Imaging Polarimetry with Polarization-Sensitive Focal Plane Arrays

Polarization is an intrinsic property of light, like frequency or coherence. Humans have long benefited from our ability to distinguish light of different frequency based on its color. However, our eyes are not sensitive to the polarization of light. Devices to measure polarization are relatively rare and expertise in polarimetry even more so. Polarization sensors based on micropolarizer arrays appear to be the first devices capable of bringing polarimetric capability to a wide range of applications. Whereas previous polarimeters were built to perform very specific measurements, the same micropolarizer-based camera can be used on a telescope, a microscope, or with a conventional camera lens. In this work, I investigate the operating principles of micropolarizer arrays using high resolution 3D simulations and describe several strategies to fabricate and characterize micropolarizer-based imaging polarimeters. Furthermore, I show how to incorporate the device characterization into a calibrated demodulation procedure to extract polarimetric quantities from the raw pixel intensities. As part of this effort, I show how the measured sensor properties, like pixel throughput and contrast ratio, can be used to construct a software model to produce synthetic observations of various scenes. These synthetic data are a powerful tool to study the many effects which can give rise to systematic and/or random errors during the data analysis process. Finally, I present the polarimetry performed on several astronomical sources using the RIT Polarization Imaging Camera and compare my results to previous measurements made with conventional polarimeters. Using the current calibration of the RIT Polarization Imaging Camera, I was able to achieve a polarimetric accuracy of ~0.3% in images of extended objects and unresolved sources

Automated Computational Techniques for High-throughput Image Analysis of Skin Structure

Biological image processing and analysis are concerned with enhancing and quantifying features that reflect different pathological states, based on the use of combinations of image processing algorithms. The integration of image processing and analysis techniques to evaluate and assess skin integrity in both human and mouse models is a major theme in this thesis. More specifically, this thesis describes computational systems for high-throughput analysis of skin tissue section images and non-invasive imaging techniques. As the skin is a largest organ in the mammalian body, and is complex in structure, manual quantification and analysis a hard task for the observer to determine an objective result, and furthermore, the analysis is complex in terms of accuracy and time taken. To look at the gross morphology of the skin, I developed high throughput analysis based on an adaptive active contour model to isolate the skin layers and provide quantification methods. This was utilised in a study to evaluate cutaneous morphology in 475 knockout mouse lines provided by the Mouse Genetics Project (MGP) pipeline, that was generated by the Wellcome Trust Sanger Institute (WTSI). This is a major international initiative to provide both functional annotation of the mammalian genome and insight into the genetic basis of disease. I found 53 interesting adipocyte phenotypes, 18 interesting dermal phenotypes and 3 interesting epidermal phenotypes. I also focussed on the analysis of collagen in the dermis of skin images in several ways. For collagen structure analysis, I developed a combined system of Gabor filtering and Fast Fourier Transform FFT. This analysis allowed the detection of subtle changes in collagen organisation. Using similar images, I also measured collagen bundle thickness by computing the maximum frequency of the FFT power spectrum. To assess collagen dynamics, I developed k-means clustering for segmentation based on colour distribution. The use of this approach allowed the measurement of dermal degradation with age and disease, which was not possible by existing means. Obtaining human skin material to facilitate the drug discovery and development process is not an easy task. The manipulation, monitoring and cost of human subjects makes the use of mouse models more suitable for high-throughput screening. Therefore, I have evaluated skin integrity from mouse tissue rather than human skin, however, mouse skin is thinner than human skin and many morphological features are easier to visualise in human skin, which has implications for analysis. Skin moulds can be used to create an impression of the skin surface. Changes in texture of skin can reflect skin conditions. I developed a skin surface structure analysis system to measure the degree of change in texture of the human skin surface. The alterations detected in texture parameters in skin mould impressions reflected changes caused by sun exposure, ageing and many other clinical parameters. I compared my analysis with the existing Beagley-Gibson scoring system to find correlations between automated and manual analysis to inform a decision on the use of optimal methods. By removing subjectivity of manual methods, I was able to develop a robust system to evaluate, for example, damage resulting from UV exposure. My experimental analysis indicated that techniques developed in this thesis were able to analyse both histological samples and skin surface images in high-throughput experiments. They could, therefore, make a contribution to biological image analysis by providing accurate results to help clinical decision making, and facilitate biological laboratory experiments to improve the quality of research in this field, and save time. Overall, my thesis demonstrated that accurate analysis of the skin to gain meaningful biological information requires an automated system that can achieve feature extraction, quantification, analysis and decision making to find interesting phenotypes and abnormalities. This will help the evaluation of the effects of a specific treatment, and answer many biological questions in fields of cosmetic dermatology and drug discovery, and improve our understanding of the genetic basis of disease

