Résumé : Thèse de DoctoratL’importance de l’imagerie médicale comme élément principal dans plusieurs application médicales et diagnostiques de soin de santé est indispensable. L’intégration des données utiles obtenues des diverses images est vitale pour une analyse appropriée de l’information contenues dans ces images sous observation. Pour que ce processus d’intégration réussisse, une procédure appelée recalage d’image est nécessaire.Le but du recalage d’image consiste à aligner deux images afin de trouver une transformation géométrique qui place une des deux images dans la meilleure correspondance spatiale possible avec l’autre image en optimisant un critère de recalage. Les deux images sont dites image cible et image source. Les méthodes de recalage d’image consistent à avoir référencées par des points de contrôle. Ceci est suivi d’une transformation de recalage qui associe les deux images et d’une fonction définie sur base de la mesure de similarité qui a pour but de mesurer la valeur qualitative de proximité ou encore de degré de concordance entre l’image cible et l’image source. Enfin, un optimisateur qui cherche à trouver la transformation optimale au sein du champ de solution de la recherche, est appliqué.Cette recherche présente un algorithme automatique de recalage d’image dont le but est de résoudre le problème du recalage d’image à multiple modes sur une paire des clichés de tomographie par ordinateur (CT) faite sur les poumons. Dans cette méthode, une étude comparative entre la méthode classique d’optimisation par algorithme du gradient à pas fixe et celle de l’algorithme évolutionniste est menée. L’objectif de cette recherche est d’effectuer l’optimisation par des techniques de recalage d’image ainsi qu’évaluer la performance de ces mêmes techniques afin de doter les spécialistes du domaine médical d’une estimation de combien précis et robuste le processus de recalage serait. Les paires des clichés obtenues de la tomographie par ordinateur faite sur les poumons sont recalées en utilisant l’information mutuelle comme mesure de similarité, la transformation affine ainsi que l’interpolation linéaire. Un optimisateur qui recherche la transformation optimale au sein de l’espace de recherche est appliqué afin de minimiser la fonction économique (fonction objectif).Les études de détermination d’un modèle de transformation qui dépend des paramètres de transformation et de l’identification des mesures de similarité basée sur l’intensité du voxel ont été menées. En alignant la transformation avec les points de control, trois modèles de transformation sont comparés. La transformation affine produit la meilleure reconstitution d’image en comparaison aux transformations non réfléchissantes et projectives. Les résultats de cette recherche sont assez comparables à celles rapportées dans le challenge de recherche EMPIRE 10 et sont conformes à la fois aux principes théoriques aussi bien qu’aux applications pratiques.La contribution de cette recherche réside dans son potentiel à améliorer la compréhension scientifique du recalage d’image des organes anatomiques du corps humain. Cette recherche établie ainsi une base pour une recherche avancée sur l’évaluation de la performance des techniques de recalage et la validation des procédures sur d’autres types d’algorithmes et domaines d’application du recalage d’images comme la détection, la communication par satellite, l’ingénierie biomédicale, la robotique, les systèmes d'information géographique (SIG) et de localisation parmi tant d’autres / D’Tech Thesis SummaryThe importance of medical imaging as a core component of several medical application and healthcare diagnosis cannot be over emphasised. Integration of useful data acquired from different images is vital for proper analysis of information contained in the images under observation. For the integration process to be successful, a procedure referred to as image registration is necessary.The purpose of image registration is to align two images in order to find a geometric transformation that brings one image into the best possible spatial correspondence with another image by optimising a registration criterion. The two images are known as the target image and the source image. Image registration methods consist of having the two images referenced with control points. This is followed by a registration transformation that relates the two images and a similarity metric function that aims to measure the qualitative value of closeness or degree of fitness between the target image and the source image. Finally, an optimiser which seeks an optimal transformation inside the defined solution search space is performed.This research presents an automated image registration algorithm for solving multimodal image registration on lung Computer Tomography (CT) scan pairs, where a comparison between regular step gradient descent optimisation technique and evolutionary optimisation was investigated. The aim of this research is to carry out optimisation and performance evaluation of image registration techniques in order to provide medical specialists with estimation on how accurate and robust the registration process is. Lung CT scan pairs are registered using mutual information as a similarity measure, affine transformation and linear interpolation. In order to minimise the cost function, an optimiser, which seeks the optimal transformation inside the defined search space is applied.Determination of a transformation model that depends on transformation parameters and identification of similarity metric based on voxel