving the challenging internal structures, however most of them do not take into account the alignment of surrounding tissues. DIR methods applied to the liver are published less frequently, but accurate registration of the liver is of high interest since, for example, knowledge of the anatomy of the vascular tree is essential when removing tumors through liver surgeries. In this work, corresponding (anatomical) points are automatically found in two images and added to the DIR algorithm. The points are found by extracting and comparing the tubular structures between the images, and with use of different distance requirements, nearby points are paired.The new method manages to achieve good registration of both internal structures and surrounding tissue. Mean target registration errors for the internal structures of lungs was 1.11 ± 0.75 and for liver 1.67 ± 1.15 mm.

<p>This thesis presents a family of automatic elastic registration methods applicable to single and multimodal images of similar or dissimilar dimensions. These registration algorithms employ a generic dynamic linear elastic continuum mechanics model of the tissue deformation which is discretized using the finite element method. The dynamic deformation model provides spatial and temporal correlation between images acquired from different orientations at different times. First, a volumetric registration algorithm is presented which estimates the deformation field by balancing internal deformation forces of the elastic model against external forces derived from an intensity-based similarity measure between images. The registration is achieved by iteratively solving a reduced form of the dynamic deformation equations in response to image-derived nodal forces. A general approach for automatic deformable image registration is also presented in this thesis which deals with different registration problems within a unified framework irrespective of the image modality and dimension. Using the dynamic deformation model, the problem of deformable image registration is approached as a classical state estimation problem with various image similarity measures providing an observation model. With this formulation, single and multiple-modality, 3D-3D and 3D-2D image registration problems can all be treated within the same framework.The registration is achieved through a Kalman-like filtering process which incorporates information from the deformation model and an observation error computed from an intensity-based similarity measure. Correlation ratio, normalized correlation coefficient, mutual information, modality independent neighborhood descriptor and sum of squared differences between images are similarity/distance measures employed for single and multiple modality image registration in this thesis</p> / Doctor of Philosophy (PhD)

This study presents two computer vision based algorithms for automated 2D detection of construction workers and equipment from site video streams. The state-of-the-art research proposes semi-automated detection methods for tracking of construction workers and equipment. Considering the number of active equipment and workers on jobsites and their frequency of appearance in a camera's field of view, application of semi-automated techniques can be time-consuming. To address this limitation, two new algorithms based on Histograms of Oriented Gradients and Colors (HOG+C), 1) HOG+C sliding detection window technique, and 2) HOG+C deformable part-based model are proposed and their performance are compared to the state-of-the-art algorithm in computer vision community. Furthermore, a new comprehensive benchmark dataset containing over 8,000 annotated video frames including equipment and workers from different construction projects is introduced. This dataset contains a large range of pose, scale, background, illumination, and occlusion variation. The preliminary results with average performance accuracies of 100%, 92.02%, and 89.69% for workers, excavators, and dump trucks respectively, indicate the applicability of the proposed methods for automated activity analysis of workers and equipment from single video cameras. Unlike other state-of-the-art algorithms in automated resource tracking, these methods particularly detects idle resources and does not need manual or semi-automated initialization of the resource locations in 2D video frames. / Master of Science

Geosynthetic tubes filled with a slurry-mix are considered. The mix is usually dredged from a nearby area and pumped directly into the tubes. The tubes are used in a variety of applications including breakwaters, groins, and temporary levees. This thesis considers single and stacked geosynthetic tubes resting on rigid and deformable foundations. A two-dimensional analysis is performed on the cross-section of a very long tube. The program Mathematica is utilized for the analysis. A few assumptions are made regarding the general behavior of the tube. The tube is assumed to be an inextensible membrane with no bending stiffness. To allow for a closed-form integral solution, it is assumed that no friction exists between the tubes and at the foundation. A single tube, two stacked tubes, and a 2-1 formation are studied. Both rigid and deformable foundations are considered. The deformable foundation is modeled as a tensionless Winkler foundation with normal forces proportional to the downward deflection of the ground. An external water load on one side is also investigated for a single tube and a 2-1 formation, with rigid blocks to prevent the structure from sliding along the ground. Example cross-sectional profiles are given. Results from the analysis include structure height, circumferential tension, and ground deflections. / Master of Science

