En imagerie par résonance magnétique (IRM) interventionnelle, des interventions percutanées minimalement-invasives (biopsies, ablations de tumeurs,...) sont réalisées sous guidage IRM. Lors de l’intervention, les plans de coupe acquis sont alignés sur l’outil chirurgical et les régions anatomiques d’intérêt afin de surveiller la progression de l’outil dans le corps du patient en temps réel. Le suivi d’objets dans l’IRM facilite et accélère les interventions guidées par IRM en permettant d’aligner automatiquement les plans de coupe avec l’outil chirurgical. Dans cette thèse, un système d’alignement automatique des plans de coupe établi sur une séquence IRM clinique est développé. Celui-ci réalise automatiquement la détection et le suivi d’un marqueur passif directement dans les images IRM tout en minimisant le temps d’imagerie dédié à la détection. L’inconvénient principal de cette approche est sa dépendance au temps d’acquisition de la séquence IRM clinique utilisée. Dans un premier temps, les performances du suivi ont pu être améliorées grâce à l’estimation et la prédiction du mouvement suivi par un filtre de Kalman. Puis un capteur optique complémentaire a été ajouté pour réaliser un suivi multi-capteurs, découplant ainsi la fréquence de rafraichissement du suivi de la fréquence de rafraichissement des images IRM. La performance du système développé a été évaluée par des simulations et des expériences utilisant un banc d’essai compatible IRM. Les résultats montrent une bonne robustesse du suivi multi-capteurs pour l’alignement des plans de coupe grâce à la combinaison des qualités individuelles de chaque capteur. / Interventional magnetic resonance imaging (MRI) aims at performing minimally invasive percutaneous interventions, such as tumor ablations and biopsies, under MRI guidance. During such interventions, the acquired MR image planes are typically aligned to the surgical instrument (needle) axis and to surrounding anatomical structures of interest in order to efficiently monitor the advancement in real-time of the instrument inside the patient’s body. Object tracking inside the MRI is expected to facilitate and accelerate MR-guided interventions by allowing to automatically align the image planes to the surgical instrument. In this PhD thesis, an image-based workflow is proposed and refined for automatic image plane alignment. An automatic tracking workflow was developed, performing detection and tracking of a passive marker directly in clinical real-time images. This tracking workflow is designed for fully automated image plane alignment, with minimization of tracking-dedicated time. Its main drawback is its inherent dependence on the slow clinical MRI update rate. First, the addition of motion estimation and prediction with a Kalman filter was investigated and improved the workflow tracking performance. Second, a complementary optical sensor was used for multi-sensor tracking in order to decouple the tracking update rate from the MR image acquisition rate. Performance of the workflow was evaluated with both computer simulations and experiments using an MR compatible testbed. Results show a high robustness of the multi-sensor tracking approach for dynamic image plane alignment, due to the combination of the individual strengths of each sensor.

