Diattenuation of Brain Tissue and its Impact on 3D Polarized Light Imaging

3D-Polarized Light Imaging (3D-PLI) reconstructs nerve fibers in histological brain sections by measuring their birefringence. This study investigates another effect caused by the optical anisotropy of brain tissue - diattenuation. Based on numerical and experimental studies and a complete analytical description of the optical system, the diattenuation was determined to be below 4 % in rat brain tissue. It was demonstrated that the diattenuation effect has negligible impact on the fiber orientations derived by 3D-PLI. The diattenuation signal, however, was found to highlight different anatomical structures that cannot be distinguished with current imaging techniques, which makes Diattenuation Imaging a promising extension to 3D-PLI.Comment: 32 pages, 15 figure

High-Resolution 3D Ptychography

Coherent imaging is a promising method in the field of x-ray microscopy allowing for the nondestructive determination of the interior structure of radiation-hard samples with a spatial resolution that is only limited by the fluence on the sample and the scattering strength of the sample. Ultimately, the achievable spatial resolution is limited by the wavelength of the incoming x-ray radiation. Combining coherent imaging with scanning microscopy to a method called ptychography enables one to also probe extended objects. In this method, a sample is scanned through a defined coherent x-ray beam and at each scan point a diffraction pattern is recorded with a diffraction camera located in the far field of the sample. Neighboring illuminated areas must have a certain overlap to guarantee the collection of sufficient information about the object for a subsequent successful and unique computational reconstruction of the object. Modern ptychographic reconstruction algorithms are even able to reconstruct the complex-valued transmission function of the sample and the complex illumination wave field at the same time. Once the 2D transmission function of a sample is known, it is an obvious step forward to combine ptychography with tomographic techniques yielding the 3D internal structure of an object with unprecedented spatial resolution. Here, projections at varying angular positions of the sample are generated via ptychographic scans and are subsequently used for the tomographic reconstruction. In this thesis the development of 3D ptychography is described. It includes the description of the required experimental environment, the numerical implementation of ptychographic phase retrieval and tomographic reconstruction routines, and a detailed analysis of the performance of 3D ptychography using an example of an experiment carried out at beamline P06 of PETRA III at DESY in Hamburg. In that experiment the investigated object was a Mo/UO2 thin film, which is a simplified model for spent nuclear fuel from nuclear power plant reactors. Such models find application in systematic scientific investigations related to the safe disposal of nuclear waste. We determined the three-dimensional interior structure of this sample with an unprecedented spatial resolution of at least 18 nm. The measurement of the fluorescence signal at each scan point of the ptychograms delivers the two- and three-dimensional elemental distribution of the sample with a spatial resolution of 80 nm. Using the fluorescence data, we assigned the chemical element to the area of the corresponding phase shift in the ptychographic reconstruction of the object phase and to the corresponding refractive index decrement in the tomographic reconstruction. The successful demonstration of the feasibility of the 3D ptychography motivates further applications, for instance, in the field of medicine, of material science, and of basic physical research.Kohärente Bildgebung ist eine vielversprechende Methode der Röntgenmikroskopie. Sie ermöglicht die zerstörungsfreie Bestimmung der inneren Struktur von strahlenharten Untersuchungsobjekten mit einer räumlichen Auflösung, die im Prinzip nur von der integralen Anzahl der Photonen auf der Probe sowie deren Streukraft abhängt. Letztendlich stellt die Wellenlänge der verwendeten Röntgenstrahlung eine Grenze für die erreichbare räumliche Auflösung dar. Die Kombination der kohärenten Bildgebung mit der Rastermikroskopie zur sogenannten Ptychographie eröffnet die Möglichkeit, auch ausgedehnte Objekte mit hoher Auflösung zu untersuchen. Dabei wird die Probe mit einem räumlich begrenzten, kohärenten Röntgenstrahl abgerastert und an jedem Rasterpunkt ein Beugungsbild von einer im Fernfeld platzierten Beugungskamera registriert. Die Beleuchtungen benachbarter Rasterpunkte müssen dabei zu einem bestimmten Prozentsatz überlappen, um genügend Informationen für eine anschließende computergestützte und eindeutige Rekonstruktion des Objektes sicherzustellen. Moderne Rekonstruktionsalgorithmen ermöglichen sogar die gleichzeitige Rekonstruktion der Transmissionsfunktion des Objektes und der Beleuchtungsfunktion des eintreffenden Röntgenstrahls. Die Verknüpfung der Ptychographie mit der Tomographie zur 3D-Ptychographie ist der nahe liegende Schritt, um nun auch die dreidimensionale innere Struktur von Objekten mit hoher räumlicher Auflösung zu bestimmen. Die Projektionen an den verschiedenen Winkelpositionen der Probe werden dabei mittels ptychographischer Abrasterung der Probe erzeugt und anschließend der tomographischen Rekonstruktion zugrunde gelegt. In dieser Arbeit wird die Entwicklung der 3D-Ptychographie beschrieben. Das beinhaltet die Beschreibung der experimentellen Umgebung, der numerischen Implementierung des ptychographischen und des tomographischen Rekonstruktionsalgorithmus als auch eine detaillierte Darstellung der Durchführung der 3D-Ptychographie am Beispiel eines Experiments, welches unter Verwendung des modernen Nanoprobe-Aufbaus des Strahlrohres P06 am PETRA III Synchrotronring des DESY in Hamburg durchgeführt wurde. Als Untersuchungsobjekt diente dabei ein dünner Mo/UO2-Film, der ein vereinfachtes Modell für die in Reaktoren von Atomkraftwerken verbrauchten Brennstäbe darstellt und deshalb im Bereich des Umweltschutzes Anwendung findet. Die dreidimensionale Struktur der Probe wurde mit einer - für diese Methode bisher einmaligen - räumlichen Auflösung von 18 nm bestimmt. Die Messung des von der Probe kommenden Fluoreszenz-Signals an jedem Rasterpunkt der Ptychogramme ermöglichte zusätzlich die Bestimmung der zwei- und dreidimensionalen Elementverteilung innerhalb der Probe mit einer räumlichen Auflösung von 80 nm. Anhand der Fluoreszenzdaten konnte sowohl den Bereichen verschiedener Phasenschübe in den ptychographischen Rekonstruktionen der Objektphase als auch den verschiedenen Werten des Dekrementes des Brechungsindex in der tomographischen Rekonstruktion, das entsprechende chemische Element zugeordnet werden. Die erfolgreiche Demonstration der Durchführbarkeit der 3D-Ptychographie motiviert weitere zukünftige Anwendungen, z. B. auf dem Gebiet der Medizin, der Materialforschung und der physikalischen Grundlagenforschung

