Precise measurements of corneal layer thickness are required to treat, evaluate risk of, and determine the progression of pathologies within the eye. The thickness measurements are typically acquired as 2d images, known as tomograms, from an optical coherence tomography (OCT) system. With the creation of ultra-high resolution OCT (UHROCT), there is active research in precisely measuring, in vivo, previously unresolvable corneal structures at arbitrary locations within the cornea to determine their relationship with corneal health. In order to obtain arbitrary corneal thickness measurements, existing reconstruction techniques require the cornea to be densely sampled so that a 3d representation can be interpolated from a stack of tomograms. Unfortunately, tomogram alignment relies solely on image properties such as pixel intensity, and does not constrain the reconstruction to corneal anatomy. Further, the reconstruction method cannot properly compensate for eye-motion. The deficiencies due to eye-motion are exacerbated due to the amount of time required in a single imaging session to acquire a sufficient number of tomograms in the region of interest. The proposed methodology is the first to incorporate models of the anatomy and the imaging system to address the limitations of existing corneal reconstruction methods. By constructing the model in such a way as to decouple anatomy from the imaging system, it becomes less computationally expensive to estimate model parameters. The decoupling provides an iterative methodology that can allow additional constraints to be introduced in the future. By combining sparsely sampled UHROCT measurements with a properly designed corneal model, reconstruction allows researchers to determine corneal layer thicknesses at arbitrary positions in both sampled and unsampled regions. The proposed methodology demonstrates an approach to decouple anatomy and physiology from measurements of a cornea, allowing for characterization of pathologies through corneal thickness measurements. Another significant contribution resulting from the corneal model allows five of the corneal layer boundaries to be automatically located and has already been used to process thousands of UHROCT tomograms. Recent studies using this method have also been used to correlate contact-lens wear to hypoxia and corneal layer swelling. While corneal reconstruction represents the main application of this work, the reconstruction methodology can be extended to other medical imaging domains and can even represent temporal changes in tissue with minor modifications to the framework.

A high speed, high resolution spectral domain optical coherence tomography (SD-OCT) system was used to study in-vivo early morphological changes and optical nerve head (ONH) blood flow in the Long Evans rat retina, induced by administration of sodium iodate (NaIO3). Linear and circular scanned OCT images were acquired at the same location in the retina from healthy control rats and from rats injected with 40mg/kg of NaIO3 solution at 1, 3, 6 12, 24, 72 and 168 hours post drug administration. Morphological OCT images showed changes in the optical reflectance and layer thickness of the photoreceptor IS and OS. The formation of a new low reflective layer between the photoreceptor OS and the RPE was observed in all tested rats. This new layer appeared as early as 1 hour, increased in thickness after 6 hours, and disappeared by 12 hours post NaIO3 injection. The low optical reflectance and the dynamics of this new layer suggest that it was most likely fluid accumulation. Comparison with H&E stained histological sections and IgG immunohistochemistry revealed minimal photoreceptor OS cell swelling at hour 1, detachment of the OS from the RPE by hour 3, and breaking of the blood-retina barrier with significant fluid accumulation by hour 6 post NaIO3 injection. The Doppler Optical Micro-Angiography (DOMAG) algorithm was used to carry out quantitative analysis of the ONH blood flow. Estimation of flow rate on each ONH vessel was done by measurements of the Doppler angle, vessel size and the axial velocity. This study has demonstrated that the capability of UHR-OCT to study optical reflectance and layer thickness changes, rearrangement and detachment of the photoreceptor OS and RPE layers, together with flow rate estimation of retinal blood vessels. Therefore, it can serve as markers in future non-invasive, in-vivo studies of disease or drug induced retinal degeneration in ophthalmic research.

The work present in this thesis report introduces a novel non-destructive technique for experimentally measuring through thickness hygro-thermal strain of Nafion membranes though digital image correlation. An Optical Coherence Tomography (OCT) system was used to acquire images of a Nafion-TiO2 (titanium dioxide powder) composite membranes in a fuel cell like device. The proposed technique, commonly known as optical coherence elastography (OCE) makes use of the normalized correlation algorithm to calculate strain between two successive scans of different relative humidity step values. Different normalized correlation parameters were compared to measured results of PDMS-TiO2 phantoms in order to analyze accuracy. The effect of TiO2 on Nafion membranbes mechanical properties was further analysed by comparing the swelling behaviour of membranes with different concentrations. It has been found that Nafion undergoes approximately 25 – 30% more strain on the land section than on the channel section, regardless gas diffusion electrode (GDE) layer presence. Furthermore, it was shown that the overall strain on the material decrease by approximately 10% when GDE layers are present. Overall this work demonstrated how OCE is a viable technique for measuring through thickness strain distribution in Nafion composite membranes and has the potential to be implemented for non-destructive in situ measurements. / Graduate / 0548 / kellerv@uvic.ca

