Abstract

Background and Objective: Accurate segmentation of the intra-retinal tissue layers in Optical Coherence Tomography (OCT) images plays an important role in the diagnosis and treatment of ocular diseases such as Age-Related Macular Degeneration (AMD) and Diabetic Macular Edema (DME). The existing energy minimization based methods employ multiple, manually handcrafted cost terms and often fail in the presence of pathologies. In this work, we eliminate the need to handcraft the energy by learning it from training images in an end-to-end manner. Our method can be easily adapted to pathologies by re-training it on an appropriate dataset. Methods: We propose a Conditional Random Field (CRF) framework for the joint multi-layer segmentation of OCT B-scans. The appearance of each retinal layer and boundary is modeled by two convolutional filter banks and the shape priors are modeled using Gaussian distributions. The total CRF energy is linearly parameterized to allow a joint, end-to-end training by employing the Structured Support Vector Machine.

Abstract

Purpose: To compare the diagnostic ability of optical coherence tomography angiography (OCT-A) derived radial peripapillary capillary (RPC) measured capillary density (CD) and inside the optic nerve head (ONH) CD measurements to differentiate between the normal and primary open angle glaucoma (POAG) eyes. Methods: AngioVue disc OCT-A images were obtained and assessed in 83 eyes of POAG patients and 74 age matched healthy eyes. RPC CD was quantitatively measured in the peripapillary area within 3.45 mm circle diameter around the ONH and inside the ONH in 8 equally divided sectors, using Bar – Selective Combination of Shifted Filter Responses method after the suppressing large vessels. Area under receiver operating characteristic (AUROC) curve was used to assess the diagnostic accuracy of the two scanning regions of CD to differentiate between the normal and POAG eyes. Results: The mean peripapillary RPC density (0.12 ± 0.03) and mean ONH CD (0.09 ± 0.03) were significantly lower in POAG eyes when compared to the normal eyes (RPC CD: 0.17 ± 0.05, p < 0.0001 and ONH CD 0.11 ± 0.02, p = 0.01 respectively). The POAG patients showed 29% reduction in the RPC CD and 19% reduction in the ONH CD when compared to the normal eyes. The AUROC for discriminating between healthy and glaucomatous eyes was 0.784 for mean RPC CD and 0.743 for the mean ONH CD. Conclusions: Diagnostic ability of OCT-A derived peripapillary CD and ONH CD was moderate for differentiating between the normal and glaucomatous eyes. Diagnostic ability of even the best peripapillary average and inferotemporal sector for RPC CD and average and superonasal sector for the ONH CD was moderate.

Abstract

Diabetic retinopathy (DR) is a disease which is widely diagnosed using (colour fundus) images. Efficiency and accuracy are critical in diagnosing DR as lack of timely intervention can lead to irreversible visual impairment. In this paper, we examine strategies for scrutinizing images which affect diagnostic performance of medical practitioners via an eye-tracking study. A total of 56 subjects with 0 to 18 years of experience participated in the study. Every subject was asked to detect DR from 40 images. The findings indicate that practitioners use mainly two types of strategies characterized by either higher dwell duration or longer track length. The main findings of the study are that higher dwell-based strategy led to higher average accuracy (> 85%) in diagnosis, irrespective of the expertise of practitioner; whereas, the average obtained accuracy with a long-track length-based strategy was dependent on the expertise of the practitioner. In the second part of the paper, we use the experimental findings to recommend a scanning strategy for fast and accurate diagnosis of DR that can be potentially used by image readers. This is derived by combining the eyetracking gaze maps of medical experts in a novel manner based on a set of rules. This strategy requires scrutiny of images in a manner which is consistent with spatial preferences found in human perception in general and in the domain of fundus images in particular. The Levenshtein distance-based assessment of gaze patterns also establish the effectiveness of the derived scanning pattern and is thus recommended for image readers.

Abstract

Annotations are critical for machine learning and developing computer aided diagnosis (CAD) algorithms. Good performance of CAD is critical to their adoption, which generally rely on training with a wide variety of annotated data. However, a vast amount of medical data is either unlabeled or annotated only at the image-level. This poses a problem for exploring data driven approaches like deep learning for CAD. In this paper, we propose a novel crowdsourcing and synthetic image generation for training deep neural net-based lesion detection. The noisy nature of crowdsourced annotations is overcome by assigning a reliability factor for crowd subjects based on their performance and requiring region of interest markings from the crowd. A generative adversarial network-based solution is proposed to generate synthetic images with lesions to control the overall severity level of the disease. We demonstrate the reliability of the crowdsourced annotations and synthetic images by presenting a solution for training the deep neural network (DNN) with data drawn from a heterogeneous mixture of annotations. Experimental results obtained for hard exudate detection from retinal images show that training with refined crowdsourced data/synthetic images is effective as detection performance in terms of sensitivity improves by 25%/27% over training with just expert-markings.

