In this paper, a new millimeter wave 3D imaging radar is proposed. The user just needs to move the radar along a circular track, and high resolution 3D imaging can be generated. The proposed radar uses the movement of itself to synthesize a large aperture in both the azimuth and elevation directions. It can utilize inverse Radon transform to resolve 3D imaging. To improve the sensing result, the compressed sensing approach is further investigated. The simulation and experimental result further illustrated the design. Because a single transceiver circuit is needed, a light, affordable and high resolution 3D mmWave imaging radar is illustrated in the paper.

Imaging Time-of-Flight secondary ion mass spectrometry (ToF-SIMS) has been developed to perform 2D imaging and depth profiling of biological systems with micron or submicron scale lateral resolution, which can be attributed to the advent of polyatomic ion beam particularly C60+ and new concept of ToF-SIMS instrument, the J105 3D Chemical Imager (J105). These recent advances in ToF-SIMS have opened a new dimension for biological analysis. In this study, 2D and 3D imaging have been performed on two biological systems, Xenopus laevis (X. laevis) zygote/embryo and murine embryonic fibroblasts NIH 3T3 BXB-ER cells to explore the capability of ToF-SIMS to handle the biological samples with extreme topography and high resolution depth profiling of microdomains, which still represent major challenges for the ToF-SIMS. The study on X. laevis embryo explored the capability of ToF-SIMS to handle spherical samples (approx. 1-1.2 mm in diameter), identify lipid species in mixtures of lipid extraction from the zygotes and image of an intact embryo in 2D/3D during dynamic biological events, e.g., fertilisation and early embryo development. For the first time the J105 and conventional BioToF-SIMS instrument were employed for the study of developmental biology. The major classes of lipid were identified through multiple lipid assay in a single analytical run using ToF-SIMS. Topography effects of the embryo were assessed through imaging a single intact zygote/embryo that revealed secondary ions loss at the edge of the single cell. However, the topography effects on the mass resolution could be minimised using the J105. Moreover, in situ lipid profiling of the zygote revealed different lipid compositions and intensities on the membrane of the animal and vegetal hemispheres. Furthermore, high resolution imaging and depth profiling that performed on a single intact cell in a time course study visualised the egg-sperm fusion sites on the membrane of the zygote 10 min post-insemination and lipids arrangement on the membrane of the embryo through the early development stages. Subcellular signalling upon the fertilisation was also spatially located on the serial cryosections of a single zygote. With the NIH 3T3 BXB-ER cells, the study firstly adopted a finely focused C60+ beam to track morphological changes and rearrangement of subcellular organelle mitochondria (0.5-2 µm) in response to the activation of Raf/ERK (extracellular signal regulated kinase) pathway using the J105. The SIMS images of the unlabelled cells showed the shifting of membrane distribution and nuclei shrinking following Raf/ERK activation. The mitochondria fluorescence probe within the cells were located 3-dimensionally using confocal microscopy and ToF-SIMS, which revealed the distribution pattern of condensing in the two sides of the nuclei following the Raf/ERK activation. Coupled with scanning electron microscopy (SEM), the three imaging modes showed good agreement in cellular morphological changes and subcellular mitochondrial rearrangement without or following Raf/ERK activation, demonstrating an integrated approaching to study the biological processes at subcellular dimension.

