In the recent years, convolutional neural networks have transformed the field of medical image analysis due to their capacity to learn discriminative image features for a variety of classification and regression tasks. However, successfully learning these features requires a large amount of manually annotated data, which is expensive to acquire and limited by the available resources of expert image analysts. Therefore, unsupervised, weakly-supervised and self-supervised feature learning techniques receive a lot of attention, which aim to utilise the vast amount of available data, while at the same time avoid or substantially reduce the effort of manual annotation. In this paper, we propose a novel way for training a cardiac MR image segmentation network, in which features are learnt in a self-supervised manner by predicting anatomical positions. The anatomical positions serve as a supervisory signal and do not require extra manual annotation. We demonstrate that this seemingly simple task provides a strong signal for feature learning and with self-supervised learning, we achieve a high segmentation accuracy that is better than or comparable to a U-net trained from scratch, especially at a small data setting. When only five annotated subjects are available, the proposed method improves the mean Dice metric from 0.811 to 0.852 for short-axis image segmentation, compared to the baseline U-net.
For natural image and video analysis problems, a number of pretext tasks have been explored, including prediction of image rotation @cite_8 , relative position @cite_6 , colorisation @cite_10 and image impainting @cite_3 etc. In medical imaging domain, self-supervised learning has also been explored but to a less extent. proposed a pretext task for subject identification @cite_4 . A Siamese network was trained to classify whether two spinal MR images came from the same subject or not. The pretrained features were used to initialise a disease grade classification network. defined re-colourisation of surgical videos as a pretext task and used the pretrained features to initialise a surgical instrument segmentation network @cite_11 . used rotation prediction as a pretext task and the self-learnt features were transferred to lung lobe segmentation and nodule detection tasks @cite_2 . Different from previous works in the medical imaging domain, we propose a novel pretext task, which is to predict anatomical positions. In particular, we leverage the rich information encoded in the cardiac MR scan view planes and DICOM headers to define the anatomical positions for the task.
@cite_4 @cite_8 @cite_3 @cite_6 @cite_2 @cite_10 @cite_11
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In self-supervised learning, one trains a model to solve a so-called pretext task on a dataset without the need for human annotation. The main objective, however, is to transfer this model to a target domain and task. Currently, the most effective transfer strategy is fine-tuning, which restricts one to use the same model or parts thereof for both pretext and target tasks. In this paper, we present a novel framework for self-supervised learning that overcomes limitations in designing and comparing different tasks, models, and data domains. In particular, our framework decouples the structure of the self-supervised model from the final task-specific fine-tuned model. This allows us to: 1) quantitatively assess previously incompatible models including handcrafted features; 2) show that deeper neural network models can learn better representations from the same pretext task; 3) transfer knowledge learned with a deep model to a shallower one and thus boost its learning. We use this framework to design a novel self-supervised task, which achieves state-of-the-art performance on the common benchmarks in PASCAL VOC 2007, ILSVRC12 and Places by a significant margin. Our learned features shrink the mAP gap between models trained via self-supervised learning and supervised learning from 5.9 to 2.6 in object detection on PASCAL VOC 2007. Alterations in the geometry and function of the heart define well-established causes of cardiovascular disease. However, current approaches to the diagnosis of cardiovascular diseases often rely on subjective human assessment as well as manual analysis of medical images. Both factors limit the sensitivity in quantifying complex structural and functional phenotypes. Deep learning approaches have recently achieved success for tasks such as classification or segmentation of medical images, but lack interpretability in the feature extraction and decision processes, limiting their value in clinical diagnosis. In this work, we propose a 3D convolutional generative model for automatic classification of images from patients with cardiac diseases associated with structural remodeling. The model leverages interpretable task-specific anatomic patterns learned from 3D segmentations. It further allows to visualise and quantify the learned pathology-specific remodeling patterns in the original input space of the images. This approach yields high accuracy in the categorization of healthy and hypertrophic cardiomyopathy subjects when tested on unseen MR images from our own multi-centre dataset (100 ) as well on the ACDC MICCAI 2017 dataset (90 ). We believe that the proposed deep learning approach is a promising step towards the development of interpretable classifiers for the medical imaging domain, which may help clinicians to improve diagnostic accuracy and enhance patient risk-stratification. Deformable image registration is a fundamental task in medical image processing. Among its most important applications, one may cite: 1) multi-modality fusion, where information acquired by different imaging devices or protocols is fused to facilitate diagnosis and treatment planning; 2) longitudinal studies, where temporal structural or anatomical changes are investigated; and 3) population modeling and statistical atlases used to study normal anatomical variability. In this paper, we attempt to give an overview of deformable registration methods, putting emphasis on the most recent advances in the domain. Additional emphasis has been given to techniques applied to medical images. In order to study image registration methods in depth, their main components are identified and studied independently. The most recent techniques are presented in a systematic fashion. The contribution of this paper is to provide an extensive account of registration techniques in a systematic manner. In this paper we study the problem of image representation learning without human annotation. By following the principles of self-supervision, we build a convolutional neural network (CNN) that can be trained to solve Jigsaw puzzles as a pretext task, which requires no manual labeling, and then later repurposed to solve object classification and detection. To maintain the compatibility across tasks we introduce the context-free network (CFN), a siamese-ennead CNN. The CFN takes image tiles as input and explicitly limits the receptive field (or context) of its early processing units to one tile at a time. We show that the CFN includes fewer parameters than AlexNet while preserving the same semantic learning capabilities. By training the CFN to solve Jigsaw puzzles, we learn both a feature mapping of object parts as well as their correct spatial arrangement. Our experimental evaluations show that the learned features capture semantically relevant content. Our proposed method for learning visual representations outperforms state of the art methods in several transfer learning benchmarks.