L’OCT plein champ est une technique d’imagerie permettant de faire de la microscopie des milieux diffusants à une profondeur donné à l’aide d’un système interférométrique. L’un des principaux objectifs qui ont motivé le développement de l’OCT plein champ ces dernières années a été de pouvoir fournir au chirurgien, durant les opérations des images similaires aux coupes histologiques mais en temps réel. Actuellement, les diagnostiques effectué à partir des images d’OCT plein champs donne de bon résultats, notamment dans le cas de certaine pathologie mammaire. Cependant, la différence majeure entre les coupes histologiques et les images d’OCT plein champs est qu’en OCT plein champ le contraste est uniquement un contraste morphologique et que dans certain cas, ce contraste seul ne suffit pas pour faire le diagnostic. Au cours des travaux de recherche décrits dans cette thèse nous nous sommes attachés à développer de nouvelles approches tomographiques, conduisant à de nouvelles formes de contraste susceptible d’enrichir les images d’OCT plein champ pour une meilleure qualité du diagnostic. Plus précisément, nous avons travaillé sur la détection optique et photo-thermique de nanoparticules d’or par OCT plein champ et la cartographie des propriétés mécaniques par trois méthodes dans le but de développer de nouveaux types de contrastes qui pourront permettre d’améliorer le diagnostic. / Full Field OCT (FF-OCT) is an imaging technic use to do microscopy inside scattering media at a given depth using an interferometric setup. One of the main objectives that motivated the development of FF-OCT was to provide during surgery to the surgeon images similar to histological slices but in real time. Currently, diagnostic made from FF-OCT images gives good results, especially in the case of some breast disease. However, the major difference between the histological and FF-OCT is that FF-OCT has only a morphological contrast and in some cases, this contrast is not enough to make the diagnosis. In the research described in this thesis we are committed to developing new tomographic approaches, leading to new forms of contrast may enhance images of FF- OCT for a better quality of diagnosis. Specifically, we worked on the optical and photothermal detection of gold nanoparticles by FF-OCT and the mechanical properties mapping by three methods in order to develop new types of contrasts that will help improve the diagnosis.

<p>The goal of my Ph.D. thesis is to enhance the visualization of the peripheral retina using wide-field optical coherence tomography (OCT) in a clinical setting.</p><p>OCT has gain widespread adoption in clinical ophthalmology due to its ability to visualize the diseases of the macula and central retina in three-dimensions, however, clinical OCT has a limited field-of-view of 300. There has been increasing interest to obtain high-resolution images outside of this narrow field-of-view, because three-dimensional imaging of the peripheral retina may prove to be important in the early detection of neurodegenerative diseases, such as Alzheimer's and dementia, and the monitoring of known ocular diseases, such as diabetic retinopathy, retinal vein occlusions, and choroid masses.</p><p>Before attempting to build a wide-field OCT system, we need to better understand the peripheral optics of the human eye. Shack-Hartmann wavefront sensors are commonly used tools for measuring the optical imperfections of the eye, but their acquisition speed is limited by their underlying camera hardware. The first aim of my thesis research is to create a fast method of ocular wavefront sensing such that we can measure the wavefront aberrations at numerous points across a wide visual field. In order to address aim one, we will develop a sparse Zernike reconstruction technique (SPARZER) that will enable Shack-Hartmann wavefront sensors to use as little as 1/10th of the data that would normally be required for an accurate wavefront reading. If less data needs to be acquired, then we can increase the speed at which wavefronts can be recorded.</p><p>For my second aim, we will create a sophisticated optical model that reproduces the measured aberrations of the human eye. If we know how the average eye's optics distort light, then we can engineer ophthalmic imaging systems that preemptively cancel inherent ocular aberrations. This invention will help the retinal imaging community to design systems that are capable of acquiring high resolution images across a wide visual field. The proposed model eye is also of interest to the field of vision science as it aids in the study of how anatomy affects visual performance in the peripheral retina.</p><p>Using the optical model from aim two, we will design and reduce to practice a clinical OCT system that is capable of imaging a large (800) field-of-view with enhanced visualization of the peripheral retina. A key aspect of this third and final aim is to make the imaging system compatible with standard clinical practices. To this end, we will incorporate sensorless adaptive optics in order to correct the inter- and intra- patient variability in ophthalmic aberrations. Sensorless adaptive optics will improve both the brightness (signal) and clarity (resolution) of features in the peripheral retina without affecting the size of the imaging system.</p><p>The proposed work should not only be a noteworthy contribution to the ophthalmic and engineering communities, but it should strengthen our existing collaborations with the Duke Eye Center by advancing their capability to diagnose pathologies of the peripheral retinal.</p> / Dissertation

