Retinal Disease Screening through Local Binary Patterns

© 2015 IEEE. Personal use of this material is permitted. Permission from IEEE must be obtained for all other uses, in any current or future media, including reprinting/republishing this material for advertising or promotional purposes, creating new collective works, for resale or redistribution to servers or lists, or reuse of any copyrighted component of this work in other works.”This work investigates discrimination capabilities in the texture of fundus images to differentiate between pathological and healthy images. For this purpose, the performance of Local Binary Patterns (LBP) as a texture descriptor for retinal images has been explored and compared with other descriptors such as LBP filtering (LBPF) and local phase quantization (LPQ). The goal is to distinguish between diabetic retinopathy (DR), agerelated macular degeneration (AMD) and normal fundus images analysing the texture of the retina background and avoiding a previous lesion segmentation stage. Five experiments (separating DR from normal, AMD from normal, pathological from normal, DR from AMD and the three different classes) were designed and validated with the proposed procedure obtaining promising results. For each experiment, several classifiers were tested. An average sensitivity and specificity higher than 0.86 in all the cases and almost of 1 and 0.99, respectively, for AMD detection were achieved. These results suggest that the method presented in this paper is a robust algorithm for describing retina texture and can be useful in a diagnosis aid system for retinal disease screening.This work was supported by NILS Science and Sustainability Programme (010-ABEL-IM-2013) and by the Ministerio de Economia y Competitividad of Spain, Project ACRIMA (TIN2013-46751-R). The work of A. Colomer was supported by the Spanish Government under the FPI Grant BES-2014-067889.Morales, S.; Engan, K.; Naranjo Ornedo, V.; Colomer, A. (2015). Retinal Disease Screening through Local Binary Patterns. IEEE Journal of Biomedical and Health Informatics. (99):1-8. https://doi.org/10.1109/JBHI.2015.2490798S189

Characterization of age-related ocular diseases in OCT images through deep learning techniques

[Abstract]: Age-Related Macular Degeneration (AMD) is the main cause of severe visual impairment and blindness in Europe, and its prevalence is expected to increase worldwide due to population aging. Optical Coherence Tomography (OCT) is a noninvasive retinal imaging technique that has become the standard of care in the diagnosis and monitoring of late AMD, where the great majority of severe symptoms are manifested. Neovascular late AMD, where new pathological blood vessels are formed that may leak fluid, often results in relatively rapid vision loss. Treatment exists for neovascular AMD, such that its detection and characterization plays a key role in patient outcomes. This project applies deep learning techniques to the task of AMD characterization. To do so, a data set of OCT scans labeled as to the presence of fluid and neovascularisation is used to train deep convolutional networks. Analysis of this initial experiment produced two hypotheses of performance limiting factors: intra-expert variability and data scarcity. The former was addressed through the development of a machine-assisted review process based on the Class Activation Mapping (CAM) interpretability technique. A small blinded trial was favorable to the methodology. The latter resulted in the adaptation of a large public data set to explore domain-specific transfer learning.[Resumo]: A Dexeneración Macular Asociada á Idade (DMAI) é a principal causa de discapacidade visual severa e cegueira en Europa, e espérase que a súa prevalencia aumente a nivel mundial debido ó envellecemento poboacional. A Tomografía de Coherencia Óptica (TCO) é un método non invasivo de imaxe retiniana que se converteu no estándar no diagnóstico e monitorización da DMAI tardía, onde se manifestan a maioría de síntomas graves. A DMAI tardía neovascular, onde se forman novos vasos sanguíneos patolóxicos que poden derramar fluído, a miúdo resulta en perda de visión de forma relativamente repentina. Existen tratamentos para a DMAI neovascular, de modo que a súa detección e caracterización xoga un papel crucial no prognóstico dos pacientes. Este proxecto aplica técnicas de aprendizaxe profunda á tarefa de caracterización de DMAI. Con ese fin, un conxunto de datos de TCO anotado en base á presenza de fluído e neovascularización foi empregado para entrenar redes convolucionais profundas. A análise deste experimento inicial produciu dúas hipóteses sobre factores que limitan o rendemento: a variabilidade intra-experto e a escaseza de datos. O primeiro foi afrontado mediante o desenvolvemento dun proceso de revisión de anotacións asistido por computadora, baseado na técnica de interpretabilidade Class Activation Mapping (CAM). Un pequeno estudo cego foi favorable á metodoloxía. A segunda hipótese resultou na adaptación dun gran conxunto de datos público para a exploración de transferencia de aprendizaxe específica ó dominio.Traballo fin de grao (UDC.FIC). Enxeñaría Informática. Curso 2021/202

