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Register a new userMedical Instrument Segmentation in 3D US by Hybrid Constrained Semi-Supervised Learning
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Hongxu Yang
Publication date
2021
fields
Informatics Engineering
and research's language is
English
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Medical instrument segmentation in 3D ultrasound is essential for image-guided intervention. However, to train a successful deep neural network for instrument segmentation, a large number of labeled images are required, which is expensive and time-consuming to obtain. In this article, we propose a semi-supervised learning (SSL) framework for instrument segmentation in 3D US, which requires much less annotation effort than the existing methods. To achieve the SSL learning, a Dual-UNet is proposed to segment the instrument. The Dual-UNet leverages unlabeled data using a novel hybrid loss function, consisting of uncertainty and contextual constraints. Specifically, the uncertainty constraints leverage the uncertainty estimation of the predictions of the UNet, and therefore improve the unlabeled information for SSL training. In addition, contextual constraints exploit the contextual information of the training images, which are used as the complementary information for voxel-wise uncertainty estimation. Extensive experiments on multiple ex-vivo and in-vivo datasets show that our proposed method achieves Dice score of about 68.6%-69.1% and the inference time of about 1 sec. per volume. These results are better than the state-of-the-art SSL methods and the inference time is comparable to the supervised approaches.
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Catheter segmentation in 3D ultrasound is important for computer-assisted cardiac intervention. However, a large amount of labeled images are required to train a successful deep convolutional neural network (CNN) to segment the catheter, which is expensive and time-consuming. In this paper, we propose a novel catheter segmentation approach, which requests fewer annotations than the supervised learning method, but nevertheless achieves better performance. Our scheme considers a deep Q learning as the pre-localization step, which avoids voxel-level annotation and which can efficiently localize the target catheter. With the detected catheter, patch-based Dual-UNet is applied to segment the catheter in 3D volumetric data. To train the Dual-UNet with limited labeled images and leverage information of unlabeled images, we propose a novel semi-supervised scheme, which exploits unlabeled images based on hybrid constraints from predictions. Experiments show the proposed scheme achieves a higher performance than state-of-the-art semi-supervised methods, while it demonstrates that our method is able to learn from large-scale unlabeled images.
Deep learning has demonstrated significant improvements in medical image segmentation using a sufficiently large amount of training data with manual labels. Acquiring well-representative labels requires expert knowledge and exhaustive labors. In this paper, we aim to boost the performance of semi-supervised learning for medical image segmentation with limited labels using a self-ensembling contrastive learning technique. To this end, we propose to train an encoder-decoder network at image-level with small amounts of labeled images, and more importantly, we learn latent representations directly at feature-level by imposing contrastive loss on unlabeled images. This method strengthens intra-class compactness and inter-class separability, so as to get a better pixel classifier. Moreover, we devise a student encoder for online learning and an exponential moving average version of it, called teacher encoder, to improve the performance iteratively in a self-ensembling manner. To construct contrastive samples with unlabeled images, two sampling strategies that exploit structure similarity across medical images and utilize pseudo-labels for construction, termed region-aware and anatomical-aware contrastive sampling, are investigated. We conduct extensive experiments on an MRI and a CT segmentation dataset and demonstrate that in a limited label setting, the proposed method achieves state-of-the-art performance. Moreover, the anatomical-aware strategy that prepares contrastive samples on-the-fly using pseudo-labels realizes better contrastive regularization on feature representations.
The success of deep learning methods in medical image segmentation tasks heavily depends on a large amount of labeled data to supervise the training. On the other hand, the annotation of biomedical images requires domain knowledge and can be laborious. Recently, contrastive learning has demonstrated great potential in learning latent representation of images even without any label. Existing works have explored its application to biomedical image segmentation where only a small portion of data is labeled, through a pre-training phase based on self-supervised contrastive learning without using any labels followed by a supervised fine-tuning phase on the labeled portion of data only. In this paper, we establish that by including the limited label in formation in the pre-training phase, it is possible to boost the performance of contrastive learning. We propose a supervised local contrastive loss that leverages limited pixel-wise annotation to force pixels with the same label to gather around in the embedding space. Such loss needs pixel-wise computation which can be expensive for large images, and we further propose two strategies, downsampling and block division, to address the issue. We evaluate our methods on two public biomedical image datasets of different modalities. With different amounts of labeled data, our methods consistently outperform the state-of-the-art contrast-based methods and other semi-supervised learning techniques.
The application of deep learning to medical image segmentation has been hampered due to the lack of abundant pixel-level annotated data. Few-shot Semantic Segmentation (FSS) is a promising strategy for breaking the deadlock. However, a high-performing FSS model still requires sufficient pixel-level annotated classes for training to avoid overfitting, which leads to its performance bottleneck in medical image segmentation due to the unmet need for annotations. Thus, semi-supervised FSS for medical images is accordingly proposed to utilize unlabeled data for further performance improvement. Nevertheless, existing semi-supervised FSS methods has two obvious defects: (1) neglecting the relationship between the labeled and unlabeled data; (2) using unlabeled data directly for end-to-end training leads to degenerated representation learning. To address these problems, we propose a novel semi-supervised FSS framework for medical image segmentation. The proposed framework employs Poisson learning for modeling data relationship and propagating supervision signals, and Spatial Consistency Calibration for encouraging the model to learn more coherent representations. In this process, unlabeled samples do not involve in end-to-end training, but provide supervisory information for query image segmentation through graph-based learning. We conduct extensive experiments on three medical image segmentation datasets (i.e. ISIC skin lesion segmentation, abdominal organs segmentation for MRI and abdominal organs segmentation for CT) to demonstrate the state-of-the-art performance and broad applicability of the proposed framework.
Generalising deep models to new data from new centres (termed here domains) remains a challenge. This is largely attributed to shifts in data statistics (domain shifts) between source and unseen domains. Recently, gradient-based meta-learning approaches where the training data are split into meta-train and meta-test sets to simulate and handle the domain shifts during training have shown improved generalisation performance. However, the current fully supervised meta-learning approaches are not scalable for medical image segmentation, where large effort is required to create pixel-wise annotations. Meanwhile, in a low data regime, the simulated domain shifts may not approximate the true domain shifts well across source and unseen domains. To address this problem, we propose a novel semi-supervised meta-learning framework with disentanglement. We explicitly model the representations related to domain shifts. Disentangling the representations and combining them to reconstruct the input image allows unlabeled data to be used to better approximate the true domain shifts for meta-learning. Hence, the model can achieve better generalisation performance, especially when there is a limited amount of labeled data. Experiments show that the proposed method is robust on different segmentation tasks and achieves state-of-the-art generalisation performance on two public benchmarks.
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