Mathematical Modelling of Optical Coherence Tomography

In this chapter a general mathematical model of Optical Coherence Tomography (OCT) is presented on the basis of the electromagnetic theory. OCT produces high resolution images of the inner structure of biological tissues. Images are obtained by measuring the time delay and the intensity of the backscattered light from the sample considering also the coherence properties of light. The scattering problem is considered for a weakly scattering medium located far enough from the detector. The inverse problem is to reconstruct the susceptibility of the medium given the measurements for different positions of the mirror. Different approaches are addressed depending on the different assumptions made about the optical properties of the sample. This procedure is applied to a full field OCT system and an extension to standard (time and frequency domain) OCT is briefly presented.Comment: 28 pages, 5 figures, book chapte

Experimental method for measuring classical concurrence of generic beam shapes

Classical entanglement is a powerful tool which provides a neat numerical estimate for the study of classical correlations. Its experimental investigation, however, has been limited to special cases. Here, we demonstrate that the experimental quantification of the level of classical entanglement can be carried out in more general instances. Our approach enables the extension to arbitrarily shaped transverse modes and hence delivering a suitable quantification tool to describe concisely the modal structure

Urban Deformation Monitoring using Persistent Scatterer Interferometry and SAR tomography

This book focuses on remote sensing for urban deformation monitoring. In particular, it highlights how deformation monitoring in urban areas can be carried out using Persistent Scatterer Interferometry (PSI) and Synthetic Aperture Radar (SAR) Tomography (TomoSAR). Several contributions show the capabilities of Interferometric SAR (InSAR) and PSI techniques for urban deformation monitoring. Some of them show the advantages of TomoSAR in un-mixing multiple scatterers for urban mapping and monitoring. This book is dedicated to the technical and scientific community interested in urban applications. It is useful for choosing the appropriate technique and gaining an assessment of the expected performance. The book will also be useful to researchers, as it provides information on the state-of-the-art and new trends in this fiel

First Demonstration of Space-Borne Polarization Coherence Tomography for Characterizing Hyrcanian Forest Structural Diversity

