The work reported in this thesis has been carried out in the following two areas of Optical metrology: 1. Measurement and correction of prism angles 2. Measurement of refractive indices using a spectrograph. The prism angles are conventionally tested by mechanical bevel protractors, autocol-limators (angle dekkors), simple interference techniques and interferometers. All these methods have their own limitations either in accuracy or in terms of cost. Mechanical methods are usually employed to measure the angles of prisms. Interference techniques and interferometers are also used but they need optically polished components. For both mechanical and simple interference methods of testing, it is essential to fabricate more than a single component in number. The process of building interferometers or purchasing interferometers, angle dekkors and standard angle gauges is not cost effective for many research laboratories, and medium scale industries. To overcome these difficulties simple and inexpensive methods without sacrificing the accuracy in the bargain are suggested for the measurement of prism angles, based on the principles of reflection of light. The refractive indices of prism materials for invisible and weaker spectral lines are usually determined from spectrograms using dispersion formulae and numerical interpolation techniques. In these methods, the accuracy of the results depends on the accuracy of determining the constants of the dispersion formulae. A simple experimental technique, using a spectrograph, is devised for the measurement of refractive indices of solids and liquids both for visible and invisible spectral lines (wavelengths). The thesis has been divided into six chapters. The first chapter starts with the general introduction. The second chapter presents the literature review of the existing methods for angle and refractive index measurements. The third chapter describes the proposed new techniques for prism angle measurements. The fourth chapter presents the experimental results of angle measurements, and the discussion of the accuracy of the results. This chapter also gives the scope for further research. The fifth chapter describes a newly proposed technique for measuring refractive indices and the experimental results. This chapter also gives the scope for further research. The summary of the results, conclusions, and suggestions for further work are presented in chapter six.

Cataract surgery is the most commonly performed surgery within the UK with 400,000 surgeries performed each year. Currently no guidelines exist for clinicians regarding target refraction discussions, spectacle provision post-operatively and driving advice following surgery. The PhD aimed to start the process of developing pre- and post-operative management guidelines for patients developed by both optometrists and ophthalmologists which could then be disseminated to both professions in the hope of improving the overall outcome of surgery. The current literature highlighted target refraction discussions were lacking or non-existent which left some myopes dissatisfied after surgery due to an emmetropic target refraction leaving them unable to read without glasses as they did prior to surgery. Target refraction discussions were found to be linked with years of experience and this needs further exposure in continuing professional development. Post-operative driving advice was found to be inconsistent and vary between practitioners and between optometry and ophthalmology. Advice was found to vary from driving “immediately” following surgery up to 6 weeks post-operatively. Re-analysis of (de Juan et al. 2013) data during our systematic review and meta-analysis found refraction to be stable 1-2 weeks following surgery for 93% of patients. It was found a large change between pre- and post-surgery cylindrical power/axis may be an indicator that refractive stability has not occurred. Although this study had limitations it confirmed refraction is stable sooner than the current guidelines of 4-6 weeks. Finally, we used a Delphi process to develop refractive management guidelines with a total of fifteen recommendations finalised.