Cette thèse porte sur la caractérisation cardiaque, qui représente un enjeu méthodologique et clinique important, à la fois pour améliorer le diagnostic des pathologies et optimiser les moyens de traitement. Des méthodes de recalage et de fusion de données sont proposées pour amener dans un même référentiel des images IRM, scanner, échographiques et électro-anatomiques et ainsi décrire le cœur suivant des caractéristiques anatomiques, électriques, mécaniques et tissulaires. Les méthodes proposées pour recaler des données multimodales reposent sur deux processus principaux : l'alignement temporel et le recalage spatial. Les dimensions temporelles des images considérées sont mises en synchronisées par une méthode de déformation temporelle dynamique adaptative. Celle-ci permet de compenser les modifications temporelles non-linéaires entre les différentes acquisitions. Pour le recalage spatial, des méthodes iconiques ont été développées pour corriger les artefacts de mouvements dans les séquences ciné-IRM, pour recaler les séquences ciné-IRM avec les séquences d'IRM de rehaussement tardif et pour recaler les ciné-IRM avec les images scanner. D'autre part, une méthode basée contours, développée dans un précédent travail, a été améliorée pour prendre en compte des acquisitions échographiques multi-vues. Ces méthodes ont été évaluées sur données réelles pour sélectionner les métriques les plus adaptées et pour quantifier les performances des approches iconiques et pour estimer la précision du recalage entre échographies et ciné-IRM. Ces méthodes sont appliquées à la caractérisation de cardiomyopathies hypertrophiques (CMH) et d'asynchronismes cardiaques. Pour la CMH, l'objectif était de mieux interpréter les données échographiques par la fusion de l'information de fibrose issue de l'IRM de rehaussement tardif avec l'information mécanique issue de l'échographie de speckle tracking. Cette analyse a permis d'évaluer le strain régional en tant qu'indicateur de la présence locale de fibrose. Concernant l'asynchronisme cardiaque, nous avons établi une description du couplage électromécanique local du ventricule gauche par la fusion de données échographiques, électro-anatomiques, scanner et, dans les cas appropriés, d'IRM de rehaussement tardif. Cette étude de faisabilité ouvre des perspectives pour l'utilisation de nouveaux descripteurs pour la sélection des sites de stimulation optimaux pour la thérapie de resynchronisation cardiaque. / This work concerns cardiac characterization, a major methodological and clinical issue, both to improve disease diagnostic and to optimize its treatment. Multisensor registration and fusion methods are proposed to bring into a common referential data from cardiac magnetic resonance (CMRI), dynamic cardiac X-ray computed tomography (CT), speckle tracking echocardiography (STE) and electro-anatomical mappings of the inner left ventricular chamber (EAM). These data is used to describe the heart by its anatomy, electrical and mechanical function, and the state of the myocardial tissue. The methods proposed to register the multimodal datasets rely on two main processes: temporal registration and spatial registration. The temporal dimensions of input data (images) are warped with an adaptive dynamic time warping (ADTW) method. This method allowed to handle the nonlinear temporal relationship between the different acquisitions. Concerning the spatial registration, iconic methods were developed, on the one hand, to correct for motion artifacts in cine acquisition, to register cine-CMRI and late gadolinium CMRI (LGE-CMRI), and to register cine-CMRI with dynamic CT. On the other hand, a contour-based method developed in a previous work was enhanced to account for multiview STE acquisitions. These methods were evaluated on real data in terms of the best metrics to use and of the accuracy of the iconic methods, and to assess the STE to cine-CMRI registration. The fusion of these multisensor data enabled to get insights about the diseased heart in the context of hypertrophic cardiomyopathy (HCM) and cardiac asynchronism. For HCM, we aimed to improve the understanding of STE by fusing fibrosis from LGE-CMRI with strain from multiview 2D STE. This analysis allowed to assess the significance of regional STE strain as a surrogate of the presence of regional myocardial fibrosis. Concerning cardiac asynchronism, we aimed to describe the intra-segment electro-mechanical coupling of the left ventricle using fused data from STE, EAM, CT and, if relevant, from LGE-CMRI. This feasibility study provided new elements to select the optimal sites for LV stimulation.

Dans le cadre de la robotique mobile extérieure, les notions de perception et de localisation sont essentielles au fonctionnement autonome d’un véhicule. Les objectifs de ce travail de thèse sont multiples et mènent vers un but de localisation et de cartographie simultanée d’un environnement extérieur dynamique avec détection et suivi d’objet mobiles (SLAMMOT) à l’aide d’un unique capteur extéroceptif tournant de type radar dans des conditions de circulation dites "réalistes", c’est-à-dire à haute vitesse soit environ 30 km/h. Il est à noter qu’à de telles vitesses, les données acquises par un capteur tournant son corrompues par le déplacement propre du véhicule. Cette distorsion, habituellement considérée comme une perturbation, est analysée ici comme une source d’information. Cette étude vise également à évaluer les potentialités d’un capteur radar de type FMCW (onde continue modulée en fréquence) pour le fonctionnement d’un véhicule robotique autonome. Nous avons ainsi proposé différentes contributions : – une correction de la distorsion à la volée par capteurs proprioceptifs qui a conduit à une application de localisation et de cartographie simultanées (SLAM), – une méthode d’évaluation de résultats de SLAM basées segment, – une considération de la distorsion des données dans un but proprioceptif menant à une application SLAM, – un principe d’odométrie fondée sur les données Doppler propres au capteur radar, – une méthode de détection et de pistage d’objets mobiles : DATMO avec un unique radar. / In outdoor robotic context, notion of perception and localization is essential for an autonomous navigation of a mobile robot. The objectives of this PhD are multiple and tend to develop a simultaneous localization and mapping approach in a dynamic outdoor environment with detection and tracking of moving objects (SLAMMOT) with a unique exteroceptive radar sensor in real driving conditions, around 30 km/h. At such high speed, data obtained with a rotating range sensor are corrupted by the own vehicle displacement. This distortion, usually considered as a disturbance, is analyzed here as a source of information. This study explores radar frequency modulated continuous wave (FMCW) technology potential for mobile robotics in extended outdoor environment. In this work, we propose : – a distortion correction on-the-fly with proprioceptive sensors in order to realize a localization and mapping application (SLAM), – a line based SLAM evaluation method, – a consideration of distortion in a proprioceptive purpose for localization and mapping, – an odometry principle based on Doppler velocimetry provided by radar sensor, – a detection and tracking of mobile objects : DATMO, with a unique radar sensor.

