SliceMamba with Neural Architecture Search for Medical Image Segmentation
School of Computer Science, Beijing University of Technology（北京工业大学计算机科学学院）；Xiaomi Inc（小米公司）；Department of Radiology, Capital Medical University Affiliated Beijing Friendship Hospital（首都医科大学附属北京友谊医院放射科）；New Laboratory of Pattern Recognition, Institute of Automation, Chinese Academy of Sciences（中国科学院自动化研究所模式识别新实验室）
Despite the progress made in Mamba-based medical image segmentation models, existing methods utilizing unidirectional or multi-directional feature scanning mechanisms struggle to effectively capture dependencies between neighboring positions, limiting the discriminant representation learning of local features. These local features are crucial for medical image segmentation as they provide critical structural information about lesions and organs. To address this limitation, we propose SliceMamba, a simple and effective locally sensitive Mamba-based medical image segmentation model. SliceMamba includes an efficient Bidirectional Slice Scan module (BSS), which performs bidirectional feature slicing and employs varied scanning mechanisms for sliced features with distinct shapes. This design ensures that spatially adjacent features remain close in the scanning sequence, thereby improving segmentation performance. Additionally, to fit the varying sizes and shapes of lesions and organs, we further introduce an Adaptive Slice Search method to automatically determine the optimal feature slice method based on the characteristics of the target data. Extensive experiments on two skin lesion datasets (ISIC2017 and ISIC2018), two polyp segmentation (Kvasir and ClinicDB) datasets, and one multi-organ segmentation dataset (Synapse) validate the effectiveness of our method.
Shanghai Jiao Tong University（上海交通大学）；Johns Hopkins University（约翰斯·霍普金斯大学）；East China Normal University（华东师范大学）
Shape information is a strong and valuable prior in segmenting organs in medical images. However, most current deep learning based segmentation algorithms have not taken shape information into consideration, which can lead to bias towards texture. We aim at modeling shape explicitly and using it to help medical image segmentation. Previous methods proposed Variational Autoencoder (VAE) based models to learn the distribution of shape for a particular organ and used it to automatically evaluate the quality of a segmentation prediction by fitting it into the learned shape distribution. Based on w…
SDC-UDA: Volumetric Unsupervised Domain Adaptation Framework for Slice-Direction Continuous Cross-Modality Medical Image Segmentation
Yonsei University（延世大学）；Harvard Medical School（哈佛医学院）；Naver AI Lab（Naver人工智能实验室）；Naver Cloud（Naver云）；Probe Medical Inc.（Probe医疗公司）；Martinos Center for Biomedical Imaging（马丁诺斯生物医学成像中心）；Korea Institute of Science and Technology（韩国科学技术研究院）
Kakao Brain；Seoul National University（首尔大学）；MILA, Université de Montréal（MILA，蒙特利尔大学）
In this paper, a neural architecture search (NAS) framework is proposed for 3D medical image segmentation, to automatically optimize a neural architecture from a large design space. Our NAS framework searches the structure of each layer including neural connectivities and operation types in both of the encoder and decoder. Since optimizing over a large discrete architecture space is difficult due to high-resolution 3D medical images, a novel stochastic sampling algorithm based on a continuous relaxation is also proposed for scalable gradient based optimization. On the 3D medical image segmenta…
Information Sciences Institute（信息科学研究所）；University of Southern California（南加州大学）
Convolutional neural networks (CNNs) have led to significant improvements in the semantic segmentation of images. When source and target datasets come from different modalities, CNN performance suffers due to domain shift. In such cases data annotation in the target domain becomes necessary to maintain model performance. To circumvent the re-annotation process, unsupervised domain adaptation (UDA) is proposed to adapt a model to new modalities using solely unlabeled target data. Common UDA algorithms require access to source domain data during adaptation, which may not be feasible in medical i…
Due to the limitation of available labeled data, medical image segmentation is a challenging task for deep learning. Traditional data augmentation techniques have been shown to improve segmentation network performances by optimizing the usage of few training examples. However, current augmentation approaches for segmentation do not tackle the strong texture bias of convolutional neural networks, observed in several studies. This work shows on the MoNuSeg dataset that style augmentation, which is already used in classification tasks, helps reducing texture over-fitting and improves segmentation…