intensity were carried out. By fitting transformation to control points, three transformation models were compared. Affine transformation produced the best recovered image when compared to non-reflective similarity and projective transformations. The results of this research compares well with documented results from EMPIRE 10 Challenge research and conforms to both theoretical principles as well as practical applications.The contribution of this research is its potential to increase the scientific understanding of image registration of anatomical body organs. It lays a basis for further research in performance evaluation of registration techniques and validation of procedures to other types of algorithms and image registration application areas, such as remote sensing, satellite communication, biomedical engineering, robotics, geographical information systems and mapping, among others

O interesse no uso de técnicas de aquisição de dados 3D em vídeos interativos e sistemas de videoconferência imersiva aumentou significativamente nos últimos anos. A disponibilidade de sensores de profundidade baseados em luz estruturada no varejo apresenta uma série de novas oportunidades em sistemas de teleconferência, entretenimento e e-learning. No entanto, problemas de oclusão frequentemente ocorrem quando é utilizado um único sensor ou técnicas de reconstrução 2,5D. Outras técnicas de interação e aplicações de teleconferências podem exigir uma reconstrução mais completa do usuário. Uma possível solução para isso implica na utilização de múltiplos dispositivos simultaneamente, o que traz novos desafios relacionados ao processo de calibração de câmaras e a aferição do aumento da superfície capturada quando é adicionado um novo sensor. Neste trabalho é apresentada a proposta VMD (Video-avatar from Multiple Depth maps), uma arquitetura de sistema que trata esses dois problemas. Com a finalidade de validar a viabilidade dessa proposta, três experimentos foram feitos resultando em uma análise qualitativa e quantitativa a fim de encontrar uma configuração adequada de múltiplos sensores de profundidade. / The interest in the use of 3D data acquisition techniques in video based interaction and immersive videoconferencing systems has noticeably increased in recent years. The availability of structured light 3D sensors as off-the-shelf hardware presents a series of new opportunities in teleconferences, entertainment and e-learning. However, occlusion issues often occur when it is used a single sensor or 2,5D reconstruction techniques. Other interaction techniques and teleconferencing applications may require a more complete reconstruction of the user. One possible solution to this involves the use of multiple devices simultaneously, which may bring new challenges related to the calibration process of cameras and measurement of the increase in covered area when it is added a new sensor. In this work we present VMD (Video-avatar from Multiple Depth maps), a system architecture that addresses this two issues. In order to validate the feasibility of this proposal, three experiments were performed resulting in a qualitative and quantitative analysis with the purpose of finding a suitable setup with multiple depth sensors.

O interesse no uso de técnicas de aquisição de dados 3D em vídeos interativos e sistemas de videoconferência imersiva aumentou significativamente nos últimos anos. A disponibilidade de sensores de profundidade baseados em luz estruturada no varejo apresenta uma série de novas oportunidades em sistemas de teleconferência, entretenimento e e-learning. No entanto, problemas de oclusão frequentemente ocorrem quando é utilizado um único sensor ou técnicas de reconstrução 2,5D. Outras técnicas de interação e aplicações de teleconferências podem exigir uma reconstrução mais completa do usuário. Uma possível solução para isso implica na utilização de múltiplos dispositivos simultaneamente, o que traz novos desafios relacionados ao processo de calibração de câmaras e a aferição do aumento da superfície capturada quando é adicionado um novo sensor. Neste trabalho é apresentada a proposta VMD (Video-avatar from Multiple Depth maps), uma arquitetura de sistema que trata esses dois problemas. Com a finalidade de validar a viabilidade dessa proposta, três experimentos foram feitos resultando em uma análise qualitativa e quantitativa a fim de encontrar uma configuração adequada de múltiplos sensores de profundidade. / The interest in the use of 3D data acquisition techniques in video based interaction and immersive videoconferencing systems has noticeably increased in recent years. The availability of structured light 3D sensors as off-the-shelf hardware presents a series of new opportunities in teleconferences, entertainment and e-learning. However, occlusion issues often occur when it is used a single sensor or 2,5D reconstruction techniques. Other interaction techniques and teleconferencing applications may require a more complete reconstruction of the user. One possible solution to this involves the use of multiple devices simultaneously, which may bring new challenges related to the calibration process of cameras and measurement of the increase in covered area when it is added a new sensor. In this work we present VMD (Video-avatar from Multiple Depth maps), a system architecture that addresses this two issues. In order to validate the feasibility of this proposal, three experiments were performed resulting in a qualitative and quantitative analysis with the purpose of finding a suitable setup with multiple depth sensors.