L'échocardiographie est la modalité d'imagerie la plus utilisée pour évaluer la morphologie et la fonction cardiaque. Il s'agit d'un outil non invasif pour le diagnostic et l'évaluation des maladies cardiaques et il permet en outre de surveiller la réponse au traitement. Cependant, la quantification des événements cardiaques rapides demeure un défi avec la cadence d’imagerie actuellement réalisable, en particulier dans des applications telles que l'échocardiographie d'effort. De plus, cette limitation devient plus prononcée en imagerie 3D conventionnelle focalisée en raison du temps nécessaire pour insonifier et acquérir un volume complet. Le fait que l’on puisse actuellement atteindre au mieux ~20 volumes par seconde est l'une des raisons qui limitent son utilisation courante dans la pratique clinique. Des améliorations dans ce domaine permettraient d'exploiter l'important potentiel de l'imagerie 3D pour la quantification complète de la déformation cardiaque.Dans ce contexte, l'objectif de cette thèse était de développer des méthodes à haute cadence d'images et de tester leur performance dans des conditions réalistes visant la prise de décision pour une transition vers la pratique clinique. Pour atteindre cet objectif, des expériences in vitro et in vivo ont été menées en utilisant l'imagerie 2D et 3D. Notre première contribution a été une comparaison 2D entre deux modalités à haute cadence d'images en termes de qualité d'image et de performance d'estimation de mouvement. Motivés par nos résultats 2D mais surtout par le défi d'implémenter le MLT dans la pratique, nous avons étendu cette approche en 3D. Nous avons étudié la faisabilité de la MLT 3D dans des conditions statiques et dynamiques. Enfin, comme l’évaluation de nouvelles approches dans des conditions physiologiques de flux complexes constitue un pas en avant vers la transition clinique, notre troisième contribution a consisté à valider des modalités 2D et 3D à haut cadence d'images sur un fantôme du vortex / Echocardiography is the most widely used imaging modality for assessing cardiac morphology and function. It does provide a non-invasive tool in diagnosis and assessment of heart diseases and it allows, in addition, monitoring the response to the treatment. However, quantifying fast cardiac events remains a challenge when using the current achievable frame rate, especially in applications such as stress-echocardiography. Moreover, this limitation becomes more pronounced in 3D conventional focused imaging due to the time needed to insonify and acquire a full volume. The fact that only ~20 volumes per second can currently be achieved is one of the reasons restricting its common usage in clinical practice. Improvements in this field would allow exploiting the important potential of 3D imaging in providing a full quantification of cardiac deformation.In this context, the aim of this thesis was to develop high frame rate methods and to test their performance in realistic conditions aiming decision making towards clinical translation. To achieve this objective, both in vitro and in vivo experiments were conducted using 2D and 3D imaging. Our first contribution was a 2D comparison between two high frame rate modalities in terms of image quality and motion estimation performance. Motivated by our 2D results but especially by the challenge of implementing MLT in practice, we extended this approach to 3D. We studied the feasibility of 3D MLT in both static and dynamic conditions. Finally, as testing novel approaches in physiological complex flows conditions is a step forward towards clinical translation, our third contribution was to validate 2D and 3D high frame rate modalities on a ring vortex phantom

Rentgenová počítačová tomografie je univerzální technika umožňující nedestruktivní trojrozměrné (3D) zobrazování. Je široce používána v průmyslu pro metrologii a charakterizaci materiálů. V poslední době našla svůj význam také v biologii a vývojové vědě, kde 3D rekonstruovaná data poskytují komplexnější informace o vzorku než konvenční 2D zobrazovací metody. Kromě toho může vytvářet vysoce kvalitní snímky různých biologických vzorků. Překážkou při zobrazování biologických vzorků může být velmi podobný koeficient útlumu měkkých tkání, a proto je nutné použít barvení chemickou látkou. Tato práce si klade za cíl pomocí mikropočítačové tomografie vizualizovat a kvalitativně vyhodnotit srdce embryonálních myší E17.5 a představit nejlepší barvící protokol. Dále byla zavedena metodika pro zvýraznění rozdílů mezi myší divokého typu a mutantem. Rigaku nano 3DX byl použit pro experimenty s mezi-komorovou přepážkou myšího srdce a po nastavení specifických parametrů zařízení byl použit algoritmus pro zvýraznění fáze. Nakonec byla provedena validace $\mu$ CT dat se snímkami z konfokálního mikroskopu.

This thesis deals with the processing of stereo images. It described the principles of calibration and rectification of stereo images. The thesis described several methods for finding important points. SURF method is then implemented for practical solution. Finding correspondences is realized using the methods of image processing library OpenCV. Reconstructed spatial coordinates of points and write by the format specified VRML97. Finally, there is introduced evaluated accuracy of spatial data acquisition and comparison of computational cost generated programs.