Nanjing University of Science and Technology（南京理工大学）
Segmentation is one of the most important and popular tasks in medical image analysis, which plays a critical role in disease diagnosis, surgical planning, and prognosis evaluation. During the past five years, on the one hand, thousands of medical image segmentation methods have been proposed for various organs and lesions in different medical images, which become more and more challenging to fairly compare different methods. On the other hand, international segmentation challenges can provide a transparent platform to fairly evaluate and compare different methods. In this paper, we present a …
South China University of Technology（华南理工大学）；University of Utah（犹他大学）
We introduce the idea of inter-slice image augmentation whereby the numbers of the medical images and the corresponding segmentation labels are increased between two consecutive images in order to boost medical image segmentation accuracy. Unlike conventional data augmentation methods in medical imaging, which only increase the number of training samples directly by adding new virtual samples using simple parameterized transformations such as rotation, flipping, scaling, etc., we aim to augment data based on the relationship between two consecutive images, which increases not only the number b…
Segmentation is a critical step in medical image analysis. Fully Convolutional Networks (FCNs) have emerged as powerful segmentation models achieving state-of-the-art results in various medical image datasets. Network architectures are usually designed manually for a specific segmentation task so applying them to other medical datasets requires extensive experience and time. Moreover, the segmentation requires handling large volumetric data that results in big and complex architectures. Recently, methods that automatically design neural networks for medical image segmentation have been present…
MAMBO-NET: Multi-Causal Aware Modeling Backdoor-Intervention Optimization for Medical Image Segmentation Network
Tianjin University（天津大学）；Tianjin Key Laboratory of Cognitive Computing and Application（天津认知计算与应用重点实验室）；Tianjin Key Laboratory of Advanced Networking（天津先进网络重点实验室）；Tianjin International Engineering Institute, Tianjin University（天津大学国际工程师学院）；Tianjin Central Hospital of Gynecology Obstetrics（天津市中心妇产科医院）；Silesian University of Technology（西里西亚工业大学）；University of Alberta（阿尔伯塔大学）；Istinye University（伊斯坦布尔耶尼大学）
Xidian University（西安电子科技大学）；University of North Carolina at Chapel Hill（北卡罗来纳大学教堂山分校）
3D image segmentation is one of the most important and ubiquitous problems in medical image processing. It provides detailed quantitative analysis for accurate disease diagnosis, abnormal detection, and classification. Currently deep learning algorithms are widely used in medical image segmentation, most algorithms trained models with full annotated datasets. However, obtaining medical image datasets is very difficult and expensive, and full annotation of 3D medical image is a monotonous and time-consuming work. Partially labelling informative slices in 3D images will be a great relief of manu…
UiT The Arctic University of Norway（特罗姆瑟大学（挪威北极圈大学））
Recent work has shown that label-efficient few-shot learning through self-supervision can achieve promising medical image segmentation results. However, few-shot segmentation models typically rely on prototype representations of the semantic classes, resulting in a loss of local information that can degrade performance. This is particularly problematic for the typically large and highly heterogeneous background class in medical image segmentation problems. Previous works have attempted to address this issue by learning additional prototypes for each class, but since the prototypes are based on…
University of Electronic Science and Technology of China（电子科技大学）；Shanghai Artificial Intelligence Laboratory（上海人工智能实验室）；Johns Hopkins University（约翰斯·霍普金斯大学）；West China Hospital, Sichuan University（四川大学华西医院）
Background and Objective: Open-source deep learning toolkits are one of the driving forces for developing medical image segmentation models. Existing toolkits mainly focus on fully supervised segmentation and require full and accurate pixel-level annotations that are time-consuming and difficult to acquire for segmentation tasks, which makes learning from imperfect labels highly desired for reducing the annotation cost. We aim to develop a new deep learning toolkit to support annotation-efficient learning for medical image segmentation. Methods: Our proposed toolkit named PyMIC is a modular de…
