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Ce travail de thèse présente une combinaison unique d'imagerie X par contraste de phase avec la fluorescence X pour des échantillons biologiques étudiés par nanosonde par fluorescence X excitée par le rayonnement synchrotron. Les récents développements dans ce domaine ouvrent la possibilité d'une imagerie chimique quantitative à l'échelle sub-cellulaire. Ceci a été rendu possible par l'utilisation d'un outil unique qui est la station de nanoimagerie X ID22NI de l'ESRF qui permet de délivrer un faisceau sub-100 nm avec un très haut flux à haute énergie entrainant une sensibilité très haute, de l'ordre de quelques centaines d'atomes pour différents éléments (Fe, Cu, Zn…). Le couplage des informations issues de l'imagerie X par contraste de phase (masse surfacique de la cellule) et de la fluorescence X (masse surfacique des éléments chimiques) a pu être obtenu pour la première fois donnant accès à une cartographie des éléments chimiques constituant les cellules et de leurs fractions massiques absolues associées. Dans l'immédiat, il n'a été possible d'étudier des cellules qui ont été congelées rapidement puis lyophilisées, cependant, une nouvelle ligne de nanoimagerie, NINA, en construction à l'ESRF, fonctionnera comme un cryomicroscope et permettra l'analyse 2D/3D d'échantillons biologiques ou non congelés hydratés. L'extension de l'imagerie chimique 2D présentée dans ce travail à une imagerie 3D représente une importante avancée pour bon nombre de problématiques scientifiques en biologie. Une des limitations de ce type d'analyse est celle des dommages radio-induits à la suite de l'irradiation de l'échantillon par un haut flux de particules ionisantes. Il existe que peu ou pas d'étude sur les effets de la nanoanalyse par fluorescence X sur les cellules lyophilisées. Nous avons combiné l'imagerie de phase à l'imagerie par fluorescence X ce qui nous permis de conclure à une rétractation des structures cellulaires accompagnée d'une volatilisation des éléments du fait de l'irradiation lors de l'analyse par fluorescence X. Ces aspects ont été confortés par des analyses utilisant une technique complémentaire non-synchrotron de microscopie ionique en transmission et à balayage (STIM). Plus important encore, nous apportons ainsi un outil rapide et non-destructif pour la cellule (imagerie X de phase) qui permet de corriger la perte de masse due à la volatilisation d'éléments légers (C, H, O, N) de la matrice cellulaire. Cette démarche permet de fiabiliser l'analyse quantitative de la composition chimique cellulaire. Cette approche sera précieuse pour corriger ces effets de perte de masse lors de futures analyses tomographiques de cellules entières congelées hydratées. Nous avons également contribué à l'étude de distribution intracellulaire de nouvelles nanoparticules d'or ou de platine fonctionnalisées. Nous avons pu exploiter les données issues de la fluorescence X pour estimer le nombre de nanoparticules et la taille des clusters internalisés au sein des cellules. Toutefois, des expériences dédiées pour des analyses sur un plus grand nombre de cellules auxquelles l'imagerie X par contraste de phase serait menée en parallèle permettraient surement de préciser plus finement ces aspects quantitatifs sur le nombre de nanoparticules intracellulaires. Dans l'ensemble ce travail ouvre la possibilité d'une imagerie chimique quantitative absolue sub-cellulaire en 2D ou 3D avec la perspective d'imagerie corrélative avec de nombreuses techniques complémentaires notamment la microscopie électronique à transmission pour l'ultrastructure, la microscopie de fluorescence pour la localisation de proteines d'intérêts et d'autres techniques d'analyses chimiques telles le NanoSIMS ou le nano-PIXE. / This work presents some recent developments in the field of hard X-ray imaging appliedto biomedical research. As the discipline is evolving quickly, new questions appear andthe list of needs becomes bigger. Some of them are dealt with in this manuscript.It has been shown that the ID22NI beamline of the ESRF can serve as a proper experimentalsetup to investigate diverse aspects of cellular research. Together with its highspatial resolution, high flux and high energy range the experimental setup providesbigger field of view, is less sensitive to radiation damages (while taking phase contrastimages) and suits well chemical analysis with emphasis on endegeneous metals (Zn, Fe,Mn) but also with a possibility for for exogoneous one’s like these found in nanoparticles(Au, Pt, Ag) study.Two synchrotron-based imaging techniques, fluorescence and phase contrast imagingwere used in this research project. They were correlated with each other on a numberof biological cases, from bacteria E.coli to various cells (HEK 293, PC12, MRC5VA,red blood cells).The explorations made in the chapter 5 allowed preparation of more establishedand detailed analysis, described in the next chapter where both techniques, X-ray