.Dans cette thèse, il a été étudié la structure des milieux poreux, en particulier sur des sols sableux et un paquet virtuel de sphères; Sur la base de références bibliographiques, nos propres outils ont été créés pour calculer la porosité, la surface spécifique et la distribution de la taille des pores. Nous avons construit un algorithme pour résoudre l'équation de diffusion de l'advection directement sur la structure du milieu poreux (en utilisant un résultat d'image 3D du scan $ mu $ CT du support poreux). Nous avons utilisé l'opérateur de division pour calculer la partie advective avec une méthode de volume fini (FV), mettant en œuvre un schéma de réduction de la variation totale (TVD). La partie diffusion a été calculée en utilisant une méthode de FV et avec l’aide du logiciel MUMPS pour résoudre le système linéaire résultant. A partir du champ de concentration obtenu avec l’algorithme et suivant une méthode de moyenne volumique, nous avons calculé les propriétés macroscopiques de: dispersivité et coefficient de dispersion à Pe = 223,23,2.3,0,23 pour un échantillon de sable de Fontainbleau NE34. Nous avons observé que ces résultats dépendent de la qualité de l'image 3D. Les propriétés structurelles et de transport ont été étudiées à l'aide d'images 3D à différentes résolutions. Les images à différentes résolutions ont été appelées images redimensionnées, elles ont été générées numériquement et prises directement à partir du micro CT scan. Comme premier résultat, nous avons proposé un critère basé sur la distribution de la taille des pores pour déterminer si une résolution d'image 3D convient ou non au calcul de la perméabilité d'un matériau granulaire avec une méthode de volume fini (FV). Dans un deuxième résultat, nous avons montré comment les propriétés des macros de transport de soluté sont moins affectées par une détérioration de la résolution que la propriété d’écoulement de la perméabilité (les deux cas sont calculés par une méthode FV). Et comme troisième résultat, nous avons montré qu'une image numérique redimensionnée préserve davantage le comportement des propriétés macroscopiques qu'une image réelle redimensionnée. / In this thesis it was studied the structure of the porous media, particularly on a sandy soils and a virtual pack of spheres; based on bibliographic references here were generated our own tools to compute the porosity, specific surface and pore size distribution. We built an algorithm to solve advection diffusion equation directly on the porous media structure (using a 3D image result of the $mu $ CT scan of the porous media). We used the splitting operator to compute the advective part with a Finite Volume (FV) method, implementing a Total Variation Diminishing (TVD) scheme. The diffusion part was computed using with a FV method with the assistance of the MUMPS software to solve the resulting linear system. From the concentration field obtained with the algorithm and following a volume averaging method, we computed the macroscopic properties of: dispersivity and dispersion coefficient at Pe=223,23,2.3,0.23 for a sample of Fontainbleau NE34 sand. We observing that these results depend on the quality of the 3D image, structural and transport properties were studied using 3D images at different resolutions. The images at different resolutions were called rescaled images, and they were generated numerically and taken directly from the micro CT scan. As a first result we proposed a criterion based on the pore size distribution to assess if a 3D image resolution is suitable or not for permeability computation of a granular material with a finite volume (FV) method. As a second result we showed how the solute transport macro properties are less affected by a deterioration of the resolution than the flow property of permeability (both cases computed through a FV method). And as a third result we showed that a numerical rescaled image preserve the behavior of the macroscopic properties more than a real rescaled image

Time domain Optical Coherence Tomography (TD-OCT), first reported in 1991, makes use of the low temporal coherence properties of a NIR broadband laser to create depth sectioning of up to 2mm under the surface using optical interferometry and point to point scanning. Prior and ongoing work in OCT in the research community has concentrated on improving axial resolution through the development of broadband sources and speed of image acquisition through new techniques such as Spectral domain OCT (SD-OCT). In SD-OCT, an entire depth scan is acquired at once with a low numerical aperture (NA) objective lens focused at a fixed point within the sample. In this imaging geometry, a longer depth of focus is achieved at the expense of lateral resolution, which is typically limited to 10 to 20 [micro]m. Optical Coherence Microscopy (OCM), introduced in 1994, combined the advantages of high axial resolution obtained in OCT with high lateral resolution obtained by increasing the NA of the microscope placed in the sample arm. However, OCM presented trade-offs caused by the inverse quadratic relationship between the