Les techniques de chirurgie assistée par ordinateur suscitent depuis quelques années un vif intérêt, depuis l’aide au diagnostic jusqu’à l’intervention chirurgicale elle-même, en passant pas les prises de décision. Dans ce but, l’Analyse par Éléments Finis (AEF) du comportement de modèles biomécaniques tridimensionnels est une des méthodes numériques les plus utilisées et les plus efficaces. Cependant, la fiabilité des solutions de l’AEF dépend fortement de la qualité et de la finesse de la représentation des organes sous la forme de maillages d'éléments finis (MEF). Or la génération de tels maillages peut être extrêmement longue et exigeante en ressources computationnelles, car il est nécessaire de procéder à l’extraction précise de la géométrie de l’organe-cible à partir d’images médicales avant de recourir à des algorithmes sophistiqués de maillage. Confrontés à ces enjeux, certains travaux se sont attachés à éviter la procédure de maillage en exploitant des méthodes fondées pour chaque patient sur la déformation géométrique d’un maillage défini sur un sujet de référence, dit « Atlas ». Mais ces méthodes nécessitent toujours une description géométrique précise de l’organe-cible du patient, sous la forme de contours, de modèles surfaciques tridimensionnels ou d’un ensemble de points de référence. Dans ce contexte, le but de la thèse est de développer une méthodologie de conception automatique de maillages « patient-spécifiques », basée sur un Atlas, mais évitant cette étape de segmentation de la géométrie de l’organe-cible du patient. Dans une première partie de la thèse, nous proposons une méthode automatique qui, dans une première phase, procède au recalage volumétrique de l'image anatomique de l’Atlas sur celle du patient, afin d’extraire la transformation géométrique permettant de passer de l’Atlas au patient, puis, dans une seconde phase, déforme le maillage de l’Atlas et l’adapte au patient en lui appliquant cette transformation. Le processus de recalage est conçu de telle manière que la transformation géométrique préserve la régularité et la haute qualité du maillage. L’évaluation de notre méthode, à savoir l'exactitude du processus de recalage inter-sujets, s’est faite en deux étapes. Nous avons d’abord utilisé un ensemble d’images CT de la cage thoracique, en accès libre. Puis nous avons exploité des données IRM de la langue que nous avons recueillies pour deux sujets sains et deux patients souffrant de cancer de la langue, en condition pré- et post-opératoire.Dans une seconde partie, nous développons une nouvelle méthode, toujours basée sur un Atlas, qui exploite à la fois l'information fournie par les images anatomiques et celle relative à la disposition des fibres musculaires telles qu’elle est décrite par imagerie par résonance magnétique du tenseur de diffusion (RM-DT). Cette nouvelle démarche s’appuie ainsi, d’abord sur le recalage anatomique proposé dans notre première méthode, puis sur l’identification et le recalage d’un ensemble de faisceaux de fibres musculaires qui seront ensuite intégrés aux maillages « patient-spécifiques ». Contrairement aux techniques usuelles de recalage d’images RM-DT, qui impliquent pour chaque image la réorientation des tenseurs de diffusion soit au cours de l'estimation de la transformation géométrique, soit après celle-ci, notre technique ne nécessite pas cette réorientation et recale directement les faisceaux de fibres de l’Atlas sur ceux du patient. Notre démarche est très importante, car la détermination et l’identification précises de toutes les sous-structures musculaires nécessiteraient une intervention manuelle pour analyser des milliers, voire des millions, de fibres, qui sont grandement influencées par les limitations et aux distorsions inhérentes aux images RM-DT et aux techniques de tractographie des fibres. L’efficacité de notre méthodologie est démontrée par son évaluation sur un ensemble d’images IRM et RM-DT de la langue d’un sujet. / During the