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Active learning is a unique abstraction of machine learning techniques where the model/algorithm could guide users for annotation of a set of data points that would be beneficial to the model, unlike passive machine learning. The primary advantage being that active learning frameworks select data points that can accelerate the learning process of a model and can reduce the amount of data needed to achieve full accuracy as compared to a model trained on a randomly acquired data set. Multiple frameworks for active learning combined with deep learning have been proposed, and the majority of them are dedicated to classification tasks. Herein, we explore active learning for the task of segmentation of medical imaging data sets. We investigate our proposed framework using two datasets: 1.) MRI scans of the hippocampus, 2.) CT scans of pancreas and tumors. This work presents a query-by-committee approach for active learning where a joint optimizer is used for the committee. At the same time, we propose three new strategies for active learning: 1.) increasing frequency of uncertain data to bias the training data set; 2.) Using mutual information among the input images as a regularizer for acquisition to ensure diversity in the training dataset; 3.) adaptation of Dice log-likelihood for Stein variational gradient descent (SVGD). The results indicate an improvement in terms of data reduction by achieving full accuracy while only using 22.69% and 48.85% of the available data for each dataset, respectively. [ABSTRACT FROM AUTHOR]

As a minimally invasive surgery to treat atrial fibrillation (AF), catheter based ablation uses high radio-frequency energy to eliminate potential sources of abnormal electrical events, especially around the ostia of pulmonary veins (PV). Fusing a patient-specific left atrium (LA) model (including LA chamber, appendage, and PVs) with electro-anatomical maps or overlaying the model onto 2-D real-time fluoroscopic images provides valuable visual guidance during the intervention. In this work, we present a fully automatic LA segmentation system on nongated C-arm computed tomography (C-arm CT) data, where thin boundaries between the LA and surrounding tissues are often blurred due to the cardiac motion artifacts. To avoid segmentation leakage, the shape prior should be exploited to guide the segmentation. A single holistic shape model is often not accurate enough to represent the whole LA shape population under anatomical variations, e.g., the left common PVs vs. separate left PVs. Instead, a part based LA model is proposed, which includes the chamber, appendage, four major PVs, and right middle PVs. Each part is a much simpler anatomical structure compared to the holistic one and can be segmented using a model-based approach (except the right middle PVs). After segmenting the LA parts, the gaps and overlaps among the parts are resolved and segmentation of the ostia region is further refined. As a common anatomical variation, some patients may contain extra right middle PVs, which are segmented using a graph cuts algorithm under the constraints from the already extracted major right PVs. Our approach is computationally efficient, taking about 2.6 s to process a volume with 256\,\times\,256\,\times\,245 voxels. Experiments on 687 C-arm CT datasets demonstrate its robustness and state-of-the-art segmentation accuracy. [ABSTRACT FROM AUTHOR]

Recent advances in deep learning for medical image segmentation demonstrate expert-level accuracy. However, application of these models in clinically realistic environments can result in poor generalization and decreased accuracy, mainly due to the domain shift across different hospitals, scanner vendors, imaging protocols, and patient populations etc. Common transfer learning and domain adaptation techniques are proposed to address this bottleneck. However, these solutions require data (and annotations) from the target domain to retrain the model, and is therefore restrictive in practice for widespread model deployment. Ideally, we wish to have a trained (locked) model that can work uniformly well across unseen domains without further training. In this paper, we propose a deep stacked transformation approach for domain generalization. Specifically, a series of ${n}$ stacked transformations are applied to each image during network training. The underlying assumption is that the “expected” domain shift for a specific medical imaging modality could be simulated by applying extensive data augmentation on a single source domain, and consequently, a deep model trained on the augmented “big” data (BigAug) could generalize well on unseen domains. We exploit four surprisingly effective, but previously understudied, image-based characteristics for data augmentation to overcome the domain generalization problem. We train and evaluate the BigAug model (with ${n}={9}$ transformations) on three different 3D segmentation tasks (prostate gland, left atrial, left ventricle) covering two medical imaging modalities (MRI and ultrasound) involving eight publicly available challenge datasets. The results show that when training on relatively small dataset (n = 10~32 volumes, depending on the size of the available datasets) from a single source domain: (i) BigAug models degrade an average of 11%(Dice score change) from source to unseen domain, substantially better than conventional augmentation (degrading 39%) and CycleGAN-based domain adaptation method (degrading 25%), (ii) BigAug is better than “shallower” stacked transforms (i.e. those with fewer transforms) on unseen domains and demonstrates modest improvement to conventional augmentation on the source domain, (iii) after training with BigAug on one source domain, performance on an unseen domain is similar to training a model from scratch on that domain when using the same number of training samples. When training on large datasets (n = 465 volumes) with BigAug, (iv) application to unseen domains reaches the performance of state-of-the-art fully supervised models that are trained and tested on their source domains. These findings establish a strong benchmark for the study of domain generalization in medical imaging, and can be generalized to the design of highly robust deep segmentation models for clinical deployment. [ABSTRACT FROM AUTHOR]