NA and the DOF of the optics used. For applications requiring high lateral resolution, such as cancer diagnostics, several solutions have been proposed including the periodic manual re-focusing of the objective lens in the time domain as well as the spectral domain C-mode configuration in order to overcome the loss in lateral resolution outside the DOF. In this research, we report for the first time, high speed, sub-cellular imaging (lateral resolution of 2 [micro]m) in OCM using a Gabor domain image processing algorithm with a custom designed and fabricated dynamic focus microscope interfaced to a Ti:Sa femtosecond laser centered at 800 nm within an SD-OCM configuration. It is envisioned that this technology will provide a non-invasive replacement for the current practice of multiple biopsies for skin cancer diagnosis. The research reported here presents three important advances to this technology all of which have been demonstrated in full functional hardware conceived and built during the course of this research. First, it has been demonstrated that the coherence gate created by the femtosecond laser can be coupled into a scanning optical microscope using optical design methods to include liquid lens technology that enables scanning below the surface of skin with no moving parts and at high resolution throughout a 2x2x2 mm imaging cube. Second, the integration the variable-focus liquid lens technology within a fixed-optics microscope custom optical design helped increase the working NA by an order of magnitude over the limitation imposed by the liquid lens alone. Thus, this design has enabled homogenous axial and lateral resolution at the micron-level (i.e., 2 [micro]m) while imaging in the spectral domain, and still maintaining in vivo speeds. The latest images in biological specimens clearly demonstrate sub-cellular resolution in all dimensions throughout the imaging volume. Third, this new modality for data collection has been integrated with an automated Gabor domain image registration and fusion algorithm to provide full resolution images across the data cube in real-time. We refer to this overall OCM method as Gabor domain OCM (GD-OCM). These advantages place GD-OCM in a unique position with respect to the diagnosis of cancer, because when fully developed, it promises to enable fast and accurate screening for early symptoms that could lead to prevention. The next step for this technology is to apply it directly, in a clinical environment. This step is underway and is expected to be reported by the next generation of researchers within this group.

<p dir="ltr">Over the last few decades, three-dimensional (3D) optical imaging and sensing techniques have attracted much attention from both academia and industries. Owing to its capability of gathering more information than conventional 2D imaging, it has been successfully adopted in many applications on the macro scale which ranges from sub-meters to meters such as entertainment, commercial electronics, manufacturing, and construction. For example, the iPhone “FaceID” sensor is used for facial recognition, and the Microsoft Kinect is used to track body motion in video games. With recent advances in many technical fields, such as semiconductor packaging, additive manufacturing, and micro-robots, there is an increasing need for microscopic 3D imaging, and several techniques including interferometry, confocal microscopy, focus variation, and structured light have been developed and adopted in these industries. Among these techniques, the structured light 3D imaging technique is considered one of the most promising techniques for in-situ metrology, owing to its advantage of simple configuration and high measurement speed. However, several challenges must be addressed in employing the structured-light 3D imaging technique in these fields.</p><p dir="ltr">The first challenge is the limited measurement range caused by the limited depth of field (DOF). Given the necessity for large magnification in the microscopic structured light system, the DOF becomes notably shallow, especially when pin-hole lenses are adopted. This issue is exacerbated by the fact that the measured objects in the aforementioned industries could contain miniaturized features spanning a broad height range. To address this problem, we introduce the idea of the focus stacking technique, wherein the focused pixels gathered from various focus settings are merged to form an all-in-focus image, into the structured-light 3D imaging. We further developed a computational framework that utilizes the phase information and fringe contrast of the projected fringe patterns to mitigate the influence of object textures.</p><p dir="ltr">The second challenge is the 3D imaging speed. The 3D measurement speed is a crucial factor for in-situ applications. We improved the large DOF 3D imaging speed by reducing the required fringe images from two aspects: 1) We developed a calibration method for multifocus pin-hole mode, which can eliminate the necessity of the 2D image alignment. The conventional method based on circle patterns will be affected during the feature extraction process by the significant camera defocusing. In contrast, our proposed method is more robust since it uses virtual features extracted from a reconstructed white flat surface under a pre-calibrated focus setting. 