last years, there has been considerable interest in using computer-aided medical design, diagnosis, and decision-making techniques that are rapidly entering the treatment mainstreams. Finite Element Analysis (FEA) of 3D models is one of the most popular and efficient numerical methods that can be utilized for solving complex problems like deformation of soft tissues or orthopedic implant designs/configurations. However, the accuracy of solutions highly depends upon the quality and accuracy of designed Finite Element Meshes (FEMs). The generation of such high-quality subject/patient-specific meshes can be extremely time consuming and labor intensive as the process includes geometry extraction of the target organ and meshing algorithms. In clinical applications where the patient specifiity has to be taken into account via the generation of adapted meshes these problems become methodological bottlenecks. In this context, various studies have addressed these challenges by bypassing the meshing phase by employing atlas-based frameworks using the deformation of an atlas FE mesh. However, these methods still rely on the geometrical description of the target organ, such as contours, 3D surface models, or a set of land-marks.In this context, the aim of this thesis is to investigate how registration techniques can overcome these bottlenecks of atlas-based approaches.We first propose an automatic atlas-based method that includes the volumetric anatomical image registration and the morphing of an atlas FE mesh. The method extracts a 3D transformation by registering the atlas' volumetric image to the subject's one. The subject-specific mesh is then generated by deforming a high-quality atlas FE mesh using the derived transformation. The registration process is designed is such a way to preserve the regularity and the quality of meshes for subsequent FEAs. A first step towards the evaluation of our approach, namely the accuracy of the inter-subject registration process, is provided using a data set of CT ribcage. Then, subject-specific tongue meshes are generated for two healthy subjects and two patients suffering from tongue cancer, in pre- and post-surgery conditions. In order to illustrate a tentative fully automatic process compatible with the clinical constraints, some functional consequences of a tongue surgery are simulated for one of the patients, where the removal of the tumor and the replacement of the corresponding tissues with a passive flap are modeled. With the extraction of any formal priorknowledge on the shape of the target organ and any meshing algorithm, high-quality subject-specific FE meshes are generated while subject’s geometrical properties are successfully captured.Following this method, we develop an original atlas-based approach that employs the information provided by the anatomical images and diffusion tensor imaging (DTI) based muscle fibers for the recognition and registration of fiber-bundles that can be integrated in the subject-specific FE meshes. In contrast to the DT MR images registration techniques that include reorientation of tensors within or after the transformation estimation, our methodology avoids this issue and directly aligns fiber-bundles. This also enables one to handel limited or distorted DTIs by deformation of an atlas fibers’ structure according to the most reliable and non-distorted subject’s ones. Such a manner becomes very important, since the classification and the determination of muscular sub-structures need manual intervention of thousands or millions of fibers for each subject, which are influenced by the limitations associated with the DTI image acquisition process and fiber tractography techniques. To evaluate the performance of our method in the recognition of subject’s fiber-bundles and accordingly in the deformation of the atlas ones, a simulated data set is utilized. In addition, feasibility of our method is demonstrated on acquired human tongue data set.

