Optical Coherence Tomography (OCT) is a novel optical imaging technique that has assumed significant importance in bio-medical imaging in the last two decades because it is non-invasive and provides accurate, high resolution images of three dimensional cross-sections of body tissue, exceeding the capabilities of the current predominant imaging technique –ultrasound. In this thesis, high resolution OCT is investigated for in vivo detection of abnormal skin pathology for the early diagnosis of cancer. The technology presented is based on a dynamic focusing microscopic imaging probe conceived for skin imaging and the detection of abnormalities in the epithelium. A novel method for dynamic focusing in the biological sample using liquid crystal (LC) lens technology to obtain three dimensional images with invariant resolution throughout the cross-section and depth of the sample is presented and discussed. Two different skin probe configurations that incorporate dynamic focusing with LC lenses, one involving a reflective microscope objective sub-system, and the other involving an all-refractive immersion microscope objective sub-system are investigated. In order to ensure high resolution imaging, a low coherence broadband source, namely a femtosecond mode-locked Ti: sapphire laser centered at a wavelength of approximately 800nm is used to illuminate the sample. An in-depth description and analysis of the optical design and predicted performance of the two microscope objectives designed for dynamic three dimensional imaging at 5ìm resolution for the chosen broadband spectrum is presented.

Microvasculature can be found in almost every part of the human body, including the internal organs. Importantly, abnormal changes in microvasculature are usually related to pathological development of the tissue cells. Monitoring of changes in blood flow properties in microvasculature, therefore, provides useful diagnostic information about pathological conditions in biological tissues as exemplified in glaucoma, diabetes, age related macular degeneration, port wine stains, burn-depth, and potentially skin cancer. However, the capillary network is typically only one cell in wall thickness with 5 to 10 microns in diameter and located in the dermis region of skin. Therefore, a non-invasive flow imaging technique that is capable of depth sectioning at high resolution and high speed is demanded. Optical coherence tomography (OCT), particularly after its advancement in frequency domain OCT (FD-OCT), is a promising tool for non-invasive high speed, high resolution, and high sensitivity depth-resolved imaging of biological tissues. Over the last ten years, numerous efforts have been paid to develop OCTbased flow imaging techniques. An important effort is the development of phase-resolved Doppler OCT (PR-DOCT). Phase-resolved Doppler imaging using FD-OCT is particularly of interest because of the direct access to the phase information of the depth profile signal. Furthermore, the high speed capability of FD-OCT is promising for real time flow monitoring as well as 3D flow segmentation applications. However, several challenges need to be addressed; 1) Flow in biological samples exhibits a wide dynamic range of flow velocity caused by, for example, the iv variation in the flow angles, flow diameters, and functionalities. However, the improvement in imaging speed of FD-OCT comes at the expense of a reduction in sensitivity to slow flow information and hence a reduction in detectable velocity range; 2) A structural ambiguity socalled 'mirror image' in FD-OCT prohibits the use of maximum sensitivity and imaging depth range; 3) The requirement of high lateral resolution to resolve capillary vessels requires the use of an imaging optics with high numerical aperture (NA) that leads to a reduction in depth of focus (DOF) and hence the imaging depth range (i.e. less than 100 microns) unless dynamic focusing is performed. Nevertheless, intrinsic to the mechanism of FD-OCT, dynamic focusing is not possible. In this dissertation, the implementation of PR-DOCT in a high speed swept-source based FD-OCT is investigated and optimized. An acquisition scheme as well as a processing algorithm that effectively extends the detectable velocity dynamic range of the PR-DOCT is presented. The proposed technique increased the overall detectable velocity dynamic range of PR-DOCT by about five times of that achieved by the conventional method. Furthermore, a novel technique of mirror image removal called ‘Dual-Detection FD-OCT’ (DD-FD-OCT) is presented. One of the advantages of DD-FD-OCT to Doppler imaging is that the full-range signal is achieved without manipulation of the phase relation between consecutive axial lines. Hence the full-range DD-FDOCT is fully applicable to phase-resolved Doppler detection without a reduction in detectable velocity dynamic range as normally encountered in other full-range techniques. In addition, PRDOCT can utilize the maximum SNR provided by the full-range capability. This capability is particularly useful for imaging of blood flow that locates deep below the sample surface, such as v blood flow at deep posterior human eye and blood vessels network in the dermis region of human skin. Beside high speed and functional imaging capability, another key parameter that will open path for optical diagnostics using OCT technology is high resolution imaging (i.e. in a regime of a few microns or sub-micron). Even though the lateral resolution of OCT can be independently improved by opening the NA of the imaging optics, the high lateral resolution is maintained only over a short range as limited by the depth of focus that varies inversely and quadratically with NA. Recently developed by our group, ‘Gabor-Domain Optical Coherence Microscopy’ (GD-OCM) is a novel imaging technique capable for invariant resolution of about 2-3 m over a 2 mm cubic field-of-view. This dissertation details the imaging protocol as well as the automatic data fusion method of GD-OCM developed to render an in-focus high-resolution image throughout the imaging depth of the sample in real time. For the application of absolute flow measurement as an example, the precise information about flow angle is required. GDOCM provides more precise interpretation of the tissue structures over a large field-of-view, which is necessary for accurate mapping of the flow structure and hence is promising for diagnostic applications particularly when combined with Doppler imaging. Potentially, the ability to perform high resolution OCT imaging inside the human body is useful for many diagnostic applications, such as providing an accurate map for biopsy, guiding surgical and other treatments, monitoring the functional state and/or the post-operative recovery process of internal organs, plaque detection in arteries, and early detection of cancers in the gastrointestinal tract. Endoscopic OCT utilizes a special miniature probe in the sample arm to vi access tubular organs inside the human body, such as the cardiovascular system, the lung, the gastrointestinal tract, the urinary tract, and the breast duct. We present an optical design of a dynamic focus endoscopic probe that is capable of about 4 to 6 m lateral resolution over a large working distance (i.e. up to 5 mm from the distal end of the probe). The dynamic focus capability allows integration of the endoscopic probe to GD-OCM imaging to achieve high resolution endoscopic tomograms. We envision the future of this developing technology as a solution to high resolution, minimally invasive, depth-resolved imaging of not only structure but also the microvasculature of in vivo biological tissues that will be useful for many clinical applications, such as dermatology, ophthalmology, endoscopy, and cardiology. The technology is also useful for animal study applications, such as the monitoring of an embryo’s heart for the development of animal models and monitoring of changes in blood circulation in response to external stimulus in small animal brains.