2)We developed a phase unwrapping method with the assistance of the electrically tunable lens (ETL), which is an optical component we used to capture fringe images under various focus settings. The proposed phase unwrapping method leverages the focal plane position of each focus setting to estimate a rough depth map for the geometric-constraint phase unwrapping algorithm. By doing this, the method eliminates the limitation on the effective working depth range and becomes feasible in large DOF 3D imaging.</p><h4>Even with all previous methodologies, the efficiency of large DOF 3D imaging is still not high enough under certain circumstances. One of the major reasons is that we can still only use a series of pre-defined focus settings to run the focus stacking, since we have no prior on the measured objects. This issue could lead to low measurement efficiency when the depth range of the measured objects does not cover the whole enlarged DOF. To improve the performance of the system under such situations, we developed a method that introduces another computational imaging technique: the focal sweep technique, to help determine the optimal focus settings adapting to different measured objects.</h4><h4>In summary, this dissertation contributed to high-speed, large depth-of-field, and automated 3D imaging, which can be used in micro-scale applications from the following aspects: (1) enlarging the DOF of the microscopic 3D imaging using the focus stacking technique; (2) developing methods to improve the speed of large DOF microscopic 3D imaging; and (3) developing a method to improve the efficiency of the focus stacking under certain circumstances. These contributions can potentially enable the structured-light 3D imaging technique to be an alternative 3D microscopy approach for many academic studies and industry applications.</h4><p></p>

La SER (Surface Équivalente Radar) est une grandeur caractérisant le pouvoir rétrodiffuseurd’une cible soumise à un champ électromagnétique. Dans de nombreuses applications,il est capital d’analyser et de contrôler la SER. L’imagerie 3D est l’outil adapté pourlocaliser et caractériser en trois dimensions les principaux contributeurs à la SER. Cependant,ce traitement est un problème de synthèse de Fourier qui n’est pas inversible car il y aplus d’inconnues que de données. Les méthodes conventionnelles telles que le Polar FormatAlgorithm, consistant en un reformatage des données avec complétion de zéro suivi d’unetransformée de Fourier inverse rapide, fournissent des résultats de qualité limitée.Dans ce travail, nous proposons une nouvelle méthode haute résolution. Elle est dénomméeSPRITE (pour SParse Radar Imaging TEchnique) et permet d’accroître considérablementla qualité des cartes de rétro-diffusion estimées. Elle repose sur une régularisation duproblème consistant en la prise en compte d’informations a priori de parcimonie et d’uneinformation de support. La solution est alors définie comme le minimiseur d’un critère pénaliséet contraint. L’optimisation est assurée par l’algorithme primal-dual ADMM (AlternatingDirection Method of Multiplier) dont une adaptation aux spécificités du problème mène à descalculs efficaces à l’aide de transformées de Fourier rapides.Finalement, la méthode est évaluée sur des données synthétiques et réelles. Comparativementà la méthode conventionnelle, la résolution est drastiquement accrue. Les images 3Dproduites sont alors un outil particulièrement adapté à l’analyse et au contrôle de SER. / The RCS (Radar Cross Section) is a quantity which characterizes the scattering power ofa target exposed to an electromagnetic field. Its analysis and control are important in manyapplications. 3D imaging is a suitable tool to accurately locate and characterize in 3D themain contributors to the RCS. However, this is a non-invertible Fourier synthesis problembecause the number of unknowns is larger than the number of data. Conventional methodssuch as the Polar Format Algorithm, which consists of data reformatting including zeropaddingfollowed by a fast inverse Fourier transform, provide results of limited quality.In this work, we propose a new high resolution method, named SPRITE (for SParse RadarImaging TEchnique), which considerably increases the quality of the estimated RCS maps. Itis based on a regularization scheme that accounts for information of sparsity and support. Thesolution is then defined as the minimizer of a penalized and constrained criterion. Optimizationis ensured by an appropriate adaptation of the ADMM (Alternating Direction Methodof Multiplier) algorithm that is able to quickly perform calculations using fast Fourier transforms.Finally, the method is evaluated on both simulated and real data. Compared to the conventionalmethod, the resolution is significantly increased and the images can support a betterRCS analysis and control.

