Browsing by Subject "Optics"
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Item Open Access A Compact Cryogenic Package Approach to Ion Trap Quantum Computing(2022) Spivey, Robert FultonIon traps are a leading candidate for scaling quantum computers. The component technologies can be difficult to integrate and manufacture. Experimental systems are also subject to mechanical drift creating a large maintenance overhead. A full system redesign with stability and scalability in mind is presented. The center of our approach is a compact cryogenic ion trap package (trap cryopackage). A surface trap is mounted to a modified ceramic pin grid array (CPGA) this is enclosed using a copper lid. The differentially pumped trap cryopackage has all necessary optical feedthroughs and an ion source (ablation target). The lid pressure is held at ultra-high vacuum (UHV) by cryogenic sorption pumping using carbon getter. We install this cryopackage into a commercial low-vibration closed-cycle cryostat which sits inside a custom monolithic enclosure. The system is tested and trapped ions are found to have common mode heating rate on the order of 10 quanta/s. The modular optical setup provides for a couterpropagating single qubit coherence time of 527 ms. We survey a population of FM two-qubit gates (gate times 120 μs - 450 μs) and find an average gate fidelity of 98\%. We study the gate survey with quantum Monte Carlo simulation and find that our two-qubit gate fidelity is limited by low frequency (30 Hz - 3 kHz) coherent electrical noise on our motional modes.
Item Embargo A Multiplexed, Multi-scale Optical Imaging Platform to Quantify Tumor Metabolic Heterogeneity(2023) Deutsch, Riley JosephThe American Cancer Society reported an estimated 300,000 new cases of breast cancer and 44,000 new breast-cancer related deaths in 2022 in the United States alone. With each new successfully treated primary tumor, there is a subsequent risk of disease recurrence. Recurrence poses a risk to 10% of patients within the first 5 years post treatment and a lifetime risk of 30% across all patients. While new tools are being developed to better understand and mitigate the risk of recurrence, triple negative breast cancers, which exhibit no targetable surface markers, offer little in the way of recurrence prediction or treatment. It is understood that tumor heterogeneity is a driving force in tumor recurrence. Temporal heterogeneity is associated with therapeutic treatment, where the administration either selects for resistance subpopulations of tumor cells that are able to recur or a de novo resistant phenotype arises that leads to recurrence. Additionally, it has been well documented that tumors vary spatially across a primary tumor. This heterogeneity takes the form of genetic, epigenetic, and phenotypic heterogeneity. One such phenotype of interest is metabolic heterogeneity. Metabolism is classified as a ‘Hallmark of Cancer’ and has been studied as a driver of tumor progression for almost a century since Otto Warburg first described the phenomenon of tumors exhibiting high rates of aerobic glycolysis. Optical imaging is well poised to study metabolic heterogeneity due to its ability to image cellular level features, to multiplex multiple endpoints, and the ability to image longitudinally. Endogenous fluorescence contrast of coenzymes NADH and FAD have been used to report on the redox state of in vivo tissue and distinguish cancerous from benign lesions. The Center for Global Women’s Health Technologies (GWHT) has employed the use of exogenous fluorescent contrast agents to provide substrate-specific metabolic information. Three fluorescent agents have been validated including: 2-[N-(7-nitrobenz-2-oxa-1, 3-diazol-4-yl) amino]-2-deoxy-D-glucose (2-NBDG), a glucose derivative that is able to report on glycolysis; Tetramethylrhodamine ethyl ester (TMRE), a cation that is selectively attracted to the charge gradient generated by the mitochondria during ATP synthesis, making it a reporter of OXPHOS; and Difluoro-5,7-Dimethyl-4-Bora-3a,4a-Diaza-s-Indacene-3-Hexadecanoic Acid (Bodipy FL C16), a long chain saturated fatty acid is taken up by the cell and undergoes beta oxidation similar to native fatty acids. More recently, GWHT has begun combing these fluorescence agents for in vivo use to provide a wholistic understanding of cancer metabolism. The work here sets out to develop a novel optical imaging platform that is capable of imaging multiplexed metabolic endpoints, for quantitative intra-image analysis of metabolic gradients. This technology is built on the use of exogenous fluorescence contrast agents to report on substrate or pathway specific axes of metabolism. By simultaneously introducing multiple contrast agents, it is possible to capture a more wholistic snapshot of tissue metabolism. To encourage the adoption of this technology, a novel low-cost instrument will also be developed. Leveraging a consumer grade CMOS camera and variable focus lens, it is possible to image over multiple length scales, capturing both bulk tumor features and also single cell features. The flexibility offered by this simple innovation will allow for metabolic imaging to be applied over a variety sample type. Three specific aims were proposed to realize this goal by developing methods of multi-parametric exogenous contrast and low-cost instrumentation for multi-scale imaging of tumor metabolic heterogeneity in preclinical models. Aim 1 validated and demonstrated a method for the simultaneous injection and measurement of Bodipy FL C16 and TMRE to report on lipid uptake and mitochondrial activity, two potentially interrelated axes of metabolism. To validate this method, three sets of experiments were performed to establish that the two probes do not exhibit chemical, optical, or biological crosstalk. Chemical compatibility was established using liquid chromatography. Briefly, high molar concentration solutions of each individual probe (Bodipy FL C16, TMRE, and 2-NBDG) were created alongside a solution of all three probes at the same concentration. Chromatograms were collected immediately upon mixing, after 1 hour and after 24 hours. The area under the curve for each probe at each time point displayed an area under the curve (AUC) within 2% of the AUC of the single probe solutions, suggesting no chemical reactions. Optical crosstalk was assessed using optical spectroscopy and tissue mimicking phantoms. Optical phantoms were created with tissue mimicking optical properties and various concentration of Bodipy FL C16, TMRE, polystyrene microspheres (tissue scattering mimic), and hemoglobin (tissue absorption mimic). Leveraging an inverse Monte Carlo algorithm, we demonstrated that accurate values for each fluorescent probe could be measured regardless of the concentration of the other optical probe or level of optical scattering or absorption, indicating optical compatibility. To address biological crosstalk, two sets of 4T1 tumor bearing mice were subject to optical spectroscopy with either 1) Bodipy FL C16 alone, 2) TMRE alone, 3) a dual injection of Bodipy FL C16 and TMRE. Fluorescence spectra were measured 2-, 4-, 6-, 8-, 10-, 20-, 