Diffusion Tensor Imaging in Pediatric Brain Tumor Patients

In this dissertation, we outline our efforts to introduce an advanced MRI imaging technique called Diffusion Tensor Imaging (DTI) to the pediatric brain tumor population. We discuss the theory and application of DTI as it was performed in a series of translational investigations at St. Jude Children’s Research Hospital. We present evidence of how the introduction of this technique impacted diagnosis, and treatment. And finally, we demonstrate how DTI was used to investigate cognitive morbidities associated with cancer treatment and how this research provided insight into the underlying pathophysiology involved in the development of these treatment sequela. This research has generated important insights into the fundamental causes of neuroanatomical and cognitive deficits associated with cancer and cancer therapy. The use of DTI has permitted us to identify potential targets for improved radiological and surgical techniques as well as targets for pharmacological and behavioral interventions that might improve cognitive function in cancer survivors. The discoveries here afford us an opportunity to reduce the negative effects of cancer therapy on patients treated in the future while maintaining successful survival rates

Development and Testing of an Implantable Perfusion and Oxygenation Sensor for Liver Transplant Monitoring

Since the first successful liver transplant in 1968 the surgery has become very common and 6,291 patients received liver transplants in 2010 in the United States. However, the monitoring methods used post-surgery, in the recovery phase, are still very basic and rely mainly on blood tests and looking for unusual symptoms. Complications are usually detected after the organ is substantially damaged which poses a risk to the patients’ life. This dissertation presents the development and testing of an implantable sensor that can potentially be used to monitor the transplant continuously and transmit the information wirelessly to the medical staff for timely intervention. Such a sensor could have a great effect on survival and reduction of retransplantation rates. The presented sensor employs near infrared spectroscopy to measure perfusion changes, arterial oxygenation and venous oxygenation in the parenchyma of the liver tissue and the supplying vessels. Light at three different wavelengths (735-, 805- and 940-nm) is shined on the tissue and the diffuse reflectance is collected via a photodetector. The collected signals can be transmitted wirelessly to an external unit for processing and display. In this dissertation, different perfusion and oxygenation monitoring techniques are reviewed and the instrumentation of an NIRS based wireless sensor is introduced. A phantom that mimics the anatomy of the liver and its optical and mechanical properties is presented. The processing methods to extract the information of interest from the diffuse reflectance are described in details. Finally, results from in vitro phantom experiments, ex vivo perfused livers and in vivo porcine studies are presented. The first in vivo wireless monitoring of hepatic perfusion and oxygenation levels is reported. The studies show that the sensor can track perfusion changes with a resolution of 0.1 mL/min/g of tissue. The possibility of tracking oxygen saturation changes is also shown as well as the ability to separate them from perfusion changes. Combining results from the pulsatile wave and DC levels, venous and arterial oxygen saturation changes were tracked with a resolution of 1.39% and 2.19% respectively. In conclusion, optical spectroscopy is shown to track perfusion, and arterial and venous oxygenation in tissue. In particular, the method was tested on hepatic and intestinal tissue

