Medinoid : computer-aided diagnosis and localization of glaucoma using deep learning

Glaucoma is a leading eye disease, causing vision loss by gradually affecting peripheral vision if left untreated. Current diagnosis of glaucoma is performed by ophthalmologists, human experts who typically need to analyze different types of medical images generated by different types of medical equipment: fundus, Retinal Nerve Fiber Layer (RNFL), Optical Coherence Tomography (OCT) disc, OCT macula, perimetry, and/or perimetry deviation. Capturing and analyzing these medical images is labor intensive and time consuming. In this paper, we present a novel approach for glaucoma diagnosis and localization, only relying on fundus images that are analyzed by making use of state-of-the-art deep learning techniques. Specifically, our approach towards glaucoma diagnosis and localization leverages Convolutional Neural Networks (CNNs) and Gradient-weighted Class Activation Mapping (Grad-CAM), respectively. We built and evaluated different predictive models using a large set of fundus images, collected and labeled by ophthalmologists at Samsung Medical Center (SMC). Our experimental results demonstrate that our most effective predictive model is able to achieve a high diagnosis accuracy of 96%, as well as a high sensitivity of 96% and a high specificity of 100% for Dataset-Optic Disc (OD), a set of center-cropped fundus images highlighting the optic disc. Furthermore, we present Medinoid, a publicly-available prototype web application for computer-aided diagnosis and localization of glaucoma, integrating our most effective predictive model in its back-end

A Survey on Deep Learning in Medical Image Analysis

Deep learning algorithms, in particular convolutional networks, have rapidly become a methodology of choice for analyzing medical images. This paper reviews the major deep learning concepts pertinent to medical image analysis and summarizes over 300 contributions to the field, most of which appeared in the last year. We survey the use of deep learning for image classification, object detection, segmentation, registration, and other tasks and provide concise overviews of studies per application area. Open challenges and directions for future research are discussed.Comment: Revised survey includes expanded discussion section and reworked introductory section on common deep architectures. Added missed papers from before Feb 1st 201

Bilateral-Fuser: A Novel Multi-cue Fusion Architecture with Anatomical-aware Tokens for Fovea Localization

Accurate localization of fovea is one of the primary steps in analyzing retinal diseases since it helps prevent irreversible vision loss. Although current deep learning-based methods achieve better performance than traditional methods, there still remain challenges such as utilizing anatomical landmarks insufficiently, sensitivity to diseased retinal images and various image conditions. In this paper, we propose a novel transformer-based architecture (Bilateral-Fuser) for multi-cue fusion. This architecture explicitly incorporates long-range connections and global features using retina and vessel distributions for robust fovea localization. We introduce a spatial attention mechanism in the dual-stream encoder for extracting and fusing self-learned anatomical information. This design focuses more on features distributed along blood vessels and significantly decreases computational costs by reducing token numbers. Our comprehensive experiments show that the proposed architecture achieves state-of-the-art performance on two public and one large-scale private datasets. We also present that the Bilateral-Fuser is more robust on both normal and diseased retina images and has better generalization capacity in cross-dataset experiments.Comment: This paper is prepared for IEEE TRANSACTIONS ON MEDICAL IMAGIN

Exploring Deep Learning Techniques for Glaucoma Detection: A Comprehensive Review

Glaucoma is one of the primary causes of vision loss around the world, necessitating accurate and efficient detection methods. Traditional manual detection approaches have limitations in terms of cost, time, and subjectivity. Recent developments in deep learning approaches demonstrate potential in automating glaucoma detection by detecting relevant features from retinal fundus images. This article provides a comprehensive overview of cutting-edge deep learning methods used for the segmentation, classification, and detection of glaucoma. By analyzing recent studies, the effectiveness and limitations of these techniques are evaluated, key findings are highlighted, and potential areas for further research are identified. The use of deep learning algorithms may significantly improve the efficacy, usefulness, and accuracy of glaucoma detection. The findings from this research contribute to the ongoing advancements in automated glaucoma detection and have implications for improving patient outcomes and reducing the global burden of glaucoma

Deep Learning based Novel Anomaly Detection Methods for Diabetic Retinopathy Screening