Yes / To introduce and evaluate the performance in detecting glaucomatous abnormalities of a novel method for extracting en face slab images (SMAS), which considers varying individual anatomy and configuration of retinal nerve fiber bundles. Dense central retinal spectral domain optical coherence tomography scans were acquired in 16 participants with glaucoma and 19 age-similar controls. Slab images were generated by averaging reflectivity over different depths below the inner limiting membrane according to several methods. SMAS considered multiple 16 µm thick slabs from 8 to 116 µm below the inner limiting membrane, whereas 5 alternative methods considered single summary slabs of various thicknesses and depths. Superpixels in eyes with glaucoma were considered abnormal if below the first percentile of distributions fitted to control data for each method. The ability to detect glaucoma defects was measured by the proportion of abnormal superpixels. Proportion of superpixels below the fitted first percentile in controls was used as a surrogate false-positive rate. The effects of slab methods on performance measures were evaluated with linear mixed models. The ability to detect glaucoma defects varied between slab methods, χ2(5) = 120.9, P

<p>Asymmetric multiple quantum wells (AMQWs) can provide broad and flat gain spectra. Broadly tunable diode lasers can be realized with AMQW active regions and without the need for antireflection coatings on cleaved facets.</p> <p> This thesis reports the application of AMQW broadly tunable lasers with uncoated facets for Fourier domain and synthesized optical coherence tomography (OCT). A depth resolution of 13 μm in air was obtained with a test bed OCT system that used diffractive optical elements, short external cavities, and AMQW InGaAsP/InP broadly tunable lasers as the light sources for the Fourier domain and the synthesized OCT measurements. The centre wavelengths of the broadly tunable sources were 1550 nm and the tunable ranges were ≤ 117 nm.</p> <p>The features of broad and flat gain spectra of AMQWs also make AMQWs ideal candidates for broad spectral width superluminescent diodes (SLDs). 1300 nm AMQW InGaAsP/InP SLDs were designed and fabricated for application to time domain OCT. For the design of the active region, it was found by simulation of gain and the comparison of two growths that the transition carrier density (TCD) has to be reasonably high to achieve high power SLDs. A transfer matrix method was used to solve for the modes of planar optical waveguides with arbitrary layers and the thicknesses of these layers were optimized with a Marquardt nonlinear fitting method. With the optimization of the optical waveguide and with AMQWs with high TCDs, the output power of SLDs could reach 2 mW with > 90 nm spectral width. It is shown by time domain OCT measurements that the depth resolution of the OCT measurements could reach 7.85 μmin air with double section SLDs.</p> <p>Two dimensional OCT images of a glass cover slip were built with the imageSC function in Matlab™. Image enhancement with blind/not-blind deconvolution was performed based on the measured point spread function (PSF) of the OCT setup. A Richardson-Lucy algorithm was used as the blind deconvolution method and a not-blind version of a Jansson-Van Cittert method was used.</p> / Thesis / Doctor of Philosophy (PhD)

Aim: To evaluate repeatability and reproducibility of macular thickness measurements in visually normal eyes using the Topcon 3D OCT-1000. Methods: Phase 1 investigated scan repeatability, the effect of age and pupil dilation. Two groups (6 younger and 6 older participants) had one eye scanned 5 times pre and post- dilation by 1 operator. Phase 2 investigated between-operator, within and between-visit reproducibility. 