Η αυτόματη ταυτοποίηση εικόνων δακτυλικών αποτυπωμάτων αποτελεί ένα δύσκολο και πολυδιάστατο πρόβλημα, το οποίο έχει απασχολήσει πλήθος ερευνητών και για το οποίο έχει αναπτυχθεί μεγάλος αριθμός τεχνικών. Η δυσκολία του προβλήματος έγκειται στο γεγονός ότι οι εικόνες των αποτυπωμάτων είναι σε μεγάλο ποσοστό αλλοιωμένες ή ακόμα σε κάποιες περιπτώσεις δεν είναι διαθέσιμη η πλήρης εικόνα του αποτυπώματος, αλλά μόνο ένα μέρος αυτής. Στη συγκεκριμένη διατριβή, προτείνονται δύο μέθοδοι αυτόματης ταυτοποίησης δακτυλικών αποτυπωμάτων: α) η μέθοδος ταυτοποίησης δακτυλικών αποτυπωμάτων με χρήση τεχνικών ευθυγράμμισης και β) μέθοδος ταυτοποίησης δακτυλικών αποτυπωμάτων από το συνδυασμό του Δικτύου Αυτό-Οργανούμενων Δικτύων του Kohonen και του ορισμού των σημείων μικρολεπτομερειών των αποτυπωμάτων ως νευρώνων του δικτύου. Επιπλέον, ιδιαίτερη βαρύτητα δόθηκε στην προεπεξεργασία των εικόνων των δακτυλικών αποτυπωμάτων βάσει της ανάπτυξης και εφαρμογής κατάλληλων τεχνικών επεξεργασίας εικόνων προκειμένου να προκύψει βελτίωση της ποιότητας της εικόνας του δακτυλικού αποτυπώματος και να εξαχθούν οι μικρολεπτομέρειες που χρησιμοποιούνται για την ταύτιση των δακτυλικών αποτυπωμάτων. Στο πλαίσιο της παρούσας διατριβής, χρησιμοποιήθηκαν δεδομένα δακτυλικών αποτυπωμάτων από τις βάσεις VeriFingerSample_DB της Neurotechnology και η DB3 του διαγωνισμού δακτυλικών αποτυπωμάτων FVC2004. Για την ποσοτική αποτίμηση της απόδοσης των προτεινόμενων μεθόδων χρησιμοποιήθηκε το κριτήριο της Αναλογίας Ίσου Σφάλματος (EqualErrorRate – EER). Σύμφωνα με το κριτήριο αυτό, η μέθοδος ταυτοποίησης δακτυλικών αποτυπωμάτων βάσει του Δικτύου Αυτό-Οργανούμενων Δικτύων παρείχε καλύτερα αποτελέσματα σε σύγκριση με οποιαδήποτε μέθοδο ευθυγράμμισης που εφαρμόστηκε. / Automatic Fingerprint Identification is a difficult and multidimensional problem. For this reason, the number of papers and techniques regarding this issue is numerous. The hardness of the problem lies with the fact that there is a large percentage of corrupted and partial fingerprint images. Throughout this Thesis, two methods were proposed for the Automatic Fingerprint Identification: a) the Automatic Fingerprint Identification based on registration techniques and b) the Automatic Fingerprint Identification based on the theory of Self Organizing Maps of Kohonen, setting the minutiae of the fingerprint images as input neurons of the Map. Furthermore, an important step prior to the application of the proposed automatic fingerprint identification methods is the pre-processing of these images by the development and implementation of a series of image processing techniques in order to enhance the image quality and to extract the minutiae which are then used for the fingerprint identification. In this Thesis, a substantial number of fingerprint images were used from the database VeriFingerSample_DB kai from the database DB3 of the competition FVC2004. The quantitative evaluation of both proposed automatic fingerprint identification methods were based on the Equal Error Rate (EER) criterion. According to this, the Automatic Fingerprint Identification based on the Self Organizing Maps outperformed against any other method based on registration techniques.

