Evaluating anesthetic protocols for functional blood flow imaging in the rat eye

The purpose of this study is to evaluate the suitability of five different anesthetic protocols (isoflurane, isoflurane–xylazine, pentobarbital, ketamine–xylazine, and ketamine–xylazine–vecuronium) for functional blood flow imaging in the rat eye. Total retinal blood flow was measured at a series of time points using an ultrahigh-speed Doppler OCT system. Additionally, each anesthetic protocol was qualitatively evaluated according to the following criteria: (1) time-stability of blood flow, (2) overall rate of blood flow, (3) ocular immobilization, and (4) simplicity. We observed that different anesthetic protocols produced markedly different blood flows. Different anesthetic protocols also varied with respect to the four evaluated criteria. These findings suggest that the choice of anesthetic protocol should be carefully considered when designing and interpreting functional blood flow studies in the rat eye.United States. National Institutes of Health (R01-EY011289-29)United States. National Institutes of Health (R44-EY022864)United States. National Institutes of Health (R01-CA075289-16)United States. Air Force Office of Scientific Research (FA9550-15-1-0473)United States. Air Force Office of Scientific Research (FA9550-12-1-0499

Mapping genetic variations to three- dimensional protein structures to enhance variant interpretation: a proposed framework

The translation of personal genomics to precision medicine depends on the accurate interpretation of the multitude of genetic variants observed for each individual. However, even when genetic variants are predicted to modify a protein, their functional implications may be unclear. Many diseases are caused by genetic variants affecting important protein features, such as enzyme active sites or interaction interfaces. The scientific community has catalogued millions of genetic variants in genomic databases and thousands of protein structures in the Protein Data Bank. Mapping mutations onto three-dimensional (3D) structures enables atomic-level analyses of protein positions that may be important for the stability or formation of interactions; these may explain the effect of mutations and in some cases even open a path for targeted drug development. To accelerate progress in the integration of these data types, we held a two-day Gene Variation to 3D (GVto3D) workshop to report on the latest advances and to discuss unmet needs. The overarching goal of the workshop was to address the question: what can be done together as a community to advance the integration of genetic variants and 3D protein structures that could not be done by a single investigator or laboratory? Here we describe the workshop outcomes, review the state of the field, and propose the development of a framework with which to promote progress in this arena. The framework will include a set of standard formats, common ontologies, a common application programming interface to enable interoperation of the resources, and a Tool Registry to make it easy to find and apply the tools to specific analysis problems. Interoperability will enable integration of diverse data sources and tools and collaborative development of variant effect prediction methods

Optical Coherence Tomography Angiography for Imaging and Analysis of the Choriocapillaris in Late Age-Related Macular Degeneration

Age-related macular degeneration (AMD), a progressive disease of the retina and choroid, is a leading cause of vision loss. At present, AMD pathogenesis remains incompletely understood, and approved treatments only exist for certain AMD subtypes. In this thesis, we investigate AMD pathophysiology with a focus on choriocapillaris impairment in macular neovascularization and geographic atrophy, the two subtypes comprising late AMD. The choriocapillaris, the capillary layer of the choroid, is responsible for nourishing the outer retina, including the photoreceptors, and has long been hypothesized to have an important role in AMD development and progression. We contribute to the existing understanding of AMD-associated choriocapillaris impairment by developing and applying optical coherence tomography angiography (OCTA) technology in conjunction with image analysis and disease modeling approaches. Key study results presented in this thesis include: (1) the development of an OCTA-based method for microvascular velocimetry that is compatible with clinical ophthalmic imaging; (2) the demonstration and quantification of choriocapillaris impairment surrounding macular neovascularization; (3) the association of macular neovascularization blood flow speeds with responses to vascular endothelial growth factor inhibitor treatment; (4) the demonstration of choriocapillaris impairment surrounding regions of geographic atrophy; and, (5) the development of a biophysical model describing the spatiotemporal expansion of geographic atrophy, and the integration of this model with spatial statistical methods to enable rigorous assessments of local correlations between choriocapillaris impairment and geographic atrophy growth.Ph.D

Optical coherence tomography angiography (OCTA) flow speed mapping technology for retinal diseases