30-, 40-, 50-, and 60-minutes post-injection to establish uptake kinetics. It was found that the uptake kinetics of the dual probe group were not statistically different from the single probe group, indicating biological compatibility. With no observable crosstalk between Bodipy FL C16 and TMRE, the two probes method was applied to characterize murine mammary gland and two tumor of differing metastatic potential (4T1 and 67NR). In addition, to Bodipy FL C16 and TMRE, oxygen saturation and total hemoglobin were extracted from estimates of optical absorption, and these 4 endpoints were used to attempt to cluster groups of tumor and normal tissue. Difficulty clustering tumor groups of varying metastatic potential suggest a need for imaging technology. In Aim 2 a low-cost fluorescence microscope was developed capable of performing quantitative fluorescence imaging over a variety of samples. The goal of this work was to design a system that could be adapted to image a number of different sample types include core-needle tissue biopsies, preclinical window chambers, and in vitro organoids. To accomplish this a low-cost CMOS detector was used with a variable magnification lens allowing for imaging at multiple length scales. Uniform illumination was a necessary criterion for quantitative imaging. To generate uniform illumination that could be scaled across multiple length scales, an LED coupled 1:4 fanout optical fiber was employed alongside a computational model to determine the positioning of each fiber. To automate the design of illumination, a computational model was employed where each optical fiber was modeled as a Lambertian emitter in a spherical coordinate system. To determine the ideal placement of each fiber such that the individual illumination contributions of all fibers summed to a uniform distribution, a global optimizer was employed. A genetic pattern search allowed for the selection of coordinates to produce uniform illumination that could be feasibly employed at the benchtop. This integrated system is referred to as the CapCell microscope. Using this computational approach, two uniform illumination profiles were designed, one with a high aspect ratio (length ≫ width) and one with a low aspect ratio (length = width). To demonstrate the utility of optimized illumination, core needle biopsies from 4T1 tumors were stained with a tumor-specific fluorescent contrast agent, HS-27 and imaged with either optimized or unoptimized gaussian illumination. The repeatability of intra-image features was compared for the two illumination scenarios, and it was found that uniform illumination repeatedly revealed the same fluorescent features across the sample. These features were further confirmed with standard histology. Window chamber imaging demonstrated the importance of designing application specific illumination. 4T1 mammary tumors were grown orthotopically before a window chamber was surgically implanted. Animals were injected with either Bodipy FL C16, 2-NBDG, or HS-27 and imaged with both the high AR and low AR illumination platforms. As expected, the low AR, designed for window chambers, had a higher power density at the sample site and thus increased contrast compared to the low AR images. With a method and a system in place, the goal of Aim 3 was to apply the optical imaging platform to observe spatiotemporal metabolic heterogeneity. To achieve this, the CapCell microscope was upgraded to enhance contrast and improve resolution for the visualization of capillaries and single cells. This was demonstrated using 4T1 window chamber models stained with acridine orange, a nucleus specific stain, and green light reflectance to highlight hemoglobin absorption in microvessels. Given the interplay between metabolism and vasculature it was desirable to employ a vessel segmentation approach to describe vascular features within an image. A Gabor filter and Djikstra segmentation approach was employed on metabolic images to enable metabolic and vascular comparisons across an image field of view. To test the improved CapCell system, 4T1 tumors were treated with combretastatin A-1, a vascular disrupting agent. Across the course of treatment, the CapCell was able to observe bulk changes in metabolism and vascular density. Additionally, by employing high resolution imaging, it was possible to observe relationships between each metabolic probe and vessel tortuosity. This analysis allowed for the identification of metabolically unique regions within each group of animals, demonstrating the ability of this technology to parse metabolically distinct regions of tumor. In total, the work outlined here describes the development of a novel optical imaging platform capable of quantifying intratumor metabolic heterogeneity of multiple metabolic endpoints over multiple length scales. The system expands on previous work developing methods for simultaneous measurement of exogenous fluorescent contrast agents to report on lipid uptake and mitochondrial activity. The system also introduced a novel computational approach to design uniform illumination for a low-cost microscope capable of imaging across multiple sample types. Together these technologies were used to observe metabolic heterogeneity in preclinical window chamber models following chemical perturbation. The technology introduced here, is primed for future exploration. First, it would be desirable to integrate all three exogenous contrast agents for simultaneous imaging of three axes of metabolism in vivo. Once accomplished, the sample technology could be applied to study metabolic and vascular changes associated with residual disease and tumors that are entering recurrence.
Item Open Access Actively Tunable Plasmonic Nanostructures(2020) Wilson, Wade MitchellActive plasmonic nanostructures with tunable resonances promise to enable smart materials with multiple functionalities, on-chip spectral-based imaging and low-power optoelectronic devices. A variety of tunable materials have been integrated with plasmonic structures, however, the tuning range in the visible regime has been limited and small on/off ratios are typical for dynamically switchable devices. An all optical tuning mechanism is desirable for on-chip optical computing applications. Furthermore, plasmonic structures are traditionally fabricated on rigid substrates, restricting their application in novel environments such as in wearable technology.
In this dissertation, I explore the mechanisms behind dynamic tuning of plasmon resonances, as well as demonstrate all-optical tuning through multiple cycles by incorporating photochromic molecules into plasmonic nanopatch antennas. Exposure to ultraviolet (UV) light switches the molecules into a photoactive state enabling dynamic control with on/off ratios up to 9.2 dB and a tuning figure of merit up to 1.43, defined as the ratio between the spectral shift and the initial line width of the plasmonic resonance. Moreover, the physical mechanisms underlying the large spectral shifts are elucidated by studying over 40 individual nanoantennas with fundamental resonances from 550 to 720 nm revealing good agreement with finite-element simulations.
