Cancer is the second leading cause of death in the United States, and its early diagnosis is critical to improving treatment options and patient outcomes. In autofluorescence (AF) imaging, light of controlled wavelengths is projected onto tissue, absorbed by specific molecules, and re-emitted at longer wavelengths. Images of re-emitted light are used together with spectral information to infer tissue functional information and diagnosis. This dissertation describes AF imaging studies of three different organs using data collected from fresh human surgical specimens. In the ovary study, illumination was at 365 nm, and images were captured at 8 emission wavelengths. Measurements from a multispectral imaging system and fiber optic probe were used to map tissue diagnosis at every image pixel. For the colon and pancreas studies, instrumentation was developed extending AF imaging capability to sub-300 nm excitation. Images excited in the deep UV revealed tryptophan and protein content which are believed to change with disease state. Several excitation wavelength bands from 280 nm to 440 nm were investigated. Microscopic AF images collected in the pancreas study included both cultured and primary cells. Several findings are reported. A method of transforming fiber optic probe spectra for direct comparison with imager spectra was devised. Normalization of AF data by green reflectance data was found useful in correcting hemoglobin absorption. Ratio images, both AF and reflectance, were formulated to highlight growths in the colon. Novel tryptophan AF images were found less useful for colon diagnostics than the new ratio techniques. Microscopic tryptophan AF images produce useful visualization of cellular protein content, but their diagnostic value requires further study.

Recent clinical studies have demonstrated that photoacoustic imaging (PAI) provides important diagnostic information for breast cancer staging. Despite these promising studies, PAI remains an unfeasible option for clinics due to the cost to implement, the required large modification in user conduct and the inflexibility of the hardware to accommodate other applications for the incremental enhancement in diagnostic information. The research described in this dissertation addresses these issues by designing attachments to clinical ultrasound probes and incorporating custom detectors into commercial ultrasound scanners. The ultimate benefit of these handheld devices is to expand the capability of current ultrasound systems and facilitate the translation of PAI to enhance cancer diagnostics and neurosurgical outcomes. Photoacoustic enabling devices (PEDs) were designed as attachments to two clinical ultrasound probes optimized for breast cancer diagnostics. PAI uses pulsed laser excitation to create transient heating (<1°C) and thermoelastic expansion that is detected as an ultrasonic emission. These ultrasonic emissions are remotely sensed to construct noninvasive images with optical contrast at depths much greater than other optical modalities. The PEDs are feasible in terms of cost, user familiarity and flexibility for various applications. Another possible application for PAI is in assisting neurosurgeons treating aneurysms. Aneurysms are often treated by placing a clip to prevent blood flow into the aneurysm. However, this procedure has risks associated with damaging nearby vessels. One of the developed PEDs demonstrated the feasibility to three-dimensionally image tiny microvasculature (<0.3mm) beyond large blood occlusions (>2.4mm) in a phantom model. The capability to use this during surgery would suggest decreasing the risks associated with these treatments. However, clinical ultrasound arrays are not clinically feasible for microsurgical applications due to their bulky size and linear scanning requirements for 3D. Therefore, capacitive micromachined ultrasound transducer (CMUT) two-dimensional arrays compatible with standard ultrasound scanners were used to generate real-time 3D photoacoustic images. Future probes, designed incorporating CMUT arrays, would be relatively simple to fabricate and a convenient upgrade to existing clinical ultrasound equipment. Eventually, a handheld tool with the ability to visualize, in real-time 3D, the desired microvasculature, would assist surgical procedures. The potential implications of PAI devices compatible with standard ultrasound equipment would be a streamlined cost efficient solution for translating photoacoustics into clinical practice. The practitioner could then explore the benefits of the enhanced contrast adjunctive to current ultrasound applications. Clinical availability of PAI could enhance breast cancer diagnostics and cerebrovascular surgical outcomes.

Current metrology methods involve technicians viewing through a microscope, increasing the time, cost, and error rate in inspection. Developing an automated inspection system eliminates these difficulties. Shown in this work is a laser scanning microscope (LSM) design for an opto-electronic detection system (OEDS), based upon the concept that intensity differences related to pattern defects can be obtained from reflections off fused silica samples coated with photoresist (PR) or Aluminum. Development of this system for data collection and processing is discussed. Results show that 2.1 μm resolution of these defects is obtainable. Preliminary results for larger-array patterns through stitching processes are also shown. The second part of this work uses the concept of phase contrast edge detection. Looking at non-metallized patterns, one can use the property that phase changes induced by a refractive-index sensitive material can be seen with a multi-cell array, rendering the image visible by comparing the respective phases. A variety of defects and samples are shown. Extrapolating results to larger arrays is also discussed. Latent imaging, or imaging without development, is also evaluated. Future work in the areas of system commercialization, sample storage, and other mass-printing techniques are discussed.