Object segmentation plays an important role in the modern medical image analysis, which benefits clinical study, disease diagnosis, and surgery planning. Given the various modalities of medical images, the automated or semi-automated segmentation approaches have been used to identify and parse organs, bones, tumors, and other regions-of-interest (ROI). However, these contemporary segmentation approaches tend to fail to predict the boundary areas of ROI, because of the fuzzy appearance contrast caused during the imaging procedure. To further improve the segmentation quality of boundary areas, w…
Unsupervised pre-training has been proven as an effective approach to boost various downstream tasks given limited labeled data. Among various methods, contrastive learning learns a discriminative representation by constructing positive and negative pairs. However, it is not trivial to build reasonable pairs for a segmentation task in an unsupervised way. In this work, we propose a novel unsupervised pre-training framework that avoids the drawback of contrastive learning. Our framework consists of two principles: unsupervised over-segmentation as a pre-train task using mutual information maxim…
Rensselaer Polytechnic Institute（伦斯勒理工学院）；Wuhan University（武汉大学）；National Institutes of Health（美国国立卫生研究院）
Automatic medical image segmentation, an essential component of medical image analysis, plays an importantrole in computer-aided diagnosis. For example, locating and segmenting the liver can be very helpful in livercancer diagnosis and treatment. The state-of-the-art models in medical image segmentation are variants ofthe encoder-decoder architecture such as fully convolutional network (FCN) and U-Net.1A major focus ofthe FCN based segmentation methods has been on network structure engineering by incorporating the latestCNN structures such as ResNet2and DenseNet.3In addition to exploring new n…
United States Food and Drug Administration（美国食品药品监督管理局）
Machine learning-based segmentation in medical imaging is widely used in clinical applications from diagnostics to radiotherapy treatment planning. Segmented medical images with ground truth are useful for investigating the properties of different segmentation performance metrics to inform metric selection. Regular geometrical shapes are often used to synthesize segmentation errors and illustrate properties of performance metrics, but they lack the complexity of anatomical variations in real images. In this study, we present a tool to emulate segmentations by adjusting the reference (truth) ma…
Beihang University（北京航空航天大学）；Hefei Innovation Research Institute, Beihang University（北京航空航天大学合肥创新研究院）；Beijing Advanced Innovation Centre for Biomedical Engineering（北京生物医学工程先进创新中心）；Beijing Advanced Innovation Centre for Big Data-Based Precision Medicine（北京大数据精准医疗先进创新中心）
Recently, deep convolutional neural networks have achieved great success for medical image segmentation. However, unlike segmentation of natural images, most medical images such as MRI and CT are volumetric data. In order to make full use of volumetric information, 3D CNNs are widely used. However, 3D CNNs suffer from higher inference time and computation cost, which hinders their further clinical applications. Additionally, with the increased number of parameters, the risk of overfitting is higher, especially for medical images where data and annotations are expensive to acquire. To issue thi…
Boston Children’s Hospital（波士顿儿童医院）；Harvard Medical School（哈佛医学院）；Massachusetts General Hospital（麻省总医院）
Deep convolutional neural networks (CNNs) have been widely used for medical image segmentation. In most studies, only the output layer is exploited to compute the final segmentation results and the hidden representations of the deep learned features have not been well understood. In this paper, we propose a prototype segmentation (ProtoSeg) method to compute a binary segmentation map based on deep features. We measure the segmentation abilities of the features by computing the Dice between the feature segmentation map and ground-truth, named as the segmentation ability score (SA score for shor…
Institute for Machine Learning, ETH Zurich（苏黎世联邦理工学院机器学习研究所）；Instituto Superior Técnico, Universidade de Lisboa（里斯本大学高等技术学院）；Champalimaud Foundation（尚帕利莫基金会）