This thesis presents an investigation of the possibility of using the fixed-point arithmetic in the inertial navigation systems, which use the local level navigation frame mechanization equations. Two square root filtering methods, the Potter's square root Kalman filter and UD factorized Kalman filter, are compared with respect to the conventional Kalman filter and its Joseph's stabilized form. The effect of rounding errors to the Kalman filter optimality and the covariance matrix or its factors conditioning is evaluated for a various lengths of the fractional part of the fixed-point computational word. Main contribution of this research lies in an evaluation of the minimal fixed-point arithmetic word length for the Phi-angle error model with noise statistics which correspond to the tactical grade inertial measurements units.

<div>This dissertation addresses the problem of how to design a convolutional neural network (CNN) for giving semantic labels to the points on the ground given the satellite image coverage over the area and, for the ground truth, given the noisy labels in OpenStreetMap (OSM). This problem is made challenging by the fact that -- (1) Most of the images are likely to have been recorded from off-nadir viewpoints for the area of interest on the ground; (2) The user-supplied labels in OSM are frequently inaccurate and, not uncommonly, entirely missing; and (3) The size of the area covered on the ground must be large enough to possess any engineering utility. As this dissertation demonstrates, solving this problem requires that we first construct a DSM (Digital Surface Model) from a stereo fusion of the available images, and subsequently use the DSM to map the individual pixels in the satellite images to points on the ground. That creates an association between the pixels in the images and the noisy labels in OSM. The CNN-based solution we present yields a 4-8% improvement in the per-class segmentation IoU (Intersection over Union) scores compared to the traditional approaches that use the views independently of one another. The system we present is end-to-end automated, which facilitates comparing the classifiers trained directly on true orthophotos vis-`a-vis first training them on the off-nadir images and subsequently translating the predicted labels to geographical coordinates. This work also presents, for arguably the first time, an in-depth discussion of large-area image alignment and DSM construction using tens of true multi-date and multi-view WorldView-3 satellite images on a distributed OpenStack cloud computing platform.</div>

This thesis presents the implementation of data fusion techniques for sustainable urban development. Recently, increasingly more geospatial data have been made easily available for no cost. The immeasurable quantities of geospatial data are mainly from four kinds of sources: remote sensing satellites, geographic information systems (GIS) data, citizen science, and sensor web. Among them, satellite images have been mostly used, due to the frequent and repetitive coverage, as well as the data acquisition over a long time period. However, the rather coarse spatial resolution of e.g. 30 m for Landsat 8 multispectral images impairs the application of satellite images in urban areas. Even though image fusion techniques have been used to improve the spatial resolution, the existing image fusion methods are neither suitable for sharpening one band thermal images nor for hyperspectral images with hundreds of bands. Therefore, simplified Ehlers fusion was developed. It adds the spatial information of a high-resolution image into a low-resolution image in the frequency domain through fast Fourier transform (FFT) and filter techniques. The developed algorithm successfully improved the spatial resolution of both one band thermal images as well as hyperspectral images. It can enhance various images, regardless of the number of bands and the spectral coverage, providing more precise measurement and richer information. To investigate the performance of simplified Ehlers fusion in practical use, it was applied for urban heat island (UHI) analysis. This was done by sharpening daytime and nighttime thermal images from Landsat 8, Landsat 7, and the Advanced Spaceborne Thermal Emission and Reflection Radiometer (ASTER). The developed algorithm effectively improved the spatial details of the original images so that the temperature differences between agricultural, forest, industrial, transportation, and residential areas could be distinguished from each other. Based on that, it was found that in the study city the causes of UHI are mainly anthropogenic heat from industrial areas as well as high temperatures from the road surface and dense urban fabric. Based on this analysis, corresponding mitigation strategies were tailored. Remote sensing images are useful yet not sufficient to retrieve land use related information, despite high spatial resolution. For sustainable urban development research, remote sensing images need to be incorporated with data from other sources. Accordingly, image fusion needs to be extended to broader data fusion. Extraction of urban vacant land was therefore taken as a second application case. Much effort was spent on the definition of vacant land as unclear definitions lead to ineffective data fusion and incorrect site extraction results. Through an intensive study of the current research and the available open data sources, a vacant land typology is proposed. It includes four categories: transportation-associated land, natural sites, unattended areas or remnant parcels, and brownfields. Based on this typology, a two-level data fusion framework was developed. On the feature level, sites are identified. For each type of vacant land, an individual site extraction rule and data fusion procedure is implemented. The overall data fusion involves satellite images, GIS data, citizen science, and social media data. In the end, four types of vacant land features were extracted from the study area. On the decision level, these extracted sites could be conserved or further developed to support sustainable urban development.

