OneSeg: Self-learning and One-shot Learning based Single-slice Annotation for 3D Medical Image Segmentation

As deep learning methods continue to improve medical image segmentation performance, data annotation is still a big bottleneck due to the labor-intensive and time-consuming burden on medical experts, especially for 3D images. To significantly reduce annotation efforts while attaining competitive segmentation accuracy, we propose a self-learning and one-shot learning based framework for 3D medical image segmentation by annotating only one slice of each 3D image. Our approach takes two steps: (1) self-learning of a reconstruction network to learn semantic correspondence among 2D slices within 3D images, and (2) representative selection of single slices for one-shot manual annotation and propagating the annotated data with the well-trained reconstruction network. Extensive experiments verify that our new framework achieves comparable performance with less than 1% annotated data compared with fully supervised methods and generalizes well on several out-of-distribution testing sets

Attention Mechanisms in Medical Image Segmentation: A Survey

Medical image segmentation plays an important role in computer-aided diagnosis. Attention mechanisms that distinguish important parts from irrelevant parts have been widely used in medical image segmentation tasks. This paper systematically reviews the basic principles of attention mechanisms and their applications in medical image segmentation. First, we review the basic concepts of attention mechanism and formulation. Second, we surveyed over 300 articles related to medical image segmentation, and divided them into two groups based on their attention mechanisms, non-Transformer attention and Transformer attention. In each group, we deeply analyze the attention mechanisms from three aspects based on the current literature work, i.e., the principle of the mechanism (what to use), implementation methods (how to use), and application tasks (where to use). We also thoroughly analyzed the advantages and limitations of their applications to different tasks. Finally, we summarize the current state of research and shortcomings in the field, and discuss the potential challenges in the future, including task specificity, robustness, standard evaluation, etc. We hope that this review can showcase the overall research context of traditional and Transformer attention methods, provide a clear reference for subsequent research, and inspire more advanced attention research, not only in medical image segmentation, but also in other image analysis scenarios.Comment: Submitted to Medical Image Analysis, survey paper, 34 pages, over 300 reference

DSFNet: Convolutional Encoder-Decoder Architecture Combined Dual-GCN and Stand-alone Self-attention by Fast Normalized Fusion for Polyps Segmentation

In the past few decades, deep learning technology has been widely used in medical image segmentation and has made significant breakthroughs in the fields of liver and liver tumor segmentation, brain and brain tumor segmentation, video disc segmentation, heart image segmentation, and so on. However, the segmentation of polyps is still a challenging task since the surface of the polyps is flat and the color is very similar to that of surrounding tissues. Thus, It leads to the problems of the unclear boundary between polyps and surrounding mucosa, local overexposure, and bright spot reflection. To counter this problem, this paper presents a novel U-shaped network, namely DSFNet, which effectively combines the advantages of Dual-GCN and self-attention mechanisms. First, we introduce a feature enhancement block module based on Dual-GCN module as an attention mechanism to enhance the feature extraction of local spatial and structural information with fine granularity. Second, the stand-alone self-attention module is designed to enhance the integration ability of the decoding stage model to global information. Finally, the Fast Normalized Fusion method with trainable weights is used to efficiently fuse the corresponding three feature graphs in encoding, bottleneck, and decoding blocks, thus promoting information transmission and reducing the semantic gap between encoder and decoder. Our model is tested on two public datasets including Endoscene and Kvasir-SEG and compared with other state-of-the-art models. Experimental results show that the proposed model surpasses other competitors in many indicators, such as Dice, MAE, and IoU. In the meantime, ablation studies are also conducted to verify the efficacy and effectiveness of each module. Qualitative and quantitative analysis indicates that the proposed model has great clinical significance.Comment: 10 pages, 6 figures, 3 table

A Comprehensive Overview of Computational Nuclei Segmentation Methods in Digital Pathology

