A deep learning model to assess and enhance eye fundus image quality

Engineering aims to design, build, and implement solutions that will increase and/or improve the life quality of human beings. Likewise, from medicine, solutions are generated for the same purposes, enabling these two knowledge areas to converge for a common goal. With the thesis work “A Deep Learning Model to Assess and Enhance Eye Fundus Image Quality", a model was proposed and implement a model that allows us to evaluate and enhance the quality of fundus images, which contributes to improving the efficiency and effectiveness of a subsequent diagnosis based on these images. On the one hand, for the evaluation of these images, a model based on a lightweight convolutional neural network architecture was developed, termed as Mobile Fundus Quality Network (MFQ-Net). This model has approximately 90% fewer parameters than those of the latest generation. For its evaluation, the Kaggle public data set was used with two sets of quality annotations, binary (good and bad) and three classes (good, usable and bad) obtaining an accuracy of 0.911 and 0.856 in the binary mode and three classes respectively in the classification of the fundus image quality. On the other hand, a method was developed for eye fundus quality enhancement termed as Pix2Pix Fundus Oculi Quality Enhancement (P2P-FOQE). This method is based on three stages which are; pre-enhancement: for color adjustment, enhancement: with a Pix2Pix network (which is a Conditional Generative Adversarial Network) as the core of the method and post-enhancement: which is a CLAHE adjustment for contrast and detail enhancement. This method was evaluated on a subset of quality annotations for the Kaggle public database which was re-classified for three categories (good, usable, and poor) by a specialist from the Fundación Oftalmolóica Nacional. With this method, the quality of these images for the good class was improved by 72.33%. Likewise, the image quality improved from the bad class to the usable class, and from the bad class to the good class by 56.21% and 29.49% respectively.La ingeniería busca diseñar, construir e implementar soluciones que permitan aumentar y/o mejorar la calidad de vida de los seres humanos. Igualmente, desde la medicina son generadas soluciones con los mismos fines, posibilitando que estas dos áreas del conocimiento convergan por un bien común. Con el trabajo de tesis “A Deep Learning Model to Assess and Enhance Eye Fundus Image Quality”, se propuso e implementó un modelo que permite evaluar y mejorar la calidad de las imágenes de fondo de ojo, lo cual contribuye a mejorar la eficiencia y eficacia de un posterior diagnóstico basado en estas imágenes. Para la evaluación de estás imágenes, se desarrolló un modelo basado en una arquitectura de red neuronal convolucional ligera, la cual fue llamada Mobile Fundus Quality Network (MFQ-Net). Este modelo posee aproximadamente 90% menos parámetros que aquellos de última generación. Para su evaluación se utilizó el conjunto de datos públicos de Kaggle con dos sets de anotaciones de calidad, binario (buena y mala) y tres clases (buena, usable y mala) obteniendo en la tareas de clasificación de la calidad de la imagen de fondo de ojo una exactitud de 0.911 y 0.856 en la modalidad binaria y tres clases respectivamente. Por otra parte, se desarrolló un método el cual realiza una mejora de la calidad de imágenes de fondo de ojo llamado Pix2Pix Fundus Oculi Quality Enhacement (P2P-FOQE). Este método está basado en tres etapas las cuales son; premejora: para ajuste de color, mejora: con una red Pix2Pix (la cual es una Conditional Generative Adversarial Network) como núcleo del método y postmejora: la cual es un ajuste CLAHE para contraste y realce de detalles. Este método fue evaluado en un subconjunto de anotaciones de calidad para la base de datos pública de Kaggle el cual fue re clasificado por un especialista de la Fundación Oftalmológica Nacional para tres categorías (buena, usable y mala). Con este método fue mejorada la calidad de estas imágenes para la clase buena en un 72,33%. Así mismo, la calidad de imagen mejoró de la clase mala a la clase utilizable, y de la clase mala a clase buena en 56.21% y 29.49% respectivamente.Línea de investigación: Visión por computadora para análisis de imágenes médicasMaestrí

NON-INVASIVE IMAGE DENOISING AND CONTRAST ENHANCEMENT TECHNIQUES FOR RETINAL FUNDUS IMAGES

The analysis of retinal vasculature in digital fundus images is important for diagnosing eye related diseases. However, digital colour fundus images suffer from low and varied contrast, and are also affected by noise, requiring the use of fundus angiogram modality. The Fundus Fluorescein Angiogram (FFA) modality gives 5 to 6 time’s higher contrast. However, FFA is an invasive method that requires contrast agents to be injected and this can lead other physiological problems. A reported digital image enhancement technique named RETICA that combines Retinex and ICA (Independent Component Analysis) techniques, reduces varied contrast, and enhances the low contrast blood vessels of model fundus images

