167 research outputs found

    Deep learning-based classification of eye diseases using Convolutional Neural Network for OCT images

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    Deep learning shows promising results in extracting useful information from medical images. The proposed work applies a Convolutional Neural Network (CNN) on retinal images to extract features that allow early detection of ophthalmic diseases. Early disease diagnosis is critical to retinal treatment. Any damage that occurs to retinal tissues that cannot be recovered can result in permanent degradation or even complete loss of sight. The proposed deep-learning algorithm detects three different diseases from features extracted from Optical Coherence Tomography (OCT) images. The deep-learning algorithm uses CNN to classify OCT images into four categories. The four categories are Normal retina, Diabetic Macular Edema (DME), Choroidal Neovascular Membranes (CNM), and Age-related Macular Degeneration (AMD). The proposed work uses publicly available OCT retinal images as a dataset. The experimental results show significant enhancement in classification accuracy while detecting the features of the three listed diseases

    Segmentation of optic disc in retinal images for glaucoma diagnosis by saliency level set with enhanced active contour model

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    Glaucoma is an ophthalmic disease which is among the chief causes of visual impairment across the globe. The clarity of the optic disc (OD) is crucial for recognizing glaucoma. Since existing methods are unable to successfully integrate multi-view information derived from shape and appearance to precisely explain OD for segmentation, this paper proposes a saliency-based level set with an enhanced active contour method (SL-EACM), a modified locally statistical active contour model, and entropy-based optical disc localization. The significant contributions are that i) the SL-EACM is introduced to address the often noticed problem of intensity inhomogeneity brought on by defects in imaging equipment or fluctuations in lighting; ii) to prevent the integrity of the OD structures from being compromised by pathological alterations and artery blockage, local image probability data is included from a multi-dimensional feature space around the region of interest in the model; and iii) the model incorporates prior shape information into the technique, for enhancing the accuracy in identifying the OD structures from surrounding regions. Public databases such as CHASE_DB, DRIONS-DB, and Drishti-GS are used to evaluate the proposed model. The findings from numerous trials demonstrate that the proposed model outperforms state-of-the-art approaches in terms of qualitative and quantitative outcomes

    Machine Learning Techniques, Detection and Prediction of Glaucoma– A Systematic Review

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    Globally, glaucoma is the most common factor in both permanent blindness and impairment. However, the majority of patients are unaware they have the condition, and clinical practise continues to face difficulties in detecting glaucoma progression using current technology. An expert ophthalmologist examines the retinal portion of the eye to see how the glaucoma is progressing. This method is quite time-consuming, and doing it manually takes more time. Therefore, using deep learning and machine learning techniques, this problem can be resolved by automatically diagnosing glaucoma. This systematic review involved a comprehensive analysis of various automated glaucoma prediction and detection techniques. More than 100 articles on Machine learning (ML) techniques with understandable graph and tabular column are reviewed considering summery, method, objective, performance, advantages and disadvantages. In the ML techniques such as support vector machine (SVM), and K-means. Fuzzy c-means clustering algorithm are widely used in glaucoma detection and prediction. Through the systematic review, the most accurate technique to detect and predict glaucoma can be determined which can be utilized for future betterment

    MFA-UNet: a vessel segmentation method based on multi-scale feature fusion and attention module

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    IntroductionThe accurate segmentation of retinal vessels is of utmost importance in the diagnosis of retinal diseases. However, the complex vessel structure often leads to poor segmentation performance, particularly in the case of microvessels.MethodsTo address this issue, we propose a vessel segmentation method composed of preprocessing and a multi-scale feature attention network (MFA-UNet). The preprocessing stage involves the application of gamma correction and contrast-limited adaptive histogram equalization to enhance image intensity and vessel contrast. The MFA-UNet incorporates the Multi-scale Fusion Self-Attention Module(MSAM) that adjusts multi-scale features and establishes global dependencies, enabling the network to better preserve microvascular structures. Furthermore, the multi-branch decoding module based on deep supervision (MBDM) replaces the original output layer to achieve targeted segmentation of macrovessels and microvessels. Additionally, a parallel attention mechanism is embedded into the decoder to better exploit multi-scale features in skip paths.ResultsThe proposed MFA-UNet yields competitive performance, with dice scores of 82.79/83.51/84.17/78.60/81.75/84.04 and accuracies of 95.71/96.4/96.71/96.81/96.32/97.10 on the DRIVE, STARE, CHASEDB1, HRF, IOSTAR and FIVES datasets, respectively.DiscussionIt is expected to provide reliable segmentation results in clinical diagnosis