fluorescenceand phase contrast imaging, were exploited in order to access absolute metalprojected mass fraction in a whole cell. The final image presents for the first timetrue quantitative information at the sub-cellular level, not biased by the cell thickness.Thus for the first time a fluorescence map serves as a complete quantitative image of acell without any risk of misinterpretation. Once both maps are divided by each otherpixel by pixel (fluorescence map divided by the phase map) they present a completeand final result of the metal (Zn in this work) projected mass fraction in ppm of dryweight. For the purpose of this calculation the analysis was extended to calibration(non-biological) samples. Polystyrene spheres of a known diameter and known densityworked very well here and allowed validation of the presented method. Different images(phase map, AFM, STIM) and profiles were compared and statement on the high accuracyof phase contrast imaging for the thickness/structures determination was made.The result on true metal projected mass fraction represents a first step to an absolutesub-cellular analysis and certainly can be improved to even closer reflect on reality.All the measurements were taken on freeze-dried cells. Thus the result is in ppm ofdry weight. In fact the measurement would have even deeper meaning if it was madeon hydrated cells. For the moment this is not possible with the existing setup of theID22NI beamline but will be possible in the future with a new beamline devoted tonano science - NINA (Nano-Imaging and Nano-Analysis). The new beamline will befurnished with a cryostage and X-ray imaging will be made on frozen-hydrated samples.Nevertheless the analysis presented in this manuscript is of undeniable importance toboth the biomedical community and to the ESRF team engaged in the NINA development.To answer the problems of cell irradiation both imaging techniques were exploitedagain. Repeating the phase contrast imaging after the fluorescence scanning allowedto show the changes induced by radiation damage during X-ray fluorescence scan. Thechanges were not only clearly visible but could be as well quantified. Together with thenumerical evaluation of damages, the dose delivered to a cell during the experiment was calculated as well. To complete the picture, a different non synchrotron-basedimaging technique, STIM, was used and compared. It is the first time that phase contrastimaging is used to monitor radiation damage effects during X-ray fluorescencemicroscopy experiments.

Les systèmes d’imagerie par rayons X conventionnels utilisent des détecteurs à base de scintillateur en mode intégration d’énergie. La nouvelle génération de détecteurs à base de semi-conducteur CdTe/CdZnTe permet de compter le nombre de photons et de mesurer l’énergie avec laquelle les photons arrivent sur le détecteur. Le laboratoire LDET (CEA LETI) a développé des détecteurs spectrométriques pixellisés à base de CdTe pour l’imagerie par rayons X associés à un circuit de lecture rapide permettant de travailler à fort taux de comptage avec une bonne résolution en énergie. Ces travaux de thèse proposent d’apporter une contribution au traitement des données acquises sur ces détecteurs résolus en énergie pour la quantification des constituants des matériaux en radiographie et en tomographie. Le cadre médical applicatif choisi est l’ostéodensitométrie. Des simulations de radiographie, qui prennent en compte les imperfections du système de détection, comme le partage de charges et les empilements, ont été réalisées. Nous avons choisi d’étudier des méthodes de traitements des données spectrales basées sur la décomposition en base de matériaux. Cette technique de réduction des données consiste à modéliser le coefficient d’atténuation linéique d’un matériau par une combinaison linéaire des fonctions d’atténuation de deux matériaux de base. Deux approches, utilisant toutes les deux un apprentissage par calibrage, ont été adaptées pour notre application. La première est une adaptation de l’approche polynômiale standard, appliquée pour deux et trois canaux d’énergie. Un processus d’optimisation des seuils des canaux a été réalisé afin de trouver la configuration optimale des bandes d’énergie. Une étude sur le nombre de canaux a permis d’évaluer les limites de la formulation polynômiale. Pour aller plus loin dans l’exploitation du potentiel des nouveaux détecteurs, une approche statistique développée dans notre laboratoire a été adaptée pour la décomposition en base de matériaux. Elle peut se généraliser à un grand nombre de canaux (100 par exemple). Une comparaison des deux approches a été réalisée selon des critères de performance comme le bruit et la précision sur l’estimation des longueurs des matériaux traversés. La validation des deux approches étudiées sur des données expérimentales acquises en radiographie, dans notre laboratoire, avec des détecteurs spectrométriques, a montré une bonne quantification des constituants des matériaux, en