This thesis describes laboratory measurements of the complex refractive index of volcanic ash particles. These measurements are needed to model the radiative impact of volcanic ash, vital for accurate satellite remote sensing. Three experimental methods have been developed, and the results for the complex refractive index and optical properties of a wide range of volcanic ash samples are presented. Measurements were made of the spectral transmission of radiation through suspended volcanic ash particles inside an aerosol cell, using a Fourier transform spectrometer at infrared wavelengths and two diffraction grating spectrometers covering ultraviolet, visible, and near-infrared wavelengths. In addition to the optical measurements, a suite of sampling and sizing instruments were connected downstream of the aerosol cell to measure the particle size distribution. The method was calibrated using two quartz samples. Mass extinction coefficients for nine volcanic ash samples, at 0.3-14 μm, are presented and show considerable variation. These variations are linked to the composition of the samples, measured using X-ray fluorescence (XRF) analysis. The complex refractive index, at 0.3-14 μm, of the two quartz samples and two samples of volcanic ash from the 2010 Eyjafjallajökull eruption were retrieved from the extinction measurements. The forward model used Mie theory and a classical damped harmonic oscillator (CDHO) model to represent the complex refractive index of the samples in terms of a finite set of band parameters, as well as the real refractive index of the sample in the small wavelength limit. Previous studies have shown that there is a redundancy in the retrievals between the band strength parameters and the real refractive index in the small wavelength limit, which can lead to spurious values for the retrieved complex refractive index. This problem was overcome by using an independent measurement of the real refractive index at a visible wavelength, to constrain the model parameter of the real refractive index in the short wavelength limit. Independent measurements of the complex refractive index at visible wavelengths are also important because the extinction produced at these wavelengths is highly sensitive to the particle size distribution, and any uncertainty in the measured size distribution will contribute to significant systematic error in the refractive index retrieved from extinction. The retrieved spectral complex refractive index of Eyjafjallajökull ash was applied using the ORAC retrieval scheme to measurements of the 2010 Eyjafjallajökull eruptionmade by theMODIS instrument aboard NASA's Terra satellite. Significant difference were found in the retrieved plume parameters of optical path, effective radius, and plume altitude, compared to assuming a literature measurement for the refractive index of pumice. For three discrete visible wavelengths (450, 546.7, and 650 nm) an optical microscope was used to make measurements of the complex refractive index of the volcanic ash samples. The long-established Becke line method was used to measure the real refractive index of the samples. For the imaginary refractive index, a new and novelmethod was developed involving measurements of the attenuation of light in individual particles. A strong linear correlation was found between the SiO₂ content of the samples and both their real and imaginary refractive indices at the visible wavelengths investigated. Furthermore, from the XRF compositional analysis of the samples values were calculated for the ratio of non-bridging oxygen atoms per tetrahedral cation (NBO/T), and it was found that NBO/T was an even stronger predictor of real refractive index at visible wavelengths. The optical microscope measurements could only be applied to particles with a radius larger than 10 μm. A new refractometer method was investigated for retrieving the real refractive index of submicron particles from colloidal reflectance measurements close to the critical angle in an internal reflection configuration. A coherent scattering model (CSM) was used to model the coherent reflection from a half-space of monodisperse or polydisperse particles, and a simple extension of the model is presented to properly account for the modified size distribution at the interface in an internal reflection set-up. A rigorous sensitivity analysis was performed to determine how experimental uncertainties propagate into uncertainty associated with the retrieved real refractive index, and the uncertainty due to non-spherical effects was estimated using T-matrix methods. Experimental reflectance data at a wavelength of 635 nm were obtained for spherical monodisperse polystyrene calibration particles, a polydisperse sand sample, and a polydisperse volcanic ash sample. The retrieved values for the real refractive index agreed, within propagated uncertainties, with values measured using other techniques. The method is shown to be a viable technique for measuring the real refractive index of small quantities of submicron particles, and can also retrieve the concentration and size of particles.

Approved for public release; distribution in unlimited. / This is a study of abnormal refractive layer occurrence over the Amazon region and possible effects on radar and ESM systems, ground or airborne based. Climatologic data from three stations in that region are analyzed using computations from the Global Tropospheric Experiment (GTE), soundings and satellite imagery. The GTE data provide monthly occurrences and seasonality of atmospheric ducts and superrefractive layers. Further, individual soundings from the March-June 2003 period and the Advanced Refractive Effects Prediction Systems (AREPS) 2.1 software are used in a case study that analyzed these layers and, in addition, subrefractive and multiple layers. Selected soundings were used in simulations to explain the effects of different types of abnormal layers on the electromagnetic propagation. Although abnormal layers did not affect ground systems, airborne ones were. For radar, a region with low or no detection is created when an abnormal layer refracts the electromagnetic energy upwards or downwards. Some combinations of multiple layers may cause effects even stronger. It is concluded that knowledge of the abnormal layers occurrence is important for operations in the Amazon region. Further, airborne radar platforms should measure local refractive conditions, if possible. A comprehensive study in time and space is recommended to provide forecasting. / Lieutenant Colonel, Brazilian Air Force

In this work, different optical techniques have been explored to study and characterize crude oil and its asphaltene. Crude oil is extremely complex fluid used to produce fuel for a wide range of applications. The characterization of this fluid is key for optimum operations in the oil and gas industry. First, we demonstrate the application of gold nanorods in characterizing a different set of crude oils. We utilize the high sensitivity of the Localized Surface Plasmon Resonance (LSPR) of the nanorods to the surrounding environment to measure the crude oil refractive index. We immobilized the nanorods on a glass substrate and took the measurement in a reflection configuration. The setup and the nanorods were calibrated using different fluids with known refractive index, and a sensitivity of 247 nm/RIU and a resolution of 0.013 RIU have been achieved. In addition to the simplicity of this approach, it has eliminated the absorption issue and made it possible to measure high optical density crude oils with typical Visible-NIR wavelengths. Surface-Enhanced Raman Spectra (SERS) can also be measured. SERS can provide additional useful information, especially to some applications such as downhole fluid analysis, where confirmation of the hydrocarbons presence is necessary. In the second part of this work, we used Terahertz Time-Domain Spectroscopy (THz-TDS) to study the asphaltene in three different crude oils. THz-TDS has a feature of measuring the amplitude and time delay and consequently the refractive index and absorption coefficient spectra simultaneously. Our approach is based on measuring the THz signal from neat crude oil samples and comparing it with the THz signal after removing the asphaltene from the samples (maltene). The results show that the difference in the time delay and the peak amplitude between the neat oil and the maltene have a linear relation with the asphaltene content. The refractive index spectra of different asphaltenes show variation in the low THz frequencies and comparable spectra in the higher frequencies. The absorption of asphaltene was mild and no distinctive absorption feature was observed except for some narrow absorption peaks that we attributed to water molecules adsorbed on the asphaltene. / Graduate