I propose and demonstrate a method by which barium titanate nanoparticle clusters can be used as exogenous contrast agents in Second Harmonic Optical Coherence Tomography imaging systems to localize and highlight desired regions of tissue. SH-OCT has previously been used to identify collagen within OCT images. However, SH-OCT signals from collagen are highly susceptible to inferior reflector artifacts because most of the second harmonic generated light is forward scattered. Second harmonic generating nanoparticle clusters exhibit high scattering properties, which can give them the advantage of backscattering a large quantity of second harmonic light while attenuating the forward scattered light. In this research project, a mathematical model is proposed in which the backward to forward scattering ratio of second harmonic generated light from nanoparticle layers is exponentially proportional to the thickness of the layer. This model was supported by measurements of the backward to forward scattering ratio of second harmonic light in barium titanate nanoparticles layers. This indicates that nanoparticle clusters can be designed and manufactured with the proper thickness so that they generate a large second harmonic signal without creating inferior reflector artifacts.

Spectral domain optical coherence tomography (SD-OCT) is a dispersed interferometric technology used to obtain tomographic images, typically of tissue for medical applications. OCT is a competing technology with confocal microscopy (CM) and confocal fluorescent microscopy (CFM), which are both used for biopsy imaging for pathology as the gold standard. OCT offers several advantages over CM/CFM: it is able to acquire a full 3D image in a single pass, it requires little or no sample preparation time, and the axial (depth) and lateral (transverse) resolution are not dependent on one another. SD-OCT is limited in imaging depth to a few millimetres due to the quality performance of the spectrograph section of the instrument--that which determines the sensitivity of the SD-OCT system. In this thesis a design for an SD-OCT system is presented that is suitable for biopsy imaging for pathological studies, i.e. an OCT microscope. The purpose of this system is to provide a fast diagnosis to be made in a surgical environment to reduce the amount of tissue removed from a patient and lower the chance of a returned visit at a later date due to insufficient tissue removal. The secondary purpose of the SD-OCT microscope is to serve as a research testbed system for implementing novel hardware advancements. One such technology, called an optical pupil slicer (OPS), will be implemented in the instrument to improve the depth imaging performance of the SD-OCT system over conventional SD-OCT systems. The OPS is a device that generally improves the performance of a dispersive-type spectrograph by increasing the spectral resolution without a loss in throughput, thereby increasing the sensitivity of the SD-OCT system.

Optical Coherence Tomography (OCT) is a relatively new interferometric technology that allows for high-resolution and non-destructive tomographic imaging. One of its primary current uses is for in vivo and ex vivo examination of medical samples. It is used for non-destructive examination of ocular disease, dermatological examination, blood vessel imaging, and many other applications. Some primary advantages of OCT imaging include rapid imaging of biological tissue with minimal sample preparation, 3D high-resolution imaging with depth penetrations of several millimeters, and the capability to obtain results in real time, allowing for fast and minimally invasive identification of many diseases. Current commercial OCT systems rely heavily on optical fiber-based designs. They depend on the robustness of the fiber to maintain system performance in variable environmental conditions but sacrifice the performance and flexibility of free-space optical designs. We discuss the design and implementation of a free-space OCT interferometer that can automatically maintain its alignment, allowing for the use of a free-space optical design outside of tightly controlled laboratory environments. In addition, we describe how similar enhancements can be made to other optical interferometric systems. By extending these techniques, we can provide similar improvements to many related fields, such as interferometric metrology and Fourier Transform Spectroscopy. Improvements in these technologies can help bring powerful interferometric tools to a wider audience.

Light delivery and sample handling systems are essential for any high performance imaging application. The custom design for two such devices with medical imaging applications are presented. The first device, a galvanometer-stage combination, is for general use optical coherence tomography and can be configured to scan over a large range of sample sizes and types. The second device, constructed in parallel, a rotation-linear stage combination, has been carefully designed for a specific imaging task: assessing tumour margins. The design of the two devices is driven by operational requirements and although requirements vary greatly from application to application, there are several common parameters that must be considered for every system. In this thesis, parameters like total scan time, scan resolution, sampling rate, and sample type flexibility are analysed and are some of the primary factors that influence the viability of a system for further development. This work's contribution to medical imaging research is the design of two light delivery systems and an analysis process that can be applied to future iterations of scan systems. The devices are shown to be flexible enough for use in test-bed systems, while providing the necessary functionality to meet the needs of medical histology and pathology. Controlling the light delivery and sample positioning of an imaging device adds important functionality to a scan system and is not a trivial task when high spatial-resolution scan spacing is required. The careful design of an imaging system to meet the unique requirements of the application enables better information and better resulting decision making. Advanced imagery provides new insights and perspectives to everyday scenes. It is these new perspectives that allow for re-evaluation and examination of problems with a fresh eye.