Intraretinal Fluid Pattern Characterization in Optical Coherence Tomography Images

[Abstract] Optical Coherence Tomography (OCT) has become a relevant image modality in the ophthalmological clinical practice, as it offers a detailed representation of the eye fundus. This medical imaging modality is currently one of the main means of identification and characterization of intraretinal cystoid regions, a crucial task in the diagnosis of exudative macular disease or macular edema, among the main causes of blindness in developed countries. This work presents an exhaustive analysis of intensity and texture-based descriptors for its identification and classification, using a complete set of 510 texture features, three state-of-the-art feature selection strategies, and seven representative classifier strategies. The methodology validation and the analysis were performed using an image dataset of 83 OCT scans. From these images, 1609 samples were extracted from both cystoid and non-cystoid regions. The different tested configurations provided satisfactory results, reaching a mean cross-validation test accuracy of 92.69%. The most promising feature categories identified for the issue were the Gabor filters, the Histogram of Oriented Gradients (HOG), the Gray-Level Run-Length matrix (GLRL), and the Laws’ texture filters (LAWS), being consistently and considerably selected along all feature selector algorithms in the top positions of different relevance rankings.Xunta de Galicia; ED431C 2016-047Xunta de Galicia; ED481A-2019/196This work is supported by the Instituto de Salud Carlos III, Government of Spain and FEDER funds of the European Union through the DTS18/00136 research projects and by the Ministerio de Ciencia, Innovación y Universidades, Government of Spain through the DPI2015-69948-R and RTI2018-095894-B-I00 research projects. Also, this work has received financial support from the European Union (European Regional Development Fund—ERDF) and the Xunta de Galicia, Grupos de Referencia Competitiva, Ref. ED431C 2016-047 and the Xunta de Galicia predoctoral grant contract ref. ED481A-2019/196

Translational Retinal Research and Therapies.

The following review summarizes the state of the art in representative aspects of gene therapy/translational medicine and evolves from a symposium held at the School of Veterinary Medicine, University of Pennsylvania on November 16, 2017 honoring Dr. Gustavo Aguirre, recipient of ARVO's 2017 Proctor Medal. Focusing on the retina, speakers highlighted current work on moving therapies for inherited retinal degenerative diseases from the laboratory bench to the clinic

Classification of SD-OCT Volumes using Local Binary Patterns: Experimental Validation for DME Detection

International audienceThis paper addresses the problem of automatic classification of Spectral Domain OCT (SD-OCT) data for automatic identification of patients with Diabetic Macular Edema (DME) versus normal subjects. Optical Coherence Tomography (OCT) has been a valuable diagnostic tool for DME, which is among the most common causes of irreversible vision loss in individuals with diabetes. Here, a classification framework with five distinctive steps is proposed and we present an extensive study of each step. Our method considers combination of various pre-processings in conjunction with Local Binary Patterns (LBP) features and different mapping strategies. Using linear and non-linear classifiers, we tested the developed framework on a balanced cohort of 32 patients. Experimental results show that the proposed method outperforms the previous studies by achieving a Sensitivity (SE) and Specificity (SP) of 81.2% and 93.7%, respectively. Our study concludes that the 3D features and high-level representation of 2D features using patches achieve the best results. However, the effects of pre-processing is inconsistent with respect to different classifiers and feature configurations