To fully explore the tuning capabilities, the molecules are incorporated into plasmonic metasurface absorbers based on the same geometry as the single nanoantennas. The increased interaction between film-coupled nanocubes and resonant dipoles in the photochromic molecules gives rise to strong coupling. The coupling strength can be quantified by the Rabi-splitting of the plasmon resonance at ~300 meV, well into the ultrastrong coupling regime.
Additionally, fluorescent emitters are incorporated into the tunable absorber platform to give dynamic control over their emission intensity. I use optical spectroscopy to investigate the capabilities of tunable plasmonic nanocavities coupled to dipolar photochromic molecules. By incorporating emission sources, active control over the peak photoluminescence (PL) wavelength and emission intensity is demonstrated with PL spectroscopy.
Beyond wavelength tuning of the plasmon resonance, design and characterization is performed towards the development of a pyroelectric photodetector that can be implemented on a flexible substrate, giving it the ability to be conformed to new shapes on demand. Photodetection in the NIR with responsivities up to 500 mV/W is demonstrated. A detailed plan is given for the next steps required to fully realize visible to short-wave infrared (SWIR) pyroelectric photodetection with a cost-effective, scalable fabrication process. This, in addition to real-time control over the plasmon resonance, opens new application spaces for photonic devices that integrate plasmonic nanoparticles and actively tunable materials.
Item Open Access Adaptive Optics in Multiphoton Microscopy(2017) Kemeldinov, AidynAny type of microscopy faces the problem in an attenuated signal level and reduced optical resolution due to optical aberration. To overcome this problem, adaptive optics was implemented in a two-photon fluorescence microscope. Using a “sensorless” approach, this study corrected the aberration in the system using two different excitation colors. As methodology, the point spread function was compared before and after applying adaptive optics. This study demonstrated that adaptive optics improves the resolution of the microscope for both excitation wavelengths. The aberration correction was then monitored as a function of depth. The result showed an improvement in the optimization metric as imaging depth is increased. Thus, adaptive optics offers improved imaging of the sample at deeper depths with better optical resolution and higher signal-to-noise ratio.
Item Open Access Advanced Applications of 3D Dosimetry and 3D Printing in Radiation Therapy(2016) Miles, DevinAs complex radiotherapy techniques become more readily-practiced, comprehensive 3D dosimetry is a growing necessity for advanced quality assurance. However, clinical implementation has been impeded by a wide variety of factors, including the expense of dedicated optical dosimeter readout tools, high operational costs, and the overall difficulty of use. To address these issues, a novel dry-tank optical CT scanner was designed for PRESAGE 3D dosimeter readout, relying on 3D printed components and omitting costly parts from preceding optical scanners. This work details the design, prototyping, and basic commissioning of the Duke Integrated-lens Optical Scanner (DIOS).
The convex scanning geometry was designed in ScanSim, an in-house Monte Carlo optical ray-tracing simulation. ScanSim parameters were used to build a 3D rendering of a convex ‘solid tank’ for optical-CT, which is capable of collimating a point light source into telecentric geometry without significant quantities of refractive-index matched fluid. The model was 3D printed, processed, and converted into a negative mold via rubber casting to produce a transparent polyurethane scanning tank. The DIOS was assembled with the solid tank, a 3W red LED light source, a computer-controlled rotation stage, and a 12-bit CCD camera. Initial optical phantom studies show negligible spatial inaccuracies in 2D projection images and 3D tomographic reconstructions. A PRESAGE 3D dose measurement for a 4-field box treatment plan from Eclipse shows 95% of voxels passing gamma analysis at 3%/3mm criteria. Gamma analysis between tomographic images of the same dosimeter in the DIOS and DLOS systems show 93.1% agreement at 5%/1mm criteria. From this initial study, the DIOS has demonstrated promise as an economically-viable optical-CT scanner. However, further improvements will be necessary to fully develop this system into an accurate and reliable tool for advanced QA.
Pre-clinical animal studies are used as a conventional means of translational research, as a midpoint between in-vitro cell studies and clinical implementation. However, modern small animal radiotherapy platforms are primitive in comparison with conventional linear accelerators. This work also investigates a series of 3D printed tools to expand the treatment capabilities of the X-RAD 225Cx orthovoltage irradiator, and applies them to a feasibility study of hippocampal avoidance in rodent whole-brain radiotherapy.
As an alternative material to lead, a novel 3D-printable tungsten-composite ABS plastic, GMASS, was tested to create precisely-shaped blocks. Film studies show virtually all primary radiation at 225 kVp can be attenuated by GMASS blocks of 0.5cm thickness. A state-of-the-art software, BlockGen, was used to create custom hippocampus-shaped blocks from medical image data, for any possible axial treatment field arrangement. A custom 3D printed bite block was developed to immobilize and position a supine rat for optimal hippocampal conformity. An immobilized rat CT with digitally-inserted blocks was imported into the SmART-Plan Monte-Carlo simulation software to determine the optimal beam arrangement. Protocols with 4 and 7 equally-spaced fields were considered as viable treatment options, featuring improved hippocampal conformity and whole-brain coverage when compared to prior lateral-opposed protocols. Custom rodent-morphic PRESAGE dosimeters were developed to accurately reflect these treatment scenarios, and a 3D dosimetry study was performed to confirm the SmART-Plan simulations. Measured doses indicate significant hippocampal sparing and moderate whole-brain coverage.
Item Open Access Analysis of High-Temperature Solar Selective Coating(2018) Xiao, QingyuAbundant and widely available solar energy is one possible solution to the increasing demands for clean energy. The Thermodynamics and Sustainable Energy Laboratory (T-SEL) in Duke University has been dedicated to investigating methods to harness solar energy. Hybrid Solar System (HSS) is one of the promising methods to use solar energy, as it absorbs sunlight to produce hydrogen, which then can electrically power equipment through fuel cells. Hydrogen is produced through a biofuel reforming process, which occurs at a high temperature (over 700℃ for methane). Methods to design a high-temperature solar selective coating are investigated in this thesis.