Indiana University-Purdue University Indianapolis (IUPUI) / Introduction: Multiphoton fluorescence excitation microscopy (MPM) is an invaluable tool for studying processes in tissue in live animals by enabling biologists to view tissues up to hundreds of microns in depth. Unfortunately, imaging depth in MPM is limited to less than a millimeter in tissue due to spherical aberration, light scattering, and light absorption. Spherical aberration is caused by refractive index mismatch between the objective immersion medium and sample. Refractive index heterogeneities within the sample cause light scattering. We investigate the effects of refractive index mismatch on imaging depth in MPM. Methods: The effects of spherical aberration on signal attenuation and resolution degradation with depth are characterized with minimal light absorption and scattering using sub-resolution microspheres mounted in test sample of agarose with varied refractive index. The effects of light scattering on signal attenuation and resolution degradation with depth are characterized using sub-resolution microspheres in kidney tissue samples mounted in optical clearing media to alter the refractive index heterogeneities within the tissue. Results: The studies demonstrate that signal levels and axial resolution both rapidly decline with depth into refractive index mismatched samples. Interestingly, studies of optical clearing with a water immersion objective show that reducing scattering increases reach even when it increases refractive index mismatch degrading axial resolution. Scattering, in the absence of spherical aberration, does not degrade axial resolution. The largest improvements in imaging depth are obtained when both scattering and refractive index mismatch are reduced. Conclusions: Spherical aberration, caused by refractive index mismatch between the immersion media and sample, and scattering, caused by refractive index heterogeneity within the sample, both cause signal to rapidly attenuate with depth in MPM. Scattering, however, seems to be the predominant cause of signal attenuation with depth in kidney tissue. Kenneth W. Dunn, Ph.D., Chair

No / This review aims to disentangle cause and effect in the relationship between anisometropia and amblyopia. Specifically, we examine the literature for evidence to support different possible developmental sequences that could ultimately lead to the presentation of both conditions. The prevalence of anisometropia is around 20% for an inter-ocular difference of 0.5D or greater in spherical equivalent refraction, falling to 2-3%, for an inter-ocular difference of 3D or above. Anisometropia prevalence is relatively high in the weeks following birth, in the teenage years coinciding with the onset of myopia and, most notably, in older adults starting after the onset of presbyopia. It has about one-third the prevalence of bilateral refractive errors of the same magnitude. Importantly, the prevalence of anisometropia is higher in highly ametropic groups, suggesting that emmetropization failures underlying ametropia and anisometropia may be similar. Amblyopia is present in 1-3% of humans and around one-half to two-thirds of amblyopes have anisometropia either alone or in combination with strabismus. The frequent co-existence of amblyopia and anisometropia at a child's first clinical examination promotes the belief that the anisometropia has caused the amblyopia, as has been demonstrated in animal models of the condition. In reviewing the human and monkey literature however it is clear that there are additional paths beyond this classic hypothesis to the co-occurrence of anisometropia and amblyopia. For example, after the emergence of amblyopia secondary to either deprivation or strabismus, anisometropia often follows. In cases of anisometropia with no apparent deprivation or strabismus, questions remain about the failure of the emmetropization mechanism that routinely eliminates infantile anisometropia. Also, the chronology of amblyopia development is poorly documented in cases of 'pure' anisometropic amblyopia. Although indirect, the therapeutic impact of refractive correction on anisometropic amblyopia provides strong support for the hypothesis that the anisometropia caused the amblyopia. Direct evidence for the aetiology of anisometropic amblyopia will require longitudinal tracking of at-risk infants, which poses numerous methodological and ethical challenges. However, if we are to prevent this condition, we must understand the factors that cause it to develop.