Structural diversity is recognized as a complementary aspect of biological diversity and plays a fundamental role in forest management, conservation, and restoration. Hence, the assessment of structural diversity has become a major effort in the primary international processes, dealing with biodiversity and sustainable forest management. Because of prohibitive costs associated with the ground measurements of forest structure, despite their high accuracy, space-borne polarization coherence tomography (PCT) can introduce an alternative approach given its ability to provide a vertical reflectivity profile and spatiotemporal resolutions related to detecting forest structural changes. In this study, for the first time ever, the potential of space-borne PCT was evaluated in a broad-leaved Hyrcanian forest of Iran over 308 circular sample plots with an area of 0.1 ha. Two aspects of horizontal structure diversity, including standard deviation of diameter at breast height (σdbh) and the number of trees (N), were predicted as important characteristics in wood production and biomass estimation. In addition, the performance of prediction algorithms, including multiple linear regression (MLR), k-nearest neighbors (k-NN), random forest (RF), and support vector regression (SVR) were compared. We addressed the issue of temporal decorrelation in space-borne PCT utilizing the single-pass TanDEM-X interferometer. The data were acquired in standard DEM mode with single polarization of HH. Consequently, airborne laser scanning (ALS) was used to estimate initial values of height hv and ground phase φ0. The Fourier–Legendre series was used to approximate the relative reflectivity profile of each pixel. To link the relative reflectivity profile averaged within each plot with corresponding ground measurements of σdbh and N, thirteen geometrical and physical parameters were defined (P1−P13). Leave-one-out cross validation (LOOCV) showed a better performance of k-NN than the other algorithms in predicting σdbh and N. It resulted in a relative root mean square error (rRMSE) of 32.80%, mean absolute error (MAE) of 4.69 cm, and R2* of 0.25 for σdbh, whereas only 22% of the variation in N was explained using the PCT algorithm with an rRMSE of 41.56%. This study revealed promising results utilizing TanDEM-X data even though the accuracy is still limited. Hence, an entire assessment of the used framework in characterizing the reflectivity profile and the possible effect of the scale is necessary for future studies

First Demonstration of Space-Borne Polarization Coherence Tomography for Characterizing Hyrcanian Forest Structural Diversity

Structural diversity is recognized as a complementary aspect of biological diversity and plays a fundamental role in forest management, conservation, and restoration. Hence, the assessment of structural diversity has become a major effort in the primary international processes, dealing with biodiversity and sustainable forest management. Because of prohibitive costs associated with the ground measurements of forest structure, despite their high accuracy, space-borne polarization coherence tomography (PCT) can introduce an alternative approach given its ability to provide a vertical reflectivity profile and spatiotemporal resolutions related to detecting forest structural changes. In this study, for the first time ever, the potential of space-borne PCT was evaluated in a broad-leaved Hyrcanian forest of Iran over 308 circular sample plots with an area of 0.1 ha. Two aspects of horizontal structure diversity, including standard deviation of diameter at breast height (σdbh) and the number of trees (N), were predicted as important characteristics in wood production and biomass estimation. In addition, the performance of prediction algorithms, including multiple linear regression (MLR), k-nearest neighbors (k-NN), random forest (RF), and support vector regression (SVR) were compared. We addressed the issue of temporal decorrelation in space-borne PCT utilizing the single-pass TanDEM-X interferometer. The data were acquired in standard DEM mode with single polarization of HH. Consequently, airborne laser scanning (ALS) was used to estimate initial values of height hv and ground phase φ0. The Fourier–Legendre series was used to approximate the relative reflectivity profile of each pixel. To link the relative reflectivity profile averaged within each plot with corresponding ground measurements of σdbh and N, thirteen geometrical and physical parameters were defined (P1−P13). Leave-one-out cross validation (LOOCV) showed a better performance of k-NN than the other algorithms in predicting σdbh and N. It resulted in a relative root mean square error (rRMSE) of 32.80%, mean absolute error (MAE) of 4.69 cm, and R2* of 0.25 for σdbh, whereas only 22% of the variation in N was explained using the PCT algorithm with an rRMSE of 41.56%. This study revealed promising results utilizing TanDEM-X data even though the accuracy is still limited. Hence, an entire assessment of the used framework in characterizing the reflectivity profile and the possible effect of the scale is necessary for future studies

Astigmatism and Pseudoaccommodation in Pseudophakic Eyes

noAdvanced IOLs with circumferential zones of different power provide pseudoaccommodation. We investigated the potential for power variation with meridian, namely astigmatism, to provide pseudo-accommodation. With appropriate power and axis orientations, acceptable pseudo-accommodation can be achieved

