OCTDL: Optical Coherence Tomography Dataset for Image-Based Deep Learning Methods
Friedrich-Alexander-Universität Erlangen-Nürnberg（弗里德里希-亚历山大-埃尔朗根-纽伦堡大学）；Ural Federal University Named after the First President of Russia B. N. Yeltsin（俄罗斯首任总统B.N.叶利钦命名的乌拉尔联邦大学）；Ophthalmosurgery Clinic "Professorskaya Plus"（“Professorskaya Plus”眼科诊所）；Ural State Medical University（乌拉尔国立医科大学）
Mikhail Kulyabin, Aleksei Zhdanov, Anastasia Nikiforova, Andrey Stepichev, Anna Kuznetsova, Mikhail Ronkin, Vasilii Borisov, Alexander Bogachev, Sergey Korotkic… 展开作者
Mikhail Kulyabin, Aleksei Zhdanov, Anastasia Nikiforova, Andrey Stepichev, Anna Kuznetsova, Mikhail Ronkin, Vasilii Borisov, Alexander Bogachev, Sergey Korotkich, Paul A Constable, Andreas Maier
Optical coherence tomography (OCT) is a non-invasive imaging technique with extensive clinical applications in ophthalmology. OCT enables the visualization of the retinal layers, playing a vital role in the early detection and monitoring of retinal diseases. OCT uses the principle of light wave interference to create detailed images of the retinal microstructures, making it a valuable tool for diagnosing ocular conditions. This work presents an open-access OCT dataset (OCTDL) comprising over 2000 OCT images labeled according to disease group and retinal pathology. The dataset consists of OCT records of patients with Age-related Macular Degeneration (AMD), Diabetic Macular Edema (DME), Epiretinal Membrane (ERM), Retinal Artery Occlusion (RAO), Retinal Vein Occlusion (RVO), and Vitreomacular Interface Disease (VID). The images were acquired with an Optovue Avanti RTVue XR using raster scanning protocols with dynamic scan length and image resolution. Each retinal b-scan was acquired by centering on the fovea and interpreted and cataloged by an experienced retinal specialist. In this work, we applied Deep Learning classification techniques to this new open-access dataset.
Technion Israel Institute of Technology（以色列理工学院）；Rambam Health Care Campus（兰巴姆医疗中心）；University of Adelaide（阿德莱德大学）；Royal Adelaide Hospital（阿德莱德皇家医院）；South Australian Institute of Ophthalmology（南澳大利亚眼科研究所）；Clinical Research Institute at Rambam（兰巴姆临床研究所）
To explore the clinical validity of elastic deformation of optical coherence tomography (OCT) images for data augmentation in the development of deep-learning model for detection of diabetic macular edema (DME).
Simon Fraser University（西蒙弗雷泽大学）；Tencent YouTu Lab（腾讯优图实验室）
Optical coherence tomography (OCT) is a non-invasive imaging technology which can provide micrometer-resolution cross-sectional images of the inner structures of the eye. It is widely used for the diagnosis of ophthalmic diseases with retinal alteration, such as layer deformation and fluid accumulation. In this paper, a novel framework was proposed to segment retinal layers with fluid presence. The main contribution of this study is two folds: 1) we developed a cascaded network framework to incorporate the prior structural knowledge; 2) we proposed a novel deep neural network based on U-Net an…
In this work we propose a ResNet-based universal method for speckle reduction in optical coherence tomography (OCT) images. The proposed model contains 3 main modules: Convolution-BN-ReLU, Branch and Residual module. Unlike traditional algorithms, the model can learn from training data instead of selecting parameters manually such as noise level. Application of this proposed method to the OCT images shows a more than 22 dB signal-to-noise ratio improvement in speckle noise reduction with minimal structure blurring. The proposed method provides strong generalization ability and can process nois…
The Pingry School（平格里学校）；Chinle Comprehensive Health Care Facility（钦利综合医疗中心）；University of Maryland, College Park（马里兰大学帕克分校）；NVIDIA（英伟达）
30 million Optical Coherence Tomography (OCT) imaging tests are issued annually to diagnose various retinal diseases, but accurate diagnosis of OCT scans requires trained eye care professionals who are still prone to making errors. With better systems for diagnosis, many cases of vision loss caused by retinal disease could be entirely avoided. In this work, we present ReLaX, a novel deep learning framework for explainable, accurate classification of retinal pathologies which achieves state-of-the-art accuracy. Furthermore, we emphasize producing both qualitative and quantitative explanations o…
Optical Coherence Tomography (OCT) is pervasive in both the research and clinical practice of Ophthalmology. However, OCT images are strongly corrupted by noise, limiting their interpretation. Current OCT denoisers leverage assumptions on noise distributions or generate targets for training deep supervised denoisers via averaging of repeat acquisitions. However, recent self-supervised advances allow the training of deep denoising networks using only repeat acquisitions without clean targets as ground truth, reducing the burden of supervised learning. Despite the clear advantages of self-superv…
