<p> An optical temperature sensor and Fourier spectrometer, working in the 1550nm telecommunications wavelength range, were fabricated in silicon-on-insulator. Both devices were based on asymmetric Mach-Zehnder Interferometer waveguide geometries. The temperature sensor underwent a two phase design. The various asymmetry factors, due to different path length differences, of the Mach-Zehnder arms resulted in different levels of temperature sensitivity, which in turn was the driving mechanism behind the Fourier spectrometer. Due to the asymmetry of the Mach-Zehnder arms, there exists an inherent optical path length difference which is further changed with temperature variation due to the thermo-optic effect. The phase I temperature sensor showed an accuracy of 1-2°C and a sensitivity of 0.5°C for ΔL of 37.23μm and 23.46μm, respectively. The phase II temperature sensor design, which allowed for self normalization, resulted in a 1°C temperature accuracy and a 0.5°C sensitivity for a ΔL of 27.85μm. Both the phase I and II temperature sensors showed repeatable and stable results for the temperature range of 20-100°C, and agreed well with the theoretical design performance. Upon analysis of the highly asymmetric Mach-Zehnder designs it was found that both the 1.05cm and 3.05cm path length differences resulted in a temperature accuracy of 0.1°C, with a 0.05°C sensitivity over a small temperature range.</p> <p> The Fourier spectrometer exhibited decent agreeability with theoretical design performance and demonstrated proof of concept. A 1.05cm path length difference was insufficient to resolve two wavelengths at 1546.12nm and 1564.68nm, which agreed with the theoretical model. However, the 3.05cm ΔL was sufficient to resolve the two wavelengths in a repeatable manner.</p> / Thesis / Master of Applied Science (MASc)

Many biological specimens are transparent and in weak intensity contrast, making it invisible using conventional bright field microscopes. Therefore, the phase-based optical microscopy techniques play important roles in the development of the modern biomedical science. Furthermore, the ability to achieve quantitative phase measurement of the tiny structures of biomedical specimens is of great importance for many biomedical applications. Thus, quantitative phase imaging becomes an important technique to measure the phase variations due to the difference of refractive index and geometric thickness of various structures and materials within the biomedical specimens. In this thesis, a spectral modulation interferometry (SMI) is developed to achieve quantitative phase imaging. In SMI, the phase and amplitude information will simultaneously be modulated onto the interference spectrum of the broadband light. Full-field phase images can be obtained by scanning along the orthogonal direction only. SMI incorporates the advantages of low coherence from broadband light source, high sensitivity from spectral domain interferometry and the high speed from the spectral modulation technique to achieve quantitative phase measurement with free of speckle, high temporal sensitivity (~0.1nm) and fast imaging rate. The principles of SMI system and programming as well as some important image processing methods will be discussed in detail. Besides, the quantitative phase measurement of the reflective object (USAF resolution target) and the transmitted biological objects (Peranema, human cheek cells) will be shown. / Master of Science

Stars with spectral type `A' (also called A-type stars or just A-stars) are bright intermediate mass stars (∼1.5-2.5 M⊙) that make up ∼1% of stars within 25 parsecs, and ∼20% of the brightest stars in the night sky (V < 3 mag). Most A-stars rotate rapidly with rotational velocities that range from ∼100 to ∼200 km/s in most cases, but can exceed 300 km/s. Such rapid rotation not only causes a star's observed properties (flux, temperature, and radius) to be inclination dependent, but also changes how the star evolves both chemically and structurally. Herein we conduct an interferometric survey of nearby A-stars using the CHARA Array. The long baselines of this optical/infrared interferometer enable us to measure the angular sizes of stars as small as ∼0.2 mas, and directly map the oblate shapes of rotationally distorted stars. This in turn allows us to more accurately determine their photospheric properties and estimate their ages and masses by comparing to evolution models that account for rotation. To facilitate this survey, we construct a census of all 232 A-stars within 50 parsecs (the 50PASS) and from that construct a sample of A-stars (the OSESNA) that lend themselves to interferometric observations with the CHARA Array (i.e., are in the northern hemisphere and have no known, bright, and nearby companions - 108 stars in total). The observations are interpreted by constructing a physical model of a rapidly rotating star from which we generate both photometric and interferometric model observations for comparison with actual observations. The stellar properties of the best fitting model are then compared to the MESA evolution models to estimate an age and a mass. To validate this physical model and the adopted MESA code, we first determine the ages of seven members of the Ursa Major moving group, which are expected to be coeval. With the exception of one star with questionable membership, these stars show a 1-σ spread in age of 56 Myr. This agreement validates our technique and provides a new estimate of the age for the group of 414 ± 23 Myr. We apply this validated technique to the directly-imaged `planet' host star κ Andromedae and determine its age to be 47+27-40 Myr. This implies the companion has a mass of 22+8-9 MJup and is thus more likely a brown dwarf than a giant planet. In total, we present new age and mass estimates for 55 nearby A-stars including six members of the Hyades open cluster, five stars with the λ Boötis chemical peculiarity, nine stars which have an infrared excess, possibly from a debris disk, and nine pulsating stars.