When exposed to light, metal nanoparticles exhibit a phenomenon known as LSPR, Localized Surface Plasmon Resonance. The wavelengths at which LSPR occurs is very dependent on the refractive index of the surrounding medium. Binding of biomolecules to the surface of gold nanoparticles result in a change in the refractive index that can be detected spectrophotometrically by monitoring the LSPR peak shift. When functionalized with the corresponding ligand(s), gold nanoparticles can be utilized in biosensors to detect the presence and concentration of a predetermined analyte. However, the system must exhibit high specificity and give rise to a detectable shift for analytes in the desired concentration range to be of commercial interest. The aim of the diploma project was to investigate and optimize the biofunctionalization and performance of a fiber optics based LSPR biosensor.  Three ligand systems were investigated for detection of antibodies (IgG), insulin and avidin. Binding of the analyte to the ligand caused a shift of a few nanometers when using spherical gold nanoparticles. The shifts were significantly larger when using gold nanorods. When using the IgG and insulin ligands, only minor unspecific binding was observed. The setup thus shows great potential for use in a wide range of sensing applications.

Analyzing the structure of a single cell based on its refractive index (RI) distribution is a common and valued approach, because it does not require any artificial markers. The RI is an inherent structural marker that can be quantified in three dimensions with optical diffraction tomography (ODT), an inverse scattering technique. This work reviews the theory of ODT and its implementation with an emphasis on single-cell analysis, identifying the Rytov approximation as the most efficient descriptor for light propagation. The accuracy of the reconstruction method is verified with in silico data and imaging artifacts associated with the inverse scattering approach are addressed. Furthermore, an experimental ODT setup is presented that consists of a bright-field microscope, a phase-imaging camera, and an optical trap combined with a microfluidic chip. A novel image analysis pipeline is proposed that addresses image corrections and frame alignment of the recorded data prior to the RI reconstruction. In addition, for a rotational axis that is tilted with respect to the image plane, an improved reconstruction algorithm is introduced and applied to single, suspended cells in vitro, achieving sub-cellular resolution.

Thesis (MSc)--Stellenbosch University, 2014. / ENGLISH ABSTRACT: Terahertz (THz) radiation is often used in many promising applications such as information and communication technology and airport security. Optimized and adapted terahertz fields hold huge promise for leading this technology further. This study is focused on terahertz time domain spectroscopy (THz-TDS). In THz-TDS the electric field is measured, therefore both amplitude and phase information of the THz pulse can be obtained. We used the pump-probe technique in order to measure a THz pulse from the photoconductive antenna. A pulsed fiber laser with FWHM of ' 100 fs was used for this. The frequency spectrum of the measured THz pulse was obtained via a fast Fourier transform. We studied the principles of the THz pulse generation as well as detection, with a photoconductive antenna as emitter and detector. In this study terahertz spectroscopy has been used to investigate the refractive index and absorption coefficient of different types of materials in the terahertz region. The last part of this study deals with a simple process for material parameter extraction of a polymer sample using commercial software called Teramat1.0. It uses the sample thickness, the reference THz pulse and the transmitted THz pulse to retrieve the complex refractive index of the sample. / AFRIKAANSE OPSOMMING: Terahertz (THz) straling word gereeld gebruik vir belowende toepassings soos inligting en kommunikasie tegnologie en lughawe sekuriteit. Geoptimeerde en aangepaste terahertz velde dra by tot die bevordering van die tegnologie. Hierdie studie fokus op terahertz tyd domein spektroskopie (THz-TDS). In THz-TDS word die elektriese veld gemeet en dus word beide amplitude en fase inligting van die THz puls verkry. Ons gebruik ’n pomp en toets tegniek om die THz puls deur ’n fotogeleidende antenna te bepaal. ’n Gepulseerde vesel laser met FWHM van 100 fs word hiervoor benut. Die frekwensie spektrum van die gemete THz puls word bereken deur ’n vinnige Fourier transvorm te bereken. Die beginsels van die generering en deteksie van THz pulse is bestudeer met ’n fotogeleidende antenna as sender en ontvanger. In die studie is terahertz spektroskopie gebruik om die brekingsindekse en die absorpsie koeffisiënte van verskillende materiale in die terahertz gebied te bepaal. Die laaste gedeelte van die studie handel oor ’n eenvoudige proses om die materiaal parameters van ’n polimeer te bepaal deur gebruik te maak van kommersiële sagteware Teramat 1.0. Die monster dikte, die THz verwysingspuls en die deurgelate puls word gebruik om die komplekse brekingsindeks van die materiaal te bereken.