Introduction. La tomographie par cohérence optique (TCO) est une modalité d'imagerie permettant de dévoiler la microarchitecture des tissus en temps réel. Compte tenu de ses propriétés, il existe un intérêt croissant pour déterminer les applications potentielles de la TCO en chirurgie endocrinienne cervico-faciale. Méthodologie. Trente-six patients opérés pour thyroïdectomie, parathyroïdectomie et/ou évidement cervical pour un cancer bien différencié de la thyroïde (CBDT) ont été recrutés prospectivement. Les spécimens de thyroïde, glandes parathyroïdes, ganglions et tissus adipeux sains et pathologiques ont été imagés avec la TCO avant l'analyse histopathologique. Les images ont été examinées par deux évaluateurs indépendants et une équipe multidisciplinaire. Résultats. Basé sur 137 spécimens chirurgicaux, la TCO ne permettait pas de différencier les nodules thyroïdiens bénins des nodules malins et les adénomes parathyroïdiens des ganglions sains. Pour les tissus sains, la TCO permettait de distinguer chaque type de tissu avec une sensibilité et une spécificité de 100% et 99% pour la thyroïde, 93% et 100% pour les glandes parathyroïdes, 100% et 99% pour les tissus adipeux, et 98% et 99% pour les ganglions. Les coefficients kappa de Cohen pour l'accord intra- et inter-évaluateurs étaient de 0,968 et 0,951. La TCO permettait également de différencier les ganglions bénins des ganglions malins avec une sensibilité, spécificité, valeur prédictive positive et négative de 85,1%, 89,5%, 80,8% et 92,2%. La fiabilité intra- et inter-évaluateurs étaient de 0,836 et 0,792. Conclusion. La TCO pourrait servir d'outil d'appoint pour confirmer l’identification des glandes parathyroïdes et différencier les ganglions métastatiques des ganglions bénins lors de la thyroïdectomie. / Background. Optical coherence tomography (OCT) is a non-invasive imaging modality that renders real-time tissue images with resolution in the order of micrometers, allowing to unveil their microarchitecture. Given its properties, there is growing interest in determining the potential applications of OCT in thyroid and parathyroid surgery. Methodology. Thirty-six patients undergoing thyroidectomy, parathyroidectomy and/or neck dissection for well-differentiated thyroid carcinoma (WDTC) were prospectively recruited in a single tertiary center. Freshly excised specimens of healthy and pathologic thyroid, parathyroid glands, lymph nodes and adipose tissues were imaged with OCT prior to histopathological analysis. Images were reviewed by two blinded independent raters, and a multidisciplinary team. Results. Based on 137 surgical specimens, OCT could not consistently differentiate benign from malignant thyroid nodules, and parathyroid adenomas from normal lymph nodes. For healthy tissues, OCT could differentiate each tissue type with high sensitivity and specificity 100% and 99% for thyroid tissue, 93% and 100% for parathyroid glands, 100% and 99% for adipose tissue, and 98% and 99% for lymph nodes. Cohen’s kappa coefficients for intra- and inter-rater agreement were 0.968 and 0.951. OCT could also differentiate benign from malignant lymph nodes in WDTC with sensitivity, specificity, positive and negative predictive values of 85.1%, 89.5%, 80.8%, and 92.2%. Cohen’s kappa coefficients for intra- and inter-rater reliability were 0.836, and 0.792. Conclusion. Evidence suggests that OCT could serve as an adjunct tool to identify parathyroid glands during thyroidectomy and differentiate benign from metastatic lymph nodes in WDTC.

