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Este trabalho discute a determinação de padrões respiratórios em sequências temporais de imagens obtidas por Ressonância Magnética (RM) e o seu uso no registro temporal de imagens coronais e sagitais. O registro é feito sem o uso de qualquer informação de sincronismo e qualquer gás especial para reforçar o contraste. As sequências temporais de imagens são adquiridas em respiração livre. O movimento real do pulmão nunca foi diretamente visto, pois é totalmente dependente dos músculos que o rodeiam. A visualização do pulmão em movimento é um tema atual de pesquisa na medicina. O movimento do pulmão não possui intervalos regulares e é suscetível a variações na respiração. Comparado à Tomografia Computadorizada (TC), a RM necessita de um maior tempo de aquisição e é preferível porque não envolve radiação. Como as sequências de imagens coronais e sagitais são ortogonais entre si, a sua intersecção corresponde a um segmento de reta no espaço tridimensional. O registro se baseia na análise deste segmento interseccional. A variação deste segmento de interseção no tempo pode ser enfileirada, definindo uma imagem espaço-temporal em duas dimensões (2DST). Supõe-se que o movimento diafragmático é o movimento principal de todas as estruturas do pulmão se movem quase que totalmente sincronicamente. A sincronização deste movimento é feita através de um padrão chamado função respiração. Este padrão é obtido através do processamento de uma imagem 2DST. Um algoritmo da transformada de Hough intervalar procura movimentos sincronizados na função respiração. O algoritmo de contornos ativos ajusta pequenas discrepâncias originadas por movimentos assíncronos nos padrões respiratórios . A saída é um conjunto de padrões respiratórios. Finalmente, a composição de imagens coronal e sagital que estão na mesma fase respiratória é realizada através da comparação de padrões respiratórios provenientes das superfícies de contorno superior e diafragmática. Quando disponíveis, os padrões respiratórios associados às estruturas internas do pulmão também são usados. Vários resultados e conclusões são apresentados. / This work addresses the determination of the breathing patterns in time sequence of images obtained from Magnetic Resonance (MR) and their use in the temporal registration of coronal and sagital images. The registration is done without the use of any triggering information and any special gas to enhance the contrast. The temporal sequences of images are acquired in free breathing. The real movement of the lung has never been seen directly, as it is totally dependent on its surrounding muscles and collapses without them. The visualization of the lung in motion is an actual topic of research in medicine. The lung movement is not periodic and it is susceptible to variations in the degree of respiration. Compared to Computerized Tomography (CT), MR imaging involves longer acquisition times and it is preferable because it does not involve radiation. As coronal and sagittal sequences of images are orthogonal to each other, their intersection corresponds to a segment in the three dimensional space. The registration is based on the analysis of this intersection segment. A time sequence of this intersection segment can be stacked, defining a two-dimension spatio-temporal (2DST) image. It is assumed that the diaphragmatic movement is the principal movement and all the lung structures move almost synchronously. The synchronization of this motion is performed through a pattern named respiratory function. This pattern is obtained by processing a 2DST image. An interval Hough transform algorithm searches for synchronized movements with the respiratory function. A greedy searches for synchronized movements with the respiratory function. A greedy active contour algorithm adjusts small discrepancies originated by asynchronous movements in the respiratory patterns. The output is a set of respiratory patterns. Finally, the composition of coronal and sagittal images that are in the same breathing phase is realized by comparing of respiratory patterns originated from diaphragmatic and upper boundary surfaces. When available, the respire tory patterns associated to lung internal structures are also used. Several results and conclusions are shown.