Indiana University-Purdue University Indianapolis (IUPUI) / With the advances in embedded technology and the omnipresence of smartphones, tracking systems do not need to be confined to a specific tracking environment. By introducing mobile devices into a tracking system, we can leverage their mobility and the availability of multiple sensors such as camera, Wi-Fi, Bluetooth and Inertial sensors. This thesis proposes to improve the existing tracking systems, enhanced Distributed Tracking System (e-DTS 2.0) [19] and enhanced Distributed Object Tracking System (eDOTS)[26], in the form of e-DTS 3.0 and provides an empirical analysis of these improvements. The enhancements proposed are to introduce Android-based mobile devices into the tracking system, to use multiple sensors on the mobile devices such as the camera, the Wi-Fi and Bluetooth sensors and inertial sensors and to utilize possible resources that may be available in the environment to make the tracking opportunistic. This thesis empirically validates the proposed enhancements through the experiments carried out on a prototype of e-DTS 3.0.

Optics are a powerful probe of chemical structure that can often be linked to theoretical predictions, providing robustness as a measurement tool. Not only do optical interactions like second harmonic generation (SHG), single and two-photon excited fluorescence (TPEF), and infrared absorption provide chemical specificity at the molecular and macromolecular scale, but the ability to image enables mapping heterogeneous behavior across complex systems such as biological tissue. This thesis will discuss nonlinear and linear optics, leveraging theoretical predictions to provide frameworks for interpreting analytical measurement. In turn, the causal mechanistic understanding provided by these frameworks will enable structurally specific quantitative tools with a special emphasis on application in biological imaging. The thesis will begin with an introduction to 2nd order nonlinear optics and the polarization analysis thereof, covering both the Jones framework for polarization analysis and the design of experiment. Novel experimental architectures aimed at reducing 1/f noise in polarization analysis will be discussed, leveraging both rapid modulation in time through electro-optic modulators (Chapter 2), as well as fixed-optic spatial modulation approaches (Chapter 3). In addition, challenges in polarization-dependent imaging within turbid systems will be addressed with the discussion of a theoretical framework to model SHG occurring from unpolarized light (Chapter 4). The application of this framework to thick tissue imaging for analysis of collagen local structure can provide a method for characterizing changes in tissue morphology associated with some common cancers (Chapter 5). In addition to discussion of nonlinear optical phenomena, a novel mechanism for electric dipole allowed fluorescence-detected circular dichroism will be introduced (Chapter 6). Tackling challenges associated with label-free chemically specific imaging, the construction of a novel infrared hyperspectral microscope for chemical classification in complex mixtures will be presented (Chapter 7). The thesis will conclude with a discussion of the inherent disadvantages in taking the traditional paradigm of modeling and measuring chemistry separately and provide the multi-agent consensus equilibrium (MACE) framework as an alternative to the classic meet-in-the-middle approach (Chapter 8). Spanning topics from pure theoretical descriptions of light-matter interaction to full experimental work, this thesis aims to unify these two fronts. <br>