Infrared cameras can directly measure the apparent temperature of objects, providing thermal imaging. However, the raw output from most infrared cameras suffers from a strong, often limiting noise source called nonuniformity. Manufacturing imperfections in infrared focal planes lead to high pixel-to-pixel sensitivity to electronic bias, focal plane temperature, and other effects. In turn, different pixels within the focal plane array give a drastically different electronic response to the same irradiance. The resulting imagery can only provide useful thermal imaging after a nonuniformity calibration has been performed. Traditionally, these calibrations are performed by momentarily blocking the field of view with a flat temperature plate or blackbody cavity. However because the pattern is a coupling of manufactured sensitivities with operational variations, periodic recalibration is required, sometimes on the order of tens of seconds. A class of computational methods called Scene-Based Nonuniformity Correction (SBNUC) has been researched for over 20 years where the nonuniformity calibration is estimated in digital processing by analysis of the video stream in the presence of camera motion. The most sophisticated SBNUC methods can completely and robustly eliminate the high-spatial frequency component of nonuniformity with only an initial reference calibration or potentially no physical calibration. I will demonstrate a novel algorithm that advances these SBNUC techniques to support all spatial frequencies of nonuniformity correction. Long-wave infrared microgrid polarimeters are a class of camera that incorporate a microscale per-pixel wire-grid polarizer directly affixed to each pixel of the focal plane. These cameras have the capability of simultaneously measuring thermal imagery and polarization in a robust integrated package with no moving parts. I will describe the necessary adaptations of my SBNUC method to operate on this class of sensor as well as demonstrate SBNUC performance in LWIR polarimetry video collected on the UA mall.

This dissertation describes the design, development, and field validation of a concentrator photovoltaic (CPV) solar energy system. The challenges of creating a highly efficient yet low-cost system architecture come from many sources. The solid-state physics of photovoltaic devices present fundamental limits to photoelectron conversion efficiency, while the electrical and thermal characteristics of widely available materials limit the design arena. Furthermore, the need for high solar spectral throughput, evenly concentrated sunlight, and tolerance to off-axis pointing places strict illumination requirements on the optical design. To be commercially viable, the cost associated with all components must be minimized so that when taken together, the absolute installed cost of the system in kWh is lower than any other solar energy method, and competitive with fossil fuel power generation. The work detailed herein focuses specifically on unique optical design and illumination concepts discovered when developing a viable commercial CPV system. By designing from the ground up with the fundamental physics of photovoltaic devices and the required system tolerances in mind, a select range of optical designs are determined and modeled. Component cost analysis, assembly effort, and development time frame further influence design choices to arrive at a final optical system design. When coupled with the collecting mirror, the final optical hardware unit placed at the focus generates more than 800W, yet is small and lightweight enough to hold in your hand. After fabrication and installation, the completed system's illumination, spectral, and thermal performance is validated with on-sun operational testing.

Plenoptic cameras and Shack-Hartmann wavefront sensors are lenslet-based optical systems that do not form a conventional image. The addition of a lens array into these systems allows for the aberrations generated by the combination of the object and the optical components located prior to the lens array to be measured or corrected with post-processing. This dissertation provides a ray selection method to determine the rays that pass through each lenslet in a lenslet-based system. This first-order, ray trace method is developed for any lenslet-based system with a well-defined fore optic, where in this dissertation the fore optic is all of the optical components located prior to the lens array. For example, in a plenoptic camera the fore optic is a standard camera lens. Because a lens array at any location after the exit pupil of the fore optic is considered in this analysis, it is applicable to both plenoptic cameras and Shack-Hartmann wavefront sensors. Only a generic, unaberrated fore optic is considered, but this dissertation establishes a framework for considering the effect of an aberrated fore optic in lenslet-based systems. The rays from the fore optic that pass through a lenslet placed at any location after the fore optic are determined. This collection of rays is reduced to three rays that describe the entire lenslet ray set. The lenslet ray set is determined at the object, image, and pupil planes of the fore optic. The consideration of the apertures that define the lenslet ray set for an on-axis lenslet leads to three classes of lenslet-based systems. Vignetting of the lenslet rays is considered for off-axis lenslets. Finally, the lenslet ray set is normalized into terms similar to the field and aperture vector used to describe the aberrated wavefront of the fore optic. The analysis in this dissertation is complementary to other first-order models that have been developed for a specific plenoptic camera layout or Shack-Hartmann wavefront sensor application. This general analysis determines the location where the rays of each lenslet pass through the fore optic establishing a framework to consider the effect of an aberrated fore optic in a future analysis.

A novel design for atmospheric laser radar (lidar) is presented, implementing a digital micromirror device (DMD) for use in (A) aligning transmitter and receiver boresight angles and in (B) field-of-view (FOV) control of such "DMD lidar" instruments. A novel technique is presented to extract the transmitter-receiver overlap-compensation function from ratioing data from different FOVs in the same pointing direction. DMD lidar design considerations and trades are surveyed. Principles of modeling DMD lidar performance are introduced and implemented in a performance-predictive system simulation with data-validated results. Operational capabilities of DMD lidar are demonstrated through a hardware prototype with field measurement examples. Additional capabilities offered by integrating DMD within lidar and other optical systems are presented, including single-pixel Radon-imaging techniques.