INTRODUCTION: Despite the advances in radiotherapy treatment delivery, target volume delineation remains one of the greatest sources of error in the radiotherapy delivery process, which can lead to poor tumour control probability and impact clinical outcome. Contouring assessments are performed to ensure high quality of target volume definition in clinical trials but this can be subjective and labour-intensive. This project addresses the hypothesis that computational segmentation techniques, with a given prior, can be used to develop an image-based tumour delineation process for contour assessments. This thesis focuses on the exploration of the segmentation techniques to develop an automated method for generating reference delineations in the setting of advanced lung cancer. The novelty of this project is in the use of the initial clinician outline as a prior for image segmentation. METHODS: Automated segmentation processes were developed for stage II and III non-small cell lung cancer using the IDEAL-CRT clinical trial dataset. Marker-controlled watershed segmentation, two active contour approaches (edge- and region-based) and graph-cut applied on superpixels were explored. k-nearest neighbour (k-NN) classification of tumour from normal tissues based on texture features was also investigated. RESULTS: 63 cases were used for development and training. Segmentation and classification performance were evaluated on an independent test set of 16 cases. Edge-based active contour segmentation achieved highest Dice similarity coefficient of 0.80 ± 0.06, followed by graphcut at 0.76 ± 0.06, watershed at 0.72 ± 0.08 and region-based active contour at 0.71 ± 0.07, with mean computational times of 192 ± 102 sec, 834 ± 438 sec, 21 ± 5 sec and 45 ± 18 sec per case respectively. Errors in accuracy of irregularly shaped lesions and segmentation leakages at the mediastinum were observed. In the distinction of tumour and non-tumour regions, misclassification errors of 14.5% and 15.5% were achieved using 16- and 8-pixel regions of interest (ROIs) respectively. Higher misclassification errors of 24.7% and 26.9% for 16- and 8-pixel ROIs were obtained in the analysis of the tumour boundary. CONCLUSIONS: Conventional image-based segmentation techniques with the application of priors are useful in automatic segmentation of tumours, although further developments are required to improve their performance. Texture classification can be useful in distinguishing tumour from non-tumour tissue, but the segmentation task at the tumour boundary is more difficult. Future work with deep-learning segmentation approaches need to be explored.

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This thesis deals with image segmentation problems that arise in various computer vision related fields such as medical imaging, satellite imaging, video surveillance, recognition and robotic vision. More specifically, this thesis deals with a special class of image segmentation technique called Snakes or Active Contour Models. In active contour models, image segmentation is posed as an energy minimization problem, where an objective energy function (based on certain image related features) is defined on the segmenting curve (contour). Typically, a gradient descent energy minimization approach is used to drive the initial contour towards a minimum for the defined energy. The drawback associated with this approach is that the contour has a tendency to get stuck at undesired local minima caused by subtle and undesired image features/edges. Thus, active contour based curve evolution approaches are very sensitive to initialization and noise. The central theme of this thesis is to develop techniques that can make active contour models robust against certain classes of local minima by incorporating global information in energy minimization. These techniques lead to energy minimization with global considerations; we call these models -- 'Non-local active contours'. In this thesis, we consider three widely used active contour models: 1) Edge- and region-based segmentation model, 2) Prior shape knowledge based segmentation model, and 3) Motion segmentation model. We analyze the traditional techniques used for these models and establish the need for robust models that avoid local minima. We address the local minima problem for each model by adding global image considerations.