The solar irradiance spectrum was assumed to be the same as Air Mass (AM) 1.5. A transfer-matrix method was adopted in this work to calculate the optical properties of the NREL #6, a design of nine-layer solar selective coating. Based on the design of NREL #6 coating, Differential Evolution (DE) algorithm was introduced to optimize this design. Two objective functions were considered: selectivity-oriented function and efficiency-oriented function, yielding the design of Revision #1 and Revision #2 respectively. The results showed a high selectivity (around 13) with low efficiency (66.6%) in Revision #1 and a high efficiency (82.6%) with moderate selectivity (around 9) in Revision #2.
Item Open Access Bounding the outcome of a two-photon interference measurement using weak coherent states(OPTICS LETTERS, 2018-08-15) Aragoneses, Andrés; Islam, Nurul T; Eggleston, Michael; Lezama, Arturo; Kim, Jungsang; Gauthier, Daniel JItem Open Access Clearly Camouflaged Crustaceans: The Physical Basis of Transparency in Hyperiid Amphipods and Anemone Shrimp(2017) Bagge, Laura ElizabethThis dissertation research focused on the ways in which clear crustaceans with complex bodies (i.e. with hard cuticles, thick muscles, and other internal organs) maintain transparency across their entire body volume. I used transparent crustacean species that had relatively large (> 25 mm long and > 2 mm thick) bodies and that occupied physically different (pelagic vs. benthic reef) habitats. Studying these transparent crustaceans and making comparisons with closely related opaque crustaceans provided some of the first insights into the puzzling problem of the physical basis of transparency in whole organisms.
First, I examined the ultrastructure of the cuticle of hyperiid amphipods, the first surface to interact with light, to understand what features may minimize reflectance. I investigated the cuticle surfaces of seven species of mostly transparent hyperiids using scanning electron microscopy and found two previously undocumented features that reduced reflectance. I found that the legs of Cystisoma spp. were covered with an ordered array of nanoprotuberances that functioned optically as a gradient refractive index material to reduce reflections. Additionally, I found that Cystisoma and six other species of hyperiids were covered with a monolayer of homogenous nanospheres (approximately 50 nm to 350 nm in diameter) that were most likely bacteria. Optical modeling demonstrated that both the nanoprotuberances and the monolayers reduced reflectance by as much as 250-fold. Even though the models only considered surface reflectance and not internal light scattering, these models showed that the nanoprotuberances and spheres could improve crypsis in a featureless habitat where the smallest reflection could render an animal vulnerable to visual predation.
Second, I took a morphological approach to investigate how light scattering may be minimized internally. Using bright field microscopy, I explored whether there were any gross anatomical differences in the abdominal muscles between a transparent species of shrimp, Ancylomenes pedersoni, and a similarly sized opaque shrimp species, Lysmata wurdemanni. I found no differences in muscle fiber size or any other features. Using transmission electron microscopy (TEM) to visualize muscle ultrastructure, I found that the myofibrils of the transparent species were twice the diameter of the opaque species (mean values of 2.2 μm compared to 1.0 μm). Over a given distance of muscle, light passes through fewer myofibrils due to their larger diameter, with fewer opportunities for light to be scattered at the interfaces between the high-index myofibrillar lattice and the surrounding lower-index fluid-filled sarcoplasmic reticulum (SR). Additionally, because transparency is not always a static trait and can sometimes be disrupted after exercise or physiological stress, I compared the ultrastructure of muscle in transparent A. pedersoni shrimp with the ultrastructure of muscle in A. pedersoni that had temporarily turned opaque after exercise. I found that in this opacified tissue, the fluid-filled space around myofibrils had an increased thickness of 360 nm as compared to a normal thickness of 20 nm. While this could have been a fixation artifact, this result still suggests that opacified tissue had some change in osmolarity or increase in fluid. Models of light scattering across a range of thicknesses and possible refractive indices showed that this observed increase in fluid-filled space dramatically reduced transparency.
Third, I further investigated how exertion or physiological stress may disrupt transparency, what may occur in the tissues to cause this disruption, and what may explain the increased fluid-filled SR interface. I hypothesized that increased perfusion, or an increase in blood volume between muscle fibers, can disrupt the normal organization of tissue, resulting in increased light scattering. I measured pre- and post-exercise perfusion via the injection of a specific fluorescent stain (Alexa Fluor 594-labeled wheat germ agglutinin) that labeled the sarcolemmal areas in contact with hemolymph and the endothelial cells of the blood vessels, and found more open vessels and greater hemolymph perfusion around fibers post-exercise. Changing salinity in the shrimps’ tanks, wounding the shrimp, and injecting proctolin (a vasodilator) were also associated with increased opacity and perfusion. To visualize the shrimps’ overall muscle morphology, I used Diffusible Iodine-based Contrast-Enhanced Computed Tomography (DICECT) to scan one control (transparent) and one experimental (opaque) A. pedersoni. The resulting images added further support to my hypothesis that hemolymph volume in the muscle increases in post-exercise opacified A. pedersoni.
Item Open Access Clinical Detection of Dysplasia Using Angle-Resolved Low Coherence Interferometry(2011) Terry, Neil GordonCancer is now the leading cause of death in developed countries. Despite advances in strategies aimed at the prevention and treatment of the disease, early detection of precancerous growths remains the most effective method of reducing associated morbidity and mortality. Pathological examination of physical tissues that are collected via systematic biopsy is the current "gold standard" in this pursuit. Despite widespread acceptance of this methodology and high confidence in its performance, it is not without limitations. Recently, much attention has been given to the development of optical biopsy techniques that can be used clinically and are able to overcome these limitations. This dissertation describes one such optical biopsy technique, angle-resolved low coherence interferometry (a/LCI), its adaptation to a clinical technology, and its evaluation in clinical studies.