accord avec les résultats obtenus en simulation. / Scintillator based integrating detectors are used in conventional X-ray imaging systems. The new generation of energy-resolved semiconductor radiation detectors, based on CdTe/CdZnTe, allows counting the number of photons incident on the detector and measure their energy. The LDET laboratory developed pixelated spectrometric detectors for X-ray imaging, associated with a fast readout circuit, which allows working with high fluxes and while maintaining a good energy resolution. With this thesis, we bring our contribution to data processing acquired in radiographic and tomographic modes for material components quantification. Osteodensitometry was chosen as a medical application. Radiographic data was acquired by simulation with a detector which presents imperfections as charge sharing and pile-up. The methods chosen for data processing are based on a material decomposition approach. Basis material decomposition models the linear attenuation coefficient of a material as a linear combination of the attenuations of two basis materials based on the energy related information acquired in each energy bin. Two approaches based on a calibration step were adapted for our application. The first is the polynomial approach used for standard dual energy acquisitions, which was applied for two and three energies acquired with the energy-resolved detector. We searched the optimal configuration of bins. We evaluated the limits of the polynomial approach with a study on the number of channels. To go further and take benefit of the elevated number of bins acquired with the detectors developed in our laboratory, a statistical approach implemented in our laboratory was adapted for the material decomposition method for quantifying mineral content in bone. The two approaches were compared using figures of merit as bias and noise over the lengths of the materials traversed by X-rays. An experimental radiographic validation of the two approaches was done in our laboratory with a spectrometric detector. Results in material quantification reflect an agreement with the simulations.

L’objectif du projet, dont le travail présenté dans cette thèse est une partie, était de développer une caméra à rayons X ultra-rapide utilisant des pixels hybrides pour l’imagerie biomédicale et la science des matériaux. La technologie à pixels hybrides permet de répondre aux besoins des ces deux champs de recherche, en particulier en apportant la possibilité de sélectionner l’énergie des rayons X détectés et de les imager à faible dose. Dans cette thèse, nous présentons une caméra ultra-rapide basée sur l’utilisation de circuits intégrés XPAD3-S développés pour le comptage de rayons X. En collaboration avec l’ESRF et SOLEIL, le CPPM a construit trois caméras XPAD3. Deux d’entre elles sont utilisée sur les lignes de faisceau des synchrotrons SOLEIL et ESRF, et le troisième est installé dans le dispositif d’irradiation PIXSCAN II du CPPM. La caméra XPAD3 est un détecteur de rayons X de grande surface composé de huit modules de détection comprenant chacun sept circuits XPAD3-S équipés d’un système d’acquisition de données ultra-rapide. Le système de lecture de la caméra est basé sur l’interface PCI Express et sur l’utilisation de circuits programmables FPGA. La caméra permet d’obtenir jusqu’à 240 images/s, le nombre maximum d’images étant limité par la taille de la mémoire RAM du PC d’acquisition. Les performances de ce dispositif ont été caractérisées grâce à plusieurs expériences à haut débit de lecture réalisées dans le système d’irradiation PIXSCAN II. Celles-ci sont décrites dans le dernier chapitre de cette thèse. / The aim of the project, of which the work described in this thesis is part, was to design a high-speed X-ray camera using hybrid pixels applied to biomedical imaging and for material science. As a matter of fact the hybrid pixel technology meets the requirements of these two research fields, particularly by providing energy selection and low dose imaging capabilities. In this thesis, high frame rate X-ray imaging based on the XPAD3-S photons counting chip is presented. Within a collaboration between CPPM, ESRF and SOLEIL, three XPAD3 cameras were built. Two of them are being operated at the beamline of the ESRF and SOLEIL synchrotron facilities and the third one is embedded in the PIXSCAN II irradiation setup of CPPM. The XPAD3 camera is a large surface X-ray detector composed of eight detection modules of seven XPAD3-S chips each with a high-speed data acquisition system. The readout architecture of the camera is based on the PCI Express interface and on programmable FPGA chips. The camera achieves a readout speed of 240 images/s, with maximum number of images limited by the RAM memory of the acquisition PC. The performance of the device was characterize by carrying out several high speed imaging experiments using the PIXSCAN II irradiation setup described in the last chapter of this thesis.

