In computational imaging, data acquired by sampling the same scene or object at different times or from different orientations result in images in different coordinate systems. Registration is a crucial step in order to be able to compare, integrate and fuse the data obtained from different measurements. Tomography is the method of imaging a single plane or slice of an object. A Computed Tomography (CT) scan, also known as a CAT scan (Computed Axial Tomography scan), is a Helical Tomography, which traditionally produces a 2D image of the structures in a thin section of the body. It uses X-ray, which is ionizing radiation. Although the actual dose is typically low, repeated scans should be limited. In dentistry, implant dentistry in specific, there is a need for 3D visualization of internal anatomy. The internal visualization is mainly based on CT scanning technologies. The most important technological advancement which dramatically enhanced the clinician's ability to diagnose, treat, and plan dental implants has been the CT scan. Advanced 3D modeling and visualization techniques permit highly refined and accurate assessment of the CT scan data. However, in addition to imperfections of the instrument and the imaging process, it is not uncommon to encounter other unwanted artifacts in the form of bright regions, flares and erroneous pixels due to dental bridges, metal braces, etc. Currently, removing and cleaning up the data from acquisition backscattering imperfections and unwanted artifacts is performed manually, which is as good as the experience level of the technician. On the other hand the process is error prone, since the editing process needs to be performed image by image. We address some of these issues by proposing novel registration methods and using stonecast models of patient's dental imprint as reference ground truth data. Stone-cast models were originally used by dentists to make complete or partial dentures. The CT scan of such stone-cast models can be used to automatically guide the cleaning of patients' CT scans from defects or unwanted artifacts, and also as an automatic segmentation system for the outliers of the CT scan data without use of stone-cast models. Segmented data is subsequently used to clean the data from artifacts using a new proposed 3D inpainting approach.

Weak optical signals have to be measured in different fields of sciences including chemistry and biology. For example, very low levels of fluorescence emission should be detected from the spots on a DNA microarray that correspond to weakly expressed genes. High sensitivity charge-coupled devices (CCDs) are used in these applications. CCDs require special fabrication and are difficult to integrate with other circuits. CMOS is the technology used for fabrication of CPUs and other widely used digital components. CMOS is not optimized for light detection. CMOS circuits are however cheap, low power and can integrate several components. Active pixel sensor (APS) is the most common pixel structure for CMOS photodetector arrays. In this work we provide an accurate analysis of the APS signal using new models for the capacitance of the photodiode. We also provide a complete noise analysis of the pixel to calculate the SNR of the pixel and provide optimum operation points. We propose a new mode of operation for APS that can achieve at least l 0 dB higher SNR, than conventional APS, at light levels of less than 1 μW/cm^2. We fabricated several APS pixels in CMOS 0.18 μm technology and measured them to confirm the proposed analyzes. There are applications like fluorescence lifetime imaging that require both sensitivity and fast response. Photomultiplier tubes (PMTs) are commonly used in these applications to detect single photons in pico- to nano-seconds regime. PMTs are bulky and require high voltage levels. Avalanche photodiodes (APDs) are the semiconductor equivalent of PMTs. We have fabricated different APDs along with different peripheral circuitries in CMOS 0.18 μm technology. Our APDs have a 5.5 percent peak probability of detection of a photon at an excess bias of 2 V, and a 30 ns dead time, which is less than the previously reported results. The low price of CMOS makes modem diagnosis devices more available. The low power of CMOS leads to battery-driven hand-held imaging solutions, and its high integration leads to miniaturized imaging and diagnosis systems. A low-light-level CMOS imager paves the way for the future generation of biomedical diagnosis solutions. / Thesis / Doctor of Philosophy (PhD)