    Robust deep learning for computational imaging through random optics

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    Light scattering is a pervasive phenomenon that poses outstanding challenges in both coherent and incoherent imaging systems. The output of a coherent light scattered from a complex medium exhibits a seemingly random speckle pattern that scrambles the useful information of the object. To date, there is no simple solution for inverting such complex scattering. Advancing the solution of inverse scattering problems could provide important insights into applications across many areas, such as deep tissue imaging, non-line-of-sight imaging, and imaging in degraded environment. On the other hand, in incoherent systems, the randomness of scattering medium could be exploited to build lightweight, compact, and low-cost lensless imaging systems that are applicable in miniaturized biomedical and scientific imaging. The imaging capabilities of such computational imaging systems, however, are largely limited by the ill-posed or ill-conditioned inverse problems, which typically causes imaging artifacts and degradation of the image resolution. Therefore, mitigating this issue by developing modern algorithms is essential for pushing the limits of such lensless computational imaging systems. In this thesis, I focus on the problem of imaging through random optics and present two novel deep-learning (DL) based methodologies to overcome the challenges in coherent and incoherent systems: 1) no simple solution for inverse scattering problem and lack of robustness to scattering variations; and 2) ill-posed problem for diffuser-based lensless imaging. In the first part, I demonstrate the novel use of a deep neural network (DNN) to solve the inverse scattering problem in a coherent imaging system. I propose a `one-to-all' deep learning technique that encapsulates a wide range of statistical variations for the model to be resilient to speckle decorrelations. I show for the first time, to the best of my knowledge, that the trained CNN is able to generalize and make high-quality object prediction through an entirely different set of diffusers of the same macroscopic parameter. I then push the limit of robustness against a broader class of perturbations including scatterer change, displacements, and system defocus up to 10X depth of field. In the second part, I consider the utility of the random light scattering to build a diffuser-based computational lensless imaging system and present a generally applicable novel DL framework to achieve fast and noise-robust color image reconstruction. I developed a diffuser-based computational funduscope that reconstructs important clinical features of a model eye. Experimentally, I demonstrated fundus image reconstruction over a large field of view (FOV) and robustness to refractive error using a constant point-spread-function. Next, I present a physics simulator-trained, adaptive DL framework to achieve fast and noise-robust color imaging. The physics simulator incorporates optical system modeling, the simulation of mixed Poisson-Gaussian noise, and color filter array induced artifacts in color sensors. The learning framework includes an adaptive multi-channel L2-regularized inversion module and a channel-attention enhancement network module. Both simulation and experiments show consistently better reconstruction accuracy and robustness to various noise levels under different light conditions compared with traditional L2-regularized reconstructions. Overall, this thesis investigated two major classes of problems in imaging through random optics. In the first part of the thesis, my work explored a novel DL-based approach for solving the inverse scattering problem and paves the way to a scalable and robust deep learning approach to imaging through scattering media. In the second part of the thesis, my work developed a broadly applicable adaptive learning-based framework for ill-conditioned image reconstruction and a physics-based simulation model for computational color imaging

    Generative Adversarial Network (GAN) for Medical Image Synthesis and Augmentation

