In this paper, we present a novel unsupervised domain adaptation (UDA) method, named Domain Adaptive Relational Reasoning (DARR), to generalize 3D multi-organ segmentation models to medical data collected from different scanners and/or protocols (domains). Our method is inspired by the fact that the spatial relationship between internal structures in medical images is relatively fixed, e.g., a spleen is always located at the tail of a pancreas, which serves as a latent variable to transfer the knowledge shared across multiple domains. We formulate the spatial relationship by solving a jigsaw puzzle task, i.e., recovering a CT scan from its shuffled patches, and jointly train it with the organ segmentation task. To guarantee the transferability of the learned spatial relationship to multiple domains, we additionally introduce two schemes: 1) Employing a super-resolution network also jointly trained with the segmentation model to standardize medical images from different domain to a certain spatial resolution; 2) Adapting the spatial relationship for a test image by test-time jigsaw puzzle training. Experimental results show that our method improves the performance by 29.60% DSC on target datasets on average without using any data from the target domain during training.
In the past ten years, with the help of deep learning, especially the rapid development of deep neural networks, medical image analysis has made remarkable progress. However, how to effectively use the relational information between various tissues or organs in medical images is still a very challenging problem, and it has not been fully studied. In this thesis, we propose two novel solutions to this problem based on deep relational learning. First, we propose a context-aware fully convolutional network that effectively models implicit relation information between features to perform medical i…
Tailored Multi-Organ Segmentation with Model Adaptation and Ensemble
Zhejiang University（浙江大学）；Suzhou Institute for Advanced Research, University of Science and Technology of China（中国科学技术大学苏州高等研究院）；Ritsumeikan University（立命馆大学）；University of Science and Technology of China（中国科学技术大学）
Automatic segmentation of abdomen organs using medical imaging has many potential applications in clinical workflows. Recently, the state-of-the-art performance for organ segmentation has been achieved by deep learning models, i.e., convolutional neural network (CNN). However, it is challenging to train the conventional CNN-based segmentation models that aware of the shape and topology of organs. In this work, we tackle this problem by introducing a novel end-to-end shape learning architecture -- organ point-network. It takes deep learning features as inputs and generates organ shape represent…
The University of Hong Kong（香港大学）；Tencent（腾讯）；Huazhong University of Science and Technology（华中科技大学）
Learning by imitation is one of the most significant abilities of human beings and plays a vital role in human's computational neural system. In medical image analysis, given several exemplars (anchors), experienced radiologist has the ability to delineate unfamiliar organs by imitating the reasoning process learned from existing types of organs. Inspired by this observation, we propose OrganNet which learns a generalized organ concept from a set of annotated organ classes and then transfer this concept to unseen classes. In this paper, we show that such process can be integrated into the one-…
Technical University of Munich（慕尼黑工业大学）；Klinikum rechts der Isar（慕尼黑 Rechts der Isar 医院）；University of Zurich（苏黎世大学）
Automatic localization and segmentation of organs-at-risk (OAR) in CT are essential pre-processing steps in medical image analysis tasks, such as radiation therapy planning. For instance, the segmentation of OAR surrounding tumors enables the maximization of radiation to the tumor area without compromising the healthy tissues. However, the current medical workflow requires manual delineation of OAR, which is prone to errors and is annotator-dependent. In this work, we aim to introduce a unified 3D pipeline for OAR localization-segmentation rather than novel localization or segmentation archite…
Accurate and robust segmentation of small organs in whole-body MRI is difficult due to anatomical variation and class imbalance. Recent deep network based approaches have demonstrated promising performance on abdominal multi-organ segmentations. However, the performance on small organs is still suboptimal as these occupy only small regions of the whole-body volumes with unclear boundaries and variable shapes. A coarse-to-fine, hierarchical strategy is a common approach to alleviate this problem, however, this might miss useful contextual information. We propose a two-stage approach with weight…
Pulmonary lobe segmentation in computed tomography scans is essential for regional assessment of pulmonary diseases. Recent works based on convolution neural networks have achieved good performance for this task. However, they are still limited in capturing structured relationships due to the nature of convolution. The shape of the pulmonary lobes affect each other and their borders relate to the appearance of other structures, such as vessels, airways, and the pleural wall. We argue that such structural relationships play a critical role in the accurate delineation of pulmonary lobes when the…
Institute of Computing Technology, Chinese Academy of Sciences（中国科学院计算技术研究所）；Southeast University（东南大学）
Annotating multiple organs in medical images is both costly and time-consuming; therefore, existing multi-organ datasets with labels are often low in sample size and mostly partially labeled, that is, a dataset has a few organs labeled but not all organs. In this paper, we investigate how to learn a single multi-organ segmentation network from a union of such datasets. To this end, we propose two types of novel loss function, particularly designed for this scenario: (i) marginal loss and (ii) exclusion loss. Because the background label for a partially labeled image is, in fact, a `merged' lab…