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<p>The introduction of the digital image sensor has triggered a revolution in the field of imaging. It has not only just replaced the conventional silver halide film based imaging system, but has also enormously widened the scope of imaging applications. Previously, charge-coupled devices (CCDs) were the most popular technology for image sensors. But in the past decade, they have been rapidly replaced by the CMOS image sensor (CIS) technology. The CCD image sensors offers higher sensitivity, wider dynamic range and better resolution compared to its CMOS imager counterparts. However, the lower power performance, higher speed of operation, easier integration with signal control and processing circuitries, and the use well-established mainstream fabrication process of CMOS technology, are key advantages that have served to propel CMOS imagers beyond CCDs in the market.</p> <p>However, CIS suffers from higher temporal noise compared to that of CCDs. One of the major noise sources in CIS is the 1/ noise generated from the in-pixel active amplifier. Due to continuous shrinking of MOS devices, the random telegraph signal (RTS) noise is emerging as a dominant noise source over other low frequency noise in CMOS imagers, resulting into reduced imaging performance.</p> <p>The RTS noise which evolves from trapping and de-trapping of electrons by the defects in the oxide, causes fluctuation in the drain current of the MOSFET. In this work, we have carried out time-domain measurement of RTS noise in CIS pixels. The time domain RTS measurements provide useful information about its characteristics in different operating conditions, which can be further used to extract the trap parameters and determine the optimum settings of operation of CIS.</p> <p>The capability of integrating various on-chip operations, higher speed and lower fabrication cost has made the CIS a good choice for various imaging applications. In order to demonstrate the extent of possible applications of CIS, we have developed an imaging system using a CIS. Two major concerns of biomedical imaging systems are their speed and cost. The system presented here is implemented using a CIS and FPGA (field programmable gate array) that provides a low-cost and high frame rate solution for biomedical microscopy.</p> / Master of Applied Science (MASc)

This case study used Zhongwei City in northwest China to quantify the urbanization and revegetation processes (1990-2011) through a unified sub-pixel measure of vegetation cover. Research strategies included: (1) Conduct sub-pixel vegetation mapping (1990, 1996, 2004, and 2011) with Random Forest (RF) algorithm by integrating high (OrbView-3) and medium spatial resolution (Landsat TM) data; (2) Examine simple Dark Object Subtraction (DOS) atmospheric correction method to support temporal generalization of sub-pixel mapping algorithm; (3) And characterize patterns of vegetation cover dynamics based on change detection analysis. We found the RF algorithm, combined with simple DOS, showed good generalization capability for sub-pixel vegetation mapping. Predicted sub-pixel vegetation proportions were consistent for "pseudo-invariant" pixels. Vegetation change analysis suggested persistent urban development within the city boundary, accompanied by a continuous expansion of revegetated area at the city fringe. Urban development occurred at both the suburban and urban core areas, and was mainly shaped by transportation networks. A transition in revegetation practices was documented: the large-scale governmental revegetation programs were replaced by the commercial afforestation conducted by industries. This study showed a slight increase in vegetation cover over the time period, balanced by losses to urban expansion, and a likely severe degradation of vegetation cover due to conversion of arable land to desert vegetation. The loss of arable land and the growth of artificial desert vegetation have yielded a dynamic equilibrium in terms of overall vegetation cover during 1990 to 2011, but in the long run vegetation quality is certainly reduced. / Master of Science

The Appalachian National Scenic Trail is a unit of the National Park System created by the National Trails Act of 1968. Commonly referred to as the Appalachian Trail, or the AT, this National Park has some of the longest boundaries of any park. The AT is routed more than 2000 miles along the mountains of the eastern United States. The land purchased for the protection of the AT creates a separate boundary on each side of the trail. Monitoring these boundaries for intrusions or encroachments is a difficult and time-consuming task when done totally by field methods. This thesis presents a more efficient and consistent monitoring process using remote sensing data and change detection algorithms. Using Landsat TM images, Normalized Difference Vegetation Index (NDVI), and image difference change detection, this research shows that major boundary encroachments can be detected. Detection of sub-pixel vegetation index decreases identifies specific locations for field inspection. Assuming low cost multispectral Landsat imagery is available, simple NDVI difference calculation allows this technique to be applied to the entire AT one or more times per year. This procedure would improve the response time for encroachment mediation. The producer's accuracy for finding possible encroachments was 100 percent and the consumer's accuracy for possible encroachments indicated was 78.3 percent. Due to limited image availability, this study only examines change between one pair of Landsat images. Further refinement of these techniques should investigate other Landsat images at other times. Use of other remote sensing systems and change detection algorithms could be the focus of further research. / Master of Science

