Optical coherence tomography (OCT) is a safe and non-invasive imaging technique providing high axial resolution. A spectral-domain OCT scanner capable of acquiring volumetric data of the retina is becoming an increasingly important modality in ophthalmology for the diagnosis and management of a variety of retinal diseases such as glaucoma, diabetic retinopathy and age related macular degeneration (AMD) which are major causes of a loss of vision. To analyze and track these ocular diseases, developments of the automated methods for detecting intraretinal layers, optic discs and retinal blood vessels from spectral-domain OCT scans are highly required recently. The major contributions of this thesis include: 1) developing a fast method that can automatically segment ten intraretinal layers in the spectral-domain macular OCT scan for the layer thickness analysis, 2) developing a method that can automatically segment the optic disc cup and neuroretinal rim in the spectral-domain OCT scan centered at the optic nerve head (ONH) to measure the cup-to-disc ratio, an important structural indicator for the progression of glaucoma, and 3) developing a method that can automatically segment the 3-D retinal blood vessels in the spectral-domain ONH-centered OCT scan to extract 3-D features of the vessels for the diagnosis of retinal vascular diseases.

Wastewater Treatment Plants (WWTPs) are sophisticated systems that have to sustain long-term qualified performance, regardless of temporally volatile volumes or compositions of the incoming wastewater. Membrane filtration in the Membrane Bioreactors (MBRs) reduces the WWTPs footprint and produces effluents of proper quality. The energy or electric power consumption of the WWTPs, mainly from aeration equipment and pumping, is directly linked to greenhouse gas emission and economic input. Biological treatment requires oxygen from aeration to perform aerobic decomposition of aquatic pollutants, while pumping consumes energy to overcome friction in the channels, piping systems, and membrane filtration. In this thesis, we researched full-scale WWTPs Influent Conditions (ICs) monitoring and forecasting models to facilitate the energy consumption budgeting and raise early alarms when facing latent abnormal events. Accurate and efficient forecasts of ICs could avoid unexpected system disruption, maintain steady product quality, support efficient downstream processes, improve reliability and save energy. We carried out a numerical study of bioreactor microbial ecology for MBRs microbial communities to identify indicator species and typical working conditions that would assist in reactor status confirmation and support energy consumption budgeting. To quantify membrane fouling and cleaning effects at various scales, we proposed quantitative methods based on Matern covariances to analyze biofouling layer thickness and roughness obtained from Optical Coherence Tomography (OCT) images taken from gravitydriven MBRs under various working conditions. Such methods would support practitioners to design suitable data-driven process operation or replacement cycles and lead to quantified WWTPs monitoring and energy saving. For future research, we would investigate data from other full-scale water or wastewater treatment process with higher sampling frequency and apply kernel machine learning techniques for process global monitoring. The forecasting models would be incorporated into optimization scenarios to support data-driven decision-making. Samples from more MBRs would be considered to gather information of microbial community structures and corresponding oxygen-energy consumption in various working conditions. We would investigate the relationship between pressure drop and spatial roughness measures. Anisotropic Matern covariance related metrics would be adopted to quantify the directional effects under various operation and cleaning working conditions.

This thesis deals mainly with perfusion modeling in optical coherence tomography (OCT). The introductory part deals with basic theory of the OCT, including a description of its basic applications. Part of the work was the testing of selected contrasting materials suitable for the OCT and the design and implementation of phantoms, which were subsequently used in the main part of the thesis. In the practical part, attention is paid to the perfusion analysis in the OCT, first the application of the dilution theory in the OCT for flow estimation, then a study testing the basic theory of perfusion on OCT by means of tissue phantom. Another part of the thesis is devoted to the method of speckle variance analysis for flow visualization.

This work describes optical coherence tomography, it's principle and methods for automatic segmentation intra-retinal layers in OCT images . There is proposed algorithm for boundary detection of two intra retinal layers, RFNL and RPE layer based on thresholding and second algorithm for detection of seven layers, which is based on graph search algorithm. In summary is compared accuracy against manualy segmented layers and there is also proposed solution for problematic parts.

Le but du projet est le développement de nouvelles techniques d’imagerie pour le diagnostic et le traitement du cancer du rein. Nous avons évalué différentes techniques comprenant la tomographie en cohérence optique et l’imagerie moléculaire. Nous avons évalué différents marqueurs potentiels pour l’imagerie moléculaire en étudiant l’expression de différents marqueurs dans le cancer du rein et leur association avec le pronostic de la maladie. Enfin, nous avons évalué deux techniques d’imagerie moléculaire sur des modèles précliniques : l’Imagerie par Résonnance Magnétique moléculaire et l’échographie moléculaire. / The aim of this project is the development of new imaging techniques for renal cancer diagnostic and treatment.We have assessed several techniques including optical coherence tomography and molecular imaging. We assessed a series of potential markers for molecular imaging by measuring some pre-defined markers expressions by immunohistochemistry in renal cell carcinoma and their association with disease’s prognostic. Finally, we assessed two molecular imaging techniques in pre-clinical models: Molecular Magnetic Resonance Imaging and Molecular Ultrasound Imaging.