Detection of Neovascularization Based on Fractal and Texture Analysis with Interaction Effects in Diabetic Retinopathy

Diabetic retinopathy is a major cause of blindness. Proliferative diabetic retinopathy is a result of severe vascular complication and is visible as neovascularization of the retina. Automatic detection of such new vessels would be useful for the severity grading of diabetic retinopathy, and it is an important part of screening process to identify those who may require immediate treatment for their diabetic retinopathy. We proposed a novel new vessels detection method including statistical texture analysis (STA), high order spectrum analysis (HOS), fractal analysis (FA), and most importantly we have shown that by incorporating their associated interactions the accuracy of new vessels detection can be greatly improved. To assess its performance, the sensitivity, specificity and accuracy (AUC) are obtained. They are 96.3%, 99.1% and 98.5% (99.3%), respectively. It is found that the proposed method can improve the accuracy of new vessels detection significantly over previous methods. The algorithm can be automated and is valuable to detect relatively severe cases of diabetic retinopathy among diabetes patients.published_or_final_versio

Quality Assessment of Retinal Fundus Images using Elliptical Local Vessel Density

Diabetic retinopathy is the leading cause of blindness in the Western world. The World Health Organisation estimates that 135 million people have diabetes mellitus worldwide and that the number of people with diabetes will increase to 300 million by the year 2025 (Amos et al., 1997). Timely detection and treatment for DR prevents severe visual loss in more than 50% of the patients (ETDRS, 1991). Through computer simulations is possible to demonstrate that prevention and treatment are relatively inexpensive if compared to the health care and rehabilitation costs incurred by visual loss or blindness (Javitt et al., 1994). The shortage of ophthalmologists and the continuous increase of the diabetic population limits the screening capability for effective timing of sight-saving treatment of typical manual methods. Therefore, an automatic or semi-automatic system able to detect various type of retinopathy is a vital necessity to save many sight-years in the population. According to Luzio et al. (2004) the preferred way to detect diseases such as diabetic retinopathy is digital fundus camera imaging. This allows the image to be enhanced, stored and retrieved more easily than film. In addition, images may be transferred electronically to other sites where a retinal specialist or an automated system can detect or diagnose disease while the patient remains at a remote location. Various systems for automatic or semi-automatic detection of retinopathy with fundus images have been developed. The results obtained are promising but the initial image quality is a limiting factor (Patton et al., 2006); this is especially true if the machine operator is not a trained photographer. Algorithms to correct the illumination or increase the vessel contrast exist (Chen & Tian, 2008; Foracchia et al., 2005; Grisan et al., 2006;Wang et al., 2001), however they cannot restore an image beyond a certain level of quality degradation. On the other hand, an accurate quality assessment algorithm can allow operators to avoid poor images by simply re-taking the fundus image, eliminating the need for correction algorithms. In addition, a quality metric would permit the automatic submission of only the best images if many are available. The measurement of a precise image quality index is not a straightforward task, mainly because quality is a subjective concept which varies even between experts, especially for images that are in the middle of the quality scale. In addition, image quality is dependent upon the type of diagnosis being made. For example, an image with dark regions might be considered of good quality for detecting glaucoma but of bad quality for detecting diabetic retinopathy. For this reason, we decided to define quality as the 'characteristics of an image that allow the retinopathy diagnosis by a human or software expert'. Fig. 1 shows some examples of macula centred fundus images whose quality is very likely to be judged as poor by many ophthalmologists. The reasons for this vary. They can be related to the camera settings like exposure or focal plane error (Fig. 1.(a,e,f)), the camera condition like a dirty or shuttered lens (Fig. 1.(d,h)), the movements of the patient which might blur the image (Fig. 1.(c)) or if the patient is not in the field of view of the camera (Fig. 1.(g)). We define an outlier as any image that is not a retina image which could be submitted to the screening system by mistake. Existing algorithms to estimate the image quality are based on the length of visible vessels in the macula region (Fleming et al., 2006), or edges and luminosity with respect to a reference image (Lalonde et al., 2001; Lee & Wang, 1999). Another method uses an unsupervised classifier that employs multi-scale filterbanks responses (Niemeijer et al., 2006). The shortcomings of these methods are either the fact that they do not take into account the natural variance encountered in retinal images or that they require a considerable time to produce a result. Additionally, none of the algorithms in the literature that we surveyed generate a 'quality measure'. Authors tend to split the quality levels into distinct classes and to classify images in particular ones. This approach is not really flexible and is error prone. In fact human experts are likely to disagree if many categories of image quality are used. Therefore, we think that a normalized 'quality measure' from 0 to 1 is the ideal way to approach the classification problem. Processing speed is another aspect to be taken into consideration. While algorithms to assess the disease state of the retina do not need to be particularly fast (within reason), the time response of the quality evaluation method is key towards the development of an automatic retinopathy screening system

