Abstract

Intra-retinal layer segmentation of Optical Coherence Tomography images is critical in the assessment of ocular diseases. Existing Energy minimization based methods employ handcrafted cost terms to define their energy and are not robust to the presence of abnormalities.We propose a novel, Linearly Parameterized, Conditional Random Field(LP-CRF) model whose energy is learnt from a set of training images in an end-to-end manner. The proposed LP-CRF comprises two convolution filter banks to capture the appearance of each tissue region and boundary, the relative weights of the shape priors and an additional term based on the appearance similarity of the adjacent boundary points. All the energy terms are jointly learnt using the Structured Support Vector Machine. The proposed method segments all retinal boundaries in a single step. Our method was evaluated on 107 Normal and 220 AMDB-scan images and found to outperform three publicly available OCT segmentation software. The average unsigned boundary localization error is 1.52±0.29 pixels for segmentation of 8 boundaries on the Normal data set and 1.9±0.65 pixels for 3 boundaries on the combined AMD and Normal data set establishing the robustness of the proposed method.

Abstract

Background and objective: Accurate segmentation of optic disc and cup from monocular color fundus images plays a significant role in the screening and diagnosis of glaucoma. Though optic cup is characterized by the drop in depth from the disc boundary, most existing methods segment the two structures separately and rely only on color and vessel kink based cues due to the lack of explicit depth information in color fundus images. Methods: We propose a novel boundary-based Conditional Random Field formulation that extracts both the optic disc and cup boundaries in a single optimization step. In addition to the color gradients, the proposed method explicitly models the depth which is estimated from the fundus image itself using a coupled, sparse dictionary trained on a set of image-depth map (derived from Optical Coherence Tomography) pairs. Results: The estimated depth achieved a correlation coefficient of 0.80 with respect to the ground truth. The proposed segmentation method outperformed several state-of-the-art methods on five public datasets. The average dice coefficient was in the range of 0.87–0.97 for disc segmentation across three datasets and 0.83 for cup segmentation on the DRISHTI-GS1 test set. The method achieved a good glaucoma classification performance with an average AUC of 0.85 for five fold cross-validation on RIM-ONE v2.

Abstract

Segmentation of retinal layers from Optical Coherence Tomography (OCT) volumes is a fundamental problem for any computer aided diagnostic algorithm development.This requires preprocessing steps such as denoising, region of interest extraction, flattening and edge detection all of which involve separate parameter tuning. In this paper,we explore deep learning techniques to automate all these steps and handle the presence/absence of pathologies. A model is proposed consisting of a combination of Convolutional Neural Network (CNN) and Long Short Term Memory (LSTM). The CNN is used to extract layers of interest image and extract the edges, while the LSTM is used to trace the layer boundary. This model is trained on a mixture of normal and AMD cases using minimal data. Validation results on three public datasets show that the pixel-wise mean absolute error obtained with our system is1.30±0.48whichis lower than the inter-marker error of1.79±0.76. Our model’s performance is also on par with the existing methods

Abstract

Annotations are critical for machine learning and developing Computer Aided Detection (CAD) algorithms. However, a majority of medical data is either unlabeled or annotated only at the image-level. This poses a problem specifically for employing deep learning based approaches for CAD development as they require large amounts of annotated data for training. Data augmentation is a popular solution to address this need. We explore crowdsourcing as a solution for training a deep neural network (DNN) for lesion detection. Our solution employs a strategy to overcome the noisy nature of crowdsourced annotations by i) assigning a reliability factor for each subject of the crowd based on their performance (at global and local levels) and experience and ii) requiring region of interest(ROI) markings rather than pixel-level markings from the crowd. We present a solution for training the DNN with data drawn from a heterogeneous mixture of annotations, namely,very limited number of pixel-level markings by experts and crowdsourced ROI markings. Experimental results obtained for hard exudate detection from color fundus images show that training with processed/refined crowdsourced data is effective as detection performance improves by 25% over training with just expert-markings and by 11% over training with annotation derived using majority voting among the crowd

Abstract

SD-OCT is a non invasive cross sectional imaging modality useful for diagnosis of macular defects. Efficient detection and segmentation of the abnormalities seen as biomarkers in OCT can help in analyzing the progression of the disease and advising effective treatment for the associated disease. In this work we proposes a fully automated Generalized Motion Pattern(GMP) based segmentation method using a cascade of fully convolutional networks for detection and segmentation of retinal fluids from SD-OCT scans. General methods for segmentation depend on domain knowledge based feature extraction , whereas we pro-pose a method based on Generalized Motion Pattern (GMP) [1] which is derived by inducing motion to an image to suppress the background.The proposed method is parallelizable and handles inter-scanner variability efficiently. Our method achieves a mean Dice score of 0.61,0.70 and0.73 during segmentation and a mean AUC of 0.85,0.84 and 0.87 during detection for the 3 types of fluids IRF,SRF and PDE respectively