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    Medical image processing aided by artificial intelligence (AI) and machine learning (ML) significantly improves medical diagnosis and decision making. However, the difficulty to access well-annotated medical images becomes one of the main constraints on further improving this technology. Generative adversarial network (GAN) is a DNN framework for data synthetization, which provides a practical solution for medical image augmentation and translation. In this study, we first perform a quantitative survey on the published studies on GAN for medical image processing since 2017. Then a novel adaptive cycle-consistent adversarial network (Ad CycleGAN) is proposed. We respectively use a malaria blood cell dataset (19,578 images) and a COVID-19 chest X-ray dataset (2,347 images) to test the new Ad CycleGAN. The quantitative metrics include mean squared error (MSE), root mean squared error (RMSE), peak signal-to-noise ratio (PSNR), universal image quality index (UIQI), spatial correlation coefficient (SCC), spectral angle mapper (SAM), visual information fidelity (VIF), Frechet inception distance (FID), and the classification accuracy of the synthetic images. The CycleGAN and variant autoencoder (VAE) are also implemented and evaluated as comparison. The experiment results on malaria blood cell images indicate that the Ad CycleGAN generates more valid images compared to CycleGAN or VAE. The synthetic images by Ad CycleGAN or CycleGAN have better quality than those by VAE. The synthetic images by Ad CycleGAN have the highest accuracy of 99.61%. In the experiment on COVID-19 chest X-ray, the synthetic images by Ad CycleGAN or CycleGAN have higher quality than those generated by variant autoencoder (VAE). However, the synthetic images generated through the homogenous image augmentation process have better quality than those synthesized through the image translation process. The synthetic images by Ad CycleGAN have higher accuracy of 95.31% compared to the accuracy of the images by CycleGAN of 93.75%. In conclusion, the proposed Ad CycleGAN provides a new path to synthesize medical images with desired diagnostic or pathological patterns. It is considered a new approach of conditional GAN with effective control power upon the synthetic image domain. The findings offer a new path to improve the deep neural network performance in medical image processing

    Deep Representation Learning with Limited Data for Biomedical Image Synthesis, Segmentation, and Detection

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    Biomedical imaging requires accurate expert annotation and interpretation that can aid medical staff and clinicians in automating differential diagnosis and solving underlying health conditions. With the advent of Deep learning, it has become a standard for reaching expert-level performance in non-invasive biomedical imaging tasks by training with large image datasets. However, with the need for large publicly available datasets, training a deep learning model to learn intrinsic representations becomes harder. Representation learning with limited data has introduced new learning techniques, such as Generative Adversarial Networks, Semi-supervised Learning, and Self-supervised Learning, that can be applied to various biomedical applications. For example, ophthalmologists use color funduscopy (CF) and fluorescein angiography (FA) to diagnose retinal degenerative diseases. However, fluorescein angiography requires injecting a dye, which can create adverse reactions in the patients. So, to alleviate this, a non-invasive technique needs to be developed that can translate fluorescein angiography from fundus images. Similarly, color funduscopy and optical coherence tomography (OCT) are also utilized to semantically segment the vasculature and fluid build-up in spatial and volumetric retinal imaging, which can help with the future prognosis of diseases. Although many automated techniques have been proposed for medical image segmentation, the main drawback is the model's precision in pixel-wise predictions. Another critical challenge in the biomedical imaging field is accurately segmenting and quantifying dynamic behaviors of calcium signals in cells. Calcium imaging is a widely utilized approach to studying subcellular calcium activity and cell function; however, large datasets have yielded a profound need for fast, accurate, and standardized analyses of calcium signals. For example, image sequences from calcium signals in colonic pacemaker cells ICC (Interstitial cells of Cajal) suffer from motion artifacts and high periodic and sensor noise, making it difficult to accurately segment and quantify calcium signal events. Moreover, it is time-consuming and tedious to annotate such a large volume of calcium image stacks or videos and extract their associated spatiotemporal maps. To address these problems, we propose various deep representation learning architectures that utilize limited labels and annotations to address the critical challenges in these biomedical applications. To this end, we detail our proposed semi-supervised, generative adversarial networks and transformer-based architectures for individual learning tasks such as retinal image-to-image translation, vessel and fluid segmentation from fundus and OCT images, breast micro-mass segmentation, and sub-cellular calcium events tracking from videos and spatiotemporal map quantification. We also illustrate two multi-modal multi-task learning frameworks with applications that can be extended to other domains of biomedical applications. The main idea is to incorporate each of these as individual modules to our proposed multi-modal frameworks to solve the existing challenges with 1) Fluorescein angiography synthesis, 2) Retinal vessel and fluid segmentation, 3) Breast micro-mass segmentation, and 4) Dynamic quantification of calcium imaging datasets