Advanced image processing techniques for detection and quantification of drusen

Dissertation presented to obtain the degree of Doctor of Philosophy in Electrical Engineering, speciality on Perceptional Systems, by the Universidade Nova de Lisboa, Faculty of Sciences and TechnologyDrusen are common features in the ageing macula, caused by accumulation of extracellular materials beneath the retinal surface, visible in retinal fundus images as yellow spots. In the ophthalmologists’ opinion, the evaluation of the total drusen area, in a sequence of images taken during a treatment, will help to understand the disease progression and effectiveness. However, this evaluation is fastidious and difficult to reproduce when performed manually. A literature review on automated drusen detection showed that the works already published were limited to techniques of either adaptive or global thresholds which showed a tendency to produce a significant number of false positives. The purpose for this work was to propose an alternative method to automatically quantify drusen using advanced digital image processing techniques. This methodology is based on a detection and modelling algorithm to automatically quantify drusen. It includes an image pre-processing step to correct the uneven illumination by using smoothing splines fitting and to normalize the contrast. To quantify drusen a detection and modelling algorithm is adopted. The detection uses a new gradient based segmentation algorithm that isolates drusen and provides basic drusen characterization to the modelling stage. These are then fitted by Gaussian functions, to produce a model of the image, which is used to compute the affected areas. To validate the methodology, two software applications, one for semi-automated (MD3RI) and other for automated detection of drusen (AD3RI), were implemented. The first was developed for Ophthalmologists to manually analyse and mark drusen deposits, while the other implemented algorithms for automatic drusen quantification.Four studies to assess the methodology accuracy involving twelve specialists have taken place. These compared the automated method to the specialists and evaluated its repeatability. The studies were analysed regarding several indicators, which were based on the total affected area and on a pixel-to-pixel analysis. Due to the high variability among the graders involved in the first study, a new evaluation method, the Weighed Matching Analysis, was developed to improve the pixel-to-pixel analysis by using the statistical significance of the observations to differentiate positive and negative pixels. From the results of these studies it was concluded that the methodology proposed is capable to automatically measure drusen in an accurate and reproducible process. Also, the thesis proposes new image processing algorithms, for image pre-processing, image segmentation,image modelling and images comparison, which are also applicable to other image processing fields

Feature Definition and Comprehensive Analysis on the Robust Identification of Intraretinal Cystoid Regions Using Optical Coherence Tomography Images

Financiado para publicación en acceso aberto: Universidade da Coruña/CISUG[Abstract] Currently, optical coherence tomography is one of the most used medical imaging modalities, offering cross-sectional representations of the studied tissues. This image modality is specially relevant for the analysis of the retina, since it is the internal part of the human body that allows an almost direct examination without invasive techniques. One of the most representative cases of use of this medical imaging modality is for the identification and characterization of intraretinal fluid accumulations, critical for the diagnosis of one of the main causes of blindness in developed countries: the Diabetic Macular Edema. The study of these fluid accumulations is particularly interesting, both from the point of view of pattern recognition and from the different branches of health sciences. As these fluid accumulations are intermingled with retinal tissues, they present numerous variants according to their severity, and change their appearance depending on the configuration of the device; they are a perfect subject for an in-depth research, as they are considered to be a problem without a strict solution. In this work, we propose a comprehensive and detailed analysis of the patterns that characterize them. We employed a pool of 11 different texture and intensity feature families (giving a total of 510 markers) which we have analyzed using three different feature selection strategies and seven complementary classification algorithms. By doing so, we have been able to narrow down and explain the factors affecting this kind of accumulations and tissue lesions by means of machine learning techniques with a pipeline specially designed for this purpose.Instituto de Salud Carlos III, Government of Spain, DTS18/00136 research project; Ministerio de Ciencia e Innovación y Universidades, Government of Spain, RTI2018-095894-B-I00 research project, Ayudas para la formación de profesorado universitario (FPU), grant ref. FPU18/02271; Ministerio de Ciencia e Innovación, Government of Spain through the research project with reference PID2019-108435RB-I00; Consellería de Cultura, Educación e Universidade, Xunta de Galicia, Grupos de Referencia Competitiva, grant ref. ED431C 2020/24 and through the postdoctoral grant contract ref. ED481B 2021/059; Axencia Galega de Innovación (GAIN), Xunta de Galicia, grant ref. IN845D 2020/38; CITIC, Centro de Investigación de Galicia ref. ED431G 2019/01, receives financial support from Consellería de Educación, Universidade e Formación Profesional, Xunta de Galicia, through the ERDF (80%) and Secretaría Xeral de Universidades (20%). Open Access funding provided thanks to the CRUE-CSIC agreement with Springer Nature. Funding for open access charge: Universidade da Coruña/CISUGXunta de Galicia; ED431C 2020/24Xunta de Galicia; ED481B 2021/059Xunta de Galicia; IN845D 2020/38Xunta de Galicia; ED431G 2019/0