Nosie is an important cause of low quality Optical coherence tomography (OCT) image. The neural network model based on Convolutional neural networks(CNNs) has demonstrated its excellent performance in image denoising. However, OCT image denoising still faces great challenges because many previous neural network algorithms required a large number of labeled data, which might cost much time or is expensive. Besides, these CNN-based algorithms need numerous parameters and good tuning techniques, which is hardware resources consuming. To solved above problems, We proposed a new Cycle-Consistent Ge…
Optical Coherence Tomography Angiography-OCTA dataset for the study of Diabetic Retinopathy
Symbiosis Institute of Technology, Symbiosis International (Deemed University)（共生国际（ deemed 大学）共生技术学院）；University of Technology Sydney（悉尼科技大学）；Natasha Eye Care（娜塔莎眼科护理中心）
In this paper, we propose the use of Optical Coherence Tomography (OCT) imaging for the problem of iris presentation attack (PA) detection. We assess its viability by comparing its performance with respect to traditional iris imaging modalities, viz., near-infrared (NIR) and visible spectrum. OCT imaging provides a cross-sectional view of an eye, whereas traditional imaging provides 2D iris textural information. PA detection is performed using three state-of-the-art deep architectures (VGG19, ResNet50 and DenseNet121) to differentiate between bonafide and PA samples for each of the three imagi…
Optical Coherence Tomography is a technique used to scan the Retina of the eye and check for tears. In this paper, we develop a Convolutional Neural Network Architecture for OCT scan classification. The model is trained to detect Retinal tears from an OCT scan and classify the type of tear. We designed a block-based approach to accompany a pre-trained VGG-19 using Transfer Learning by writing customised layers in blocks for better feature extraction. The approach achieved substantially better results than the baseline we initially started out with.
Shanghai Jiao Tong University（上海交通大学）；EPFL（洛桑联邦理工学院）；Shanghai General Hospital（上海市第一人民医院）
Projection map (PM) from optical coherence tomography (OCT) B-scan is an important tool to diagnose retinal diseases, which typically requires retinal layer segmentation. In this study, we present a novel end-to-end framework to predict PMs from B-scans. Instead of segmenting retinal layers explicitly, we represent them implicitly as predicted coordinates. By pixel interpolation on uniformly sampled coordinates between retinal layers, the corresponding PMs could be easily obtained with pooling. Notably, all the operators are differentiable; therefore, this Differentiable Projection Module (DPM…
Georgia Institute of Technology（佐治亚理工学院）；Retina Consultants Texas（得克萨斯视网膜咨询中心）；Retina Consultants of America（美国视网膜咨询中心）
In this paper, we propose a framework that incorporates experts diagnostics and insights into the analysis of Optical Coherence Tomography (OCT) using multi-modal learning. To demonstrate the effectiveness of this approach, we create a medical diagnostic attribute dataset to improve disease classification using OCT. Although there have been successful attempts to deploy machine learning for disease classification in OCT, such methodologies lack the experts insights. We argue that injecting ophthalmological assessments as another supervision in a learning framework is of great importance for th…
Optical coherence tomography (OCT) is a non-invasive imaging modality which is widely used in clinical ophthalmology. OCT images are capable of visualizing deep retinal layers which is crucial for early diagnosis of retinal diseases. In this paper, we describe a comprehensive open-access database containing more than 500 highresolution images categorized into different pathological conditions. The image classes include Normal (NO), Macular Hole (MH), Age-related Macular Degeneration (AMD), Central Serous Retinopathy (CSR), and Diabetic Retinopathy (DR). The images were obtained from a raster s…
Optical Coherence Tomography allows ophthalmologist to obtain cross-section imaging of eye retina. Assisted with digital image analysis methods, effective disease detection could be performed. Various methods exist to extract feature from OCT images. The proposed study aims to compare the effectiveness of handcrafted and deep neural network features. The evaluated dataset consist of 32339 instances distributed in four classes, namely CNV, DME, DRUSEN, and NORMAL. The methods are Histogram of Oriented Gradient (HOG), Local Binary Pattern (LBP), DenseNet-169, and ResNet50. As a result, the deep …
Wellman Center for Photomedicine, Massachusetts General Hospital（马萨诸塞州总医院韦尔曼光医学中心）；Harvard Medical School（哈佛医学院）；Computer Science and Artificial Intelligence Laboratory (CSAIL), Massachusetts Institute of Technology（麻省理工学院计算机科学与人工智能实验室）；Erasmus Medical Center（伊拉斯谟医学中心）