The main objective of this thesis is to investigate the intrinsic optical signals (IOSs) with an ultra-high resolution optical coherence tomography system (UHROCT). In order to study the retinal IOSs evoked by visible light, an UHROCT and an Electroretinogram (ERG) system was combined. An animal model (chicken retina) based on its retinal avascularity and cone dominance, was selected. Imaging the chicken retina with OCT resulted in high contrast, high resolution (~3μm axial and ~5 μm lateral resolution) 2D and 3D volumetric tomograms, in which all retina layers were clearly distinguishable. Using the combined UHROCT and ERG system to image IOSs from the chicken retina exposed to visible light (7ms green flash) resulted in highly reproducible IOS recordings from all retinal layers for the first time. All inner retinal layers showed an initial increase and subsequently a decrease in the intensity of the backreflected imaging light within the first 100 ms after the onset of the stimulus. Outer segments of the photoreceptors also showed a decrease in the backreflected imaging light within 100 ms after the onset of the flash. All retinal layers showed a strong decrease in the backreflected light within 150 to 175 ms after the onset of the flash. Imaging the pupil dynamics of the chicken with a modified combined UHROCT and ERG system showed that part of the strong negative IOSs observed in all retinal layers resulted from the vignetting of the imaging beam due to the light induced pupil constriction. Thorough analysis of the pupil dynamics acquired with UHROCT showed a time dependent effect of the anesthesia agent on pupil constriction. Further experiments to investigate an anesthesia effects on retinal function showed significant changes in ERG components. Statistical analysis showed that Isoflurane anesthesia severely affects the inner retinal response. In conclusion, it was hypothesized that the fast IOSs within ~50-100 ms after the onset of the visual stimulus originated from the neuronal tissue in the retina and are related to tissue optical property changes as a result of the electrical signal propagation in the light activated retina. Longer term decreases in backreflected light are likely due to pupil changes.

The changes in the human crystalline lens shape and its internal structure during accommodation and with aging are a fundamental component of the dynamic mechanism of accommodation and presbyopia, the loss of near vision with age. A better understanding of the crystalline lens changes during accommodation will help in developing new treatments to correct for presbyopia. The goal of this dissertation is to design and develop an imaging system to study the dynamic changes in lens shape during accommodative response. An imaging system based on spectral domain optical coherence tomography (SD-OCT) was developed with long axial range, high axial and lateral resolution and high speed for in vivo imaging the anterior segment along its entire length at video-rate. A slit-lamp mounted optical delivery scanning device for the extended depth SD-OCT system was developed. The delivery system was combined with a custom made unit that provides accommodation and disaccommodation step stimuli. A method to correct for the distortions of the OCT images was also developed that provides corrected two dimensional biometric data at different accommodative states.

The main objective of this thesis is to investigate the intrinsic optical signals (IOSs) with an ultra-high resolution optical coherence tomography system (UHROCT). In order to study the retinal IOSs evoked by visible light, an UHROCT and an Electroretinogram (ERG) system was combined. An animal model (chicken retina) based on its retinal avascularity and cone dominance, was selected. Imaging the chicken retina with OCT resulted in high contrast, high resolution (~3μm axial and ~5 μm lateral resolution) 2D and 3D volumetric tomograms, in which all retina layers were clearly distinguishable. Using the combined UHROCT and ERG system to image IOSs from the chicken retina exposed to visible light (7ms green flash) resulted in highly reproducible IOS recordings from all retinal layers for the first time. All inner retinal layers showed an initial increase and subsequently a decrease in the intensity of the backreflected imaging light within the first 100 ms after the onset of the stimulus. Outer segments of the photoreceptors also showed a decrease in the backreflected imaging light within 100 ms after the onset of the flash. All retinal layers showed a strong decrease in the backreflected light within 150 to 175 ms after the onset of the flash. Imaging the pupil dynamics of the chicken with a modified combined UHROCT and ERG system showed that part of the strong negative IOSs observed in all retinal layers resulted from the vignetting of the imaging beam due to the light induced pupil constriction. Thorough analysis of the pupil dynamics acquired with UHROCT showed a time dependent effect of the anesthesia agent on pupil constriction. Further experiments to investigate an anesthesia effects on retinal function showed significant changes in ERG components. Statistical analysis showed that Isoflurane anesthesia severely affects the inner retinal response. In conclusion, it was hypothesized that the fast IOSs within ~50-100 ms after the onset of the visual stimulus originated from the neuronal tissue in the retina and are related to tissue optical property changes as a result of the electrical signal propagation in the light activated retina. Longer term decreases in backreflected light are likely due to pupil changes.