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Register a new userSystematic Clinical Evaluation of A Deep Learning Method for Medical Image Segmentation: Radiosurgery Application
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We systematically evaluate a Deep Learning (DL) method in a 3D medical image segmentation task. Our segmentation method is integrated into the radiosurgery treatment process and directly impacts the clinical workflow. With our method, we address the relative drawbacks of manual segmentation: high inter-rater contouring variability and high time consumption of the contouring process. The main extension over the existing evaluations is the careful and detailed analysis that could be further generalized on other medical image segmentation tasks. Firstly, we analyze the changes in the inter-rater detection agreement. We show that the segmentation model reduces the ratio of detection disagreements from 0.162 to 0.085 (p < 0.05). Secondly, we show that the model improves the inter-rater contouring agreement from 0.845 to 0.871 surface Dice Score (p < 0.05). Thirdly, we show that the model accelerates the delineation process in between 1.6 and 2.0 times (p < 0.05). Finally, we design the setup of the clinical experiment to either exclude or estimate the evaluation biases, thus preserve the significance of the results. Besides the clinical evaluation, we also summarize the intuitions and practical ideas for building an efficient DL-based model for 3D medical image segmentation.
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The astounding success made by artificial intelligence (AI) in healthcare and other fields proves that AI can achieve human-like performance. However, success always comes with challenges. Deep learning algorithms are data-dependent and require large datasets for training. The lack of data in the medical imaging field creates a bottleneck for the application of deep learning to medical image analysis. Medical image acquisition, annotation, and analysis are costly, and their usage is constrained by ethical restrictions. They also require many resources, such as human expertise and funding. That makes it difficult for non-medical researchers to have access to useful and large medical data. Thus, as comprehensive as possible, this paper provides a collection of medical image datasets with their associated challenges for deep learning research. We have collected information of around three hundred datasets and challenges mainly reported between 2013 and 2020 and categorized them into four categories: head & neck, chest & abdomen, pathology & blood, and ``others. Our paper has three purposes: 1) to provide a most up to date and complete list that can be used as a universal reference to easily find the datasets for clinical image analysis, 2) to guide researchers on the methodology to test and evaluate their methods performance and robustness on relevant datasets, 3) to provide a ``route to relevant algorithms for the relevant medical topics, and challenge leaderboards.
Deep learning has been widely used for medical image segmentation and a large number of papers has been presented recording the success of deep learning in the field. In this paper, we present a comprehensive thematic survey on medical image segmentation using deep learning techniques. This paper makes two original contributions. Firstly, compared to traditional surveys that directly divide literatures of deep learning on medical image segmentation into many groups and introduce literatures in detail for each group, we classify currently popular literatures according to a multi-level structure from coarse to fine. Secondly, this paper focuses on supervised and weakly supervised learning approaches, without including unsupervised approaches since they have been introduced in many old surveys and they are not popular currently. For supervised learning approaches, we analyze literatures in three aspects: the selection of backbone networks, the design of network blocks, and the improvement of loss functions. For weakly supervised learning approaches, we investigate literature according to data augmentation, transfer learning, and interactive segmentation, separately. Compared to existing surveys, this survey classifies the literatures very differently from before and is more convenient for readers to understand the relevant rationale and will guide them to think of appropriate improvements in medical image segmentation based on deep learning approaches.
Automated medical image segmentation is an important step in many medical procedures. Recently, deep learning networks have been widely used for various medical image segmentation tasks, with U-Net and generative adversarial nets (GANs) being some of the commonly used ones. Foreground-background class imbalance is a common occurrence in medical images, and U-Net has difficulty in handling class imbalance because of its cross entropy (CE) objective function. Similarly, GAN also suffers from class imbalance because the discriminator looks at the entire image to classify it as real or fake. Since the discriminator is essentially a deep learning classifier, it is incapable of correctly identifying minor changes in small structures. To address these issues, we propose a novel context based CE loss function for U-Net, and a novel architecture Seg-GLGAN. The context based CE is a linear combination of CE obtained over the entire image and its region of interest (ROI). In Seg-GLGAN, we introduce a novel context discriminator to which the entire image and its ROI are fed as input, thus enforcing local context. We conduct extensive experiments using two challenging unbalanced datasets: PROMISE12 and ACDC. We observe that segmentation results obtained from our methods give better segmentation metrics as compared to various baseline methods.
Accurate image segmentation is crucial for medical imaging applications. The prevailing deep learning approaches typically rely on very large training datasets with high-quality manual annotations, which are often not available in medical imaging. We introduce Annotation-effIcient Deep lEarning (AIDE) to handle imperfect datasets with an elaborately designed cross-model self-correcting mechanism. AIDE improves the segmentation Dice scores of conventional deep learning models on open datasets possessing scarce or noisy annotations by up to 30%. For three clinical datasets containing 11,852 breast images of 872 patients from three medical centers, AIDE consistently produces segmentation maps comparable to those generated by the fully supervised counterparts as well as the manual annotations of independent radiologists by utilizing only 10% training annotations. Such a 10-fold improvement of efficiency in utilizing experts labels has the potential to promote a wide range of biomedical applications.
Current Computer-Aided Diagnosis (CAD) methods mainly depend on medical images. The clinical information, which usually needs to be considered in practical clinical diagnosis, has not been fully employed in CAD. In this paper, we propose a novel deep learning-based method for fusing Magnetic Resonance Imaging (MRI)/Computed Tomography (CT) images and clinical information for diagnostic tasks. Two paths of neural layers are performed to extract image features and clinical features, respectively, and at the same time clinical features are employed as the attention to guide the extraction of image features. Finally, these two modalities of features are concatenated to make decisions. We evaluate the proposed method on its applications to Alzheimers disease diagnosis, mild cognitive impairment converter prediction and hepatic microvascular invasion diagnosis. The encouraging experimental results prove the values of the image feature extraction guided by clinical features and the concatenation of two modalities of features for classification, which improve the performance of diagnosis effectively and stably.
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