In this work, a characterization and optimization of the grating-based x-ray imaging technique is presented. The investigations are introduced by analytical considerations, are underpinned with numerical simulations and validated using exemplary experiments. A detailed examination of the image formation in a grating interferometer is given, highlighting the dependence of the measured signal on the profile of the gratings. Subsequently, it is shown analytically and in experiments that grating-based imaging can be performed using three basic grating arrangements, which differ in their requirements on grating fabrication and experimental implementation. By a characterization of the measurement signal for each arrangement, a dependence of the signal strength on the sample position within the interferometer is identified. The consecutive evaluation of the impact of this position dependence on radiographic and tomographic data leads to the derivation of optimized reconstruction algorithms and to a correction of resulting image artifacts. Additionally, it is shown that the simultaneous measurement of attenuation and phase images allows the determination of the atomic number of the sample, opening new possibilities for material discrimination. Apart from these investigations on the contrast formation, various imperfections of the technique are investigated: The properties of the image noise are examined in a detailed statistical analysis, yielding a fundamental understanding of the signal-to-noise behavior of the three available contrast channels. Additionally, beam-hardening artifacts at polychromatic x-ray sources are investigated and their correction by a linearization approach is resented. By a subsequent analysis of the influence of various different grating imperfections on the image quality, tolerance limits for grating fabrication are specified. Furthermore, analytical considerations show that gratings with a duty cycle of 1/3 are advantageous with respect to the signal-to-noise ratio in comparison to common gratings with a duty cycle of 1/2. In conclusion, the results, concepts and methods developed in this work broaden the understanding of grating-based x-ray imaging and constitute a step forward towards the practical implementations of the technique in imaging applications.

<p>A variety of methods have been developed to enhance solid propellant burning rates, including adjusting oxidizer particle size, modifying metal additives, tailoring the propellant core geometry, and adding catalysts or wires. Fully consumable reactive wires embedded in propellant have been used to increase the burning rate by increasing the surface area; however, the manufacture of propellant grains and the observation of geometric effects with reactive components has been restricted by traditional manufacturing and viewing methods. In this work, a printable reactive filament was developed that is tailorable to a number of use cases spanning reactive fibers to photosensitive igniters. The filament employs aluminum fuel within a printable polyvinylidene fluoride matrix that can be tailored to a desired burning rate through stoichiometry or aluminum fuel configuration such as particle size and modified aluminum composites. The material is printable with fused filament fabrication, enabling access to more complex geometries such as spirals and branches that are inaccessible to traditionally cast reactive materials. However, additively manufacturing the reactive fluoropolymer and propellant together comes attendant with many challenges given the significantly different physical properties, particularly regarding adhesion. To circumvent the challenges posed by multiple printing techniques required for such dissimilar materials, the reactive fluoropolymer was included within a solid propellant carrier matrix as small fibers. The fibers were varied in aspect ratio (AR) and orientation, with aspect ratios greater than one exhibiting a self-alignment behavior in concordance with the prescribed extrusion direction. The effective burning rate of the propellant was improved nearly twofold with 10 wt.% reactive fibers with an AR of 7 and vertical orientation. </p> <p>The reactive wires and fibers in propellant proved difficult to image in realistic sample designs, given that traditional visible imaging techniques restrict the location and dimensions of the reactive wire due to the necessity of an intrusive window next to the wire, a single-view dynamic X-ray imaging technique was employed to analyze the evolution of the internal burning profile of propellant cast with embedded additively manufacture reactive components. To image complex branching geometries and propellant with multiple reactive components stacked within the same line of sight, the dynamic X-ray imaging technique was expanded to two views. Topographic reconstructions of propellants with multiple reactive fibers showed the evolution of the burning surface enhanced by the geometric effects caused by the faster burning fibers. These dual-view reconstructions provide a method for accurate quantitative analysis of volumetric burning rates that can improve the accessibility and viability of novel propellant grain designs.</p>