Introduction: Optical coherence tomography angiography (OCTA) is a noninvasive imaging modality for depth-resolved visualization of retinal vasculature. Angiographic data couples with structural data to generate a cube scan, from which en-face images of vasculature can be obtained at various axial positions. OCTA has expanded understanding of retinal vascular disorders and has primarily been used for qualitative analysis. Areas covered: Recent studies have explored the quantitative properties of OCTA, which would allow for objective assessment and follow-up of retinal pathologies. Various quantitative metrics have been developed, such as foveal avascular zone area and vessel density. However, quantitative assessment of the characteristics of retinal blood flow remains limited, as OCTA provides an image depicting either the presence or absence of flow at a particular region without information of relative velocities. The development of variable interscan time analysis (VISTA) overcomes this limitation. The VISTA algorithm generates a color-coded map of relative blood flow speeds. VISTA has already demonstrated utility in furthering our understanding of various retinal pathologies, such as geographic atrophy, choroidal neovascularization, aneurysmal type 1 neovascularization, and diabetic retinopathy. Expert commentary: VISTA, an OCTA flow speed mapping technique, may have a role in developing the utility of OCTA as a screening tool.United States. Air Force. Office of Scientific Research (Grant AFOSR FA9550–15-1–0473)National Institutes of Health (U.S.) (Grant NIH 5-R01-EY011289–31

Ultrahigh Speed OCT Angiography of Retinal and Choriocapillaris Alterations in Diabetic Patients with and without Retinopathy Using Swept Source Optical Coherence Tomography

Purpose: To investigate the utility of ultrahigh speed, swept source optical coherence tomography angiography in visualizing retinal microvascular and choriocapillaris (CC) changes in diabetic patients. Methods: The study was prospective and cross-sectional. A 1,050 nm wavelength, 400 kHz A-scan rate swept source optical coherence tomography prototype was used to perform volumetric optical coherence tomography angiography of the retinal and CC vasculatures in diabetic patients and normal subjects. Sixty-three eyes from 32 normal subjects, 9 eyes from 7 patients with proliferative diabetic retinopathy, 29 eyes from 16 patients with nonproliferative diabetic retinopathy, and 51 eyes from 28 diabetic patients without retinopathy were imaged. Results: Retinal and CC microvascular abnormalities were observed in all stages of diabetic retinopathy. In nonproliferative diabetic retinopathy and proliferative diabetic retinopathy, optical coherence tomography angiography visualized a variety of vascular abnormalities, including clustered capillaries, dilated capillary segments, tortuous capillaries, regions of capillary dropout, reduced capillary density, abnormal capillary loops, and foveal avascular zone enlargement. In proliferative diabetic retinopathy, retinal neovascularization above the inner limiting membrane was visualized. Regions of CC flow impairment in patients with proliferative diabetic retinopathy and nonproliferative diabetic retinopathy were also observed. In 18 of the 51 of eyes from diabetic patients without retinopathy, retinal mircrovascular abnormalities were observed and CC flow impairment was found in 24 of the 51 diabetic eyes without retinopathy. Conclusion: The ability of optical coherence tomography angiography to visualize retinal and CC microvascular abnormalities suggests it may be a useful tool for understanding pathogenesis, evaluating treatment response, and earlier detection of vascular abnormalities in patients with diabetes.National Institutes of Health (U.S.) (Grants NIH R01-EY011289-28, R44-EY022864-03, R01-CA075289-17)United States. Air Force. Office of Scientific Research (Grants AFOSR FA9550-10-1-0551 and FA9550-12-1-0499

Developing a potential retinal OCT biomarker for local growth of geographic atrophy

Geographic atrophy (GA), the advanced stage of age-related macular degeneration, is a leading cause of blindness. GA lesions are characterized by anisotropic growth and the ability to predict growth patterns would be valuable in assessing potential therapeutics. In this study, we propose an OCT-based marker of local GA growth rate based on an axial projection of the OCT volume in the Henle fiber layer (HFL) and outer nuclear layer (ONL). We analyze the association between our proposed metric and local GA growth rates in a small longitudinal cohort of patients with AMD. These methods can potentially be used to identify risk markers, stratify patients, or assess response in future therapeutic studies.China Scholarship Council (201806010297)National Institutes of Health (U.S.) (Grant 5-R01-EY011289-31

Correction propagation for user-assisted optical coherence tomography segmentation: general framework and application to Bruch’s membrane segmentation