Le Large Hadron Collider (LHC), située au CERN, Genève, produit des collisions de protons accélérés à une énergie de 3.5 TeV depuis le 23 Novembre 2009. L’expérience ATLAS enregistre depuis des données et poursuit sa recherche de nouvelle physique à travers l’analyse de la cinématique des événements issues des collisions. L’augmentation prévue de la luminosité sur la période s’étalant de 2011 2020 apportera de nouveaux défis pour le détecteur qui doivent être considérés pour maintenir les bonnes performance de la configuration actuelle. Le détecteur interne sera le sous-détecteur le plus affecté par l’augmentation de la luminosité qui se traduira par une augmentation des dommages occasionnés par la forte radiation et par la multiplication du nombre de traces associées à chaque croisement de faisceau. Les dommages causés par l’irradiation intense entrainera une perte d’efficacité de détection et une réduction du nombre de canaux actifs. Un intense effort de Recherche et Développement (R&D) est présentement en cours pour concevoir un nouveau détecteur pixel plus tolérant aux radiations et au cumul des événements générant un grand nombre de traces à reconstruire. Un premier projet de mise-à-jour du détecteur interne, nommé Insertable B-Layer (IBL) consiste à ajouter un couche de détection entre le tube à vide du faisceau et la première couche de silicium. Le projet SLHC prévoit de remplacer l’ensemble du détecteur interne par une version améliorée plus tolérante aux radiations et aux cumuls des événements. Dans cet ouvrage, je présente une étude utilisant la simulation technologique assisté par ordinateur (TCAD) portant sur les méthodes de conception des détecteurs pixels planaires permettant de réduire les zones inactives des détecteurs et d’augmenter leurs tolérances aux radiations. Les différents modèles physiques disponible ont étés étudiés pour développer un modèle cohérent capablede prédire le fonctionnement des détecteurs pixels planaires après irradiation. La structure d’anneaux de gardes utilisée dans le détecteur interne actuel a été étudié pour obtenir de l’information sur les possible méthodes permettant de réduire l’étendu de la surface occupée par cette structure tout en conservant un fonctionnement stable tout au long de la vie du détecteur dans l’expérience ATLAS. Une campagne de mesures sur des structures pixels fut organisée pour comparer les résultats obtenue grâce à la simulation avec le comportement des structures réelles. Les paramètres de fabrication ainsi que le comportement électrique ont été mesurés et comparés aux simulations pour valider et calibrer le modèle de simulation TCAD. Un modèle a été développé pour expliquer la collection de charge excessive observée dans les détecteurs planaires en silicium lors de leur exposition a une dose extrême de radiations. Finalement, un modèle simple de digitalisation à utiliser pour la simulation de performances détecteurs pixels individuels exposés à des faisceau de haute énergie ou bien de l’ensemble du détecteur interne est présenté. Ce modèle simple permets la comparaison entre les données obtenue en faisceau test aux modèle de transport de charge inclut dans ladigitalisation. Le dommage dû à la radiation , l’amincissement et l’utilisation de structures à bords minces sont autant de structures dont les effets sur la collecte de charges affectent les performance du détecteur. Le modèle de digititalisation fut validé pour un détecteur non-irradié en comparant les résultats obtenues avec les données acquises en test faisceau de haut énergie. Le modèle validé sera utilisé pour produire la première simulation de l’IBL incluant les effets d’amincissement du substrat, de dommages dûes aux radiations et de structure dotés de bords fins. / In this work, is presented a study, using TCAD simulation, of the possible methods of designing of a planar pixel sensors by reducing their inactive area and improving their radiation hardness for use in the Insertable B-Layer (IBL) project and for SLHC upgrade phase for the ATLAS experiment. Different physical models available have been studied to develop a coherent model of radiation damage in silicon that can be used to predict silicon pixel sensor behavior after exposure to radiation. The Multi-Guard Ring Structure,a protection structure used in pixel sensor design was studied to obtain guidelines for the reduction of inactive edges detrimental to detector operation while keeping a good sensor behavior through its lifetime in the ATLAS detector. A campaign of measurement of the sensor’s process parameters and electrical behavior to validate and calibrate the TCAD simulation models and results are also presented. A model for diode charge collection in highly irradiated environment was developed to explain the high charge collection observed in highly irradiated devices. A simple planar pixel sensor digitization model to be used in test beam and full detector system is detailed. It allows for easy comparison between experimental data and prediction by the various radiation damage models available. The digitizer has been validated using test beam data for unirradiated sensors and can be used to produce the first full scale simulation of the ATLAS detector with the IBL that include sensor effects such as slim edge and thinning of the sensor.