Detection and Classification of Diabetic Retinopathy Pathologies in Fundus Images

Diabetic Retinopathy (DR) is a disease that affects up to 80% of diabetics around the world. It is the second greatest cause of blindness in the Western world, and one of the leading causes of blindness in the U.S. Many studies have demonstrated that early treatment can reduce the number of sight-threatening DR cases, mitigating the medical and economic impact of the disease. Accurate, early detection of eye disease is important because of its potential to reduce rates of blindness worldwide. Retinal photography for DR has been promoted for decades for its utility in both disease screening and clinical research studies. In recent years, several research centers have presented systems to detect pathology in retinal images. However, these approaches apply specialized algorithms to detect specific types of lesion in the retina. In order to detect multiple lesions, these systems generally implement multiple algorithms. Furthermore, some of these studies evaluate their algorithms on a single dataset, thus avoiding potential problems associated with the differences in fundus imaging devices, such as camera resolution. These methodologies primarily employ bottom-up approaches, in which the accurate segmentation of all the lesions in the retina is the basis for correct determination. A disadvantage of bottom-up approaches is that they rely on the accurate segmentation of all lesions in order to measure performance. On the other hand, top-down approaches do not depend on the segmentation of specific lesions. Thus, top-down methods can potentially detect abnormalities not explicitly used in their training phase. A disadvantage of these methods is that they cannot identify specific pathologies and require large datasets to build their training models. In this dissertation, I merged the advantages of the top-down and bottom-up approaches to detect DR with high accuracy. First, I developed an algorithm based on a top-down approach to detect abnormalities in the retina due to DR. By doing so, I was able to evaluate DR pathologies other than microaneurysms and exudates, which are the main focus of most current approaches. In addition, I demonstrated good generalization capacity of this algorithm by applying it to other eye diseases, such as age-related macular degeneration. Due to the fact that high accuracy is required for sight-threatening conditions, I developed two bottom-up approaches, since it has been proven that bottom-up approaches produce more accurate results than top-down approaches for particular structures. Consequently, I developed an algorithm to detect exudates in the macula. The presence of this pathology is considered to be a surrogate for clinical significant macular edema (CSME), a sight-threatening condition of DR. The analysis of the optic disc is usually not taken into account in DR screening systems. However, there is a pathology called neovascularization that is present in advanced stages of DR, making its detection of crucial clinical importance. In order to address this problem, I developed an algorithm to detect neovascularization in the optic disc. These algorithms are based on amplitude-modulation and frequency-modulation (AM-FM) representations, morphological image processing methods, and classification algorithms. The methods were tested on a diverse set of large databases and are considered to be the state-of the art in this field

Image Quality Improvement of Medical Images using Deep Learning for Computer-aided Diagnosis

Retina image analysis is an important screening tool for early detection of multiple dis eases such as diabetic retinopathy which greatly impairs visual function. Image analy sis and pathology detection can be accomplished both by ophthalmologists and by the use of computer-aided diagnosis systems. Advancements in hardware technology led to more portable and less expensive imaging devices for medical image acquisition. This promotes large scale remote diagnosis by clinicians as well as the implementation of computer-aided diagnosis systems for local routine disease screening. However, lower cost equipment generally results in inferior quality images. This may jeopardize the reliability of the acquired images and thus hinder the overall performance of the diagnos tic tool. To solve this open challenge, we carried out an in-depth study on using different deep learning-based frameworks for improving retina image quality while maintaining the underlying morphological information for the diagnosis. Our results demonstrate that using a Cycle Generative Adversarial Network for unpaired image-to-image trans lation leads to successful transformations of retina images from a low- to a high-quality domain. The visual evidence of this improvement was quantitatively affirmed by the two proposed validation methods. The first used a retina image quality classifier to confirm a significant prediction label shift towards a quality enhance. On average, a 50% increase of images being classified as high-quality was verified. The second analysed the perfor mance modifications of a diabetic retinopathy detection algorithm upon being trained with the quality-improved images. The latter led to strong evidence that the proposed solution satisfies the requirement of maintaining the images’ original information for diagnosis, and that it assures a pathology-assessment more sensitive to the presence of pathological signs. These experimental results confirm the potential effectiveness of our solution in improving retina image quality for diagnosis. Along with the addressed con tributions, we analysed how the construction of the data sets representing the low-quality domain impacts the quality translation efficiency. Our findings suggest that by tackling the problem more selectively, that is, constructing data sets more homogeneous in terms of their image defects, we can obtain more accentuated quality transformations

Comprehensive retinal image analysis: image processing and feature extraction techniques oriented to the clinical task