Restoration of image data has become an essential part of the processing of medical images obtained by any system. The same applies in the case of optical coherence tomography. The aim of this work is to study the first restoration methods. Second, the description of the data representation from optical coherence tomography and subsequent discussions that restoration methods based on deconvolution would potentially find application in processing of Optical coherence tomography. Finally, the third to create a program solution of the OCT data restoration process in MATLAB environment and followed by discussion of effectiveness of the presented solutions.

The main target of this work is a design of the program for border localization of the optic disc in OCT data. Part of this program is also localization of the „optic cup“ and calculation of several values that characterize optic disc. The work is also dealing with a description of the optical coherence tomography principle which is used in ophthalmology. One chapter describes some published methods of optic cup localization. Success of the program and its comparison with OCT Zeiss Stratus 3000 is evaluated at the end of the work.

L’activité plaquettaire joue un rôle clé dans la physiopathologie de l’infarctus du myocarde avec sus-décalage du segment ST (IDM ST+). La réactivité plaquettaire est augmentée lors d’un IDM ST+, traité par angioplastie primaire ou par fibrinolyse avec succès. La relation entre la réactivité plaquettaire résiduelle après un pré-traitement, la charge athérothrombotique et la qualité de la reperfusion myocardique reste peu décrite dans le cadre des IDM ST+. La tomographie par cohérence optique et celle plus récente par domaine de fréquence offrent une imagerie de haute résolution permettant l’identification et la quantification précise de la charge athérothrombotique intracoronaire (CAT). La CAT résiduelle intra-stent peut aider à mieux comprendre la relation entre la réactivité plaquettaire et la reperfusion. Dans un premier temps, nous avons évalué la précision des tests VerifyNow et PFA en comparaison à l’agrégométrie optique pour la détection de l’hyperréactivité plaquettaire dans le contexte particulier des IDM ST+ traités par fibrinolyse avec succès. Nous avons aussi décrit les caractéristiques de la CAT avant et après angioplastie selon la présence d’une rupture de plaque ou d’une érosion coronaire chez des patients traités par fibrinolyse avec succès. Ensuite, nous avons étudié la relation entre la réactivité plaquettaire résiduelle (en réponse au ticagrelor et à l’aspirine) mesurée par VerifyNow et la reperfusion myocardique chez des patients traités par angioplastie primaire. En parallèle, nous avons décrit la relation entre la reperfusion myocardique et la CAT résiduelle intra-stent dans la même cohorte. / Platelet activity plays a key role in the pathophysiology of ST-segment elevation myocardial infarction (STEMI). Platelet reactivity is enhanced after STEMI treated with primary percutaneous coronary intervention (PCI) or successful thrombolysis. The relationship between residual platelet reactivity after pre-treatment, the atherothrombotic burden and the quality of reperfusion remains poorly described in STEMI. Optical coherence tomography (OCT) and optical frequency domain imaging (OFDI) provide high resolution imaging allowing identification and accurate quantification of intracoronary atherothrombotic burden (ATB). Residual in-stent ATB may help to better understand the relation between platelet reactivity and reperfusion. First, we assessed the accuracy of the point-of-care tests VerifyNow and PFA in comparison to light transmittance aggregometry to detect high on-treatment platelet reactivity (HPR) in the particular setting of STEMI successfully treated with fibrinolysis. We also described the characteristics of ATB before and after PCI according to the underlying presence of rupture or erosion in patients successfully treated with fibrinolysis. Then, we assessed the relationship between residual platelet reactivity (in response to ticagrelor and aspirin) using VerifyNow and myocardial reperfusion in primary PCI patients. In parallel, we studied the relationship between myocardial reperfusion and residual in-stent ATB in the same cohort.

