Abstract

Deep learning based approaches to Computer Aided Diagnosis (CAD) typically pose the problem as an image classification (Normal or Abnormal) problem. These systems achieve high to very high accuracy in specific disease detection for which they are trained but lack in terms of an explanation for the provided decision/classification result. The activation maps which correspond to decisions do not correlate well with regions of interest for specific diseases. This paper examines this problem and proposes an approach which mimics the clinical practice of looking for an evidence prior to diagnosis. A CAD model is learnt using a mixed set of information: class labels for the entire training set of images plus a rough localisation of suspect regions as an extra input for a smaller subset of training images for guiding the learning. The proposed approach is illustrated with detection of diabetic macular edema (DME) from …

Abstract

Disease diagnosis often requires segmentation of structures from a given image followed by shape analysis. Shape analysis entails quantifying the variability in a shape by constructing a template for a given population. We propose an orientation-invariant representation using varifolds for the shape elements in a given shape population and present a novel diffeomorphic Log-demons based template creation pipeline. The proposed method generates a good quality template at a significantly less computation time compared to state of the art method.

Abstract

Anatomical variabilities seen in longitudinal data or inter-subject data is usually described by the underlying deformation, captured by non-rigid registration of these images. Stationary Velocity Field (SVF) based non-rigid registration algorithms are widely used for registration. SVF based methods form a metric-free framework which captures a finite dimensional submanifold of deformations embedded in the infinite dimensional smooth manifold of diffeomorphisms. However, these methods cover only a limited degree of deformations. In this paper, we address this limitation and define an approximate metric space for the manifold of diffeomorphisms . We propose a method to break down the large deformation into finite compositions of small deformations. This results in a broken geodesic path on and its length now forms an approximate registration metric. We illustrate the method using a simple, intensity-based, log-demon implementation. Validation results of the proposed method show that it can capture large and complex deformations while producing qualitatively better results than the state-of-the-art methods. The results also demonstrate that the proposed registration metric is a good indicator of the degree of deformation.

Abstract

Optical coherence tomographic (OCT) images provide valuable information for understanding the changes occurring in the retina due to glaucoma, specifically, related to the retinal nerve fiber layer and the optic nerve head. In this paper, we propose a deep learning approach using Capsule network for glaucoma classification, which directly operates on 3D OCT volumes. The network is trained only on labelled volumes and does not attempt any region/structure segmentation. The proposed network was assessed on 50 volumes and found to achieve 0.97 for the area under the ROC curve (AUC). This is considerably higher than the existing approaches which are majorly based on machine learning or rely on segmentation of the required structures from OCT. Our network also outperforms 3D convolutional neural networks despite the fewer network parameters and fewer epochs needed for training.

Abstract

The Optic Disc (OD) and Optic Cup (OC) boundaries play a critical role in the detection of glaucoma. However, very few annotated datasets are available for both OD and OC that are required for segmentation. Recently, Convolutional Neural Networks have shown significant improvements in segmentation performance. However, the full potential of CNNs is hindered by the lack of a large amount of annotated training images. To address this issue, we explore a method to generate synthetic images which can be used to augment the training data. Given the segmentation masks of OD, OC and vessels from arbitrarily different fundus images, the proposed method employs a combination of B-spline registration and GAN to generate high quality images that ensure that the vessels bend at the edge of the OC in a realistic manner. In contrast, the existing GAN based methods for fundus image synthesis fail to capture the local details and vasculature in the Optic Nerve Head (ONH) region. The utility of the proposed method in training deep networks for the challenging problem of OC segmentation is explored and an improvement in the dice score from 0.85 to 0.902 is seen with the inclusion of the synthetic images in the training set.

Abstract

Fundus imaging with a Smartphone camera (SC) is a cost effective solution for the assessment of retina. However, imaging at high magnification and low light levels, results in loss of details, uneven illumination and noise especially in the peripheral region. We address these problems by matching the characteristics of images from SC to those from a regular fundus camera (FC) with an architecture called ResCycleGAN. It is based on the CycleGAN with two significant changes: A residual connection is introduced to aid learning only the correction required; A structure similarity based loss function is used to improve the clarity of anatomical structures and pathologies. The proposed method can handle variations seen in normal and pathological images, acquired even without mydriasis, which is attractive in screening. The method produces consistently balanced results, outperforms CycleGAN both qualitatively and quantitatively, and has more pleasing results.

Abstract

: A brain magnetic resonanace imaging (MRI) atlas plays an important role in many neuroimage analysis tasks as it provides an atlas with a standard coordinate system which is needed for spatial normalization of a brain MRI. Ideally, this atlas should be as near to the average brain of the population being studied as possible.

Abstract

Fingerprint is a common biometric used for authentication and verification of an individual. These images are degraded when fingers are wet, dirty, dry or wounded and due to the failure of the sensors, etc. The extraction of the fingerprint from a degraded image requires denoising and inpainting. We propose to address these problems with an endto-end trainable Convolutional Neural Network based architecture called FPD-M-net, by posing the fingerprint denoising and inpainting problem as a segmentation (foreground) task. Our architecture is based on the M-net with a change: structure similarity loss function, used for better extraction of the fingerprint from the noisy background. Our method outperforms the baseline method and achieves an overall 3rd rank in the Chalearn LAP Inpainting Competition Track 3 −Fingerprint Denoising and Inpainting, ECCV 2018.

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

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.