Medical digital imaging has become a key element of modern health care procedures. It provides a visual documentation, a permanent record for the patients, and most importantly the ability to extract information about many diseases. Ophthalmology is a field that is heavily dependent on the analysis of digital images because they can aid in establishing an early diagnosis even before the first symptoms appear. This dissertation contributes to the digital analysis of such images and the problems that arise along the imaging pipeline, a field that is commonly referred to as retinal image analysis. We have dealt with and proposed solutions to problems that arise in retinal image acquisition and longitudinal monitoring of retinal disease evolution. Specifically, non-uniform illumination, poor image quality, automated focusing, and multichannel analysis. However, there are many unavoidable situations in which images of poor quality, like blurred retinal images because of aberrations in the eye, are acquired. To address this problem we have proposed two approaches for blind deconvolution of blurred retinal images. In the first approach, we consider the blur to be space-invariant and later in the second approach we extend the work and propose a more general space-variant scheme. For the development of the algorithms we have built preprocessing solutions that have enabled the extraction of retinal features of medical relevancy, like the segmentation of the optic disc and the detection and visualization of longitudinal structural changes in the retina. Encouraging experimental results carried out on real retinal images coming from the clinical setting demonstrate the applicability of our proposed solutions

NON-INVASIVE IMAGE ENHANCEMENT OF COLOUR RETINAL FUNDUS IMAGES FOR A COMPUTERISED DIABETIC RETINOPATHY MONITORING AND GRADING SYSTEM

Diabetic Retinopathy (DR) is a sight threatening complication due to diabetes mellitus affecting the retina. The pathologies of DR can be monitored by analysing colour fundus images. However, the low and varied contrast between retinal vessels and the background in colour fundus images remains an impediment to visual analysis in particular in analysing tiny retinal vessels and capillary networks. To circumvent this problem, fundus fluorescein angiography (FF A) that improves the image contrast is used. Unfortunately, it is an invasive procedure (injection of contrast dyes) that leads to other physiological problems and in the worst case may cause death. The objective of this research is to develop a non-invasive digital Image enhancement scheme that can overcome the problem of the varied and low contrast colour fundus images in order that the contrast produced is comparable to the invasive fluorescein method, and without introducing noise or artefacts. The developed image enhancement algorithm (called RETICA) is incorporated into a newly developed computerised DR system (called RETINO) that is capable to monitor and grade DR severity using colour fundus images. RETINO grades DR severity into five stages, namely No DR, Mild Non Proliferative DR (NPDR), Moderate NPDR, Severe NPDR and Proliferative DR (PDR) by enhancing the quality of digital colour fundus image using RETICA in the macular region and analysing the enlargement of the foveal avascular zone (F AZ), a region devoid of retinal vessels in the macular region. The importance of this research is to improve image quality in order to increase the accuracy, sensitivity and specificity of DR diagnosis, and to enable DR grading through either direct observation or computer assisted diagnosis system

Towards Learning Representations in Visual Computing Tasks

abstract: The performance of most of the visual computing tasks depends on the quality of the features extracted from the raw data. Insightful feature representation increases the performance of many learning algorithms by exposing the underlying explanatory factors of the output for the unobserved input. A good representation should also handle anomalies in the data such as missing samples and noisy input caused by the undesired, external factors of variation. It should also reduce the data redundancy. Over the years, many feature extraction processes have been invented to produce good representations of raw images and videos. The feature extraction processes can be categorized into three groups. The first group contains processes that are hand-crafted for a specific task. Hand-engineering features requires the knowledge of domain experts and manual labor. However, the feature extraction process is interpretable and explainable. Next group contains the latent-feature extraction processes. While the original feature lies in a high-dimensional space, the relevant factors for a task often lie on a lower dimensional manifold. The latent-feature extraction employs hidden variables to expose the underlying data properties that cannot be directly measured from the input. Latent features seek a specific structure such as sparsity or low-rank into the derived representation through sophisticated optimization techniques. The last category is that of deep features. These are obtained by passing raw input data with minimal pre-processing through a deep network. Its parameters are computed by iteratively minimizing a task-based loss. In this dissertation, I present four pieces of work where I create and learn suitable data representations. The first task employs hand-crafted features to perform clinically-relevant retrieval of diabetic retinopathy images. The second task uses latent features to perform content-adaptive image enhancement. The third task ranks a pair of images based on their aestheticism. The goal of the last task is to capture localized image artifacts in small datasets with patch-level labels. For both these tasks, I propose novel deep architectures and show significant improvement over the previous state-of-art approaches. A suitable combination of feature representations augmented with an appropriate learning approach can increase performance for most visual computing tasks.Dissertation/ThesisDoctoral Dissertation Computer Science 201