Intravascular ultrasound and optical coherence tomography are widely available for characterizing coronary stenoses and provide critical vessel parameters to optimize percutaneous intervention. Intravascular polarization-sensitive optical coherence tomography (PS-OCT) simultaneously provides high-resolution cross-sectional images of vascular structures while also revealing preponderant tissue components such as collagen and smooth muscle and thereby enhances plaque characterization. Automated interpretation of these features promises to facilitate the objective clinical investigation of the na…
Automated drusen segmentation in retinal optical coherence tomography (OCT) scans is relevant for understanding age-related macular degeneration (AMD) risk and progression. This task is usually performed by segmenting the top/bottom anatomical interfaces that define drusen, the outer boundary of the retinal pigment epithelium (OBRPE) and the Bruch's membrane (BM), respectively. In this paper we propose a novel multi-decoder architecture that tackles drusen segmentation as a multitask problem. Instead of training a multiclass model for OBRPE/BM segmentation, we use one decoder per target class …
Noise in speckle-prone optical coherence tomography tends to obfuscate important details necessary for medical diagnosis. In this paper, a denoising approach that preserves disease characteristics on retinal optical coherence tomography images in ophthalmology is presented. By combining a deep convolutional autoencoder with a priorly trained ResNet image classifier as regularizer, the perceptibility of delicate details is encouraged and only information-less background noise is filtered out. With our approach, higher peak signal-to-noise ratios with $ \mathrm{PSNR} = 31.2\,\mathrm{dB} $ and hi…
Massachusetts Institute of Technology（麻省理工学院）；Friedrich-Alexander-Universität Erlangen-Nürnberg（埃尔朗根-纽伦堡弗里德里希-亚历山大大学）；Tufts Medical Center（塔夫茨医疗中心）
Recent advances in optical coherence tomography such as the development of high speed ultrahigh resolution scanners and corresponding signal processing techniques may reveal new potential biomarkers in retinal diseases. Newly visible features are, for example, small hyperreflective specks in age-related macular degeneration. Identifying these new markers is crucial to investigate potential association with disease progression and treatment outcomes. Therefore, it is necessary to reliably detect these features in 3D volumetric scans. Because manual labeling of entire volumes is infeasible a nee…
National University of Singapore（新加坡国立大学）；Duke-NUS, Graduate Medical School（杜克-新加坡国立大学医学院）；Singapore Eye Research Institute（新加坡眼科研究所）；Singapore National Eye Centre（新加坡全国眼科中心）；Université de la Polynésie francaise（法属波利尼西亚大学）；Moorfields Eye Hospital NHS Foundation Trust（Moorfields眼科医院NHS基金会信托）；UCL Institute of Ophthalmol（伦敦大学学院眼科研究所）
Given that the neural and connective tissues of the optic nerve head (ONH) exhibit complex morphological changes with the development and progression of glaucoma, their simultaneous isolation from optical coherence tomography (OCT) images may be of great interest for the clinical diagnosis and management of this pathology. A deep learning algorithm was designed and trained to digitally stain (i.e. highlight) 6 ONH tissue layers by capturing both the local (tissue texture) and contextual information (spatial arrangement of tissues). The overall dice coefficient (mean of all tissues) was $0.91 \…
Medical University Vienna（维也纳医科大学）；Department of Biomedical Imaging and Image-guided Therapy, Computational Imaging Research Lab, Medical University Vienna, Austria（维也纳医科大学生物医学成像与影像引导治疗系计算成像研究实验室）；Christian Doppler Laboratory for Ophthalmic Image Analysis, Department of Ophthalmology and Optometry, Medical University Vienna, Austria（维也纳医科大学眼科与视光学系眼科图像分析基督教多普勒实验室）；Department of Ophthalmology and Optometry, Medical University Vienna, Austria（维也纳医科大学眼科与视光学系）
The automatic detection of disease related entities in retinal imaging data is relevant for disease- and treatment monitoring. It enables the quantitative assessment of large amounts of data and the corresponding study of disease characteristics. The presence of hyperreflective foci (HRF) is related to disease progression in various retinal diseases. Manual identification of HRF in spectral-domain optical coherence tomography (SD-OCT) scans is error-prone and tedious. We present a fully automated machine learning approach for segmenting HRF in SD-OCT scans. Evaluation on annotated OCT images o…
Optical coherence tomography (OCT) is an important interferometric diagnostic technique which provides cross-sectional views of the subsurface microstructure of biological tissues. However, the imaging quality of high-speed OCT is limited due to the large speckle noise. To address this problem, this paper proposes a multi-frame algorithmic method to denoise OCT volume. Mathematically, we build an optimization model which forces the temporally registered frames to be low rank, and the gradient in each frame to be sparse, under logarithmic image formation and noise variance constraints. Besides,…