Orientador: João Antonio Pereira / Resumo: O objetivo específico deste trabalho é estender as capacidades da técnica de rastreamento de pontos em 3 dimensões (three-dimensional point tracking – 3DPT) para identificar as características dinâmicas de estruturas grandes e complexas, tais como pás de turbina eólica. Um sistema multi-camera (composto de múltiplos sistemas de estéreo visão calibrados independentemente) é desenvolvido para obter alta resolução espacial de pontos discretos a partir de medidas de deslocamento sobre grandes áreas. Uma proposta de técnica de costura é apresentada e empregada para executar o alinhamento de duas nuvens de pontos, obtidas com a técnica 3DPT, de uma estrutura sob excitação dinâmica. Três diferentes algoritmos de registro de nuvens de pontos são propostos para executar a junção das nuvens de pontos de cada sistema estéreo, análise de componentes principais (Principal Component Analysis - PCA), decomposição de valores singulares (Singular value Decomposition - SVD) e ponto mais próximo iterativo (Iterative Closest Point - ICP). Além disso, análise modal operacional em conjunto com o sistema de medição multi-camera e as técnicas de registro de nuvens de pontos são usadas para determinar a viabilidade de usar medidas ópticas (e.g. three-dimensional point tracking – 3DPT) para estimar os parâmetros modais de uma pá de gerador eólico comparando seus resultados com técnicas de medição mais convencionais. / Abstract: The specific objective of this research is to extend the capabilities of three-dimensional (3D) Point Tracking (PT) to identify the dynamic characteristics of large and complex structures, such as utility-scale wind turbine blades. A multi-camera system (composed of multiple independently calibrated stereovision systems) is developed to obtain high spatial resolution of discrete points from displacement measurement over very large areas. A proposal of stitching techniques is presented and employed to perform the alignment of two point clouds, obtained with 3DPT measurement, of a structure under dynamic excitation. The point cloud registration techniques are exploited as a technique for dynamic measuring (displacement) of large structures with high spatial resolution of the model. Three different image registration algorithms are proposed to perform the junction of the points clouds of each stereo system, Principal Component Analysis (PCA), Singular value Decomposition (SVD) and Iterative Closest Point (ICP). Furthermore, operational modal analysis in conjunction with the multi-camera measurement system and registration techniques are used to determine the feasibility of using optical measurements (e.g. three-dimensional point tracking (3DPT)) to estimate the modal parameters of a utility-scale wind turbine blade by comparing with traditional techniques. / Doutor

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Ce travail portant sur l’imagerie tomodensitométrique double énergie de la ventilation a permis d’établir les points suivants :• L’irradiation d’un examen thoracique acquis en double énergie peut être abaissée à celle d’un examen acquis en simple énergie, grâce à l’utilisation de la reconstruction itérative.• L’analyse qualitative du parenchyme pulmonaire en imagerie double énergie doit se faire sur les reconstructions monochromatiques 50-55keV.• L’atténuation théorique maximale du Krypton dosé à 80% est modérément inférieure à celle du Xénon dosé à 30%.• La décomposition des matériaux en tomodensitométrie double énergie simple source est possible sur le Xénon et le Krypton.• L’utilisation d’un produit de contraste gazeux n’a pas d’impact significatif sur le Workflow en routine clinique.• Le Krypton est cliniquement sûr à la dose de 80%.• La technique ne permet pas de détecter le Krypton au-delà de la carène de manière satisfaisante, probablement en raison d’une concentration en gaz atteinte insuffisante.• Le recalage élastique augmente les performances diagnostiques de détection de la bronchiolite oblitérante par rapport à une simple analyse visuelle. / This work on dual energy CT ventilation imaging has established the following:• The radiation dose of a dual energy chest CT can be reduced to that of a single energy examination through the use of iterative reconstruction.• The qualitative analysis of the lung parenchyma should be made on the 50-55keV monochromatic reconstructions.• The maximum theoretical attenuation obtained with 80% Krypton is moderately inferior to that of 30% Xenon.• Dual energy material decomposition of Xenon and Krypton is efficient with a single source technique.• The use of a gaseous contrast agent has no significant impact on the workflow in the clinical setting.• The Krypton is safe at 80% concentration.• The technique does not satisfactorily detect Krypton beyond the carina, probably due to insufficient gas concentration.• The elastic registration increases the diagnostic performance of bronchiolitis obliterans syndrome detection, compared to a simple visual analysis.