La tomographie par cohérence optique plein champ (OCT plein champ) est une technique de microscopie interférométrique basée sur l’utilisation d’une source de lumière faiblement cohérente, telle qu’une lampe halogène. Elle permet de réaliser, de façon non invasive, des images tomographiques à plusieurs centaines de micromètres de profondeur dans les tissus biologiques et avec une résolution spatiale isotrope de l’ordre de 1 µm. Ces travaux de thèse concernent le développement de plusieurs systèmes d'OCT plein champ, dans le but de proposer de nouvelles performances et de nouveaux contrastes destinés à l’imagerie en trois dimensions de tissus biologiques. Nous avons dans un premier temps exploité la large bande spectrale d’émission d’une lampe halogène, afin d’apporter une information spectroscopique et d’être capable de distinguer et de caractériser des zones d’un échantillon qui seraient sinon indiscernables. Puis nous avons optimisé la résolution spatiale d’un montage d’OCT plein champ pour atteindre une valeur record de 0,5 µm (dans l’eau) dans les trois directions de l’espace, notamment grâce à l’utilisation d’une bande spectrale adaptée à l’imagerie de tissus, tels que la peau. Un montage dont le champ de vision est élargi à 18 mm x 18 mm a ensuite été développé et appliqué à l’imagerie du signal d’amplitude ainsi qu’à la mesure quantitative du signal de phase résolu en profondeur. Enfin un système utilisant un laser à balayage spectral comme source de lumière combiné à un traitement numérique de correction de la focalisation a été mis en œuvre. Nous avons ainsi démontré la possibilité de réaliser des images en trois dimensions avec une résolution latérale relativement élevée, sans utiliser le moindre déplacement mécanique durant l’acquisition. / Full-field optical coherence tomography (FF-OCT) is an optical technology based on low-coherence interference microscopy for tomographic imaging of semitransparent samples. Non-invasive three-dimensional imaging can be performed with an isotropic spatial resolution of the order of 1 µm. During the PhD thesis, several FF-OCT systems have been reported achieving extended performances or contrast enhanced images relevant for biological tissues imaging. Firstly, a three-band, 1.9-μm axial resolution FF-OCT system has been implemented to perform spectroscopic contrast enhanced imaging of biological tissues over a 530-1700 nm wavelength range. Then, a study of the FF-OCT axial response has been carried out for maximizing the axial resolution of the system. An isotropic spatial resolution of 0.5 µm (in water) has been obtained by combining 1.2-NA microscope objectives with an optimized broad spectral band adapted to biological tissues imaging, such as skin samples. A set-up with an extended field of view of 18 mm x 18 mm has been also designed and applied to amplitude signal detection as well as depth-resolved quantitative phase signal measurement. At last, we developed a technique based on the combination of full-field swept-source optical coherence tomography (FF-SSOCT) with low spatial coherence illumination and a special numerical processing that allows for numerically focused mechanical motion-free three-dimensional imaging.