Abstract

Optical coherence tomography (OCT) images are corrupted by speckle noise due to the underlying coherence-based strategy. Speckle suppression/removal in OCT images plays a significant role in both manual and automatic detection of diseases, especially in early clinical diagnosis. In this paper, we propose a new method for denoising OCT images based on Convolutional Neural Network by learning common features from unpaired noisy and clean OCT images in an unsupervised, end-to-end manner. The proposed method consists of a combination of two autoencoders with shared encoder layers, which we call as Shared Encoder (SE) architecture. The SE is trained to reconstruct noisy and clean OCT images with respective autoencoders. The denoised OCT image is obtained using a cross-model prediction. The proposed method can be used for denoising OCT images with or without pathology from any scanner. The SE architecture was assessed using public datasets and found to perform better than baseline methods exhibiting a good balance of retaining anatomical integrity and speckle reduction.

Abstract

Automated segmentation of cortical and noncortical human brain structures has been hither to approached using nonrigid registration followed by label fusion. We propose an alternative approach for this using a convolutional neural network (CNN) which classifies a voxel into one of many structures. Four different kinds of two-dimensional and three-dimensional intensity patches are extracted for each voxel, providing local and global (context) information to the CNN. The proposed approach is evaluated on five different publicly available datasets which differ in the number of labels per volume. The obtained mean Dice coefficient varied according to the number of labels, for example, it is0.844
0.031and0.743
0.019for datasets with the least(32) and the most (134) number of labels, respectively. These figures are marginally better or on par with those obtained with the current state-of-the-art methods on nearly all datasets, at a reduced computational time. The consistently good performance of the proposed method across datasets and no requirement for registration make it attractive for many applications where reduced computational time is necessary.

Abstract

Retinal vessel keypoint detection and classification is a fundamental step in tracking the physiological changes that occur in the retina which is linked to various retinal and systemic diseases. In this paper, we propose a novel Vessel Keypoint Detector (VKD) which is derived from the projection of log-polar transformed binary patches around vessel points.VKD is used to design a two stage solution for junction detection and classification. In the first stage, the keypoints detected using VKD are refined using curvature orientation information to extract candidate junctions. True junctions from these candidates are identified in a supervised manner using a Random Forest classifier. In the next stage, a novel combination of local orientation and shape based features is extracted from the junction points and classified using asecond Random Forest classifier. Evaluation results on five datasets show that the designed system is robust to changes in resolution and other variations across datasets, with average values of accuracy/sensitivity/specificity for junction detection being 0.78/0.79/0.75 and for junction classification being 0.87/0.85/0.88. Our system outperforms the state of the art method [1] by at least 11%, on the DRIVE and IOSTAR datasets. These results demonstrate the effectiveness of VKDfor vessel analysis.

Abstract

Retinal Neovascularization (NV) is a critical stage of Diabetic Retinopathy (DR) and its detection is important to prevent blindness. Existing fully supervised frameworks typically take a patch-based approach and report good results only on limited number of images due to sparsity of annotated data.We propose a patch-based semi-supervised framework which paves the way for including unlabeled data in training. In this framework, NV patches are modeled using oriented energy and vesselness based features. These features are fused within a co-training based semi-supervised framework by using neighborhood information in feature space. Rule-based criteria on patch-level neovascularity scores is used to derive the final image-level decision. The proposed approach was evaluated on 1 private and 3 public datasets, both at patch and image level detection on nearly 200,000 patches. An AUCof 0.985 with sensitivity of 96.2% at specificity of 92.6% was obtained for abnormality detection at patch-level, while at the image-level, a sensitivity of 96.76% at a specificity of 91.85%were obtained. The achieved performance on a large number of patches indicates the robustness of our approach.

Abstract

In this paper, we propose an end-to-end trainable Convolutional Neural Network (CNN) architecture called the M-net,for segmenting deep (human) brain structures from Magnetic Resonance Images (MRI). A novel scheme is used to learn to combine and represent 3D context information of a given slice in a 2D slice. Consequently, the M-netutilizes only 2D convolution though it operates on 3D data, which makes M-net memory efficient. The segmentation method is evaluated on two publicly available datasets and is compared against publicly available model based segmentation algorithms as well as other classification based algorithms such as Random For-rest and 2D CNN based approaches. Experiment results show that the M-net out performs all these methods in terms of dice coefficient and is at least 3 times faster than other methods in segmenting a new volume which is attractive for clinical use

Abstract

Computer-assisted diagnostic (CAD) tools are of interest as they enable efficient decision-making in clinics and the screening of diseases. The traditional approach to CAD algorithm design focuses on the automated detection of abnormalities independent of the end-user, who can be an image reader or an expert.We propose a reader-centric system design wherein a reader’s attention is drawn to abnormal regions in a least-obtrusive yet effective manner, using saliency-based emphasis of abnormalities and without altering the appearance of the background tissues. We present an assistive lesion-emphasis system (ALES) based on the above idea, for fundus image-based diabetic retinopathy diagnosis. Lesion-saliency is learnt using a convolutional neural network (CNN), inspired by the saliency model of Itti and Koch. The CNN is used to fine-tune standard low-level filters and learn high-level filters for deriving a lesion-saliency map, which is then used to perform lesion-emphasis via a spatially variant version of gamma correction. The proposed system has been evaluated on public datasets and bench marked against other saliency models. It was found to outperform other saliency models by 6% to 30% and boost the contrast-to-noise ratio of lesions by more than 30%. Results of a perceptual study also underscore the effectiveness and, hence, the potential of ALES as an assistive tool for readers