Este trabalho discute a determinação de padrões respiratórios em sequências temporais de imagens obtidas por Ressonância Magnética (RM) e o seu uso no registro temporal de imagens coronais e sagitais. O registro é feito sem o uso de qualquer informação de sincronismo e qualquer gás especial para reforçar o contraste. As sequências temporais de imagens são adquiridas em respiração livre. O movimento real do pulmão nunca foi diretamente visto, pois é totalmente dependente dos músculos que o rodeiam. A visualização do pulmão em movimento é um tema atual de pesquisa na medicina. O movimento do pulmão não possui intervalos regulares e é suscetível a variações na respiração. Comparado à Tomografia Computadorizada (TC), a RM necessita de um maior tempo de aquisição e é preferível porque não envolve radiação. Como as sequências de imagens coronais e sagitais são ortogonais entre si, a sua intersecção corresponde a um segmento de reta no espaço tridimensional. O registro se baseia na análise deste segmento interseccional. A variação deste segmento de interseção no tempo pode ser enfileirada, definindo uma imagem espaço-temporal em duas dimensões (2DST). Supõe-se que o movimento diafragmático é o movimento principal de todas as estruturas do pulmão se movem quase que totalmente sincronicamente. A sincronização deste movimento é feita através de um padrão chamado função respiração. Este padrão é obtido através do processamento de uma imagem 2DST. Um algoritmo da transformada de Hough intervalar procura movimentos sincronizados na função respiração. O algoritmo de contornos ativos ajusta pequenas discrepâncias originadas por movimentos assíncronos nos padrões respiratórios . A saída é um conjunto de padrões respiratórios. Finalmente, a composição de imagens coronal e sagital que estão na mesma fase respiratória é realizada através da comparação de padrões respiratórios provenientes das superfícies de contorno superior e diafragmática. Quando disponíveis, os padrões respiratórios associados às estruturas internas do pulmão também são usados. Vários resultados e conclusões são apresentados. / This work addresses the determination of the breathing patterns in time sequence of images obtained from Magnetic Resonance (MR) and their use in the temporal registration of coronal and sagital images. The registration is done without the use of any triggering information and any special gas to enhance the contrast. The temporal sequences of images are acquired in free breathing. The real movement of the lung has never been seen directly, as it is totally dependent on its surrounding muscles and collapses without them. The visualization of the lung in motion is an actual topic of research in medicine. The lung movement is not periodic and it is susceptible to variations in the degree of respiration. Compared to Computerized Tomography (CT), MR imaging involves longer acquisition times and it is preferable because it does not involve radiation. As coronal and sagittal sequences of images are orthogonal to each other, their intersection corresponds to a segment in the three dimensional space. The registration is based on the analysis of this intersection segment. A time sequence of this intersection segment can be stacked, defining a two-dimension spatio-temporal (2DST) image. It is assumed that the diaphragmatic movement is the principal movement and all the lung structures move almost synchronously. The synchronization of this motion is performed through a pattern named respiratory function. This pattern is obtained by processing a 2DST image. An interval Hough transform algorithm searches for synchronized movements with the respiratory function. A greedy searches for synchronized movements with the respiratory function. A greedy active contour algorithm adjusts small discrepancies originated by asynchronous movements in the respiratory patterns. The output is a set of respiratory patterns. Finally, the composition of coronal and sagittal images that are in the same breathing phase is realized by comparing of respiratory patterns originated from diaphragmatic and upper boundary surfaces. When available, the respire tory patterns associated to lung internal structures are also used. Several results and conclusions are shown.

Today, tool center point calibration is mostly done by a manual procedure. The method is very time consuming and the result may vary due to how skilled the operators are. This thesis proposes a new automated iterative method for tool center point calibration of industrial robots, by making use of computer vision and image processing techniques. The new method has several advantages over the manual calibration method. Experimental verifications have shown that the proposed method is much faster, still delivering a comparable or even better accuracy. The setup of the proposed method is very easy, only one USB camera connected to a laptop computer is needed and no contact with the robot tool is necessary during the calibration procedure. The method can be split into three different parts. Initially, the transformation between the robot wrist and the tool is determined by solving a closed loop of homogeneous transformations. Second an image segmentation procedure is described for finding point correspondences on a rotation symmetric robot tool. The image segmentation part is necessary for performing a measurement with six degrees of freedom of the camera to tool transformation. The last part of the proposed method is an iterative procedure which automates an ordinary four point tool center point calibration algorithm. The iterative procedure ensures that the accuracy of the tool center point calibration only depends on the accuracy of the camera when registering a movement between two positions.