L'imagerie mono-pixel est un concept récent qui permet l'obtention d'images à un coût relativement faible par une compression des données durant l'acquisition. L'architecture d'une caméra mono-pixel comprend seulement deux éléments, un modulateur spatial de la lumière et un détecteur ponctuel. L'idée est de mesurer, au niveau du détecteur, la projection de la scène observée -l'image- avec un certain motif. Le post-traitement d'une séquence de mesures obtenues avec différents motifs permet de restaurer l'image de la scène. L'imagerie mono-pixel possède plusieurs avantages qui sont d'un intérêt pour différentes applications, en particulier dans le domaine biomédical. Par exemple, une caméra mono-pixel résolue en temps bas coût est bénéfique pour l'imagerie de temps de vie de fluorescence. Un tel système peut également être couplé à un spectromètre afin de compléter le temps de vie avec une information spectrale. Cependant, la limite principale de l'imagerie mono-pixel est la vitesse d'acquisition et/ou de l'étape de restauration d'image qui est, à ce jour, non compatible avec des applications temps réel. Le but de cette thèse est de développer des méthodes rapides d'acquisition et de restauration des images à visée d'applications biomédicales. Tout d'abord, une stratégie d'acquisition basée sur les algorithmes de compression dans le domaine ondelettes est proposée. Celle-ci accélère le temps de restauration de l'image par rapport aux schémas d'acquisition classiques basés sur l'acquisition comprimée. Dans un second temps, une nouvelle méthode pour lever une contrainte expérimentale de positivité sur les motifs est détaillée. Comparée aux approches classiques, cette méthode basée sur une factorisation en matrices non-négatives permet de diviser par deux le nombre de motifs envoyés au modulateur spatial de la lumière, entrainant ainsi une division par deux du temps d'acquisition total. Enfin, l'applicabilité de ces techniques est démontrée pour de l'imagerie multispectrale et/ou résolue en temps, modalités courantes dans le domaine biomédical. / Single-pixel imaging is a recent paradigm that allows the acquisition of images at a reasonably low cost by exploiting hardware compression of the data. The architecture of a single-pixel camera consists of only two elements, a spatial light modulator and a single point detector. The key idea is to measure, at the detector, the projection (i.e., inner product) of the scene under view -the image- with some patterns. The post-processing of a measurements sequence obtained with different patterns permits to restore the desired image. Single-pixel imaging has several advantages, which are of interest for different applications, especially in the biomedical field. In particular, a time-resolved single-pixel imaging system benefits to fluorescence lifetime sensing. Such a setup can be coupled to a spectrometer to supplement lifetime with spectral information. However, the main limitation of single-pixel imaging is the speed of the acquisition and/or image restoration that is, as of today, not compatible with real-time applications. This thesis investigates fast acquisition/restoration schemes for single-pixel camera targeting biomedical applications. First, a new acquisition strategy based on wavelet compression algorithms is reported. It is shown that it can significantly accelerate image recovery compared to conventional schemes belonging to the compressive sensing framework. Second, a novel technique is proposed to alleviate an experimental positivity constraint of the modulation patterns. With respect to the classical approaches, the proposed non-negative matrix factorization based technique permits to divide by two the number of patterns sent to the spatial light modulator, hence dividing the overall acquisition time by two. Finally, the applicability of these techniques is demonstrated for multispectral and/or time-resolved imaging, which are common modalities in biomedical imaging.