The dissertation presents the theory that underlies the operation of the a/LCI technique, the design and validation of the clinical instrument, and its evaluation by means of two clinical trials. First, an account of the manner in which the depth-resolved angular scattering profiles that are collected by a/LCI can be used to determine nuclear characteristics of the investigated tissues is given. The design of the clinical system that is able to collect these scattering profiles through an optical fiber probe that can be passed through the accessory channel of an endoscope for in vivo use is presented. To demonstrate the ability of this system to accurately determine the size of cell nuclei, a set of validation experiments are described.
In order to evaluate the clinical utility of this a/LCI system, two clinical trials intended to assess the ability of a/LCI to detect the presence of early, pre-cancerous dysplasias in human tissues are presented. The first of these, an in vivo study of Barrett's esophagus (BE) patients undergoing routine surveillance for the early signs of esophageal adenocarcinoma, is described. This study represents the first use of the a/LCI technique in vivo, and confirms its ability to provide clinically useful information regarding the disease state of the tissue that it examines, with performance that compares favorably to other optical biopsy techniques. Next, an ex vivo study of resected intestinal tissue is presented. The results of this study demonstrate the ability of a/LCI to provide information that can be used to detect dysplasia in the lower gastrointestinal tract with high accuracy. This study will enable future development of the technology to allow conduction of in vivo trials of intestinal tissue. The results of these two clinical studies demonstrate the clinical utility a/LCI, illustrating its potential as an optical biopsy technique that has great potential to provide diagnostically relevant information during surveillance procedures. This is particularly relevant in the case of BE, where its successful use has been demonstrated in vivo.
Item Open Access Coding Strategies and Implementations of Compressive Sensing(2016) Tsai, Tsung-HanThis dissertation studies the coding strategies of computational imaging to overcome the limitation of conventional sensing techniques. The information capacity of conventional sensing is limited by the physical properties of optics, such as aperture size, detector pixels, quantum efficiency, and sampling rate. These parameters determine the spatial, depth, spectral, temporal, and polarization sensitivity of each imager. To increase sensitivity in any dimension can significantly compromise the others.
This research implements various coding strategies subject to optical multidimensional imaging and acoustic sensing in order to extend their sensing abilities. The proposed coding strategies combine hardware modification and signal processing to exploiting bandwidth and sensitivity from conventional sensors. We discuss the hardware architecture, compression strategies, sensing process modeling, and reconstruction algorithm of each sensing system.
Optical multidimensional imaging measures three or more dimensional information of the optical signal. Traditional multidimensional imagers acquire extra dimensional information at the cost of degrading temporal or spatial resolution. Compressive multidimensional imaging multiplexes the transverse spatial, spectral, temporal, and polarization information on a two-dimensional (2D) detector. The corresponding spectral, temporal and polarization coding strategies adapt optics, electronic devices, and designed modulation techniques for multiplex measurement. This computational imaging technique provides multispectral, temporal super-resolution, and polarization imaging abilities with minimal loss in spatial resolution and noise level while maintaining or gaining higher temporal resolution. The experimental results prove that the appropriate coding strategies may improve hundreds times more sensing capacity.
Human auditory system has the astonishing ability in localizing, tracking, and filtering the selected sound sources or information from a noisy environment. Using engineering efforts to accomplish the same task usually requires multiple detectors, advanced computational algorithms, or artificial intelligence systems. Compressive acoustic sensing incorporates acoustic metamaterials in compressive sensing theory to emulate the abilities of sound localization and selective attention. This research investigates and optimizes the sensing capacity and the spatial sensitivity of the acoustic sensor. The well-modeled acoustic sensor allows localizing multiple speakers in both stationary and dynamic auditory scene; and distinguishing mixed conversations from independent sources with high audio recognition rate.
Item Open Access Coherence in Dynamic Metasurface Aperture Microwave Imaging Systems(2020) Diebold, Aaron VincentMicrowave imaging systems often utilize electrically large arrays for remote characterization of spatial and spectral content. Image reconstruction involves computational processing, the success of which depends on adequate spatial and temporal sampling at the array as dictated by the nature of the radiation and sensing strategy. Effective design of an imaging system, consisting of its hardware and algorithmic components, thus requires detailed understanding of the nature of the involved fields and their impact on the processing capabilities. One can sufficiently characterize many of the properties of such fields and systems via coherence, which quantifies their interferometric capacity in terms of statistical correlations and point spread functions. Recent work on dynamic metasurface apertures (DMAs) for microwave imaging has demonstrated the utility of these structures in active, coherent systems, supplanting traditional array architectures with lower-cost designs capable of powerful wavefront shaping. In contrast to arrays of distinct antennas, DMAs are composed of electrically large arrays of dynamically-tunable, radiating metamaterial elements to realize diverse gain patterns that can function as an encoding mechanism for coded aperture image reconstruction. With the appropriate formulation, well-established concepts from the realm of Fourier optics can be transposed from conventional array systems to DMA architectures. This dissertation furthers that task by modeling DMA imaging systems involving partial coherence and incoherence, and demonstrating new reconstruction algorithms in these contexts. Such an undertaking provides convenient opportunities for examining the origins of coherence in computational and holographic imaging systems. This insight is necessary for the development of modern approaches that seek to smoothly integrate hardware and computational elements for powerful, efficient, and innovative imaging tasks.
Accommodating different degrees of coherence in a microwave imaging system can substantially relax demands on hardware components including phase stability and synchronization, or on algorithmic procedures such as calibration. In addition, incoherent operation can yield improved images free of coherent diffraction artifacts and speckle. Finally, an understanding of coherence can unlock fundamentally distinct applications, such as passive imaging and imaging with ambient illumination, that can benefit from the flexibility of a DMA system but have yet to be demonstrated under such an architecture. To this end, I formulate a unified framework for analyzing and processing array imaging systems in the Fourier domain, and demonstrate a method for transforming a DMA-based system to an equivalent array representation under active, coherent operation. I then investigate the role of spatial coherence in a two-dimensional holographic imaging system, and experimentally demonstrate some results using a collection of DMAs. I conduct a similar investigation in the context of single-pixel ghost imaging, which allows coherent and incoherent imaging directly from intensity measurements, thereby relaxing hardware phase requirements. I then formulate a model for partially coherent fields in a DMA imaging system, and provide several reconstruction strategies and example simulations. I finally restrict this general case to passive, spectral imaging of spatially and temporally incoherent sources, and experimentally demonstrate a compressive imaging strategy in this context.
