The murine eye naturally undergoes post-natal changes in eye size. This dissertation quantifies longitudinal structural and functional changes in control mice (C57BL/6J (B6), D2-Gpnmb+/SjJ) and in DBA/2J (D2) mice, which spontaneously develop elevated intraocular pressure (IOP). IOP elevation results in abnormal eye elongation, retinal nerve fiber layer (RNFL) thickness thinning and retinal ganglion cell (RGC) dysfunction and demise resembling human glaucoma. I measured structural changes with Optical Coherence Tomography (OCT), and RGC function with Pattern Electroretinogram (PERG). I also developed and refined provocation approaches (IOP elevation with changes in body posture; metabolic load with flickering light) to probe susceptibility of RGC function in D2 mice prone to glaucoma. Finally, I developed a novel system for recording, simultaneously but independently, the PERG from both eyes using asynchronous visual stimuli and deconvolution analysis. Simultaneous PERG recording from each eye was hitherto impossible due to the interocular cross-talk of the PERG signal. Altogether, the combination of these measures (OCT, PERG) and provocative conditions may represent powerful tools for glaucoma research using mouse models.

Radiotherapy plays a significant role in cancer treatment, and is thought to be curative by mainly killing tumor cells through damage to their genetic material. However, recent findings indicate that the tumor’s vascular blood supply is also a major determinant of radiation response. The goals of this thesis are to: (1) develop an experimental platform for small animals to deliver ionizing radiation and perform high-resolution optical imaging to treatment targets, and (2) use this toolkit to longitudinally monitor the response of tumors and the associated vasculature. The thesis has achieved: (1) customization of a novel micro-irradiator for mice, (2) technical development of an improved optical coherence tomography imaging system, (3) comprehensive experimental protocol and imaging optimization for optical microscopy in a specialized animal model, and (4) completion of a feasibility study to demonstrate the capabilities of the experimental platform in monitoring the response of tumor and vasculature to radiotherapy.

Radiotherapy plays a significant role in cancer treatment, and is thought to be curative by mainly killing tumor cells through damage to their genetic material. However, recent findings indicate that the tumor’s vascular blood supply is also a major determinant of radiation response. The goals of this thesis are to: (1) develop an experimental platform for small animals to deliver ionizing radiation and perform high-resolution optical imaging to treatment targets, and (2) use this toolkit to longitudinally monitor the response of tumors and the associated vasculature. The thesis has achieved: (1) customization of a novel micro-irradiator for mice, (2) technical development of an improved optical coherence tomography imaging system, (3) comprehensive experimental protocol and imaging optimization for optical microscopy in a specialized animal model, and (4) completion of a feasibility study to demonstrate the capabilities of the experimental platform in monitoring the response of tumor and vasculature to radiotherapy.

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.

<p>Cancer is a disease that affects millions of people each year. While methods for the prevention and treatment of the disease continue to advance, the early detection of precancerous development remains a key factor in reducing mortality and morbidity among patients. The current gold standard for cancer detection is the systematic biopsy. While this method has been used for decades, it is not without limitations. Fortunately, optical detection of cancer techniques are particularly well suited to overcome these limitations. This dissertation chronicles the development of one such technique called Fourier domain low coherence interferometry (fLCI). </p><p>The presented work first describes a detailed analysis of temporal and spatial coherence. The study shows that temporal coherence information in time frequency distributions contains valuable structural information about experimental samples. Additionally, the study of spatial coherence demonstrates the necessity of spatial resolution in white light interferometry systems. The coherence analysis also leads to the development of a new data processing technique that generates depth resolved spectroscopic information with simultaneously high depth and spectral resolution. </p><p>The development of two new fLCI optical systems is also presented. These systems are used to complete a series of controlled experiments validating the theoretical basis and functionality of the fLCI system and processing methods. First, the imaging capabilities of the fLCI system are validated through scattering standard experiments and animal tissue imaging. Next, the new processing method is validated by a series of absorption phantom experiments. Additionally, the nuclear sizing capabilities of the fLCI technique are validated by a study measuring the nuclear morphology of in vitro cell monolayers.</p><p>The validation experiments set the stage for two animal studies: an initial, pilot study and a complete animal trial. The results of these animal studies show that fLCI can distinguish between normal and dyplastic epithelial tissue with high sensitivity and specificity. The results of the work presented in this dissertation show that fLCI has great potential to develop into an effective method for early cancer detection.</p> / Dissertation