The Event Horizon Telescope (EHT) is a millimeter-wavelength, very-long-baseline interferometry (VLBI) experiment that is capable of observing black holes with horizon-scale resolution. Early observations have revealed variable horizon-scale emission in the Galactic Center black hole, Sagittarius. A* (Sgr A*). Comparing such observations to time-dependent general relativistic magnetohydrodynamic (GRMHD) simulations requires statistical tools that explicitly consider the variability in both the data and the models. We develop here a Bayesian method to compare time-resolved simulation images to variable VLBI data, in order to infer model parameters and perform model comparisons. We use mock EHT data based on GRMHD simulations to explore the robustness of this Bayesian method and contrast it to approaches that do not consider the effects of variability. We find that time-independent models lead to offset values of the inferred parameters with artificially reduced uncertainties. Moreover, neglecting the variability in the data and the models often leads to erroneous model selections. We finally apply our method to the early EHT data on Sgr A*.

Aims. This article describes the implementation of a focal plane based wavefront control loop on the high-contrast imaging instrument SCExAO (Subaru Coronagraphic Extreme Adaptive Optics). The sensor relies on the Fourier analysis of conventional focal-plane images acquired after an asymmetric mask is introduced in the pupil of the instrument. Methods. This absolute sensor is used here in a closed-loop to compensate for the non-common path errors that normally affects any imaging system relying on an upstream adaptive optics system. This specific implementation was used to control low-order modes corresponding to eight zernike modes (from focus to spherical). Results. This loop was successfully run on-sky at the Subaru Telescope and is used to offset the SCExAO deformable mirror shape used as a zero-point by the high-order wavefront sensor. The paper details the range of errors this wavefront-sensing approach can operate within and explores the impact of saturation of the data and how it can be bypassed, at a cost in performance. Conclusions. Beyond this application, because of its low hardware impact, the asymmetric pupil Fourier wavefront sensor (APF-WFS) can easily be ported in a wide variety of wavefront sensing contexts, for ground-as well space-borne telescopes, and for telescope pupils that can be continuous, segmented or even sparse. The technique is powerful because it measures the wavefront where it really matters, at the level of the science detector.

Label free detection of biologically relevant binding pairs has provided critical insight into the characterization of reagents used in both therapeutic and diagnostic applications. The Interferometric Reflectance Imaging Sensor (IRIS) platform has been developed for the multiplexed, real-time detection of such binding interactions. Improvements to experimental methodology and analysis applied to the latest iteration of the IRIS provided heretofore unseen binding characterizations with this multiplexed platform. Here, we extend and demonstrate the utility of the IRIS system to (1) evaluate and compare kinetic parameters to those obtained with more traditional label free methods (2) characterize multiple, disease relevant antibodies in multiple disease systems (anthrax, Zika, dengue and plague) (3) determine appropriate binding pairs in multiplexed label free formats and (4) obtain 10-fold improvements to the limits of detection for analyte in solution over previous IRIS iterations. Applications to immunoassay development are discussed throughout with exemplary datasets provided. Observations regarding additional IRIS utilities are also discussed, including qualifications of genetically engineered ligands, evaluating subcloned antibodies and screening unpurified antibody supernatants.