New optical designs strive to achieve extreme performance, and continually increase the complexity of prescribed optical shapes, which often require wide dynamic range and high resolution. SCOTS, or the Software Configurable Optical Test System, can measure a wide range of optical surfaces with high sensitivity using surface slope. This dissertation introduces a high resolution version of SCOTS called SPOTS, or the Slope measuring Portable Optical Test System. SPOTS improves the metrology of surface features on the order of sub-millimeter to decimeter spatial scales and nanometer to micrometer level height scales. Currently there is no optical surface metrology instrument with the same utility. SCOTS uses a computer controlled display (such as an LCD monitor) and camera to measure surface slopes over the entire surface of a mirror. SPOTS differs in that an additional lens is placed near the surface under test. A small prototype system is discussed in general, providing the support for the design of future SPOTS devices. Then the SCOTS instrument transfer function is addressed, which defines the way the system filters surface heights. Lastly, the calibration and performance of larger SPOTS device is analyzed with example measurements of the 8.4-m diameter aspheric Large Synoptic Survey Telescope's (LSST) primary mirror. In general optical systems have a transfer function, which filters data. In the case of optical imaging systems the instrument transfer function (ITF) follows the modulation transfer function (MTF), which causes a reduction of contrast as a function of increasing spatial frequency due to diffraction. In SCOTS, ITF is shown to decrease the measured height of surface features as their spatial frequency increases, and thus the SCOTS and SPOTS ITF is proportional to their camera system's MTF. Theory and simulations are supported by a SCOTS measurement of a test piece with a set of lithographically written sinusoidal surface topographies. In addition, an example of a simple inverse filtering technique is provided. The success of a small SPOTS proof of concept instrument paved the way for a new larger prototype system, which is intended to measure subaperture regions on large optical mirrors. On large optics, the prototype SPOTS is light weight and it rests on the surface being tested. One advantage of this SPOTS is stability over time in maintaining its calibration. Thus the optician can simply place SPOTS on the mirror, perform a simple alignment, collect measurement data, then pick the system up and repeat at a new location. The entire process takes approximately 5 to 10 minutes, of which 3 minutes is spent collecting data. SPOTS' simplicity of design, light weight, robustness, wide dynamic range, and high sensitivity make it a useful tool for optical shop use during the fabrication and testing process of large and small optics.

Measurement of the quality and performance of soft contact lenses is not new and is continually evolving as manufacturing methods develop and more complicated contact lenses become available. Qualification of soft contact lenses has not been a simple task since they are fundamentally difficult to measure. The shape of the lens is extremely sensitive to how the lens is supported and the material properties can change quickly with time. These lenses have been measured in several different ways, the most successful being non-contact optical methods that measure the lens while it is immersed in saline solution. All of these tests measure the lens in transmission and do not directly measure the surface structure of the lens. The reason for this is that the Fresnel reflectivity of the surface of a contact lens in saline solution is about 0.07%. Surface measurements have been performed in air, but not in saline. The lens needs to be measured in solution so that it can maintain its true shape. An interferometer is proposed, constructed, verified, and demonstrated to measure the aspheric low reflectivity surfaces of a contact lens while they are immersed in saline solution. The problem is extremely difficult and requires delicate balance between stray light mitigation, color correction, and polarization management. The resulting system implements reverse raytracing algorithms to correct for retrace errors so that highly aspheric, toric, and distorted contact lens surfaces can be measured. The interferometer is capable of measuring both surfaces from the same side of the contact lens as well as the lens thickness. These measurements along with the index of refraction of the lens material are enough build a complete 3D model of the lens. A simulated transmission test of the 3D model has been shown to match the real transmission test of the same lens to within 32nm RMS or 1/20th of a wave at the test wavelength.

Our burgeoning appetite for data relentlessly demands exponential scaling of computing and communications resources leading to an overbearing and ever-present drive to improve efficiency while reducing on-chip area even as photonic components expand to fill application spaces no longer satisfied by their electronic counterparts. With a high index contrast, low optical loss, and compatibility with the CMOS fabrication infrastructure, silicon-on-insulator technology delivers a mechanism by which efficient, sub-micron waveguides can be fabricated while enabling monolithic integration of photonic components and their associated electronic infrastructure. The result is a solution leveraging the superior bandwidth of optical signaling on a platform capable of delivering the optical analogue to Moore's Law scaling of transistor density. Device size is expected to end Moore's Law scaling in photonics as Maxwell's equations limit the extent to which this parameter may be reduced. The focus of the work presented here surrounds photonic device miniaturization and the development of 3D optical interconnects as approaches to optimize performance in densely integrated optical interconnects. In this dissertation, several technological barriers inhibiting widespread adoption of photonics in data communications and telecommunications are explored. First, examination of loss and crosstalk performance in silicon nitride over SOI waveguide crossings yields insight into the feasibility of 3D optical interconnects with the first experimental analysis of such a structure presented herein. A novel measurement platform utilizing a modified racetrack resonator is then presented enabling extraction of insertion loss data for highly efficient structures while requiring minimal on-chip area. Finally, pioneering work in understanding the statistical nature of doublet formation in microphotonic resonators is delivered with the resulting impact on resonant device design detailed.