Modeling of Subsurface Scattering from Ice Sheets for Pol-InSAR Applications

Remote sensing is a fundamental tool to measure the dynamics of ice sheets and provides valuable information for ice sheet projections under a changing climate. There is, however, the potential to further reduce the uncertainties in these projections by developing innovative remote sensing methods. One of these remote sensing techniques, the polarimetric synthetic aperture radar interferometry (Pol-InSAR), is known since decades to have the potential to assess the geophysical properties below the surface of ice sheets, because of the penetration of microwave signals into dry snow, firn, and ice. Despite this, only very few studies have addressed this topic and the development of robust Pol-InSAR applications is at an early stage. Two potential Pol-InSAR applications are identified as the motivation for this thesis. First, the estimation and compensation of the penetration bias in digital elevation models derived with SAR interferometry. This bias can lead to errors of several meters or even tens of meters in surface elevation measurements. Second, the estimation of geophysical properties of the subsurface of glaciers and ice sheets using Pol-InSAR techniques. There is indeed potential to derive information about melt-refreeze processes within the firn, which are related to density and affect the mass balance. Such Pol-InSAR applications can be a valuable information source with the potential for monthly ice sheet wide coverage and high spatial resolution provided by the next generation of SAR satellites. However, the required models to link the Pol-InSAR measurements to the subsurface properties are not yet established. The aim of this thesis is to improve the modeling of the vertical backscattering distribution in the subsurface of ice sheets and its effect on polarimetric interferometric SAR measurements at different frequencies. In order to achieve this, polarimetric interferometric multi-baseline SAR data at different frequencies and from two different test sites on the Greenland ice sheet are investigated. This thesis contributes with three concepts to a better understanding and to a more accurate modeling of the vertical backscattering distribution in the subsurface of ice sheets. First, the integration of scattering from distinct subsurface layers. These are formed by refrozen melt water in the upper percolation zone and cause an interesting coherence undulation pattern, which cannot be explained with previously existing models. This represents a first link between Pol-InSAR data and geophysical subsurface properties. The second step is the improved modeling of the general vertical backscattering distribution of the subsurface volume. The advantages of more flexible volume models are demonstrated, but interestingly, the simple modification of a previously existing model with a vertical shift parameter lead to the best agreement between model and data. The third contribution is the model based compensation of the penetration bias, which is experimentally validated. At the investigated test sites, it becomes evident that the model based estimates of the surface elevations are more accurate than the interferometric phase center locations, which are conventionally used to derive surface elevations of ice sheets. This thesis therefore improves the state of the art of subsurface scattering modeling for Pol-InSAR applications, demonstrates the model-based penetration bias compensation, and makes a further research step towards the retrieval of geophysical subsurface information with Pol-InSAR

The Use of Optical Coherence Tomography as a Diagnostic Tool for Dental Caries

Dental caries is one of the most common human diseases, 60-90% of school children world-wide have dental cavities. Severity can vary, from early demineralisation, which preventive measures can improve, to cavitation, leading to fillings. Different diagnostic tools are available, such as clinical examination, radiographic investigation and Enhanced Visual examination/In-ternational Caries Detection and Assessment System (ICDAS). To date, there is no universal diagnostic tool that can be used to detect carious lesions at the very early stages. Optical Coherence Tomography (OCT) is a non-invasive and ionising radiation free technique that has been used in dentistry, but not to diagnose caries. // The aim of this research was to investigate the use of OCT imaging in dentistry as a routine, and adjunct clinical diagnostic tool for dental caries, by developing standardised markers for each ICDAS score, and to compare the results with conventional clinical methods i.e. radio-graphs and ICDAS. In addition, markers in the OCT scan and scattering profile intensity plots for both sound and carious affected teeth were determined, to aid diagnosis. // All specimens were collected from patients undergoing dental treatment at Eastman Dental Hospital. Extracted human primary and permanent teeth (N>180) with varying caries severity were collected under ethical approval, after obtaining informed consent according to the inclu-sion and exclusion criteria. Photographic and radiographic images of tooth samples were taken and categorised according to the ICDAS system. Samples were then imaged using OCT (VivoSight OCT Scanner) with each lesion scanned separately (N>200). The scattering inten-sity profiles were plotted. In healthy samples, OCT B-scans showed a homogenous pattern of scattering intensity throughout enamel structure indicating healthy structure while in carious teeth, a non-homogenous scattering intensity was observed indicating changes in enamel structure. // Different scattering intensity profiles for each ICDAS score were observed, and empirical markers were developed for each score. This led to establishing scattering fingerprints for each type of ICDAS lesion. A multi-assessor’s analysis, followed by a kappa analysis, was carried to evaluate the selectivity and accuracy of the makers. The results showed moderate to substantial strength of agreement in both intra-rater and inter-rater reliability. // In conclusion, OCT has been shown to be a safe, useful, reliable and non-destructive tech-nique that can investigate the internal structure by measuring the back-scattered light from enamel and dentine. OCT provides an understanding of the lesion in terms of depth and ex-tent, therefore helping in predicting the lesion’s prognosis, which is not found in conventional methods. In addition, OCT helps to differentiate between carious and sound teeth, and addi-tionally between different ICDAS scores. The definition of specific scattering markers for each type of caries lesions will enable us to bring this technique one-step closer to the clinic