<div>The Sentinel-1 (S1) mission is a part of the European Space Agency (ESA) Copernicus program. In 2014 and 2016, the mission launched the twin Synthetic Aperture Radar (SAR) satellites, Sentinel-1A (S1A) and Sentinel-1B (S1B). The S1 mission has started a new era for earth observations missions with its higher spatial resolution, shorter revisit days, more precise control of satellites orbits and the unprecedented free-to-public distribution policy. More importantly, S1 adopts a new wide swath mode, the TOPS mode as it default acquisition mode. The TOPS mode scans several different subswaths for gaining a larger coverage. Because the S1 mission is aimed at earth observation missions, for example, earthquakes, oods, ice sheets flow, etc., thus it is desired to have large monitoring areas. Although TOPS is still a relatively new idea, the high quality data and wide application scopes from S1 has earned tremendous attention in the SAR community.</div><div><br></div><div><div>The signal properties of wide swath mode such as TOPS are different from the more conventional stripmap mode, and it requires special techniques for successfully processing such data in the sense of interferometry. For the purpose of doing Interferometric SAR (InSAR), the coregistration step is of most critical because it requires a 1/1000 accuracy. In addition, processing wide swath mode requires special steps such as bursts stitching, deramping and reramping, and so on. Compared with stripmap, the processing techniques of wide swath mode are less developed. Much exploitations are still needed for how to design a generic and robust wide swath interferometric</div><div>processing chain.</div></div><div><br></div><div><div>Driven by the application needs of S1 wide swath interferometric processing, this research studies the key methodologies, explores and implements new processing chain, designs a generic wide swath processing </div><div>flow that would utilize the existing stripmap processing platform, as well as carries out preliminary applications. For studying key methods, this study carries out a quantitative analysis between two different coregistration methods, namely the cross-correlation approach and the geometrical</div><div>approach. The advantages and disadvantages for each method are given by the author, and it is proposed to choose the suitable method based on one's study area. For the implementation of the new processing chain, the author proposes a user-friendly stripmap-like processing </div><div>ow with all the wide swath related process done behind the scene. This approach allows people with basic knowledge in InSAR and very few knowledge in wide swath mode to be able to process and get interferometric products. For designing the generic process flow, the author applied TOPS's work flow to the other wide swath mode, ScanSAR mode and demonstrated the feasibility of processing two different wide swath mode with the same processing chain.</div><div>For preliminary applications, the author shows a large number of interferometric data throughout the research and presents a case study with multi temporal time series analysis using a stack of S1 dataset.</div></div><div><br></div><div><div>This research is application oriented, which means the study serves for real-world applications. Up to now, the processing chain and methodologies implemented in this</div><div>research has been shared by many research groups around the world and has seen a number of promising outcomes. The recognition from others is also an affrmation to the value of this research.</div></div>

The Soil Moisture and Ocean Salinity (SMOS) mission is an Earth Explorer Opportunity mission from the European Space Agency (ESA). It was a direct response to the global observations of soil moisture and ocean salinity. Its goal is to produce global of these parameters using a dual-polarization L-band interferometric radiometer the Microwave Imaging Radiometer by Aperture Synthesis (MIRAS). This instrument is a new polarimetric two-dimensional (2-D) Y-shaped synthetic aperture interferometric radiometer based on the techniques used in radio-astronomy to obtain high resolution avoiding large antenna structures. MIRAS measures remotely the brightness temperature (TB) emitted by the Earth's surface, which is not isotropic, since it depends on the incidence angle and polarization, the Soil Moisture (SM) or the Sea Surface (SSS), the surface roughness etc. among others. The scope of this doctoral thesis is the study of some potential improvements could eventually be implemented in future interferometric radiometers. To validate improvements a ground-based instrument concept demonstrator the Passive Advanced Unit Synthetic Aperture or (PAU-SA) has being designed and implemented. Both MIRAS and PAU-SA are Y-shaped array, but the receiver topology and the processing unit are different. This Ph.D. thesis has been developed in the frame of The European Investigator Awards (EURYI) 2004 project entitled "Passive Advanced Unit (PAU): Hybrid L-band Radiometer, GNSS Refectometer and IR-Radiometer for Passive Sensing of the Ocean", and supported by the European Science Foundation (ESF).