Deep learning analysis of eye fundus images to support medical diagnosis

Machine learning techniques have been successfully applied to support medical decision making of cancer, heart diseases and degenerative diseases of the brain. In particular, deep learning methods have been used for early detection of abnormalities in the eye that could improve the diagnosis of different ocular diseases, especially in developing countries, where there are major limitations to access to specialized medical treatment. However, the early detection of clinical signs such as blood vessel, optic disc alterations, exudates, hemorrhages, drusen, and microaneurysms presents three main challenges: the ocular images can be affected by noise artifact, the features of the clinical signs depend specifically on the acquisition source, and the combination of local signs and grading disease label is not an easy task. This research approaches the problem of combining local signs and global labels of different acquisition sources of medical information as a valuable tool to support medical decision making in ocular diseases. Different models for different eye diseases were developed. Four models were developed using eye fundus images: for DME, it was designed a two-stages model that uses a shallow model to predict an exudate binary mask. Then, the binary mask is stacked with the raw fundus image into a 4-channel array as an input of a deep convolutional neural network for diabetic macular edema diagnosis; for glaucoma, it was developed three deep learning models. First, it was defined a deep learning model based on three-stages that contains an initial stage for automatically segment two binary masks containing optic disc and physiological cup segmentation, followed by an automatic morphometric features extraction stage from previous segmentations, and a final classification stage that supports the glaucoma diagnosis with intermediate medical information. Two late-data-fusion methods that fused morphometric features from cartesian and polar segmentation of the optic disc and physiological cup with features extracted from raw eye fundus images. On the other hand, two models were defined using optical coherence tomography. First, a customized convolutional neural network termed as OCT-NET to extract features from OCT volumes to classify DME, DR-DME and AMD conditions. In addition, this model generates images with highlighted local information about the clinical signs, and it estimates the number of slides inside a volume with local abnormalities. Finally, a 3D-Deep learning model that uses OCT volumes as an input to estimate the retinal thickness map useful to grade AMD. The methods were systematically evaluated using ten free public datasets. The methods were compared and validated against other state-of-the-art algorithms and the results were also qualitatively evaluated by ophthalmology experts from Fundación Oftalmológica Nacional. In addition, the proposed methods were tested as a diagnosis support tool of diabetic macular edema, glaucoma, diabetic retinopathy and age-related macular degeneration using two different ocular imaging representations. Thus, we consider that this research could be potentially a big step in building telemedicine tools that could support medical personnel for detecting ocular diseases using eye fundus images and optical coherence tomography.Las técnicas de aprendizaje automático se han aplicado con éxito para apoyar la toma de decisiones médicas sobre el cáncer, las enfermedades cardíacas y las enfermedades degenerativas del cerebro. En particular, se han utilizado métodos de aprendizaje profundo para la detección temprana de anormalidades en el ojo que podrían mejorar el diagnóstico de diferentes enfermedades oculares, especialmente en países en desarrollo, donde existen grandes limitaciones para acceder a tratamiento médico especializado. Sin embargo, la detección temprana de signos clínicos como vasos sanguíneos, alteraciones del disco óptico, exudados, hemorragias, drusas y microaneurismas presenta tres desafíos principales: las imágenes oculares pueden verse afectadas por artefactos de ruido, las características de los signos clínicos dependen específicamente de fuente de adquisición, y la combinación de signos locales y clasificación de la enfermedad no es una tarea fácil. Esta investigación aborda el problema de combinar signos locales y etiquetas globales de diferentes fuentes de adquisición de información médica como una herramienta valiosa para apoyar la toma de decisiones médicas en enfermedades oculares. Se desarrollaron diferentes modelos para diferentes enfermedades oculares. Se desarrollaron cuatro modelos utilizando imágenes de fondo de ojo: para DME, se diseñó un modelo de dos etapas que utiliza un modelo superficial para predecir una máscara binaria de exudados. Luego, la máscara binaria se apila con la imagen de fondo de ojo original en una matriz de 4 canales como entrada de una red neuronal convolucional profunda para el diagnóstico de edema macular diabético; para el glaucoma, se desarrollaron tres modelos de aprendizaje profundo. Primero, se definió un modelo de aprendizaje profundo basado en tres etapas que contiene una etapa inicial para segmentar automáticamente dos máscaras binarias que contienen disco óptico y segmentación fisiológica de la copa, seguido de una etapa de extracción de características morfométricas automáticas de segmentaciones anteriores y una etapa de clasificación final que respalda el diagnóstico de glaucoma con información médica intermedia. Dos métodos de fusión de datos tardíos que fusionaron características morfométricas de la segmentación cartesiana y polar del disco óptico y la copa fisiológica con características extraídas de imágenes de fondo de ojo crudo. Por otro lado, se definieron dos modelos mediante tomografía de coherencia óptica. Primero, una red neuronal convolucional personalizada denominada OCT-NET para extraer características de los volúmenes OCT para clasificar las condiciones DME, DR-DME y AMD. Además, este modelo genera imágenes con información local resaltada sobre los signos clínicos, y estima el número de diapositivas dentro de un volumen con anomalías locales. Finalmente, un modelo de aprendizaje 3D-Deep que utiliza volúmenes OCT como entrada para estimar el mapa de espesor retiniano útil para calificar AMD. Los métodos se evaluaron sistemáticamente utilizando diez conjuntos de datos públicos gratuitos. Los métodos se compararon y validaron con otros algoritmos de vanguardia y los resultados también fueron evaluados cualitativamente por expertos en oftalmología de la Fundación Oftalmológica Nacional. Además, los métodos propuestos se probaron como una herramienta de diagnóstico de edema macular diabético, glaucoma, retinopatía diabética y degeneración macular relacionada con la edad utilizando dos representaciones de imágenes oculares diferentes. Por lo tanto, consideramos que esta investigación podría ser potencialmente un gran paso en la construcción de herramientas de telemedicina que podrían ayudar al personal médico a detectar enfermedades oculares utilizando imágenes de fondo de ojo y tomografía de coherencia óptica.Doctorad