<p>Generative Adversarial Networks (GANs) have consistently defined the state-of-the-art in the generative modelling of high-quality images in several applications.  The images generated using GANs, however, do not lend themselves to being directly used in supervised learning tasks without first being curated through annotations.  This dissertation investigates how to carry out automatic on-the-fly segmentation of GAN-generated images and how this can be applied to the problem of producing high-quality simulated data for X-ray based security screening.  The research exploits the hidden layer properties of GAN models in a self-supervised learning framework for the automatic one-shot segmentation of images created by a style-based GAN.  The framework consists of a novel contrastive learner that is based on a Sinkhorn distance-based clustering algorithm and that learns a compact feature space for per-pixel classification of the GAN-generated images.  This facilitates faster learning of the feature vectors for one-shot segmentation and allows on-the-fly automatic annotation of the GAN images.  We have tested our framework on a number of standard benchmarks (CelebA, PASCAL, LSUN) to yield a segmentation performance that not only exceeds the semi-supervised baselines by an average wIoU margin of 1.02 % but also improves the inference speeds by a factor of 4.5.  This dissertation also presents BagGAN, an extension of our framework to the problem domain of X-ray based baggage screening.  BagGAN produces annotated synthetic baggage X-ray scans to train machine-learning algorithms for the detection of prohibited items during security screening.  We have compared the images generated by BagGAN with those created by deterministic ray-tracing models for X-ray simulation and have observed that our GAN-based baggage simulator yields a significantly improved performance in terms of image fidelity and diversity.  The BagGAN framework is also tested on the PIDRay and other baggage screening benchmarks to produce segmentation results comparable to their respective baseline segmenters based on manual annotations.</p>

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We investigate the signal and noise transform characteristics from the projection domain to the image domain in a linear systems theory framework and predictions of the DQE within this framework are made. A simulation study of a photon counting silicon detector is made from which the energy information is used in order to produce synthetic monoenergetic images. From these images the MTF, NPS, and DQE are estimated and are compared to the respective quantities predicted from the model. Within this model we find that the DQE in the projection domain has similar global characteristics as in the image domain, and that the sampling step in the imaging chain affects the DQE close to the zero frequency. / Vi undersöker hur signal och brus egenskaper transformeras från projektionsdomänen till bilddomänen i ett linjärt-skiftinvariant system och förutsägelser av DQE inom detta ramverk görs. Vidare görs en simuleringsstudie av en fotonräknande kiseldetektor från vilken energiinformationen används för att producera syntetiska monoenergetiska bilder. Från dessa bilder uppskattas MTF, NPS och DQE och jämförs med respektive storheter förutspådda från modellen. Inom modellen finner vi att DQE i projektionsdomänen har liknande globala egenskaper som i bilddomänen, och att samplingssteget i bildkedjan påverkar DQE nära nollfrekvensen.

Yes / Dynamic X-ray imaging systems are used for interventional cardiac procedures to treat coronary heart disease. X-ray settings are controlled automatically by specially-designed X-ray dose control mechanisms whose role is to ensure an adequate level of image quality is maintained with an acceptable radiation dose to the patient. Current commonplace dose control designs quantify image quality by performing a simple technical measurement directly from the image. However, the utility of cardiac X-ray images is in their interpretation by a cardiologist during an interventional procedure, rather than in a technical measurement. With the long term goal of devising a clinically-relevant image quality metric for an intelligent dose control system, we aim to investigate the relationship of image noise with clinical professionals’ perception of dynamic image sequences. Computer-generated noise was added, in incremental amounts, to angiograms of five different patients selected to represent the range of adult cardiac patient sizes. A two alternative forced choice staircase experiment was used to determine the amount of noise which can be added to a patient image sequences without changing image quality as perceived by clinical professionals. Twenty-five viewing sessions (five for each patient) were completed by thirteen observers. Results demonstrated scope to increase the noise of cardiac X-ray images by up to 21% ± 8% before it is noticeable by clinical professionals. This indicates a potential for 21% radiation dose reduction since X-ray image noise and radiation dose are directly related; this would be beneficial to both patients and personnel. / This work was funded by Philips Healthcare, NL. Part of this work has been performed in the project PANORAMA, cofunded by grants from Belgium, Italy, France, the Netherlands, and the United Kingdom, and the ENIAC Joint Undertaking.