The present thesis is on the error estimates of different energy based quasicontinuum (QC) methods, which are a class of computational methods for the coupling of atomistic and continuum models for micro- or nano-scale materials. The thesis consists of two parts. The first part considers the a priori error estimates of three energy based QC methods. The second part deals with the a posteriori error estimates of a specific energy based QC method which was recently developed. In the first part, we develop a unified framework for the a priori error estimates and present a new and simpler proof based on negative-norm estimates, which essentially extends previous results. In the second part, we establish the a posteriori error estimates for the newly developed energy based QC method for an energy norm and for the total energy. The analysis is based on a posteriori residual and stability estimates. Adaptive mesh refinement algorithms based on these error estimators are formulated. In both parts, numerical experiments are presented to illustrate the results of our analysis and indicate the optimal convergence rates. The thesis is accompanied by a thorough introduction to the development of the QC methods and its numerical analysis, as well as an outlook of the future work in the conclusion.

Two important components of a visual recognition system are representation and model. Both involves the selection and learning of the features that are indicative for recognition and discarding those features that are uninformative. This thesis, in its general form, proposes different techniques within the frameworks of two learning systems for representation and modeling. Namely, latent support vector machines (latent SVMs) and deep learning. First, we propose various approaches to group the positive samples into clusters of visually similar instances. Given a fixed representation, the sampled space of the positive distribution is usually structured. The proposed clustering techniques include a novel similarity measure based on exemplar learning, an approach for using additional annotation, and augmenting latent SVM to automatically find clusters whose members can be reliably distinguished from background class.  In another effort, a strongly supervised DPM is suggested to study how these models can benefit from privileged information. The extra information comes in the form of semantic parts annotation (i.e. their presence and location). And they are used to constrain DPMs latent variables during or prior to the optimization of the latent SVM. Its effectiveness is demonstrated on the task of animal detection. Finally, we generalize the formulation of discriminative latent variable models, including DPMs, to incorporate new set of latent variables representing the structure or properties of negative samples. Thus, we term them as negative latent variables. We show this generalization affects state-of-the-art techniques and helps the visual recognition by explicitly searching for counter evidences of an object presence. Following the resurgence of deep networks, in the last works of this thesis we have focused on deep learning in order to produce a generic representation for visual recognition. A Convolutional Network (ConvNet) is trained on a largely annotated image classification dataset called ImageNet with $\sim1.3$ million images. Then, the activations at each layer of the trained ConvNet can be treated as the representation of an input image. We show that such a representation is surprisingly effective for various recognition tasks, making it clearly superior to all the handcrafted features previously used in visual recognition (such as HOG in our first works on DPM). We further investigate the ways that one can improve this representation for a task in mind. We propose various factors involving before or after the training of the representation which can improve the efficacy of the ConvNet representation. These factors are analyzed on 16 datasets from various subfields of visual recognition. / <p>QC 20160908</p>

Capillaries in tumours are often severely buckled (in a plane perpendicular to the axis) and / or chaotic in their direction. We develop a model of these phenomena using nonlinear solid mechanics. Our model focusses on the immediate surrounding of a capillary. The vessel and surrounding tissue are modelled as concentric annulii. The growth is dependent on the concentration of a nutrient (oxygen) diffusing from the vessel into the tumour interstitium. The stress is modelled using a multiplicative decomposition of the deformation gradient F=F_e F_g. The stress is determined by substituting the elastic deformation gradient F_e (which gives the deformation gradient from the hypothetical configuration to the current configuration) into a hyperelastic constitutive model as per classical solid mechanics. We use a Blatz-Ko model, parameterised using uniaxial compression experiments. The entire system is in quasi-static equilibrium, with the divergence of the stress tensor equal to zero. We determine the onset of buckling using a linear stability analysis. We then investigate the postbuckling behaviour by introducing higher order perturbations in the deformation and growth before using the Fredholm Alternative to obtain the magnitude of the buckle. Our results demonstrate that the growth-induced stresses are sufficient for the capillary to buckle in the absence of external loading and / or constraints. Planar buckling usually occurs after 2-5 times the cellular proliferation timescale. Buckles with axial variation almost always go unstable after planar buckles. Buckles of fine wavelength are initially preferred by the system, but over time buckles of large wavelength become energetically more favourable. The tumoural hoop stress T_{ThetaTheta} is the most invariant (Eulerian) variable at the time of buckling: it is typically of the order of the tumoural Young's Modulus when this occurs.