Dans l'objectif de développer des nouveaux capteurs d'image 3D pour des applications émergeantes, nous avons étudié un pixel de mesure de distance de type « temps de vol ». Nous avons proposé une nouvelle architecture de pixel basée sur la méthode « Continuous-Wave modulation » à trois échantillons par pixel. Cette méthode repose sur la mesure d'un déphasage entre la source lumineuse modulée en amplitude envoyée (source proche infrarouge) et le signal réfléchi par la scène à capturer. Le pixel de dimensions 6,2μm x 6,2μm intègre une photodiode pincée, trois chemins de transfert de charges pour l'échantillonnage successif du signal modulé reçu, et d'un quatrième chemin pour évacuer les charges excédentaires. Les différents chemins de transfert sont constitués d'une grille de transfert de charges de la photodiode vers une mémoire de stockage à canal enterré pour améliorer le rendement et la vitesse de transfert de charges; d'une mémoire à stockage en volume à base de tranchées capacitives profondes afin d'augmenter la dynamique; d'un substrat dont l'épaisseur et le profil de dopage ont été optimisés afin de collecter efficacement les charges photogénérées et ainsi augmenter les performances de démodulation. Un véhicule de test constitué d'une matrice de résolution de 464x197 pixels (QVGA) a été fabriqué, différentes variantes de pixels et différents essais technologiques ont été étudiées et analysées. La fonctionnalité du pixel a été vérifiée pour des fréquences de démodulation de 20MHz à 165MHz, utilisant une source laser de longueur d'onde 850nm ou 950nm. Une première image de profondeur acquise utilisant une matrice de test est une validation du pixel proposé / In order to develop new 3D image sensors for emerging applications, we studied “time of flight” pixel for distance measurement. We have proposed a new pixel architecture based on the "Continuous-Wave Modulation" method with three samples per pixel. This method is based on the measurement of a phase shift between the transmitted amplitude modulated light source (near-infrared source) and the signal reflected by the scene to be captured. The pixel of dimensions 6.2 μm x 6.2 μm integrates a pinned photodiode, three charge transfer paths for successive sampling of the received modulated signal, and a fourth path for anti-blooming purpose. The different paths are controlled by a buried-channel transfer gate for charges transfer from the photodiode to memory in order to improve the efficiency and speed of the charge transfer; A fully depleted memory based on capacitive deep trenches is used to increase the memory storage capacitance; thickness and doping profile of the substrate have been optimized to efficiently collect photogenerated and increase demodulation performance. The designed 464x197-pixel (QVGA) test chip has been fabricated, different pixel variants and different technology trials have been studied and analyzed. Pixel functionality has been verified for demodulation frequencies from 20 to 165MHz, using a laser source of wavelength 850nm or 950nm. A first acquired depth image using the test chip made is a validation of the proposed pixel

What are the elementary particles and how did the universe originate are the main driving forces in the high energy physics. In order to further demonstrate the standard model and discover new physics, several detectors are built for the high energy physics experiments. CMOS pixel sensors (CPS) can achieve an attractive tradeoff among many performance parameters, such as readout speed, granularity, material budget, power dissipation, radiation tolerance and integrating readout circuitry on the same substrate, compared with the hybrid pixel sensors and charge coupled devices. Thus, the CPS is a good candidate for tracking the charged particles in vertex detectors and beam telescopes.The power distribution becomes an important issue in the future detectors, since a considerable amount of sensors will be installed. Unfortunately, the independent powering has been proved to fail. In order to solve the power distribution challenges and to provide noiseless voltages, this thesis focuses on the design of a low noise, limited area, low power consumption and full on-chip power management in CPS chips. The CPS are firstly introduced drawing the design requirements of the power management. The power distribution dedicated to CPS chips is then proposed, in which the power management is utilized as the second power conversion stage. Two full on-chip regulators are proposed to generate the analog power supply voltage and the reference voltage required by correlated double sampling operation, respectively. Two prototypes have verified these regulators. They can meet the requirements of CPS. Moreover, the power management techniques and the radiation tolerance design are also presented in this thesis.