Optical coherence tomography (OCT) is commonly used to analyze retinal layers for assessment of ocular diseases. In this paper, we propose a method for retinal layer segmentation and quantification of uncertainty based on Bayesian deep learning. Our method not only performs end-to-end segmentation of retinal layers, but also gives the pixel wise uncertainty measure of the segmentation output. The generated uncertainty map can be used to identify erroneously segmented image regions which is useful in downstream analysis. We have validated our method on a dataset of 1487 images obtained from 15 …
With the introduction of spectral-domain optical coherence tomography (OCT), much larger image datasets are routinely acquired compared to what was possible using the previous generation of time-domain OCT. Thus, the need for 3-D segmentation methods for processing such data is becoming increasingly important. We present a new 3D segmentation method for retinal OCT volume data, which generates an enhanced volume data by using pixel intensity, boundary position information, intensity changes on both sides of the border simultaneously, and preliminary discrete boundary points are found from all …
Chromatic dispersion is a common problem to degrade the system resolution in optical coherence tomography (OCT). This study is to develop a deep learning network for automated dispersion compensation (ADC-Net) in OCT. The ADC-Net is based on a redesigned UNet architecture which employs an encoder-decoder pipeline. The input section encompasses partially compensated OCT B-scans with individual retinal layers optimized. Corresponding output is a fully compensated OCT B-scans with all retinal layers optimized. Two numeric parameters, i.e., peak signal to noise ratio (PSNR) and structural similari…
As a non-invasive imaging modality, optical coherence tomography (OCT) can provide micrometer-resolution 3D images of retinal structures. Therefore it is commonly used in the diagnosis of retinal diseases associated with edema in and under the retinal layers. In this paper, a new framework is proposed for the task of fluid segmentation and detection in retinal OCT images. Based on the raw images and layers segmented by a graph-cut algorithm, a fully convolutional neural network was trained to recognize and label the fluid pixels. Random forest classification was performed on the segmented flui…
Technische Universität München（慕尼黑工业大学）；Ludwig-Maximilians-University（路德维希-马克西米利安大学）；Indian Institute of Technology Kharagpur（印度理工学院克勒格布尔分校）；Johns Hopkins University（约翰斯·霍普金斯大学）
Optical coherence tomography (OCT) is used for non-invasive diagnosis of diabetic macular edema assessing the retinal layers. In this paper, we propose a new fully convolutional deep architecture, termed ReLayNet, for end-to-end segmentation of retinal layers and fluid masses in eye OCT scans. ReLayNet uses a contracting path of convolutional blocks (encoders) to learn a hierarchy of contextual features, followed by an expansive path of convolutional blocks (decoders) for semantic segmentation. ReLayNet is trained to optimize a joint loss function comprising of weighted logistic regression and…
In this paper we present a new method for cystoid macular edema (CME) segmentation in retinal Optical Coherence Tomography (OCT) images, using a fully convolutional neural network (FCN) and a fully connected conditional random fields (dense CRFs). As a first step, the framework trains the FCN model to extract features from retinal layers in OCT images, which exhibit CME, and then segments CME regions using the trained model. Thereafter, dense CRFs are used to refine the segmentation according to the edema appearance. We have trained and tested the framework with OCT images from 10 patients wit…
As a non-invasive optical imaging technique, optical coherence tomography (OCT) has proven promising for automatic fingerprint recognition system (AFRS) applications. Diverse approaches have been proposed for OCT-based fingerprint presentation attack detection (PAD). However, considering the complexity and variety of PA samples, it is extremely challenging to increase the generalization ability with the limited PA dataset. To solve the challenge, this paper presents a novel supervised learning-based PAD method, denoted as ISAPAD, which applies prior knowledge to guide network training and enha…
University of Canterbury（坎特伯雷大学）；Nicolaus Copernicus University（尼古拉斯·哥白尼大学）