The Ground-Based Synthetic Aperture Radar (GB-SAR) is a relatively new technique, which in the last ten years has gained interest as deformation measurement and monitoring tool. The GB-SAR technique is based on an imaging radar-based sensor, which o ers high sensitivity to small displacements, in the region of sub-millimetres to millimetres, long-range measurements, which can work up to some kilometres, and massive deformation measurement capability. These features confer to the GB-SAR technique interesting advantages with respect to other point-wise deformation measurement techniques. The process of estimating deformation from the GB-SAR data is not straightforward: it requires complex data processing and analysis tools. This dissertation is focused on these tools, covering the whole deformation estimation process. This thesis collects the main research results achieved on this topic during my work at the Active Remote Sensing Unit of the Institute of Geomatics. Two di erent approaches for measuring deformation with GB-SAR data are described and discussed. The irst one is the interferometric approach, based on the exploitation of the phase component of the GB-SAR data, which is the commonly used GB-SAR method. The second one is a non-interferometric approach, which exploits the amplitude component of the GB-SAR data, o ering an interesting alternative way to exploit the GB-SAR data. This dissertation has two main objectives. The first one is presenting, step by step, a complete interferometric GB-SAR procedure for deformation measuring and monitoring. The second one is presenting two new algorithms, which represent the most innovative part of this thesis. The first algorithm faces the phase unwrapping problem, providing an automatic solution for detecting and correcting unwrapping errors, which is called 2+1D phase unwrapping. The second algorithm is the base of the above mentioned non- interferometric approach, which overcomes some of the most critical limitation of GB-SAR interferometry, at the expense of getting less precise deformation estimates. The dissertation is divided in 6 chapters. The first one is the introduction, while the second one provides an overview of GB-SAR interferometry, introducing the main aspects that are the basics of the subsequent chapters. Chapter 3 describes a complete GB-SAR processing chain. Chapters 4 and 5 contain the most original part of the dissertation, i.e. the 2D+1 phase unwrapping algorithm, and the non-interferometric approach. Finally, in Chapter 6 the conclusions are discussed and further research is proposed. / El radar terrestre d’obertura sintètica (GB-SAR) és una tècnica relativament nova que, en els últims deu anys, ha guanyat interès com a eina per a mesurar i monitorar deformacions. La tècnica GB-SAR es basa en un sistema radar amb capacitat per proporcionar imatges, que ofereix una alta sensibilitat a petits desplaçaments, d’ordre mil·limètric o submil·limètric, que és capaç de mesurar a llargues distàncies (alguns km) i que té una alta capacitat per fer mesures massives. Aquestes característiques donen a la tècnica interessants avantatges respecte a altres tècniques clàssiques de mesura de deformacions, típicament basades en mesures puntuals. Derivar mesures de deformació a partir de dades GB-SAR no és un procés senzill, ja que requereix uns procediments complexos de processat i anàlisi de dades. Aquesta tesi es centra en aquests processos. Aquesta tesi recull alguns dels resultats més destacats de la investigació que he desenvolupat sobre aquest tema a la unitat de Teledetecció Activa de l'Institut de Geomàtica. Al llarg del document es descriuen dues aproximacions diferents per mesurar deformacions amb GB-SAR. Una es basa en la explotació de la tècnica de la interferometria, és a dir explotant la component de la fase de les imatges GB-SAR: és la tècnica GB-SAR usada habitualment. La segona, anomenada tècnica no-interferomètrica, es basa en la component de l’amplitud de les dades GB-SAR i ofereix una interessant alternativa a la primera. La tesi acompleix dos objectius principals. En primer lloc presenta un procediment complet per la mesura i monitoratge de deformacions mitjançant interferometria GB-SAR. En segon lloc, descriu dos nous algorismes que resolen problemes específics de la interferometria clàssica aplicada al GB-SAR i que representen la part més innovadora d’aquesta tesi. El primer algorisme aborda un dels problemes oberts de la interferometria, el phase unwrapping, proposant un mètode automàtic per detectar-ne i corregir-ne els errors. El segon algorisme proposa un nou mètode per a l'explotació de les dades GB-SAR per mesurar deformacions sense utilitzar la interferometria. La estructura de la tesi consisteix en sis capítols. Després de la introducció, el Capítol 2 proporciona una visió general de la interferometria GB-SAR, introduint els conceptes principals utilitzats en la tesi. En el tercer capítol es descriu una cadena de processament basada en GB-SAR interferomètric. Els capítols quart i cinquè contenen la part més original de la tesi: l'algorisme de phase unwrapping i el mètode no-interferomètric per la mesura de deformacions. Finalment, es discuteixen les conclusions principals i es proposen futures línies d’investigació.

A fully integrated optical chem/bio sensor complete with integrated source, chemically sensitive waveguide, detector arrays, and associated signal processing electronics on a Si-CMOS chip is a challenging, but highly desirable goal. An evanescent-wave multimode interferometric sensing element is a sensitive method for sensing, which is easily integrated on Si-CMOS. This work is concerned with the design, analysis, and demonstration of a planar multimode interferometric chem/bio sensor that is compatible with the fabrication constraints of Si-CMOS. A 4000-micron-long interferometric that can be adapted for different agents by a particular sensing layer has been fabricated on silicon using silicon dioxide and silicon oxynitride. Hexaflouro-isopropanol substituted polynorbornene is the sensing layer. This sensor has also been fabricated on a Si-CMOS circuit with embedded photodetectors. A sensor on silicon was demonstrated with a minimum detectable index change of 2.0x10-6 using an accurate gas delivery system and a custom hermetic waveguide test chamber. A modal pattern analysis strategy has also been developed to extract the optimal SNR from the measured modal patterns. An understanding of the noise processes and spatial bandwidth effects has enabled an experimentally-based prediction of the index sensitivity of a fully integrated multimode chem/bio sensor on Si-CMOS at 9.2 x10-7. Theoretically, the sensitivity enhancement of high over low index sensing layers and transverse-magnetic over transverse electric modes is described. Also, the sensitivity enhancement of higher-order-transverse modes has been quantified. The wide-angle beam propagation method has been used to simulate the sensor. This simulation showed the relation between the modal pattern repetition period and sensor sensitivity. Further, the modal coupling properties of the multimode y-junction have been described. A second multimode y-junction has been designed to change the modal excitation under the SL, and thus the sensitivity. The chemo-optic response of the `substituted polynorbornene' polymer., hexaflouro-isopropanol substituted polynorbornene to methanol, water, iso-propanol, and benzene has been measured. Also, its thermo-optic response has been measured. Athermal interferometric chem/bio sensors have then been suggested.