In clinical practice, regions of interest in medical imaging often need to be identified through a process of precise image segmentation. The quality of this image segmentation step critically affects the subsequent clinical assessment of the patient status. To enable high accuracy, automatic image segmentation, we introduce a novel deep neural network architecture that exploits the inherent spatial coherence of anatomical structures and is well equipped to capture long-range spatial dependencies in the segmented pixel/voxel space. In contrast to the state-of-the-art solutions based on convolu…
University of Science and Technology Beijing（北京科技大学）；University of Central Florida（中佛罗里达大学）
Transformer, benefiting from global (long-range) information modeling using self-attention mechanism, has been successful in natural language processing and computer vision recently. Convolutional Neural Networks, capable of capturing local features, are difficult to model explicit long-distance dependencies from global feature space. However, both local and global features are crucial for dense prediction tasks, especially for 3D medical image segmentation. In this paper, we present the further attempt to exploit Transformer in 3D CNN for 3D medical image volumetric segmentation and propose a…
Vanderbilt University（范德堡大学）；The George Washington University（乔治华盛顿大学）；Korea University（高丽大学）
Segmenting medical images accurately and reliably is important for disease diagnosis and treatment. It is a challenging task because of the wide variety of objects' sizes, shapes, and scanning modalities. Recently, many convolutional neural networks (CNN) have been designed for segmentation tasks and achieved great success. Few studies, however, have fully considered the sizes of objects, and thus most demonstrate poor performance for small objects segmentation. This can have a significant impact on the early detection of diseases. This paper proposes a Context Axial Reserve Attention Network …
The University of British Columbia（不列颠哥伦比亚大学）；Harvard Medical School（哈佛医学院）
Fully convolutional neural networks (FCNs), and in particular U-Nets, have achieved state-of-the-art results in semantic segmentation for numerous medical imaging applications. Moreover, batch normalization and Dice loss have been used successfully to stabilize and accelerate training. However, these networks are poorly calibrated i.e. they tend to produce overconfident predictions both in correct and erroneous classifications, making them unreliable and hard to interpret. In this paper, we study predictive uncertainty estimation in FCNs for medical image segmentation. We make the following co…
Automated and accurate 3D medical image segmentation plays an essential role in assisting medical professionals to evaluate disease progresses and make fast therapeutic schedules. Although deep convolutional neural networks (DCNNs) have widely applied to this task, the accuracy of these models still need to be further improved mainly due to their limited ability to 3D context perception. In this paper, we propose the 3D context residual network (ConResNet) for the accurate segmentation of 3D medical images. This model consists of an encoder, a segmentation decoder, and a context residual decod…
Beihang University（北京航空航天大学）；Hefei Innovation Research Institute, Beihang University（北京航空航天大学合肥创新研究院）；Beijing Advanced Innovation Centre for Biomedical Engineering（北京生物医学工程高精尖创新中心）；Beijing Advanced Innovation Centre for Big Data-Based Precision Medicine（北京大数据精准医疗高精尖创新中心）
The success of deep learning methods in medical image segmentation tasks usually requires a large amount of labeled data. However, obtaining reliable annotations is expensive and time-consuming. Semi-supervised learning has attracted much attention in medical image segmentation by taking the advantage of unlabeled data which is much easier to acquire. In this paper, we propose a novel dual-task mutual learning framework for semi-supervised medical image segmentation. Our framework can be formulated as an integration of two individual segmentation networks based on two tasks: learning region-ba…
Johns Hopkins University（约翰斯·霍普金斯大学）；NVIDIA（英伟达）；Arizona State University（亚利桑那州立大学）
Semantic segmentation of 3D medical images is a challenging task due to the high variability of the shape and pattern of objects (such as organs or tumors). Given the recent success of deep learning in medical image segmentation, Neural Architecture Search (NAS) has been introduced to find high-performance 3D segmentation network architectures. However, because of the massive computational requirements of 3D data and the discrete optimization nature of architecture search, previous NAS methods require a long search time or necessary continuous relaxation, and commonly lead to sub-optimal netwo…