10 participants had 1 un-dilated eye scanned 3 times on 2 separate visits by 2 operators. Results: Phase 1: No significant difference existed between repeat scans (p=0.75) and no significant difference was found pre- and post-dilation (p=0.54). In the younger group variation was low (95% limits ± 3.62 m) and comparable across all retinal regions. The older group demonstrated greater variation (95% limits ± 7.6 m). Phase 2: For a given retinal location, 95% confidence limits for within-operator, within-visit reproducibility was 5.16 m. This value increased to 5.56 m for the same operator over two visits and to 6.18 m for two operators over two visits. Conclusion: A high level repeatability, close to 6 m, of macular thickness measurement is possible using the 3D OCT- 1000. Measured differences in macular thickness between successive visits that exceed 6 m in pre-presbyopic individuals are therefore likely to reflect actual structural change. OCT measures are more variable in older individuals and it is advisable to take a series of scans so that outliers can be more easily identified.

No description available.

Regenerative medicine involves formation of tissue or organ for replacement of a wounded or dysfunctional tissue. Healthy cells extracted from the patient are expanded and are seeded on a three-dimensional biodegradable scaffold. The structure is then placed in a bioreactor and is provided with nutrients for the cells, which proliferate and migrate throughout the scaffold to eventually form a desired to tissue that can be transplanted into the patient's body.  Inability to monitor this complex process of regeneration in real-time makes control and optimization of this process extremely difficult. Histology, the gold standard used for tissue structural assessment, is a static technique that only provides "snapshots" of the progress and requires the specimen to be sacrificed. This inefficiency severely limits our understanding of the biological processes associated with tissue growth during the in vitro pre-conditioning phase. Optical Coherence Tomography (OCT) enables imaging of cross sectional structure in biological tissues by measuring the echo time delay of backreflected light. OCT has recently emerged as an important method to assess the structures of physiological, pathological as well as tissue engineered blood vessels. The goal of the present study is to develop an imaging system for non-destructive monitoring of blood vessels maturing within a bioreactor. Non-destructive structural imaging of tissue-engineered blood vessels cultured in a novel bioreactor was performed using free-space and catheter-based OCT imaging, while monitoring of the endothelium development was performed using a fluorescence imaging system that utilizes a commercial OCT catheter. The project included execution of three specific aims. Firstly, we developed OCT instrumentation to determine geometrical and optical properties of porcine and human skin in real-time. The purpose of the second aim was to assess structural development of tissue-engineered blood vessels maturing in a bioreactor. We constructed a novel quartz-based bioreactor that will permit free space and catheter-based OCT imaging of vascular grafts. The grafts were made of biodegradable PCL-collagen and seeded with multipotent mesenchymal cells. We imaged the maturing grafts over 30 days to assess changes in graft wall thickness. We also monitored change in optical properties of the grafts based on free-space OCT scanning.   Finally, in order to visualize the proliferation of endothelial cells and development of the endothelium, we developed an imaging system that utilizes a commercial OCT catheter for single-cell-level imaging of the growing endothelium of a tissue-engineered blood vessel. We have developed two modules of an imaging system for non-destructive monitoring of maturing bioengineered vascular grafts. The first module provides the ability to non-destructively examine the structure of the grafts while the second module can track the progress of endothelialization. As both modules use the same endoscope for imaging, when operated in sequence, they will produce high-resolution, three-dimensional, structural details of the graft and two-dimensional spatial distribution of ECs on the lumen. This non-destructive, multi-modality imaging can be potentially used to monitor and assess the development of luminal bioengineered constructs such as colon or trachea. / Ph. D.