In der vorliegenden Arbeit wurde die Netzhaut einiger tagaktiver Raubvögel hinsichtlich ihrer morphologischen und morphometrischen Eigenschaften mit verschiedenen Methoden untersucht. Über die Histologie werden Gestalt und Subspezialisierungen der Netzhaut von neun Vögel sieben verschiedener Spezies in ihrer nasal-temporalen und superior-inferioren Ausdehnung betrachtet. Besonderes Augenmerk lag hierbei auf dem Verhältnis der Photorezeptor- und Neuronenpopulationen zueinander, da hier über den Grad von Konvergenz oder Divergenz der Verschaltung Informationen über die intraretinale Signalverarbeitung gewonnen werden können. Über das Verfahren der Immunhistochemie wurde zudem untersucht, ob sich die Spezies hinsichtlich der intraretinalen Verteilung einiger ausgewählter Marker von Strukturen der Müllerzellen und der Photorezeptoren unterscheiden. Eine weitere angewandte Methode war die optische Kohärenztomographie, ein bildgebendes Verfahren, das non-invasiv in vivo Schnittbilder der Netzhaut erzeugt. Hier konnte gezeigt werden, dass diese aus der humanen Augenheilkunde bekannte Untersuchungstechnik auch am aviären Patienten anwendbar ist. Desweiteren wurde die Darstellbarkeit der aviären Netzhaut, ihrer Besonderheiten und pathologischer Veränderungen bei den verschiedenen Raubvogelspezies untersucht. Für bestimmte Regionen in der Raubvogelnetzhaut wie die Fovea centralis und temporalis, sind in historischen Untersuchungen Formunterschiede beschrieben worden und es konnte gezeigt werden, dass diese auch in vivo bestehen. Zuletzt wird die Frage behandelt, welche Unterschiede der Vergleich zwischen den beiden Verfahren der Netzhautdarstellung aufdeckt, inwiefern beide fehlerbehaftet sind und was bei der Interpretation beachtet werden sollte.:Inhaltsverzeichnis 1 Einleitung 1 1.1 Grundlagen zur Netzhaut 1 1.2 Die optische Kohärenztomographie (OCT) 6 1.3 Aufgabenstellung und klinische Relevanz 7 2 Material und Methoden 10 2.1 Untersuchungsmaterial 10 2.2 Spezies der histomorphologischen Untersuchung 10 2.3 Histologie und Immunhistochemie 14 2.4 Vergleich von OCT-Abbildung und histologischem Korrelat 25 2.5 Untersuchung der Ultrastruktur der aviären Netzhaut 28 3 Ergebnisse 30 3.1 Histologische und immunhistochemische Analyse der Netzhaut von tagaktiven Raubvogelspezies 30 3.2 Untersuchung retinaler Strukturen bei tagaktiven Raubvögeln mittels OCT 84 3.3 Vergleich der Darstellung in OCT und Histologie 91 3.4 Elektronenmikroskopie der äußeren Netzhaut des Raubvogels 95 4 Diskussion 98 4.1 Morphometrische Untersuchungen in Histologie und Immunhistochemie 98 4.2 OCT-Untersuchung von tagaktiven Raubvögeln 110 4.3 Verhältnis von OCT und histologischem Abbild 113 4.4 Fazit und Ausblick 115 Zusammenfassung 117 Literatur 121 Anhang

Auf Basis der vorgestellten Untersuchungen lässt sich ein großes Potenzial der OCT für die Erkennung initialer Kariesstadien sowie für die Darstellung der dentalen Mikrostruktur ableiten. Die eingeführte Depolarisationsbildgebung stellt dabei eine Erweiterung bisheriger OCT-basierter Ansätze dar und wurde im Rahmen dieser Arbeit erstmalig für die Anwendung am Zahn präsentiert. Darüber hinaus bilden die Ergebnisse der Untersuchungen die Grundlage für die Entwicklung weiterer Prototypen für die intraorale OCT-Bildgebung, die zukünftig eine vielversprechende Ergänzung zu klinisch etablierten Verfahren bei der Diagnostik der Approximalbereiche und Okklusalflächen darstellen könnte.

The heart and its mechanical components, especially the heart valves and leaflets, are under enormous strain during lifetime. Like all highly stressed materials, also these biological components undergo fatigue and signs of wear, which impinge upon cardiac output and in the end on health and living comfort of affected patients. Thereby pathophysiological changes of the aortic valve leading to calcific aortic valve stenosis (AVS) as most frequent heart valve disease in humans are of particular interest. The knowledge about changes of the dynamic behavior during the course of this disease and the possibility of early stage diagnosis could lead to the development of new treatment strategies and drug-based options of prevention or therapy. ApoE-/- mice as established model of AVS versus wildtype mice were introduced in an ex vivo artificially stimulated heart model. 4D optical coherence tomography (OCT) in combination with high-speed video microscopy were applied to characterize dynamic behavior of the murine aortic valve and to characterize dynamic properties during artificial stimulation. OCT and high-speed video microscopy with high spatial and temporal resolution represent promising tools for the investigation of dynamic behavior and their changes in calcific aortic stenosis disease models in mice.

Besides structural imaging, OCT can be used to estimate axial velocities of the sample resolved in depth by Dopplerprocessing. In Fourier domain OCT (FD-OCT), this is accomplished by measuring the phase difference (i.e. phase shift) between timely separated A-scans at the same depth. In most cases, these data are disturbed by noise caused by intrinsic noise of the OCT system, specified by the SNR, and decorrelation noise caused by the transversal movement of the optical beam relative to the sample. Since the first use of Doppler methods in OCT, many methods to reduce the phase shift noise by averaging have been presented. While all these methods use a fixed set of consecutive A-scans, the best method, exhibiting no bias and having the smallest standard deviation, was questionable. Recently, Doppler processing methods depending on the mentioned noise sources and delivering the most likely phase shift and thereby axial velocity became available. The relation of these methods to previously known methods like the Kasai estimator, maximum likelihood estimator (MLE) and joint spectral and time domain OCT (jSTdOCT) will be discussed.