Abstract

Automated classification of glaucoma is of interest in early detection and treatment. Existing methods employ featureswhich are either image-based or derived from Optic Disc(OD) and Cup (OC) segmentation. While the latter suffers from segmentation inaccuracies, the image-based features tend to overf it in limited availability of training data. We propose a solution to overcome these issues and present a classification framework that fuses both type of features within a co-training based semi-supervised setting to over-come the paucity of labelled data. A novel set of features is proposed to represent the segmented OD-OC regions. Additionally, features based on Texture of projections and color Bag of Visual Words have been designed to be sensitive to the sector-wise deformations in OD. The proposed method was trained on 386 labelled and 717 unlabelled images. It outperformed existing methods with an accuracy and AUC of73.28%,0.79on a private test set of 696 unseen images and76.77%,0.78when cross-tested on DRISHTI-GS1 dataset

Abstract

A variety of imaging modalities have been used for developing diagnostic aids for glaucoma assessment. Structural imaging modalities such as colour fundus imaging and optical coherence tomography (OCT) have been investigated for automatically estimating key parameters for glaucoma assessment such as cup to disc diameter ratio and thickness of there tinal nerve fibre layer (RNFL). OCT-based angiography or OCTA is a new modality which provides structural and angiographic information about the retinal layers. We present a method for glaucoma detection using OCTA images. Specifically, the capillary density at various layers and thickness of RNFL are estimated and used to classify a given OCTA volume as glaucamatous or not. RNFL thickness is estimated using polynomial fitting to intensity profiles of OCT slices. The capillary density is estimated from the angio flow images using morphological processing to extract the optic nerve head(ONH) and vessel detection in a region of interest define daround the ONH. A system trained on these two features was evaluated on a dataset of 67 eyes (49 normal and 18 glaucomatous) and found to have a sensitivity of 94.44%and specificity of 91.67%. This demonstrates the potential of the new modality for glaucoma assessment.

Abstract

The variations in the intensity scale in Magnetic Resonance Images pose a problem for many tasks and Intensity Standardization (IS) aims to solve this problem. Existing methods generally use landmark values of the image histogram and match it to a standard scale. The landmarks are often chosen to be percentiles from different segmented tissues. We propose a method for IS in which tissue information (via segmentation) is needed during training but not during testing by using landmark propagation. A KL divergence-based technique is employed for identifying volumes from the training set, which are similar to a given non-standardized testing volume. The landmarks from the similar volumes are then propagated to the given test volume. Evaluation of the proposed method on 24 MRI volumes from 3 different scanners shows that the IS results are better than L4 and at par with a method which uses prior segmentation, to get percentile-based land-marks. The proposed method aids speeding up and expanding the scope of IS to volumes with no tissue information

Abstract

Cardiac motion analysis from B-mode ultrasound sequence is a key task in assessing the health of the heart. The paper proposes a new methodology for cardiac motion analysis based on the temporal behaviour of points of interest on the myocardium. We define a new signal called the Temporal Flow Graph(TFG) which depicts the movement of a point of interest over time. It is a graphical representation derived from a flow field and describes the temporal evolution of a point. We prove that TFG for an object undergoing periodic motion is also periodic. This principle can be utilized to derive both global and local information from a given sequence. We demonstrate this for detecting motion irregularities at the sequence, as well as regional levels on real and synthetic data. A coarse localisation of anatomical landmarks such as centres of left/right cavities and valve points is also demonstrated using TFGs.

Abstract

Color fundus photographs of 2252 eyes from1126 subjects were collected from 2 centers: Aravind Eye Hospital,Madurai and Coimbatore, India. The images of 1926 eyes (963 subjects) were used to train an automated image analysis-based system,which was developed to provide a decision on a given fundus image.A total of 163 subjects were clinically examined by 2 ophthalmologists independently and their diagnostic decisions were recorded. The consensus decision was defined to be the clinical reference (gold standard). Fundus images of eyes with disagreement in diagnosis were excluded from the study. The fundus images of the remaining 314eyes (157 subjects) were presented to 4 graders and their diagnostic decisions on the same were collected. The performance of the system was evaluated on the 314 images, using the reference standard. The sensitivity and specificity of the system and 4 independent graders were determined against the clinical reference standard