Programa Oficial de Doutoramento en Computación. 5009V01[Abstract] Computer-Aided Screening (CAS) systems are getting popularity in disease diagnosis. Modern CAS systems exploit data driven machine learning algorithms including supervised and unsupervised methods. In medical imaging, annotating pathological samples are much harder and time consuming work than healthy samples. Therefore, there is always an abundance of healthy samples and scarcity of annotated and labelled pathological samples. Unsupervised anomaly detection algorithms can be implemented for the development of CAS system using the largely available healthy samples, especially when disease/nodisease decision is important for screening. This thesis proposes unsupervised machine learning methodologies for anomaly detection in retinal fundus images. A novel patchbased image reconstructor architecture for DR detection is presented, that addresses the shortcomings of standard autoencoders-based reconstructors. Furthermore, a full-size image based anomaly map generation methodology is presented, where the potential DR lesions can be visualized at the pixel-level. Afterwards, a novel methodology is proposed to extend the patch-based architecture to a fully-convolutional architecture for one-shot full-size image reconstruction. Finally, a novel methodology for supervised DR classification is proposed that utilizes the anomaly maps

Computational Analysis of Fundus Images: Rule-Based and Scale-Space Models

Fundus images are one of the most important imaging examinations in modern ophthalmology because they are simple, inexpensive and, above all, noninvasive. Nowadays, the acquisition and storage of highresolution fundus images is relatively easy and fast. Therefore, fundus imaging has become a fundamental investigation in retinal lesion detection, ocular health monitoring and screening programmes. Given the large volume and clinical complexity associated with these images, their analysis and interpretation by trained clinicians becomes a timeconsuming task and is prone to human error. Therefore, there is a growing interest in developing automated approaches that are affordable and have high sensitivity and specificity. These automated approaches need to be robust if they are to be used in the general population to diagnose and track retinal diseases. To be effective, the automated systems must be able to recognize normal structures and distinguish them from pathological clinical manifestations. The main objective of the research leading to this thesis was to develop automated systems capable of recognizing and segmenting retinal anatomical structures and retinal pathological clinical manifestations associated with the most common retinal diseases. In particular, these automated algorithms were developed on the premise of robustness and efficiency to deal with the difficulties and complexity inherent in these images. Four objectives were considered in the analysis of fundus images. Segmentation of exudates, localization of the optic disc, detection of the midline of blood vessels, segmentation of the vascular network and detection of microaneurysms. In addition, we also evaluated the detection of diabetic retinopathy on fundus images using the microaneurysm detection method. An overview of the state of the art is presented to compare the performance of the developed approaches with the main methods described in the literature for each of the previously described objectives. To facilitate the comparison of methods, the state of the art has been divided into rulebased methods and machine learningbased methods. In the research reported in this paper, rulebased methods based on image processing methods were preferred over machine learningbased methods. In particular, scalespace methods proved to be effective in achieving the set goals. Two different approaches to exudate segmentation were developed. The first approach is based on scalespace curvature in combination with the local maximum of a scalespace blob detector and dynamic thresholds. The second approach is based on the analysis of the distribution function of the maximum values of the noise map in combination with morphological operators and adaptive thresholds. Both approaches perform a correct segmentation of the exudates and cope well with the uneven illumination and contrast variations in the fundus images. Optic disc localization was achieved using a new technique called cumulative sum fields, which was combined with a vascular enhancement method. The algorithm proved to be reliable and efficient, especially for pathological images. The robustness of the method was tested on 8 datasets. The detection of the midline of the blood vessels was achieved using a modified corner detector in combination with binary philtres and dynamic thresholding. Segmentation of the vascular network was achieved using a new scalespace blood vessels enhancement method. The developed methods have proven effective in detecting the midline of blood vessels and segmenting vascular networks. The microaneurysm detection method relies on a scalespace microaneurysm detection and labelling system. A new approach based on the neighbourhood of the microaneurysms was used for labelling. Microaneurysm detection enabled the assessment of diabetic retinopathy detection. The microaneurysm detection method proved to be competitive with other methods, especially with highresolution images. Diabetic retinopathy detection with the developed microaneurysm detection method showed similar performance to other methods and human experts. The results of this work show that it is possible to develop reliable and robust scalespace methods that