Evaluation of fractal dimension effectiveness for damage detection in retinal background

[EN] This work investigates the characterization of bright lesions in retinal fundus images using texture analysis techniques. Exudates and drusen are evidences of retinal damage in diabetic retinopathy (DR) and age-related macular degeneration (AMD) respectively. An automatic detection of pathological tissues could make possible an early detection of these diseases. In this work, fractal analysis is explored in order to discriminate between pathological and healthy retinal texture. After a deep preprocessing step, in which spatial and colour normalization are performed, the fractal dimension is extracted locally by computing the Hurst exponent (H) along different directions. The greyscale image is described by the increments of the fractional Brownian motion model and the H parameter is computed by linear regression in the frequency domain. The ability of fractal dimension to detect pathological tissues is demonstrated using a home-made system, based on fractal analysis and Support Vector Machine, able to achieve around a 70% and 83% of accuracy in E-OPHTHA and DIARETDB1 public databases respectively. In a second experiment, the fractal descriptor is combined with texture information, extracted by the Local Binary Patterns, improving the bright lesion detection. Accuracy, sensitivity and specificity values higher than 89%, 80% and 90% respectively suggest that the method presented in this paper is a robust algorithm for describing retina texture and can be useful in the automatic detection of DR and AMD.This paper was supported by the European Union's Horizon 2020 research and innovation programme under the Project GALAHAD [H2020-ICT-2016-2017, 732613]. In addition, this work was partially funded by the Ministerio de Economia y Competitividad of Spain, Project SICAP [DPI2016-77869-C2-1-R]. The work of Adrian Colomer has been supported by the Spanish Government under a FPI Grant [BES-2014-067889]. We gratefully acknowledge the support of NVIDIA Corporation with the donation of the Titan Xp GPU used for this research.Colomer, A.; Naranjo Ornedo, V.; Janvier, T.; Mossi García, JM. (2018). Evaluation of fractal dimension effectiveness for damage detection in retinal background. Journal of Computational and Applied Mathematics. 337:341-353. https://doi.org/10.1016/j.cam.2018.01.005S34135333