La segmentation d'image constitue une étape importante dans le traitement d'image et de nombreuses questions restent ouvertes. Il a été montré récemment, dans le cas d'une segmentation à deux régions homogènes, que l'utilisation de contours actifs polygonaux fondés sur la minimisation d'un critère issu de la théorie de l'information permet d'aboutir à un algorithme ultra-rapide qui ne nécessite ni paramètre à régler dans le critère d'optimisation, ni connaissance a priori sur les fluctuations des niveaux de gris. Cette technique de segmentation rapide et non supervisée devient alors un outil élémentaire de traitement.L'objectif de cette thèse est de montrer les apports de cette brique élémentaire pour la conception de nouvelles techniques de segmentation plus complexes, permettant de dépasser un certain nombre de limites et en particulier :- d'être robuste à la présence dans les images de fortes inhomogénéités ;- de segmenter des objets non connexes par contour actif polygonal sans complexifier les stratégies d'optimisation ;- de segmenter des images multi-régions tout en estimant de façon non supervisée le nombre de régions homogènes présentes dans l'image.Nous avons pu aboutir à des techniques de segmentation non supervisées fondées sur l'optimisation de critères sans paramètre à régler et ne nécessitant aucune information sur le type de bruit présent dans l'image. De plus, nous avons montré qu'il était possible de concevoir des algorithmes basés sur l'utilisation de cette brique élémentaire, permettant d'aboutir à des techniques de segmentation rapides et dont la complexité de réalisation est faible dès lors que l'on possède une telle brique élémentaire. / Image segmentation is an important step in many image processing systems and many problems remain unsolved. It has recently been shown that when the image is composed of two homogeneous regions, polygonal active contour techniques based on the minimization of a criterion derived from information theory allow achieving an ultra-fast algorithm which requires neither parameter to tune in the optimized criterion, nor a priori knowledge on the gray level fluctuations. This algorithm can then be used as a fast and unsupervised processing module. The objective of this thesis is therefore to show how this ultra-fast and unsupervised algorithm can be used as a module in the conception of more complex segmentation techniques, allowing to overcome several limits and particularly:- to be robust to the presence of strong inhomogeneity in the image which is often inherent in the acquisition process, such as non-uniform illumination, attenuation, etc.;- to be able to segment disconnected objects by polygonal active contour without complicating the optimization strategy;- to segment multi-region images while estimating in an unsupervised way the number of homogeneous regions in the image.For each of these three problems, unsupervised segmentation techniques based on the optimization of Minimum Description Length criteria have been obtained, which do not require the tuning of parameter by user or a priori information on the kind of noise in the image. Moreover, it has been shown that fast segmentation techniques can be achieved using this segmentation module, while keeping reduced implementation complexity.

Optic nerve head and macula are important structures in fundus images. Detection and measurement plays crucial role in several diagnosis methods of optic disease. This work is focused on the detection of the central point of macula and optic nerve head, where the inner border is detected too. There are many methods for extracting this structure in retinal images. Due to the unique properties of each acquisition technique, a single generally acknowledged detection algorithm does not exist. The whole detection process is described from preprocessing through segmentation towards postprocessing. Presented methods are based on the combination of correlation techniques, Hough transform, active contours and morphological operations. The detected contours of the optic nerve head are evaluated and quantitatively compared with the contour drawn by experienced ophthalmologist. The master thesis contains quantity of images that help to describe detection methods.

This thesis focuses on advanced methods of detecting contours of the cardiac cells and measuring their contraction. The theoretical section describes the types of confocal microscopes, which are used for capturing biological samples. The following chapter is devoted to the methods of cardiac cells segmentation, where we are introduced to the generally applied approaches. The most widely spread methods of segmentation are active contours and mathematical morphology, which are the crucial topics of this thesis. Thanks to the those methods we are able in the visual data to accurately detect required elements and measure their surface chnage in time. Acquired theoretical knowledge leads us to the practical realization of the methods in MATLAB.