Artefacts in quantum-mimic Optical Coherence Tomography are considered detrimental because they scramble the images even for the simplest objects. They are a side effect of autocorrelation which is used in the quantum entanglement mimicking algorithm behind this method. Interestingly, the autocorrelation imprints certain characteristics onto an artefact - it makes its shape and characteristics depend on the amount of dispersion exhibited by the layer that artefact corresponds to. This unique relationship between the artefact and the layer's dispersion can be used to determine Group Velocity Di…
Despite significant advances in artificial intelligence (AI) for computer vision, its application in medical imaging has been limited by the burden and limits of expert-generated labels. We used images from optical coherence tomography angiography (OCTA), a relatively new imaging modality that measures perfusion of the retinal vasculature, to train an AI algorithm to generate vasculature maps from standard structural optical coherence tomography (OCT) images of the same retinae, both exceeding the ability and bypassing the need for expert labeling. Deep learning was able to infer perfusion of …
Optical coherence tomography offers astounding opportunities to image the complex structure of living tissue, but lacks functional information. We present dynamic full-field optical coherence tomography to image living human induced pluripotent stem cell-derived retinal organoids non-invasively. Colored images with an endogenous contrast linked to organelle motility are generated, with sub-micrometer spatial resolution and millisecond temporal resolution, opening an avenue to identify specific cell types in living tissue via their function.
Friedrich-Alexander-Universität Erlangen-Nürnberg（埃尔朗根-纽伦堡弗里德里希-亚历山大大学）；Massachusetts Institute of Technology（麻省理工学院）；Tufts School of Medicine（塔夫茨医学院）
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…
National Taiwan University（台湾大学）；Chang Gung Memorial Hospital（长庚纪念医院）；Chang Gung University（长庚大学）
Automated vascular segmentation on optical coherence tomography angiography (OCTA) is important for the quantitative analyses of retinal microvasculature in neuroretinal and systemic diseases. Despite recent improvements, artifacts continue to pose challenges in segmentation. Our study focused on removing the speckle noise artifact from OCTA images when performing segmentation. Speckle noise is common in OCTA and is particularly prominent over large non-perfusion areas. It may interfere with the proper assessment of retinal vasculature. In this study, we proposed a novel Supervision Vessel Seg…
This dissertation relates to the transition of the state of the art of swept source optical coherence tomography (SS-OCT) systems to a new realm in which the image acquisition speed is improved by an order of magnitude. With the aid of a better quality imaging technology, the speed-up factor will considerably shorten the eye-exam clinical visits which in turn improves the patient and doctor interaction experience. These improvements will directly lower associated medical costs for eye-clinics and patients worldwide. There are several other embodiments closely related to Optical Coherence Tomog…
Indian Institute of Information Technology, Sri City（印度信息技术学院，斯里城）
Image to Image Translation (I2I) is a challenging computer vision problem used in numerous domains for multiple tasks. Recently, ophthalmology became one of the major fields where the application of I2I is increasing rapidly. One such application is the generation of synthetic retinal optical coherence tomographic (OCT) scans. Existing I2I methods require training of multiple models to translate images from normal scans to a specific pathology: limiting the use of these models due to their complexity. To address this issue, we propose an unsupervised multi-domain I2I network with pre-trained s…
Imperial College London（帝国理工学院）；UCLA（加州大学洛杉矶分校）；Jules Stein Eye Institute（朱尔斯·斯坦眼科研究所）；California State University（加州州立大学）；David Geffen School of Medicine（大卫·格芬医学院）；Technische Universität München（慕尼黑工业大学）
The estimation of glaucoma progression is a challenging task as the rate of disease progression varies among individuals in addition to other factors such as measurement variability and the lack of standardization in defining progression. Structural tests, such as thickness measurements of the retinal nerve fiber layer or the macula with optical coherence tomography (OCT), are able to detect anatomical changes in glaucomatous eyes. Such changes may be observed before any functional damage. In this work, we built a generative deep learning model using the conditional GAN architecture to predict…
We have developed a multimodal photoacoustic remote sensing (PARS) microscope combined with swept source optical coherence tomography for in vivo, non-contact retinal imaging. Building on the proven strength of multiwavelength PARS imaging, the system is applied for estimating retinal oxygen saturation in the rat retina. The capability of the technology is demonstrated by imaging both microanatomy and the microvasculature of the retina in vivo. To our knowledge this is the first time a non-contact photoacoustic imaging technique is employed for in vivo oxygen saturation measurement in the reti…
