Explainable cardiac pathology classification on cine MRI with motion characterization by semi-supervised learning of apparent flow

We propose a method to classify cardiac pathology based on a novel approach to extract image derived features to characterize the shape and motion of the heart. An original semi-supervised learning procedure, which makes efficient use of a large amount of non-segmented images and a small amount of images segmented manually by experts, is developed to generate pixel-wise apparent flow between two time points of a 2D+t cine MRI image sequence. Combining the apparent flow maps and cardiac segmentation masks, we obtain a local apparent flow corresponding to the 2D motion of myocardium and ventricular cavities. This leads to the generation of time series of the radius and thickness of myocardial segments to represent cardiac motion. These time series of motion features are reliable and explainable characteristics of pathological cardiac motion. Furthermore, they are combined with shape-related features to classify cardiac pathologies. Using only nine feature values as input, we propose an explainable, simple and flexible model for pathology classification. On ACDC training set and testing set, the model achieves 95% and 94% respectively as classification accuracy. Its performance is hence comparable to that of the state-of-the-art. Comparison with various other models is performed to outline some advantages of our model

Stratified decision forests for accurate anatomical landmark localization in cardiac images

Accurate localization of anatomical landmarks is an important step in medical imaging, as it provides useful prior information for subsequent image analysis and acquisition methods. It is particularly useful for initialization of automatic image analysis tools (e.g. segmentation and registration) and detection of scan planes for automated image acquisition. Landmark localization has been commonly performed using learning based approaches, such as classifier and/or regressor models. However, trained models may not generalize well in heterogeneous datasets when the images contain large differences due to size, pose and shape variations of organs. To learn more data-adaptive and patient specific models, we propose a novel stratification based training model, and demonstrate its use in a decision forest. The proposed approach does not require any additional training information compared to the standard model training procedure and can be easily integrated into any decision tree framework. The proposed method is evaluated on 1080 3D highresolution and 90 multi-stack 2D cardiac cine MR images. The experiments show that the proposed method achieves state-of-theart landmark localization accuracy and outperforms standard regression and classification based approaches. Additionally, the proposed method is used in a multi-atlas segmentation to create a fully automatic segmentation pipeline, and the results show that it achieves state-of-the-art segmentation accuracy

A Survey on Deep Learning in Medical Image Analysis

Deep learning algorithms, in particular convolutional networks, have rapidly become a methodology of choice for analyzing medical images. This paper reviews the major deep learning concepts pertinent to medical image analysis and summarizes over 300 contributions to the field, most of which appeared in the last year. We survey the use of deep learning for image classification, object detection, segmentation, registration, and other tasks and provide concise overviews of studies per application area. Open challenges and directions for future research are discussed.Comment: Revised survey includes expanded discussion section and reworked introductory section on common deep architectures. Added missed papers from before Feb 1st 201

Combining Shape and Learning for Medical Image Analysis

Automatic methods with the ability to make accurate, fast and robust assessments of medical images are highly requested in medical research and clinical care. Excellent automatic algorithms are characterized by speed, allowing for scalability, and an accuracy comparable to an expert radiologist. They should produce morphologically and physiologically plausible results while generalizing well to unseen and rare anatomies. Still, there are few, if any, applications where today\u27s automatic methods succeed to meet these requirements.\ua0The focus of this thesis is two tasks essential for enabling automatic medical image assessment, medical image segmentation and medical image registration. Medical image registration, i.e. aligning two separate medical images, is used as an important sub-routine in many image analysis tools as well as in image fusion, disease progress tracking and population statistics. Medical image segmentation, i.e. delineating anatomically or physiologically meaningful boundaries, is used for both diagnostic and visualization purposes in a wide range of applications, e.g. in computer-aided diagnosis and surgery.The thesis comprises five papers addressing medical image registration and/or segmentation for a diverse set of applications and modalities, i.e. pericardium segmentation in cardiac CTA, brain region parcellation in MRI, multi-organ segmentation in CT, heart ventricle segmentation in cardiac ultrasound and tau PET registration. The five papers propose competitive registration and segmentation methods enabled by machine learning techniques, e.g. random decision forests and convolutional neural networks, as well as by shape modelling, e.g. multi-atlas segmentation and conditional random fields

Recovering 6D Object Pose and Predicting Next-Best-View in the Crowd

Object detection and 6D pose estimation in the crowd (scenes with multiple object instances, severe foreground occlusions and background distractors), has become an important problem in many rapidly evolving technological areas such as robotics and augmented reality. Single shot-based 6D pose estimators with manually designed features are still unable to tackle the above challenges, motivating the research towards unsupervised feature learning and next-best-view estimation. In this work, we present a complete framework for both single shot-based 6D object pose estimation and next-best-view prediction based on Hough Forests, the state of the art object pose estimator that performs classification and regression jointly. Rather than using manually designed features we a) propose an unsupervised feature learnt from depth-invariant patches using a Sparse Autoencoder and b) offer an extensive evaluation of various state of the art features. Furthermore, taking advantage of the clustering performed in the leaf nodes of Hough Forests, we learn to estimate the reduction of uncertainty in other views, formulating the problem of selecting the next-best-view. To further improve pose estimation, we propose an improved joint registration and hypotheses verification module as a final refinement step to reject false detections. We provide two additional challenging datasets inspired from realistic scenarios to extensively evaluate the state of the art and our framework. One is related to domestic environments and the other depicts a bin-picking scenario mostly found in industrial settings. We show that our framework significantly outperforms state of the art both on public and on our datasets.Comment: CVPR 2016 accepted paper, project page: http://www.iis.ee.ic.ac.uk/rkouskou/6D_NBV.htm

A Comprehensive Performance Evaluation of Deformable Face Tracking "In-the-Wild"

Recently, technologies such as face detection, facial landmark localisation and face recognition and verification have matured enough to provide effective and efficient solutions for imagery captured under arbitrary conditions (referred to as "in-the-wild"). This is partially attributed to the fact that comprehensive "in-the-wild" benchmarks have been developed for face detection, landmark localisation and recognition/verification. A very important technology that has not been thoroughly evaluated yet is deformable face tracking "in-the-wild". Until now, the performance has mainly been assessed qualitatively by visually assessing the result of a deformable face tracking technology on short videos. In this paper, we perform the first, to the best of our knowledge, thorough evaluation of state-of-the-art deformable face tracking pipelines using the recently introduced 300VW benchmark. We evaluate many different architectures focusing mainly on the task of on-line deformable face tracking. In particular, we compare the following general strategies: (a) generic face detection plus generic facial landmark localisation, (b) generic model free tracking plus generic facial landmark localisation, as well as (c) hybrid approaches using state-of-the-art face detection, model free tracking and facial landmark localisation technologies. Our evaluation reveals future avenues for further research on the topic.Comment: E. Antonakos and P. Snape contributed equally and have joint second authorshi