Spintronic Operations Driven by Terahertz Electromagnetic Pulses

Spintronic devices, supplementing and surpassing charge-based electronics by including the electron spin, have recently begun to reach the market. Information carriers such as electrons (in field-effect transistors) and photons (in optical fibers) have already reached the terahertz range (THz, 10^12 Hz). To make the electron spin compatible and competitive, spintronic operations need to be pushed to THz frequencies. So far, is is unclear whether fundamental spintronic effects such as spin accumulation or spin-orbit torque can be transferred to THz frequencies. In this respect, it is also important to note that the THz range coincides with many fundamental excitations, for instance phonons, magnons, and the relaxation of electronic currents. Strong THz electromagnetic pulses can be used to study such fundamental excitations, making use of both the electric and magnetic fields of the electromagnetic pulse. In this thesis, strong THz electromagnetic pulses are applied to spintronic thinfilm stacks to drive charge and spin currents, apply torque and manipulate magnetic order. A short optical probe pulse or a resistance probe interrogate the transient magnetic response. First, a measurement strategy is developed to simultaneously detect all components of the vector magnetization of thin film magnets in optical transmission probe experiments at normal incidence, requiring only a variation in the initial probe polarization. To this end, the magnetic circular and linear birefringence (MCB, MLB) effects are measured simultaneously and a calibration strategy for the often neglected MLB effect is presented. Second, using this detection scheme, we study the THz frequency operation of spintronic effects in ferromagnetic(FM)/non-magnetic (NM) heavy metal stacks. We find signatures of THz spin accumulation at the FM/NM interface. The spins injected into a ferromagnet relax within ∼ 100 fs, in line with electron-spin equilibration times measured by ultrafast optically induced demagnetization. Indications of the field-like spin-orbit torque (FL-SOT) are found. Third, an effective method to modulate the relative THz electric and magnetic field amplitudes in thin film samples is presented, enabling one to disentangle effects driven by the electric or the magnetic component of the THz electromagnetic pulse. A nearperfect conductor (THz mirror) quenches the THz electric field in a region close to the mirror, while doubling the THz magnetic field. Measurements with a ferromagnetic thin film confirmed a THz magnetic field increase of 1.97 ± 0.06 and a suppression of the THz electric field in the sample. Finally, we utilize the electric-field suppression effect close to metals to optically gate the THz electric field driven resistance modulation of an antiferromagnet (AFM) grown on a semiconducting substrate. An optically induced transient substrate conductance depletes the THz electric field in the AFM layer, while not perturbing the AFM magnetic order directly. A simple model of parallel conductances is presented, confirming the experimental observations. In conclusion, this thesis is an important contribution to push fundamental spintronic effects such as spin accumulation and spin-orbit torque to the THz range. The developed methodologies are helpful to advance nonlinear THz spectroscopy of magnetic materials.Da die ersten auf spintronischen Prinzipien erbauten Speicher den Markt erreichen und gleichzeitig Informationsträger wie Elektronen (in Feldeffekttransistoren) und Photonen (in Glasfaserkabeln) in den Terahertz-Frequenzbereich (THz, 10^12 Hz) vordringen, stellt sich die Frage, ob die Spintronik, welche die Elektronik um den Elektronenspin erweitert, mit solch hohen Frequenzen kompatibel ist. Gleichzeitig ist der THz-Frequenzbereich, welcher elementare Anregungen wie Phononen und Magnonen enthält, auch fur die Grundlagenforschung interessant. Um diese Anregungen zu untersuchen bieten sich elektromagnetische THz-Pulse mit hohen Feldstärken an, denn sie können direkt an elektrische und magnetische Resonanzen koppeln. Diese Arbeit untersucht mit THz-Lichtpulsen, die in spintronischen Dünnfilmproben Spin- und Ladungsströme induzieren, ob elementare spintronische Effekte, wie die Spin-Akkumulation oder das Spin-Bahn-Drehmoment, auch bei THz-Frequenzen aktiv sind. Die magnetische Antwort wird mit kurzen optischen Pulsen oder mittels elektrischer Messungen zeitaufgelöst abgefragt. Die spintronischen Effekte werden in ferromagnetischen (FM)/nichtmagnetischen (NM) Dunnfilm-Metallmultilagen untersucht, wobei zuerst eine Messmethode erarbeitet ¨ wird, um alle räumlichen Anteile der Probenmagnetisierung gleichzeitig zu bestimmen. Hierzu werden die magnetische zirkuläre Doppelbrechung (MCB) und die, oft vernachlässigte, magnetische lineare Doppelbrechung (MLB), welche der Abfragepuls beim Durchdringen der Probe entlang der Probennormale erfährt, gleichzeitig bestimmt. Ein besonderes Augenmerk liegt auf der Normierung des MLB-Signals. Mithilfe dieser neuartigen Messmethode werden Indizien fur eine THz Spin-Akkumulation und das feldartige Spin- ¨ Bahn-Drehmoment (FL-SOT) an der FM/NM Grenzfläche gefunden, welche auf einen Spinaustausch zwischen dem nichtmagnetischen Schwermetall und dem FM zuruckgeführt ¨ werden. Die in den FM eindringenden Spins relaxieren auf einer Zeitskala von ∼ 100 fs, was mit Ergebnissen aus ultraschnellen optischen Demagnetisierungsstudien ubereinstimmt. ¨ Zusätzlich wird die nichtlineare THz-Spektroskopie dahingehend erweitert, vom elektrischen oder magnetischen THz-Feld getriebene Signale unterscheiden zu können, indem die relativen Stärken der elektromagnetischen Felder im Inneren einer Dunnfilmprobe beeinflusst werden. Hierbei unterdruckt ein elektrisch leitender THz Spiegel das THz elektrische Feld in der Probe, während das THz magnetische Feld um einen Faktor 1.97±0.06 verstärkt wird. Diese Unterdruckung des THz elektrischen Feldes in der Nähe eines Leiters wird genutzt, um die vom THz elektrischen Feld getriebene Widerstandsmodulation in einem, auf einem (optisch angeregten) halbleitenden Substrat gewachsenen, Antiferromagneten (AFM) zu steuern. Dabei wird die Wirkung des THz elektrischen Feldes im AFM unterdruckt ohne den magnetischen Zustand des AFM zu stören. Ein einfaches Modell stutzt die Interpretation der Beobachtungen. Zusammenfassend leistet diese Arbeit einen wichtigen Beitrag, um spintronische Effekte wie die Spin-Akkumulation und das Spin-Bahn-Drehmoment im THz-Frequenzbereich zu etablieren und erweitert zusätzlich die Möglichkeiten der nichtlinearen THz-Spektroskopie an Magneten