Item Open Access Collective light-matter interactions via emergent order in cold atoms(2012) Greenberg, JoelCollective behavior in many-body systems, where the dynamics of an individual element depend on the state of the entire ensemble, play an important role in both basic science research and applied technologies. Over the last twenty years, studies of such effects in cold atomic vapors have lead to breakthroughs in areas such as quantum information science and atomic and condensed matter physics. Nevertheless, in order to generate photon-mediated atom-atom coupling strengths that are large enough to produce collective behavior, these studies employ techniques that intrinsically limit their applicability. In this thesis, I describe a novel nonlinear optical process that enables me to overcome these limitations and realize a new regime of collective light-matter interaction.
My experiment involves an anisotropic cloud of cold rubidium atoms illuminated by a pair of counterpropagating optical (pump) fields propagating at an angle to the trap's long axis. When the pump beam intensities exceed a threshold value, a collective instability occurs in which new beams of light are generated spontaneously and counterpropagate along the trap's long axis. In order to understand the physical mechanism responsible for this behavior, I study first the system's nonlinear optical response when driven below the instability threshold. I find that the incident optical fields produce an optical lattice that causes the atoms to become spatially organized on the sub-wavelength length scale. This organization corresponds to the formation of an atomic density grating, which effectively couples the involved fields to one another and enables the transfer of energy between them. The loading of atoms into this grating is enhanced by my choice of field polarizations, which simultaneously results in cooling of the atoms from T~30 μK to T~3 μK via the Sisyphus effect. As a result, I observe a fifth-order nonlinear susceptibility χ^{(5)}=1.9x10^-12 (m/V)^4 that is 7 orders of magnitude larger than previously observed. In addition, because of the unique scaling of the resulting nonlinear response with material parameters, the magnitude of the nonlinearity can be large for small pump intensities (\ie, below the resonant electronic saturation intensity 1.6 mW/cm^2) while simultaneously suffering little linear absorption. I confirm my interpretation of the nonlinearity by developing a theoretical model that agrees quantitatively with my experimental observations with no free parameters.
The collective instability therefore corresponds to the situation where the cold vapor transitions spontaneously from a spatially-homogeneous state to an ordered one. This emergent organization leads to the simultaneous emission of new optical fields in a process that one can interpret either in terms of mirrorless parametric self-oscillation or superradiance. By mapping out the phase diagram for this transition, I find that the instability can occur for pump intensities as low as 1 mW/cm^2, which is approximately 50 times smaller than previous observations of similar phenomena. The intensity of the emitted light can be up to 20% of the pump beam intensity and depends superlinearly on the number of atoms, which is a clear signature of collective behavior. In addition, the generated light demonstrates temporal correlations between the counterpropagating modes of up to 0.987 and is nearly coherent over several hundred μs. The most significant attributes of the light, though, are that it consists of multiple transverse spatial modes and persists in steady-state. This result represents the first observation of such dynamics, which have been shown theoretically to lead to a rich array of new phenomena and possible applications.
Item Unknown Computational 3D Optical Imaging Using Wavevector Diversity(2021) Zhou, KevinThe explosion in the popularity and success of deep learning in the past decade has accelerated the development of computationally efficient, GPU-accelerated frameworks, such as TensorFlow and PyTorch, for rapid prototyping of neural networks. In this dissertation, we show that these deep learning tools are also well-suited for computational 3D imaging problems, specifically optical diffraction tomography (ODT), photogrammetry, and our newly proposed optical coherence refraction tomography (OCRT). Underlying these computational 3D imaging techniques is a physical model that demands multiple measurements taken with either angular diversity, wavelength diversity, or both. This requirement can be compactly summarized as wavevector (or k-vector) diversity, where the magnitude and direction of the wavevector correspond to the color and angle of the light, respectively.
To understand the importance of wavevector diversity for 3D imaging, this dissertation starts by advancing a unified k-space theory of optical coherence tomography (OCT), the most comprehensive and inclusive theoretical description of OCT to date that not only describes the transfer functions of all major forms of OCT and other coherent techniques (e.g., confocal microscopy, holography, ODT), but also includes the fundamental concepts of OCT, such as speckle, dispersion, aberration, and the tradeoff between lateral resolution and depth of focus (DOF).
Consistent with this unified theory, we implemented in TensorFlow a reconstruction algorithm for ODT, a technique that relies on illumination angular diversity to achieve 3D refractive index (RI) imaging. We propose a new method for filling the well-known “missing cone” of the ODT transfer function by reparameterizing the 3D sample as the output of an untrained neural network known as a deep image prior (DIP), which we show to outperform traditional regularization strategies.
Next, we introduce OCRT, a computational extension of OCT that incorporates extreme angular diversity over OCT's already high wavelength diversity to enable resolution-enhanced, speckle-reduced reconstructions that overcome the lateral-resolution-DOF tradeoff. OCRT also jointly reconstructs quantitative RI maps of the sample using a ray-based physical model implemented in TensorFlow. We also demonstrate spectroscopic OCRT (SOCRT), an extension of spectroscopic OCT (SOCT) that overcomes its tradeoff between spectral and axial resolution.
Motivated to make OCRT more widely applicable, we propose a new use of conic-section (e.g., parabolic, ellipsoidal) mirrors to allow fast multi-view imaging over very high angular ranges (up to 360°) using galvanometers without requiring sample rotation. We theoretically characterize the achievable fields of view (FOVs) as a function of many imaging system parameters (e.g., NA, wavelength, incidence angle, focal length, and telecentricity). Based on these predictions, we constructed a parabolic-mirror-based imaging system that facilitates multi-view OCT volume capture with millimetric FOVs over up to ±75°, which we combined to perform 3D OCRT reconstructions of zebrafish, fruitfly, and mouse tissue.