Sun Yat-Sen University（中山大学）；Xidian University（西安电子科技大学）；The Sixth Affiliated Hospital, Sun Yat-sen University（中山大学附属第六医院）
Semi-supervised learning (SSL), which aims at leveraging a few labeled images and a large number of unlabeled images for network training, is beneficial for relieving the burden of data annotation in medical image segmentation. According to the experience of medical imaging experts, local attributes such as texture, luster and smoothness are very important factors for identifying target objects like lesions and polyps in medical images. Motivated by this, we propose a cross-level contrastive learning scheme to enhance representation capacity for local features in semi-supervised medical image …
Curating a large set of fully annotated training data can be costly, especially for the tasks of medical image segmentation. Scribble, a weaker form of annotation, is more obtainable in practice, but training segmentation models from limited supervision of scribbles is still challenging. To address the difficulties, we propose a new framework for scribble learning-based medical image segmentation, which is composed of mix augmentation and cycle consistency and thus is referred to as CycleMix. For augmentation of supervision, CycleMix adopts the mixup strategy with a dedicated design of random …
Vanderbilt University（范德比尔特大学）；The George Washington University（乔治华盛顿大学）
Segmenting medical images accurately and reliably is important for disease diagnosis and treatment. It is a challenging task because of the wide variety of objects' sizes, shapes, and scanning modalities. Recently, many convolutional neural networks (CNN) have been designed for segmentation tasks and achieved great success. Few studies, however, have fully considered the sizes of objects, and thus most demonstrate poor performance for small objects segmentation. This can have a significant impact on the early detection of diseases. This paper proposes a Context Axial Reverse Attention Network …
SimulaMet；UiT The Arctic University of Norway（挪威北极大学）；Oslo Metropolitan University（奥斯陆城市大学）
Semantic image segmentation is the process of labeling each pixel of an image with its corresponding class. An encoder-decoder based approach, like U-Net and its variants, is a popular strategy for solving medical image segmentation tasks. To improve the performance of U-Net on various segmentation tasks, we propose a novel architecture called DoubleU-Net, which is a combination of two U-Net architectures stacked on top of each other. The first U-Net uses a pre-trained VGG-19 as the encoder, which has already learned features from ImageNet and can be transferred to another task easily. To capt…
Medical image segmentation is one of the most challenging tasks in medical image analysis and has been widely developed for many clinical applications. Most of the existing metrics have been first designed for natural images and then extended to medical images. While object surface plays an important role in medical segmentation and quantitative analysis i.e. analyze brain tumor surface, measure gray matter volume, most of the existing metrics are limited when it comes to analyzing the object surface, especially to tell about surface smoothness or roughness of a given volumetric object or to a…
University of Arkansas（阿肯色大学）；Cyberlogitec Vietnam（越南赛博罗吉泰克公司）；VinAI（越南人工智能研究院）
Capsule network is a recent new deep network architecture that has been applied successfully for medical image segmentation tasks. This work extends capsule networks for volumetric medical image segmentation with self-supervised learning. To improve on the problem of weight initialization compared to previous capsule networks, we leverage self-supervised learning for capsule networks pre-training, where our pretext-task is optimized by self-reconstruction. Our capsule network, SS-3DCapsNet, has a UNet-based architecture with a 3D Capsule encoder and 3D CNNs decoder. Our experiments on multiple…
Fudan University（复旦大学）；Ruijin Hospital, Shanghai Jiaotong University（上海交通大学医学院附属瑞金医院）；Tongji Hospital, Huazhong University of Science and Technology（华中科技大学同济医学院附属同济医院）；Leiden University Medical Center（莱顿大学医学中心）