can detect various anatomical structures and pathological features of the retina. Furthermore, the results obtained in this work show that although recent research has focused on machine learning methods, scalespace methods can achieve very competitive results and typically have greater independence from image acquisition. The methods developed in this work may also be relevant for the future definition of new descriptors and features that can significantly improve the results of automated methods.As imagens do fundo do olho são hoje um dos principais exames imagiológicos da oftalmologia moderna, pela sua simplicidade, baixo custo e acima de tudo pelo seu carácter nãoinvasivo. A aquisição e armazenamento de imagens do fundo do olho com alta resolução é também relativamente simples e rápida. Desta forma, as imagens do fundo do olho são um exame fundamental na identificação de alterações retinianas, monitorização da saúde ocular, e em programas de rastreio. Considerando o elevado volume e complexidade clínica associada a estas imagens, a análise e interpretação das mesmas por clínicos treinados tornase uma tarefa morosa e propensa a erros humanos. Assim, há um interesse crescente no desenvolvimento de abordagens automatizadas, acessíveis em custo, e com uma alta sensibilidade e especificidade. Estas devem ser robustas para serem aplicadas à população em geral no diagnóstico e seguimento de doenças retinianas. Para serem eficazes, os sistemas de análise têm que conseguir detetar e distinguir estruturas normais de sinais patológicos. O objetivo principal da investigação que levou a esta tese de doutoramento é o desenvolvimento de sistemas automáticos capazes de detetar e segmentar as estruturas anatómicas da retina, e os sinais patológicos retinianos associados às doenças retinianas mais comuns. Em particular, estes algoritmos automatizados foram desenvolvidos segundo as premissas de robustez e eficácia para lidar com as dificuldades e complexidades inerentes a estas imagens. Foram considerados quatro objetivos de análise de imagens do fundo do olho. São estes, a segmentação de exsudados, a localização do disco ótico, a deteção da linha central venosa dos vasos sanguíneos e segmentação da rede vascular, e a deteção de microaneurismas. De acrescentar que usando o método de deteção de microaneurismas, avaliouse também a capacidade de deteção da retinopatia diabética em imagens do fundo do olho. Para comparar o desempenho das metodologias desenvolvidas neste trabalho, foi realizado um levantamento do estado da arte, onde foram considerados os métodos mais relevantes descritos na literatura para cada um dos objetivos descritos anteriormente. Para facilitar a comparação entre métodos, o estado da arte foi dividido em metodologias de processamento de imagem e baseadas em aprendizagem máquina. Optouse no trabalho de investigação desenvolvido pela utilização de metodologias de análise espacial de imagem em detrimento de metodologias baseadas em aprendizagem máquina. Em particular, as metodologias baseadas no espaço de escalas mostraram ser efetivas na obtenção dos objetivos estabelecidos. Para a segmentação de exsudados foram usadas duas abordagens distintas. A primeira abordagem baseiase na curvatura em espaço de escalas em conjunto com a resposta máxima local de um detetor de manchas em espaço de escalas e limiares dinâmicos. A segunda abordagem baseiase na análise do mapa de distribuição de ruído em conjunto com operadores morfológicos e limiares adaptativos. Ambas as abordagens fazem uma segmentação dos exsudados de elevada precisão, além de lidarem eficazmente com a iluminação nãouniforme e a variação de contraste presente nas imagens do fundo do olho. A localização do disco ótico foi conseguida com uma nova técnica designada por campos de soma acumulativos, combinada com métodos de melhoramento da rede vascular. O algoritmo revela ser fiável e eficiente, particularmente em imagens patológicas. A robustez do método foi verificada pela sua avaliação em oito bases de dados. A deteção da linha central dos vasos sanguíneos foi obtida através de um detetor de cantos modificado em conjunto com filtros binários e limiares dinâmicos. A segmentação da rede vascular foi conseguida com um novo método de melhoramento de vasos sanguíneos em espaço de escalas. Os métodos desenvolvidos mostraram ser eficazes na deteção da linha central dos vasos sanguíneos e na segmentação da rede vascular. Finalmente, o método para a deteção de microaneurismas assenta num formalismo de espaço de escalas na deteção e na rotulagem dos microaneurismas. Para a rotulagem foi utilizada uma nova abordagem da vizinhança dos candidatos a microaneurismas. A deteção de microaneurismas permitiu avaliar também a deteção da retinopatia diabética. O método para a deteção de microaneurismas mostrou ser competitivo quando comparado com outros métodos, em particular em imagens de alta resolução. A deteção da retinopatia diabética exibiu um desempenho semelhante a outros métodos e a especialistas humanos. Os trabalhos descritos nesta tese mostram ser possível desenvolver uma abordagem fiável e robusta em espaço de escalas capaz de detetar diferentes estruturas anatómicas e sinais patológicos da retina. Além disso, os resultados obtidos mostram que apesar de a pesquisa mais recente concentrarse em metodologias de aprendizagem máquina, as metodologias de análise espacial apresentam resultados muito competitivos e tipicamente independentes do equipamento de aquisição das imagens. As metodologias desenvolvidas nesta tese podem ser importantes na definição de novos descritores e características, que podem melhorar significativamente o resultado de métodos automatizados