Optical coherence tomography (OCT) is a commonly used ophthalmic imaging modality. While OCT has traditionally been viewed cross-sectionally (i.e., as a sequence of B-scans), higher A-scan rates have increased interest in en face OCT visualization and analysis. The recent clinical introduction of OCT angiography (OCTA) has further spurred this interest, with chorioretinal OCTA being predominantly displayed via en face projections. Although en face visualization and quantitation are natural for many retinal features (e.g., drusen and vasculature), it requires segmentation. Because manual segmentation of volumetric OCT data is prohibitively laborious in many settings, there has been significant research and commercial interest in developing automatic segmentation algorithms. While these algorithms have achieved impressive results, the variability of image qualities and the variety of ocular pathologies cause even the most robust automatic segmentation algorithms to err. In this study, we develop a user-assisted segmentation approach, complementary to fully-automatic methods, wherein correction propagation is used to reduce the burden of manually correcting automatic segmentations. The approach is evaluated for Bruch’s membrane segmentation in eyes with advanced age-related macular degeneration.National Eye Institute (Grant R01-EY011289

High-Speed, Ultrahigh-Resolution Spectral-Domain OCT with Extended Imaging Range Using Reference Arm Length Matching

Purpose: To develop high-speed, extended-range, ultrahigh-resolution spectraldomain optical coherence tomography (UHR SD-OCT) and demonstrate scan protocols for clinical retinal imaging. Methods: A UHR SD-OCT operating at 840-nm with 150-nm bandwidths was developed. The axial imaging range was extended by dynamically matching reference arm length to the retinal contour during acquisition. Two scan protocols were demonstrated for imaging healthy participants and patients with dry age-related macular degeneration. A high-definition raster protocol with intra–B-scan reference arm length matching (ReALM) was used for high-quality cross-sectional imaging. A cube volume scan using horizontal and vertical rasters with inter–B-scan ReALM and software motion correction was used for en face and cross-sectional imaging. Linear OCT signal display enhanced visualization of outer retinal features. Results: UHR SD-OCT was demonstrated at 128-and 250-kHz A-scan rates with 2.7 μm axial resolution and a 1.2-mm, 6-dB imaging range in the eye. Dynamic ReALM was used to maintain the retina within the 6-dB imaging range over wider fields of view. Outer retinal features, including the rod and cone interdigitation zones, retinal pigment epithelium, and Bruch’s membrane were visualized and alterations observed in agerelated macular degeneration eyes. Conclusions: Technological advances and dynamic ReALM improve the imaging performance and clinical usability of UHR SD-OCT. Translational Relevance: These advances should simplify clinical imaging workflow, reduce imaging session times, and improve yield of high quality images. Improved visualization of photoreceptors, retinal pigment epithelium, and Bruch’s membrane may facilitate diagnosis and monitoring of age-related macular degeneration and other retinal diseases.National Institutes of Health (U.S.) (Grant 5-R01-EY011289-33)United States. Air Force. Office of Scientific Research (Grant FA9550-15-1-0473

Optical Coherence Tomography Angiography of Dry Age-Related Macular Degeneration

Optical coherence tomography angiography (OCTA) can be used to visualize alterations in the choriocapillaris of patients with dry age-related macular degeneration (AMD). These changes seem to be present during all stages of the disease. Earlier stages are associated with patchy thinning of the choriocapillaris, while geographic atrophy is associated with loss of choriocapillaris lying under the area of geographic atrophy and asymmetric alteration of choriocapillaris at the margins of the geographic atrophy. The use of high-speed, long-wave-length swept-source OCT for angiography, with its better penetration into the choroid and high acquisition speeds, enable OCTA with scaled slowest detectable flow and fastest distinguishable flow. This will enable us to better investigate choriocapillaris changes in patients with dry AMD. The ability to image the choriocapillaris structure and flow impairments may be useful in the future for detecting and monitoring the progression of dry AMD and for monitoring treatment responses in clinical trials to therapies that target disease progression in dry AMD

Maximum a posteriori signal recovery for optical coherence tomography angiography image generation and denoising

Optical coherence tomography angiography (OCTA) is a novel and clinically promising imaging modality to image retinal and sub-retinal vasculature. Based on repeated optical coherence tomography (OCT) scans, intensity changes are observed over time and used to compute OCTA image data. OCTA data are prone to noise and artifacts caused by variations in flow speed and patient movement. We propose a novel iterative maximum a posteriori signal recovery algorithm in order to generate OCTA volumes with reduced noise and increased image quality. This algorithm is based on previous work on probabilistic OCTA signal models and maximum likelihood estimates. Reconstruction results using total variation minimization and wavelet shrinkage for regularization were compared against an OCTA ground truth volume, merged from six co-registered single OCTA volumes. The results show a significant improvement in peak signal-to-noise ratio and structural similarity. The presented algorithm brings together OCTA image generation and Bayesian statistics and can be developed into new OCTA image generation and denoising algorithms.German Research Foundation (Grant (MA 4898/12-1)National Institutes of Health (U.S.) (Grant 5-R01- EY011289-31