While dental caries represents the major chronic disease of humans, visual and tactile inspection are the methods of choice in daily dental practice. Several optical technologies have been developed in recent years for the purpose of dental examination, including near-infrared light transillumination as a promising tool for the supplementation and partial replacement of radiography. In case of occlusal alterations, the incidence of surface discolorations impedes the visual assessment, whereas tactile inspection appears to yield little diagnostic information or might be detrimental. Optical coherence tomography (OCT) facilitates depth-resolved imaging with μm resolution, utilizing near-infrared light, and has already shown its potential for various dental applications. We have recently demonstrated that depolarization imaging utilizing the degree of polarization uniformity (DOPU) extends those abilities by the detection of early carious lesions, as it provides an unambiguous demineralization contrast. Here, we show that this approach also enables the assessment of occlusal enamel lesions in the presence of stains, and compare PS-OCT cross sections with polarized light microscopy (PLM) images of thin sections. For tooth samples with discoloration or demineralization, respectively, PS-OCT and PLM results are in good agreement.

Ce mémoire par article décrit le développement d’instrumentation optique et d’algorithmes qui ont servi à l’étude du développement rétinien du modèle murin par tomographie par cohérence optique (OCT de l’anglais, Optical Coherence Tomography). Le document est divisé en deux parties importantes. Le Chapitre 1 introduit les bases théoriques nécessaires à la compréhension de la problématique, alors que le Chapitre 2 décrit les outils qui ont été développés ou adaptés durant le projet pour mener à bien les expériences. Spécifiquement, les particularités du système optique développé pour permettre la focalisation d’un faisceau sur la rétine, maximiser le signal et minimiser l’impact des aberrations sphériques et de dispersion sur la qualité de l’image sont détaillées. Les algorithmes de traitement de signal OCT permettant la visualisation une tomographie sont aussi détaillés. La seconde partie est un manuscrit en préparation pour soumission au journal Investigative Ophthalmology & Visual Science pour publication. Le but de ce manuscrit est d’établir des chartes de référence détaillant la croissance et la maturation morphologique des tissus rétiniens de la souris wild-type (129S1/SvImJ) entre 7 et 21 jours de vie (Chapitre 3). L’article détaille l’algorithme de traitement d’images et de segmentation dédié à la quantification de l’épaisseur des tissus rétiniens dans le temps. Enfin, un aperçu des travaux de recherche rendus possibles par les outils développés dans ce projet est présenté. Cette section montre entre autres le potentiel de ces outils pour étudier des maladies développementales de la rétine. / This master thesis is including a manuscript submitted for publication and is divided into two sections. In particular, the document describes the development of optical instrumentation and methodological tools to study the retinal development in an animal model through optical coherence tomography (OCT). The first section is divided into two chapters. Chapter 1 describes the theoretical basis and the problem to solve. Chapter 2 describes the tools developed or adapted to enable the performance of the experiments. In particular, this chapter details the optical system designed to allow the optimal focalization of the light beam onto the retina, which maximizes the signal and minimizes the impact of spherical aberrations and light dispersion on image quality. Also, the processing algorithm used to segment retinal tissues from OCT tomography is discussed. The second section is divided into two chapters. Chapter 3 is a manuscript that was submitted for publication to Investigative Ophthalmology & Visual Science. This work describes the growth and maturation of specific retinal layers in the wild type mouse (129S1/SvImJ) between 7 and 21 days of life. The manuscript also describes the image processing and segmentation algorithm that allows the quantification of the thickness of the layers over time. Then, Chapter 4 describes specific research projects where these OCT imaging tools can be applied. Specifically, this chapter shows the potential to study retinal developmental diseases as well as perfusion methods.

Large-scale and cost-effective manufacturing of ceramic micro devices based on tape stacking requires the development of inspection systems to perform high-resolution in-process quality control of embedded manufactured cavities, metal structures and defects. In this work, alumina ceramic samples are evaluated by optical coherence tomography (OCT) operating at 1.3μm wavelength and some dimensional data are obtained by dedicated image processing and segmentation. Layer thicknesses can be measured and laser-machined channels can be verified embedded at around 100μm depth. Moreover, detection of internal defects is enabled. Monte Carlo ray tracing simulations are employed to analyze the abilities of OCT in imaging of the embedded channels. The light scattering mechanism is studied for the alumina ceramics, and different scattering origins and models are discussed. The scattering parameters required as input data for simulations are evaluated from the integrating sphere measurements of collimated and diffuse transmittance spectra using a reconstruction algorithm based on refined diffusion approximation approach. / <p>QC 20120628</p>

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