High-resolution optical imaging methods, such as confocal microscopy and full-field optical coherence tomography, capture flat optical sections of the sample. If the sample is curved, the optical field sections through several sample layers and the view of each layer is reduced. Here we present curved-field optical coherence tomography, capable of capturing optical sections of arbitrary curvature. We test the device on a challenging task of imaging the human cornea in vivo and achieve 10x larger viewing area comparing to the clinical state-of-the-art. This enables more precise cell and nerve c…
Intrinsic optical signal (IOS) imaging of the retina, also termed as optoretinography (ORG), promises a noninvasive method for objective assessment of retinal function. By providing unparalleled capability to differentiate individual layers of the retina, functional optical coherence tomography (OCT) has been actively investigated for intrinsic signal ORG measurements. However, clinical deployment of functional OCT for quantitative ORG is still challenging due to the lack of a standardized imaging protocol and the complication of IOS sources and mechanisms. This article aims to summarize recen…
This study is to demonstrate deep learning for automated artery-vein (AV) classification in optical coherence tomography angiography (OCTA). The AV-Net, a fully convolutional network (FCN) based on modified U-shaped CNN architecture, incorporates enface OCT and OCTA to differentiate arteries and veins. For the multi-modal training process, the enface OCT works as a near infrared fundus image to provide vessel intensity profiles, and the OCTA contains blood flow strength and vessel geometry features. A transfer learning process is also integrated to compensate for the limitation of available da…
We present a cascade deep neural network to segment retinal vessels in volumetric optical coherence tomography (OCT). Two types of knowledge are infused into the network for confining the searching regions. (1) Histology. The retinal vessels locate between the inner limiting membrane and the inner nuclear layer of human retina. (2) Imaging. The red blood cells inside the vessels scatter the OCT probe light forward and form projection shadows on the retinal pigment epithelium (RPE) layer, which is avascular thus perfect for localizing the retinal vessel in transverse plane. Qualitative and quan…
Modern optical coherence tomography (OCT) devices provide volumetric images with micrometer-scale spatial resolution and a temporal resolution beyond video rate. In this work, we analyze an OCT-based prototypical tracking system which processes 831 volumes per second, estimates translational motion, and automatically adjusts the field-of-view, which has a size of few millimeters, to follow a sample even along larger distances. The adjustment is realized by two galvo mirrors and a motorized reference arm, such that no mechanical movement of the scanning setup is necessary. Without requiring a m…
We consider the use of optical coherence tomography (OCT) imaging to predict the quality of meat. We find that intramuscular fat (IMF) absorbs infrared light about nine times stronger than muscle, which enables us to estimate fat content in intact meat samples. The method is made very efficient by extracting relevant information from the three-dimensional high-resolution images generated by OCT using principal component analysis (PCA). The principal components are then used as regressors into a support vector regression (SVR) prediction model. The SVR model is found to predict IMF content stab…
Optical coherence tomography (OCT) has seen widespread success as an in vivo clinical diagnostic 3D imaging modality, impacting areas including ophthalmology, cardiology, and gastroenterology. Despite its many advantages, such as high sensitivity, speed, and depth penetration, OCT suffers from several shortcomings that ultimately limit its utility as a 3D microscopy tool, such as its pervasive coherent speckle noise and poor lateral resolution required to maintain millimeter-scale imaging depths. Here, we present 3D optical coherence refraction tomography (OCRT), a computational extension of O…
Simon Fraser University（西蒙弗雷泽大学）；Wake Forest University School of Medicine（维克森林大学医学院）；University of British Columbia（不列颠哥伦比亚大学）；University College London（伦敦大学学院）
Optical coherence tomography (OCT) captures cross-sectional data and is used for the screening, monitoring, and treatment planning of retinal diseases. Technological developments to increase the speed of acquisition often results in systems with a narrower spectral bandwidth, and hence a lower axial resolution. Traditionally, image-processing-based techniques have been utilized to reconstruct subsampled OCT data and more recently, deep-learning-based methods have been explored. In this study, we simulate reduced axial scan (A-scan) resolution by Gaussian windowing in the spectral domain and in…