Interrogating nonadiabatic molecular dynamics using ultrafast nonlinear optics

The field of femtochemistry seeks to comprehend the fundamental underlying mechanisms of the interaction between light and molecules and to study the ultrafast timescales on which these processes occur. In particular, the photoresistance of biologically relevant molecules to potential damage caused by absorption of ultraviolet radiation is of great interest. The so called “building blocks” of life use ultrafast non-radiative relaxation pathways for the dissipation of the high excess UV energy as vibrational energy into the surroundings, which is the key of their photoprotective function. The use of a “bottom-up” methodology for such investigations is applied to understand basic model UV chromophores, which are molecular sub-units of various bio-molecules such as, for example, the DNA bases and the melanin pigmentation system. The photophysics of the basic model chromophores, indole and the aniline derivatives N,N-dimethylaniline and 3,5-dimethylaniline, were investigated in the gas phase to understand the link between their molecular structure, the ultrafast non-adiabatic dynamics and thus their potential photoprotection function. This study was done with the powerful time-resolved photoelectron imaging (TRPEI) technique, which provides temporal, energy- and angle-resolved information related to the non-adiabatic relaxation dynamics operating within each molecular system. TRPEI is a highly differential pump-probe spectroscopic technique providing a detailed picture of the underlying processes, since it is sensitive to both electronic and nuclear motion within the molecule. The observation of the complete dynamical process using the TRPEI method is however restricted by the energy of the utilised probe pulse. For this reason the spectroscopic technique was improved with the integration of a newly built femtosecond vacuum ultraviolet (VUV) light source. The VUV laser pulses are generated in a four wave frequency mixing process in third order nonlinear media, such as noble gases. First results from this instrument are presented for the butadiene molecule. The combination of the new VUV laser light and the already powerful spectroscopic technique enables, in principle, the detection of the complete non-radiative relaxation process of a large variety of molecular systems