<p>Spectral Domain Optical Coherence Tomography (SDOCT) is a high-speed, high resolution imaging modality capable of structural and functional resolution of tissue microstructure. SDOCT fills a niche between histology and ultrasound imaging, providing non-contact, non-invasive backscattering amplitude and phase from a sample. Due to the translucent nature of the tissue, ophthalmic imaging is an ideal space for SDOCT imaging. </p><p>Structural imaging of the retina has provided new insights into ophthalmic disease. The phase component of SDOCT images remains largely underexplored, though. While Doppler SDOCT has been explored in a research setting, it remains to catch on in the clinic. Other, functional exploitations of the phase are possible and necessary to expand the utility of SDOCT. Spectral Domain Phase Microscopy (SDPM) is an extension of SDOCT that is capable of resolving sub-wavelength displacements within a focal volume. Application of sub-wavelength displacement measurement ophthalmic imaging could provide a new method for imaging of optophysiology. </p><p>This body of work encompasses both hardware and software design and development for implementation of SDOCT. Structural imaging was proven in both the lab and the clinic. Coarse phase changes associated with Doppler flow frequency shifts were recorded and a study was conducted to validate Doppler measurement. Fine phase changes were explored through SDPM applications. Preliminary optophysiology data was acquired to study the potential of sub-wavelength measurements in the retina. To remove the complexity associated with in-vivo human retinal imaging, a first principles approach using isolated nerve samples was applied using standard SDPM and a depth-encoded technique for measuring conduction velocity. </p><p>Results from amplitude as well as both coarse and fine phase processing are presented. In-vivo optophysiology using SDPM is a promising avenue for exploration, and projects furthering or extending this body of work are discussed.</p> / Dissertation

<p>Spectral&#8208;domain optical&#8208;coherence tomography (SDOCT) has recently emerged as a powerful new tool for noninvasive human retinal imaging. I have developed a low&#8208;cost, high resolution real&#8208;time Spectral Domain Optical Coherence Tomography (SDOCT) system optimized for rapid 3D imaging of the human retina in vivo. Then functional retinal OCT imaging such as polarization sensitive OCT (PSOCT) and Doppler OCT were also developed based on phase technique. Unique phase unwrapping method in retina is described to extract the total reflectivity, accumulative retardance and fast axis orientation of the retinal nerve fiber layer (RNFL). The polarization scrambling layer of the retinal pigment epithelium was segmented by employing single camera sequential scan bsed PSOCT. As an extension, synthetic wavelength method will be also introduced for phase unwrapping in cell imaging. Finally I present an algorithm for 3D refraction correction based on a vector representation which accounts for refraction of CT light in the cornea. Following 3D refraction correction of volumetric corneal datasets, we can estimate the corneal optical power, thickness and the individual wavefront aberrations of the epithelial and the refraction&#8208;corrected endothelial surfaces by using Zernike spectrum analysis.</p> / Dissertation

Atherosclerosis and specifically rupture of vulnerable plaques account for 23% of all deaths worldwide, far surpassing both infectious diseases and cancer. Plaque-based macrophages, often associated with lipid deposits, contribute to atherogenesis from initiation through progression, plaque rupture and ultimately, thrombosis. Therefore, the macrophage is an important early cellular marker related to vulnerability of atherosclerotic plaques. The objective of my research is to assess the ability of multiple optical imaging modalities to detect, and further characterize the distribution of macrophages (having taken up plasmonic gold nanoparticles as a contrast agent) and lipid deposits in atherosclerotic plaques. Tissue phantoms and macrophage cell cultures were used to investigate the capability of nanorose as an imaging contrast agent to target macrophages. Ex vivo aorta segments from a rabbit model of atherosclerosis after intravenous nanorose injection were imaged by optical coherence tomography (OCT), photothermal imaging (PTW) and two-photon luminescence microscopy (TPLM), respectively. OCT images depicted detailed surface structure of atherosclerotic plaques. PTW images identified nanorose-loaded macrophages (confirmed by co-registration of a TPLM image and corresponding RAM-11 stain on a histological section) associated with lipid deposits at multiple depths. TPLM images showed three-dimensional distribution of nanorose-loaded macrophages with a high spatial resolution. Imaging results suggest that superficial nanorose-loaded macrophages are distributed at shoulders on the upstream side of atherosclerotic plaques at the edges of lipid deposits. Combination of OCT with PTW or TPLM can simultaneously reveal plaque structure and composition, permitting assessment of plaque vulnerability during cardiovascular interventions. / text