<p>Optical coherence tomography (OCT) is a non-invasive optical imaging modality that provides micron-scale resolution of tissue micro-structure over depth ranges of several millimeters. This imaging technique has had a profound effect on the field of ophthalmology, wherein it has become the standard of care for the diagnosis of many retinal pathologies. Applications of OCT in the anterior eye, as well as for imaging of coronary arteries and the gastro-intestinal tract, have also shown promise, but have not yet achieved widespread clinical use.</p><p>The usable imaging depth of OCT systems is most often limited by one of three factors: optical attenuation, inherent imaging range, or depth-of-focus. The first of these, optical attenuation, stems from the limitation that OCT only detects singly-scattered light. Thus, beyond a certain penetration depth into turbid media, essentially all of the incident light will have been multiply scattered, and can no longer be used for OCT imaging. For many applications (especially retinal imaging), optical attenuation is the most restrictive of the three imaging depth limitations. However, for some applications, especially anterior segment, cardiovascular (catheter-based) and GI (endoscopic) imaging, the usable imaging depth is often not limited by optical attenuation, but rather by the inherent imaging depth of the OCT systems. This inherent imaging depth, which is specific to only Fourier Domain OCT, arises due to two factors: sensitivity fall-off and the complex conjugate ambiguity. Finally, due to the trade-off between lateral resolution and axial depth-of-focus inherent in diffractive optical systems, additional depth limitations sometimes arises in either high lateral resolution or extended depth OCT imaging systems. The depth-of-focus limitation is most apparent in applications such as adaptive optics (AO-) OCT imaging of the retina, and extended depth imaging of the ocular anterior segment.</p><p>In this dissertation, techniques for extending the imaging range of OCT systems are developed. These techniques include the use of a high spectral purity swept source laser in a full-field OCT system, as well as the use of a peculiar phenomenon known as coherence revival to resolve the complex conjugate ambiguity in swept source OCT. In addition, a technique for extending the depth of focus of OCT systems by using a polarization-encoded, dual-focus sample arm is demonstrated. Along the way, other related advances are also presented, including the development of techniques to reduce crosstalk and speckle artifacts in full-field OCT, and the use of fast optical switches to increase the imaging speed of certain low-duty cycle swept source OCT systems. Finally, the clinical utility of these techniques is demonstrated by combining them to demonstrate high-speed, high resolution, extended-depth imaging of both the anterior and posterior eye simultaneously and in vivo.</p> / Dissertation

Indiana University-Purdue University Indianapolis (IUPUI) / An algorithm was developed in to efficiently segment the inner-limiting membrane (ILM) and retinal pigmented epithelium (RPE) from spectral domain-optical coherence tomography image volumes. A deformable model framework is described and implemented in which free-form deformations (FFD) are used to direct two deformable sheets to the two high-contrast layers of interest. Improved accuracy in determining retinal thickness (the distance between the ILM and the RPE) is demonstrated against the commercial state-of-the-art Spectralis OCT native segmentation software. A novel adaptation of the highest confidence first (HCF) algorithm is utilized to improve upon the initial results. The proposed adaptation of HCF provides distance-based clique potentials and an efficient solution to layer-based segmentation, reducing a 3D problem to 2D inference.

No description available.