Finally, we adapted the OCRT reconstruction algorithm to photogrammetric 3D mesoscopic imaging with tens-of-micron accuracy, using a sequence of smartphone camera images taken at close range under freehand motion. 3D estimation was possible due to the angular diversity afforded by the nontelecentricity of smartphone cameras, using a similar ray-based model as for OCRT. We show that careful modeling of lens distortion and incorporation of a DIP are both pivotal for obtaining high 3D accuracy using devices not designed for close-range imaging.
Item Unknown Computational Bio-Optical Imaging with Novel Sensor Arrays(2023) Xu, ShiqiOptical imaging is an essential tool for studying life sciences. Existing biomedical optical systems range from microscopes in clinics that use wave optics principles to examine pathological samples at high resolution, to photoplethysmography in everyday smartwatches utilizing diffuse optics technologies for monitoring deep tissue physiology. An optical system, such as a photography solution in a studio, typically consists of three parts: illumination, objects of interest, and recording devices. Over the past decades, thanks to rapid advancements in semiconductor manufacturing, numerous new and exciting optical devices have emerged. These include low-cost, small form-factor LEDs and CMOS camera sensors in budget tablet devices, as well as high-density time-of-flight array detectors in recent generations of iPhones, for example. Moore's Law, on the other hand, has driven significant development in powerful yet inexpensive computational tools. As a result, nowadays, analogous to other medical imaging modalities such as X-ray CT and MRI, multiplexed optical measurements that may not resemble the object of interest can be recorded and post-processed to reconstruct useful images for human perception. In this thesis, several new computational optical imaging techniques at different scales will be discussed. These range from vectorial tomographic microscopies for imaging anisotropic cells and tissue, to high-throughput imaging systems capable of recording eukaryotic colonies at mesoscopic scales, and novel single-photon-sensitive sensing methods for non-invasive imaging of macroscopic transient dynamics deep within turbid volumes.
Item Unknown Computational Optical Imaging Systems for Spectroscopy and Wide Field-of-View Gigapixel Photography(2013) Kittle, David S.This dissertation explores computational optical imaging methods to circumvent the physical limitations of classical sensing. An ideal imaging system would maximize resolution in time, spectral bandwidth, three-dimensional object space, and polarization. Practically, increasing any one parameter will correspondingly decrease the others.
Spectrometers strive to measure the power spectral density of the object scene. Traditional pushbroom spectral imagers acquire high resolution spectral and spatial resolution at the expense of acquisition time. Multiplexed spectral imagers acquire spectral and spatial information at each instant of time. Using a coded aperture and dispersive element, the coded aperture snapshot spectral imagers (CASSI) here described leverage correlations between voxels in the spatial-spectral data cube to compressively sample the power spectral density with minimal loss in spatial-spectral resolution while maintaining high temporal resolution.
Photography is limited by similar physical constraints. Low f/# systems are required for high spatial resolution to circumvent diffraction limits and allow for more photon transfer to the film plain, but require larger optical volumes and more optical elements. Wide field systems similarly suffer from increasing complexity and optical volume. Incorporating a multi-scale optical system, the f/#, resolving power, optical volume and wide field of view become much less coupled. This system uses a single objective lens that images onto a curved spherical focal plane which is relayed by small micro-optics to discrete focal planes. Using this design methodology allows for gigapixel designs at low f/# that are only a few pounds and smaller than a one-foot hemisphere.
Computational imaging systems add the necessary step of forward modeling and calibration. Since the mapping from object space to image space is no longer directly readable, post-processing is required to display the required data. The CASSI system uses an undersampled measurement matrix that requires inversion while the multi-scale camera requires image stitching and compositing methods for billions of pixels in the image. Calibration methods and a testbed are demonstrated that were developed specifically for these computational imaging systems.
Item Unknown Control of Optical Processes in Diamond using Plasmonic Nanogap Cavities(2022) Boyce, Andrew MichaelSolid-state quantum emitters embedded in carefully engineered nanostructures could enable a new generation of quantum information and sensing technologies, including networked processors for quantum computing and precise monitors of temperature and strain at the nanoscale. The primary goal when designing these nanostructures is to utilize the Purcell effect to improve the emission rate, directionality and brightness of quantum emitters, as long decay times, nondirectional emission and weak fluorescence limit their applications. One particularly promising emitter is the silicon vacancy (SiV) in diamond, which offers excellent photostability and minimal spectral diffusion, in addition to coherent emission at its zero-phonon line (ZPL) comprising 80% of its total fluorescence. In this dissertation, up to 121-fold enhancement of the spontaneous emission rate of SiVs coupled to plasmonic nanogap cavities is demonstrated. The vacancy centers are implanted into a monolithic diamond thin film, which is then etched to nanometer-scale thickness, an approach with a clear path towards wafer-scale fabrication. A novel approach to creating film-coupled nanogap metasurfaces was developed to support this research and consists of transferring EBL-fabricated nanoparticles by using a PDMS stamp. Up to seven orders of magnitude of enhancement of nonlinear frequency conversion was also observed in diamond thin films coupled to these metasurfaces. Furthermore, a robust mechanism for actively tuning the nanocavity absorption resonance by integrating sub-10-nm films of the phase-change material vanadium dioxide. This platform opens up opportunities for on-chip quantum networks and nanoscale sensors based on nanocavity-coupled SiVs with the potential for in-situ frequency conversion to outcouple to photonic circuits and reconfigurable properties by incorporating VO2 thin films.
Item Open Access Control of Surface Plasmon Substrates and Analysis of Near field Structure(2011) Chen, Shiuan-YehThe electromagnetic properties of various plasmonic nanostructures are investigated. These nanostructures, which include random clusters, controlled clusters and particle-film hybrids are applied to surface-enhanced Raman scattering (SERS). A variety of techniques are utilized to fabricate, characterize, and model these SERS-active structures, including nanoparticle functionalization, thin film deposition, extinction spectroscopy, elastic scattering spectroscopy, Raman scattering spectroscopy, single-assembly scattering spectroscopy, transmission electron microscopy, generalized Mie theory, and finite element method.