    Machine Learning Approaches for Automated Glaucoma Detection using Clinical Data and Optical Coherence Tomography Images

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    Glaucoma is a multi-factorial, progressive blinding optic-neuropathy. A variety of factors, including genetics, vasculature, anatomy, and immune factors, are involved. Worldwide more than 80 million people are affected by glaucoma, and around 300,000 in Australia, where 50% remain undiagnosed. Untreated glaucoma can lead to blindness. Early detection by Artificial intelligence (AI) is crucial to accelerate the diagnosis process and can prevent further vision loss. Many proposed AI systems have shown promising performance for automated glaucoma detection using two-dimensional (2D) data. However, only a few studies had optimistic outcomes for glaucoma detection and staging. Moreover, the automated AI system still faces challenges in diagnosing at the clinicians’ level due to the lack of interpretability of the ML algorithms and integration of multiple clinical data. AI technology would be welcomed by doctors and patients if the "black box" notion is overcome by developing an explainable, transparent AI system with similar pathological markers used by clinicians as the sign of early detection and progression of glaucomatous damage. Therefore, the thesis aimed to develop a comprehensive AI model to detect and stage glaucoma by incorporating a variety of clinical data and utilising advanced data analysis and machine learning (ML) techniques. The research first focuses on optimising glaucoma diagnostic features by combining structural, functional, demographic, risk factor, and optical coherence tomography (OCT) features. The significant features were evaluated using statistical analysis and trained in ML algorithms to observe the detection performance. Three crucial structural ONH OCT features: cross-sectional 2D radial B-scan, 3D vascular angiography and temporal-superior-nasal-inferior-temporal (TSNIT) B-scan, were analysed and trained in explainable deep learning (DL) models for automated glaucoma prediction. The explanation behind the decision making of DL models were successfully demonstrated using the feature visualisation. The structural features or distinguished affected regions of TSNIT OCT scans were precisely localised for glaucoma patients. This is consistent with the concept of explainable DL, which refers to the idea of making the decision-making processes of DL models transparent and interpretable to humans. However, artifacts and speckle noise often result in misinterpretation of the TSNIT OCT scans. This research also developed an automated DL model to remove the artifacts and noise from the OCT scans, facilitating error-free retinal layers segmentation, accurate tissue thickness estimation and image interpretation. Moreover, to monitor and grade glaucoma severity, the visual field (VF) test is commonly followed by clinicians for treatment and management. Therefore, this research uses the functional features extracted from VF images to train ML algorithms for staging glaucoma from early to advanced/severe stages. Finally, the selected significant features were used to design and develop a comprehensive AI model to detect and grade glaucoma stages based on the data quantity and availability. In the first stage, a DL model was trained with TSNIT OCT scans, and its output was combined with significant structural and functional features and trained in ML models. The best-performed ML model achieved an area under the curve (AUC): 0.98, an accuracy of 97.2%, a sensitivity of 97.9%, and a specificity of 96.4% for detecting glaucoma. The model achieved an overall accuracy of 90.7% and an F1 score of 84.0% for classifying normal, early, moderate, and advanced-stage glaucoma. In conclusion, this thesis developed and proposed a comprehensive, evidence-based AI model that will solve the screening problem for large populations and relieve experts from manually analysing a slew of patient data and associated misinterpretation problems. Moreover, this thesis demonstrated three structural OCT features that could be added as excellent diagnostic markers for precise glaucoma diagnosis
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