Les changements anatomiques des patients au cours du traitement de radiothérapie peuvent engendrer des conséquences dosimétriques significatives sur les volumes cibles (VC) ou les organes à risques (OARs). Le processus de radiothérapie adaptative peut compenser ces variations, cependant son déploiement en clinique est ralentit par une charge de travail supplémentaire considérable pour les équipes médicales et aucun logiciel n'est disponible pour une utilisation en clinique. Nous avons développé un outil d'alerte dosimétrique in vivo simple permettant d'identifier rapidement les situations où une adaptation de traitement est requise pour un patient. L'évaluation dosimétrique des traitements délivrés a été réalisée sur l'imagerie embarquée 3D (CBCT) dont la précision des calculs de dose a dû être évaluée. L'outil d'alerte permet de s'affranchir d'une nouvelle délinéation de volumes d'intérêt et est basé sur des critères objectifs et quantifiables constitués par le dépassement des limites dosimétriques définies pour chacun des volumes considérés. La précision et la détectabilité de l'outil ont été validées puis il a été appliqué dans une étude rétrospective de 10 patients ORL afin de surveiller l'administration du traitement et d'identifier les patients pour lesquels une adaptation du traitement aurait pu être envisagée. Dans son implémentation clinique, le processus de radiothérapie adaptative requiert des algorithmes de recalage déformable capable de suivre les déformations locales d'un patient se produisant au cours du traitement, seulement leur utilisation n'est pas encore validée. Nous avons procédé à l'évaluation de la précision d'un algorithme de recalage déformable, de type Block Matching présentant l'avantage d'être adapté à l'imagerie multimodale CT/CBCT, en comparaison par rapport à un algorithme de recalage rigide. Une étude a été menée pour 10 patients ORL en se basant sur la comparaison de contours de volumes d'intérêt pour 76 CBCT. Les paramètres de similarité utilisés consistaient en l'Indice de Similarité Dice, la distance de Hausdorff robuste (en mm) et la différence de volume absolu (en cm3) / Changing anatomy during radiotherapy can lead to significant dosimetric consequences for organs at risk (OARs) and/or target volumes. Adaptive radiotherapy can compensate for these variations however its deployment for clinical work is hampered by the increased workload for the medical staff and there is still no commercialized software available for clinical use. We developed a simple in vivo dosimetric alert tool allowing rapid identification of patients who might benefit from an adaptive radiotherapy. Dosimetric evaluation of delivered treatment has been conducted onto 3D on board imaging (CBCT) whose dose calculation accuracy has been evaluated. The tool does not require a new volume of interest delineation. Tool alert is based on objectives and quantifiable criteria defined by the exceeding volumes of interest dose thresholds. Tool precision and detectability have been validated and applied in a retrospective study on 10 head and neck patients. The tool allows detecting patients where an adaptive treatment could have been considered. In its clinical implementation, adaptive radiotherapy process requires deformable matching algorithms to follow patient local's deformations occurring during treatment. Nevertheless, their use has not been validated. We conducted an evaluation of the Block Matching deformable algorithm, suitable for multimodality imaging (CT/CBCT), in comparison to rigid algorithm. A study has been conducted for 10 head and neck patients based on volume of interest contours comparison for 76 CBCT. Similarity parameters used consisted on Dice Similarity Index, Robust Hausdorff Distance (in mm) and the absolute volume difference (in cc)