Optical coherence tomography (OCT) is a volumetric imaging modality that empowers clinicians and scientists to noninvasively visualize the cross-sections of biological samples. As the latest generation of its kind, Fourier-domain OCT (FD-OCT) offers a micrometer-scale axial resolution by taking advantage of coherence gating. Based on the current theory, it is believed the only way to obtain a higher-axial-resolution OCT image is to physically extend the system's spectral bandwidth given a certain central wavelength. Here, we showed the belief is wrong. We proposed a novel reconstruction framew…
Accurate choroid segmentation in optical coherence tomography (OCT) image is vital because the choroid thickness is a major quantitative biomarker of many ocular diseases. Deep learning has shown its superiority in the segmentation of the choroid region but subjects to the performance degeneration caused by the domain discrepancies (e.g., noise level and distribution) among datasets obtained from the OCT devices of different manufacturers. In this paper, we present an unsupervised perceptual-assisted adversarial adaptation (PAAA) framework for efficiently segmenting the choroid area by narrowi…
Spectral domain optical coherence tomography (OCT) offers high resolution multidimensional imaging, but generally suffers from defocussing, intensity falloff and shot noise, causing artifacts and image degradation along the imaging depth. In this work, we develop an iterative statistical reconstruction technique, based upon the interferometric synthetic aperture microscopy (ISAM) model with additive noise, to actively compensate for these effects. For the ISAM re-sampling, we use a non uniform FFT with Kaiser-Bessel interpolation, offering efficiency and high accuracy. We then employ an accele…
We demonstrate swept-source optical coherence tomography in real-time by high throughput digital Fresnel hologram rendering from optically-acquired interferograms with a high-speed camera. The interferogram stream is spatially rescaled with respect to wavelength to compensate for field-of-view dilation inherent to discrete Fresnel transformation. Holograms are calculated from an input stream of 16-bit, 1024-by-1024-pixel interferograms recorded at up to 512 frames per second with a digital camera. All calculations are performed by a NVIDIA TITAN Xp graphics card on single-precision floating-po…
We present a pseudo-real-time retinal layer segmentation for high-resolution Sensorless Adaptive Optics-Optical Coherence Tomography (SAO-OCT). Our pseudo-real-time segmentation method is based on Dijkstra's algorithm that uses the intensity of pixels and the vertical gradient of the image to find the minimum cost in a geometric graph formulation within a limited search region. It segments six retinal layer boundaries in an iterative process according to their order of prominence. The segmentation time is strongly correlated to the number of retinal layers to be segmented. Our program permits …
Optical coherence tomography angiography (OCTA) requires high transverse sampling density for visualizing retinal and choroidal capillaries. Low transverse sampling causes resolution degradation, such as the angiograms in wide-field OCTA. In this paper, we propose to address this problem using deep learning. We conducted extensive experiments on converting the centrally cropped 3 x 3 mm2 field of view (FOV) of the 8 x 8 mm2 foveal OCTA images (a sampling density of 22.9 $μ$m) to the native 3 x 3 mm2 en face OCTA images (a sampling density of 12.2 $μ$m). We employed a cycle-consistent adversari…
Due to its noninvasive character, optical coherence tomography (OCT) has become a popular diagnostic method in clinical settings. However, the low-coherence interferometric imaging procedure is inevitably contaminated by heavy speckle noise, which impairs both visual quality and diagnosis of various ocular diseases. Although deep learning has been applied for image denoising and achieved promising results, the lack of well-registered clean and noisy image pairs makes it impractical for supervised learning-based approaches to achieve satisfactory OCT image denoising results. In this paper, we p…
Clinical tracking systems are popular but typically require specific tracking markers. During the last years, scanning speed of optical coherence tomography (OCT) has increased to A-scan rates above 1 MHz allowing to acquire volume scans of moving objects. Thorefore, we propose a markerless tracking system based on OCT to obtain small volumetric images including information of sub-surface structures at high spatio-temporal resolution. In contrast to conventional vision based approaches, this allows identifying natural landmarks even for smooth and homogeneous surfaces. We describe the optomech…