Initially, the generalized Mie theory is applied to calculate the near-field of the small random clusters to explain their SERS signal distribution. The nonlinear trend of SERS intensity versus size of clusters is demonstrated in experiments and near-field simulations.
Subsequently, controlled nanoparticle clusters are fabricated for quantitative SERS. A 50 nm gold nanoparticle and 20nm gold nanoparticles are tethered to form several hot spots between them. The SERS signal from this assembly is compared with SERS signals from single particles and the relative intensities are found to be consistent with intensity ratios predicted by near-field calculation.
Finally, the nanoparticle/film hybrid structure is studied. The scattering properties and SERS activity are observed from gold nanoparticles on different substrates. The gold nanoparticle on gold film demonstrates high field enhancement. Raman blinking is observed and implies a single molecule signal. Furthermore, the doughnut shape of Raman images indicates that this hybrid structure serves as nano-antenna and modifies the direction of molecular emission.
In additional to the primary gap dipole utilized for SERS, high order modes supported by the nanoparticle/film hybrid also are investigated. In experiments, the HO mode show less symmetry compared to the gap dipole mode. The simulation indicates that the HO modes observed may be comprised of two gap modes. One is quadrupole-like and the other is dipole-like in terms of near-field profile. The analytical treatment of the coupled dipole is performed to mimic the imaging of the quadrupole radiation.
Item Open Access Decoy-state quantum key distribution with nonclassical light generated in a one-dimensional waveguide.(Optics letters, 2013-03) Zheng, Huaixiu; Gauthier, Daniel J; Baranger, Harold UWe investigate a decoy-state quantum key distribution (QKD) scheme with a sub-Poissonian single-photon source, which is generated on demand by scattering a coherent state off a two-level system in a one-dimensional waveguide. We show that, compared to coherent state decoy-state QKD, there is a two-fold increase of the key generation rate. Furthermore, the performance is shown to be robust against both parameter variations and loss effects of the system.Item Open Access Design, Analysis, And Characterization Of Metamaterial Quasi-Optical Components For Millimeter-Wave Automotive Radar(2013) Nguyen, Vinh NgocSince their introduction by Mercedes Benz in the late 1990s, W-band radars operating at 76-77 GHz have found their way into more and more passenger cars. These automotive radars are typically used in adaptive cruise control, pre-collision sensing, and other driver assistance systems. While these systems are usually only about the size of two stacked cigarette packs, system size, and weight remains a concern for many automotive manufacturers.
In this dissertation, I discuss how artificially structured metamaterials can be used to improve lens-based automotive radar systems. Metamaterials allow the fabrication of smaller and lighter systems, while still meeting the frequency, high gain, and cost requirements of this application. In particular, I focus on the development of planar artificial dielectric lenses suitable for use in place of the injection-molded lenses now used in many automotive radar systems.
I begin by using analytic and numerical ray-tracing to compare the performance of planar metamaterial GRIN lenses to equivalent aspheric refractive lenses. I do this to determine whether metamaterials are best employed in GRIN or refractive automotive radar lenses. Through this study I find that planar GRIN lenses with the large refractive index ranges enabled by metamaterials have approximately optically equivalent performance to equivalent refractive lenses for fields of view approaching ±20°. I also find that the uniaxial nature of most planar metamaterials does not negatively impact planar GRIN lens performance.
I then turn my attention to implementing these planar GRIN lenses at W-band automotive radar frequencies. I begin by designing uniform sheets of W-band electrically-coupled LC resonator-based metamaterials. These metamaterial samples were fabricated by the Jokerst research group on glass and liquid crystal polymer (LCP) substrates and tested at Toyota Research Institute- North America (TRI-NA). When characterized at W-band frequencies, these metamaterials show material properties closely matching those predicted by full-wave simulations.
Due to the high losses associated with resonant metamaterials, I shift my focus to non-resonant metamaterials. I discuss the design, fabrication, and testing of non-resonant metamaterials for fabrication on multilayer LCP printed circuit boards (PCBs). I then use these non-resonant metamaterials in a W-band planar metamaterial GRIN lens. Radiation pattern measurements show that this lens functions as a strong collimating element.
Using similar lens design methods, I design a metamaterial GRIN lens from polytetrafluoroethylene-based (PTFE-based) non-resonant metamaterials. This GRIN lens is designed to match a target dielectric lens's radiation characteristics across a ±6° field of view. Measurements at automotive radar frequencies show that this lens has approximately the same radiation characteristics as the target lens across the desired field of view.
Finally, I describe the development of electrically reconfigurable metamaterials using thin-film silicon semiconductors. These silicon-based reconfigurable metamaterials were developed in close collaboration with several other researchers. My major contribution to the development of these reconfigurable metamaterials consisted of the initial metamaterial design. The Jokerst research group fabricated this initial design while TRI-NA characterized the fabricated metamaterial experimentally. Measurements showed approximately 8% variation in transmission under a 5 Volt DC bias. This variation in transmission closely matched the variation in transmission predicted by coupled electronic-electromagnetic simulation run by Yaroslav Urzhumov, one of other contributors to the development of the reconfigurable metamaterial.
Item Open Access Design, Characterization, and Evaluation of a Surface Plasmon Resonance Sensor(2012) Greenley, MichaelCharacterization of thin films, prominently including self-assembled monolayers is important to the understanding of interfacial events in both biological and manufactured systems. To facilitate such work, a surface plasmon resonance device, or SPR, was constructed, and tests were conducted to evaluate the performance of the system relative to current systems and mathematical models. First, relevant analytical equations are introduced to describe the behavior of the system. In subsequent chapters, the design of the device, its calibration, and operating procedure are explained. Finally, the system is tested against samples with known behaviors, and the experimental and analytical results are compared.