Convolutional neural network (CNN), in particular the Unet, is a powerful method for medical image segmentation. To date Unet has demonstrated state-of-art performance in many complex medical image segmentation tasks, especially under the condition when the training and testing data share the same distribution (i.e. come from the same source domain). However, in clinical practice, medical images are acquired from different vendors and centers. The performance of a U-Net trained from a particular source domain, when transferred to a different target domain (e.g. different vendor, acquisition pa…
Shaanxi University of Science and Technology（陕西科技大学）；Lanzhou Jiaotong University（兰州交通大学）；Brunel University London（伦敦布鲁内尔大学）
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…
University of Glasgow（格拉斯哥大学）；University of York（约克大学）；Mohamed bin Zayed University of Artificial Intelligence（穆罕默德·本·扎耶德人工智能大学）；NAAMII
We propose a new residual block for convolutional neural networks and demonstrate its state-of-the-art performance in medical image segmentation. We combine attention mechanisms with group convolutions to create our group attention mechanism, which forms the fundamental building block of our network, FocusNet++. We employ a hybrid loss based on balanced cross entropy, Tversky loss and the adaptive logarithmic loss to enhance the performance along with fast convergence. Our results show that FocusNet++ achieves state-of-the-art results across various benchmark metrics for the ISIC 2018 melanoma…
The paper is a short review of medical image segmentation using U-Net and its variants. As we understand going through a medical images is not an easy job for any clinician either radiologist or pathologist. Analysing medical images is the only way to perform non-invasive diagnosis. Segmenting out the regions of interest has significant importance in medical images and is key for diagnosis. This paper also gives a bird eye view of how medical image segmentation has evolved. Also discusses challenge's and success of the deep neural architectures. Following how different hybrid architectures hav…
National Institute of Technology Karnataka（卡纳塔克邦国家技术研究所）
Computer-aided medical image analysis plays a significant role in assisting medical practitioners for expert clinical diagnosis and deciding the optimal treatment plan. At present, convolutional neural networks (CNN) are the preferred choice for medical image analysis. In addition, with the rapid advancements in three-dimensional (3D) imaging systems and the availability of excellent hardware and software support to process large volumes of data, 3D deep learning methods are gaining popularity in medical image analysis. Here, we present an extensive review of the recently evolved 3D deep learn…
University of California, Los Angeles（加州大学洛杉矶分校）；NVIDIA（英伟达）
Fully convolutional neural networks (CNNs) have proven to be effective at representing and classifying textural information, thus transforming image intensity into output class masks that achieve semantic image segmentation. In medical image analysis, however, expert manual segmentation often relies on the boundaries of anatomical structures of interest. We propose boundary aware CNNs for medical image segmentation. Our networks are designed to account for organ boundary information, both by providing a special network edge branch and edge-aware loss terms, and they are trainable end-to-end. W…
Ecole nationale Supérieure en Informatique（国立高等计算机学院）；Université de Bourgogne（勃艮第大学）
Segmentation of medical images is an essential part in the process of diagnostics. Physicians require an automatic, robust and valid results. Hidden Markov Random Fields (HMRF) provide powerful model. This latter models the segmentation problem as the minimization of an energy function. Cuckoo search (CS) algorithm is one of the recent nature-inspired meta-heuristic algorithms. It has shown its efficiency in many engineering optimization problems. In this paper, we use three cuckoo search algorithm to achieve medical image segmentation.
South China University of Technology（华南理工大学）；Rochester Institute of Technology（罗切斯特理工学院）
We introduce a novel frame-interpolation-based method for slice imputation to improve segmentation accuracy for anisotropic 3D medical images, in which the number of slices and their corresponding segmentation labels can be increased between two consecutive slices in anisotropic 3D medical volumes. Unlike previous inter-slice imputation methods, which only focus on the smoothness in the axial direction, this study aims to improve the smoothness of the interpolated 3D medical volumes in all three directions: axial, sagittal, and coronal. The proposed multitask inter-slice imputation method, in …