In the cancer diagnosis pipeline, digital pathology plays an instrumental role in the identification, staging, and grading of malignant areas on biopsy tissue specimens. High resolution histology images are subject to high variance in appearance, sourcing either from the acquisition devices or the H\&E staining process. Nuclei segmentation is an important task, as it detects the nuclei cells over background tissue and gives rise to the topology, size, and count of nuclei which are determinant factors for cancer detection. Yet, it is a fairly time consuming task for pathologists, with reportedly high subjectivity. Computer Aided Diagnosis (CAD) tools empowered by modern Artificial Intelligence (AI) models enable the automation of nuclei segmentation. This can reduce the subjectivity in analysis and reading time. This paper provides an extensive review, beginning from earlier works use traditional image processing techniques and reaching up to modern approaches following the Deep Learning (DL) paradigm. Our review also focuses on the weak supervision aspect of the problem, motivated by the fact that annotated data is scarce. At the end, the advantages of different models and types of supervision are thoroughly discussed. Furthermore, we try to extrapolate and envision how future research lines will potentially be, so as to minimize the need for labeled data while maintaining high performance. Future methods should emphasize efficient and explainable models with a transparent underlying process so that physicians can trust their output.Comment: 47 pages, 27 figures, 9 table

Medical Image Segmentation Review: The success of U-Net

Automatic medical image segmentation is a crucial topic in the medical domain and successively a critical counterpart in the computer-aided diagnosis paradigm. U-Net is the most widespread image segmentation architecture due to its flexibility, optimized modular design, and success in all medical image modalities. Over the years, the U-Net model achieved tremendous attention from academic and industrial researchers. Several extensions of this network have been proposed to address the scale and complexity created by medical tasks. Addressing the deficiency of the naive U-Net model is the foremost step for vendors to utilize the proper U-Net variant model for their business. Having a compendium of different variants in one place makes it easier for builders to identify the relevant research. Also, for ML researchers it will help them understand the challenges of the biological tasks that challenge the model. To address this, we discuss the practical aspects of the U-Net model and suggest a taxonomy to categorize each network variant. Moreover, to measure the performance of these strategies in a clinical application, we propose fair evaluations of some unique and famous designs on well-known datasets. We provide a comprehensive implementation library with trained models for future research. In addition, for ease of future studies, we created an online list of U-Net papers with their possible official implementation. All information is gathered in https://github.com/NITR098/Awesome-U-Net repository.Comment: Submitted to the IEEE Transactions on Pattern Analysis and Machine Intelligence Journa

Deep segmentation of the liver and the hepatic tumors from abdomen tomography images

A pipelined framework is proposed for accurate, automated, simultaneous segmentation of the liver as well as the hepatic tumors from computed tomography (CT) images. The introduced framework composed of three pipelined levels. First, two different transfers deep convolutional neural networks (CNN) are applied to get high-level compact features of CT images. Second, a pixel-wise classifier is used to obtain two output-classified maps for each CNN model. Finally, a fusion neural network (FNN) is used to integrate the two maps. Experimentations performed on the MICCAI’2017 database of the liver tumor segmentation (LITS) challenge, result in a dice similarity coefficient (DSC) of 93.5% for the segmentation of the liver and of 74.40% for the segmentation of the lesion, using a 5-fold cross-validation scheme. Comparative results with the state-of-the-art techniques on the same data show the competing performance of the proposed framework for simultaneous liver and tumor segmentation

Graph Flow: Cross-layer Graph Flow Distillation for Dual Efficient Medical Image Segmentation

With the development of deep convolutional neural networks, medical image segmentation has achieved a series of breakthroughs in recent years. However, the higher-performance convolutional neural networks always mean numerous parameters and high computation costs, which will hinder the applications in clinical scenarios. Meanwhile, the scarceness of large-scale annotated medical image datasets further impedes the application of high-performance networks. To tackle these problems, we propose Graph Flow, a comprehensive knowledge distillation framework, for both network-efficiency and annotation-efficiency medical image segmentation. Specifically, our core Graph Flow Distillation transfer the essence of cross-layer variations from a well-trained cumbersome teacher network to a non-trained compact student network. In addition, an unsupervised Paraphraser Module is designed to purify the knowledge of the teacher network, which is also beneficial for the stabilization of training procedure. Furthermore, we build a unified distillation framework by integrating the adversarial distillation and the vanilla logits distillation, which can further refine the final predictions of the compact network. Extensive experiments conducted on Gastric Cancer Segmentation Dataset and Synapse Multi-organ Segmentation Dataset demonstrate the prominent ability of our method which achieves state-of-the-art performance on these different-modality and multi-category medical image datasets. Moreover, we demonstrate the effectiveness of our Graph Flow through a new semi-supervised paradigm for dual efficient medical image segmentation. Our code will be available at Graph Flow