Optical coherence tomography (OCT) is becoming an increasingly important modality for the noninvasive assessment of a variety of ocular diseases such as glaucoma, diabetic macular edema, and age-related macular degeneration. Even though individual layers of the retina are visible on OCT images, current commercial quantitative assessment is limited to measuring the thickness of only one layer. Because each intraretinal layer may be affected differently by disease, an intraretinal layer segmentation approach is needed to enable quantification of individual layer properties, such as thickness or texture. Furthermore, with the latest generation of OCT scanner systems producing true volumetric image data, processing these images using 3-D methods is important for maximal extraction of image information. In this thesis, an optimal 3-D graph search approach for the intraretinal layer segmentation of OCT images is presented. It is built upon the optimal 3-D multiple surface graph-theoretic approach presented by Li et al. (K. Li, X. Wu, D. Z. Chen, and M. Sonka, "Optimal surface segmentation in volumetric images - a graph-theoretic approach," IEEE Transactions on Pattern Analysis and Machine Intelligence, vol. 28, no. 1, pp. 119-134, 2006). In this method, multiple surfaces can be found simultaneously by transforming the 3-D segmentation problem into finding a minimum-cost closed set in a corresponding vertex-weighted geometric graph. However, the original formulation of this approach did not incorporate varying feasibility constraints or true regional information, two extensions that would aid in the intraretinal layer segmentation of OCT images. Thus, the major contributions of this thesis include: 1) extending the optimal 3-D graph-theoretic segmentation approach to allow for the incorporation of varying feasibility constraints and regional information, 2) developing a method for learning varying constraints and cost functions from examples for use in the approach, 3) developing and validating a method for the 3-D segmentation of intraretinal layers in both time-domain and spectral-domain OCT images (achieving error rates comparable to that of multiple human experts), and 4) analyzing layer thickness properties in normal subjects and in patients with anterior ischemic optic neuropathy (AION).

Optical coherence tomography (OCT) is becoming an increasingly important modality for the diagnosis and management of a variety of eye diseases, such as age-related macular degeneration (AMD), glaucoma, and diabetic macular edema (DME). Spectral domain OCT (SD-OCT), an advanced type of OCT, produces three dimensional high-resolution cross-sectional images and demonstrates delicate structure of the functional portion of posterior eye, including retina, choroid, and optic nerve head. As the clinical importance of OCT for retinal disease management and the need for quantitative and objective disease biomarkers grows, fully automated three-dimensional analysis of the retina has become desirable. Previously, our group has developed the Iowa Reference Algorithms (http://www.biomed-imaging.uiowa.edu/downloads/), a set of fully automated 3D segmentation algorithms for the analysis of retinal layer structures in subjects without retinal disease. This is the first method of segmenting and quantifying individual layers of the retina in three dimensions. However, in retinal disease, the normal architecture of the retina - specifically the outer retina - is disrupted. Fluid and deposits can accumulate, and normal tissue can be replaced by scar tissue. These abnormalities increase the irregularity of the retinal structure and make quantitative analysis in the image data extra challenging. In this work, we focus on the segmentation of the retina of patients with age-related macular degeneration, the most important cause of blindness and visual loss in the developed world. Though early and intermediate AMD results in some vision loss, the most devastating vision loss occurs in the two endstages of the disease, called geographic atrophy (GA) respectively choroidal neovascularization (CNV). In GA, because of pathological changes that are not fully understood, the retinal pigment epithelium disappears and photoreceptors lose this supporting tissue and degenerate. Second, in CNV, the growth of abnormal blood vessels originating from the choroidal vasculature causes fluid to enter the surrounding retina, causing disruption of the tissues and eventual visual loss. The severity and progress of early AMD is characterized by the formation of drusen and subretinal drusenoid deposits, structures containing photoreceptor metabolites - primarily lipofuscin - the more drusen the more severe the disease and the higher the risk of progressing to GAD or CNV. Thus, to improve the image guided management of AMD, we will study automated methods for segmenting and quantifying these intraretinal, subretinal and choroidal structures, including different types of abnormalities and layers, focusing on the outer retina. The major contributions of this thesis include: 1) developing an automated method of segmenting the choroid and quantifying the choroidal thickness in 3D OCT images; 2) developing an automated method of quantifying the presence of drusen in early and intermediate AMD; 3) developing an method of identifying the different ocular structures simultaneously; 4) studying the relationship among intraretinal, subretinal and choroidal structures.

Optical coherence tomography (OCT), being a noninvasive imaging modality, has begun to find vast use in the diagnosis and management of retinal diseases. These high-resolution images of the retina allow structural changes to be detected and tracked. For instance, in glaucoma, the retinal nerve fiber layer (RNFL) has been known to thin. The recent availability of the considerably larger volumetric data from the spectral-domain OCT scanners has further increased the need for new processing techniques. This body of work is centered around an automated 3-D graph-theoretic approach for the segmentation of 7 surfaces (6 layers) of the retina from 3-D spectral-domain OCT images centered on the optic nerve head (ONH). The multiple surfaces are detected through the computation of a minimum-cost closed set in a vertex-weighted graph constructed using edge/regional information, and subject to a priori determined varying surface interaction and smoothness constraints. The method also addresses the challenges posed by presence of the neural canal and the large blood vessels found at the ONH. The method was used to study RNFL thickness maps of normal and glaucomatous eyes, which showed average thicknesses of 73.72 +/- 32.72um and 60.38 +/- 25.22um (p < 0.01), respectively.

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