Johns Hopkins University（约翰斯·霍普金斯大学）；Huazhong University of Science and Technology（华中科技大学）；Shanghai University（上海大学）；The Johns Hopkins University School of Medicine（约翰斯·霍普金斯大学医学院）
Deep convolutional neural networks (CNNs), especially fully convolutional networks, have been widely applied to automatic medical image segmentation problems, e.g., multi-organ segmentation. Existing CNN-based segmentation methods mainly focus on looking for increasingly powerful network architectures, but pay less attention to data sampling strategies for training networks more effectively. In this paper, we present a simple but effective sample selection method for training multi-organ segmentation networks. Sample selection exhibits an exploitation-exploration strategy, i.e., exploiting har…
Nuclei segmentation is a fundamental task that is critical for various computational pathology applications including nuclei morphology analysis, cell type classification, and cancer grading. Conventional vision-based methods for nuclei segmentation struggle in challenging cases and deep learning approaches have proven to be more robust and generalizable. However, CNNs require large amounts of labeled histopathology data. Moreover, conventional CNN-based approaches lack structured prediction capabilities which are required to distinguish overlapping and clumped nuclei. Here, we present an appr…
Chest X-ray (CXR) is one of the most commonly prescribed medical imaging procedures, often with over 2-10x more scans than other imaging modalities such as MRI, CT scan, and PET scans. These voluminous CXR scans place significant workloads on radiologists and medical practitioners. Organ segmentation is a crucial step to obtain effective computer-aided detection on CXR. In this work, we propose Structure Correcting Adversarial Network (SCAN) to segment lung fields and the heart in CXR images. SCAN incorporates a critic network to impose on the convolutional segmentation network the structural …
Nagoya University（名古屋大学）；Aichi Cancer Center Hospital（爱知县癌症中心医院）
Deep learning-based methods achieved impressive results for the segmentation of medical images. With the development of 3D fully convolutional networks (FCNs), it has become feasible to produce improved results for multi-organ segmentation of 3D computed tomography (CT) images. The results of multi-organ segmentation using deep learning-based methods not only depend on the choice of networks architecture, but also strongly rely on the choice of loss function. In this paper, we present a discussion on the influence of Dice-based loss functions for multi-class organ segmentation using a dataset …
New York University（纽约大学）；New York University Abu Dhabi（纽约大学阿布扎比分校）；Winship Cancer Institute of Emory University（埃默里大学温希普癌症研究所）
CT organ segmentation on computed tomography (CT) images becomes a significant brick for modern medical image analysis, supporting clinic workflows in multiple domains. Previous segmentation methods include 2D convolution neural networks (CNN) based approaches, fed by CT image slices that lack the structural knowledge in axial view, and 3D CNN-based methods with the expensive computation cost in multi-organ segmentation applications. This paper introduces an adversarial performance validation network into a 2D-to-3D segmentation framework. The classifier and performance validator competition c…
Automated abdominal multi-organ segmentation is a crucial yet challenging task in the computer-aided diagnosis of abdominal organ-related diseases. Although numerous deep learning models have achieved remarkable success in many medical image segmentation tasks, accurate segmentation of abdominal organs remains challenging, due to the varying sizes of abdominal organs and the ambiguous boundaries among them. In this paper, we propose a boundary-aware network (BA-Net) to segment abdominal organs on CT scans and MRI scans. This model contains a shared encoder, a boundary decoder, and a segmentati…
Accurate automatic organ segmentation is an important yet challenging problem for medical image analysis. The pancreas is an abdominal organ with very high anatomical variability. This inhibits traditional segmentation methods from achieving high accuracies, especially compared to other organs such as the liver, heart or kidneys. In this paper, we present a holistic learning approach that integrates semantic mid-level cues of deeply-learned organ interior and boundary maps via robust spatial aggregation using random forest. Our method generates boundary preserving pixel-wise class labels for p…
Simon Fraser University（西蒙弗雷泽大学）；Siemens Healthineers（西门子医疗）
Simultaneous segmentation of multiple organs from different medical imaging modalities is a crucial task as it can be utilized for computer-aided diagnosis, computer-assisted surgery, and therapy planning. Thanks to the recent advances in deep learning, several deep neural networks for medical image segmentation have been introduced successfully for this purpose. In this paper, we focus on learning a deep multi-organ segmentation network that labels voxels. In particular, we examine the critical choice of a loss function in order to handle the notorious imbalance problem that plagues both the …
Muroran Institute of Technology（室兰工业大学）；Niigata University of Health and Welfare（新潟医疗福祉大学）
To promote the development of medical image segmentation technology, AMOS, a large-scale abdominal multi-organ dataset for versatile medical image segmentation, is provided and AMOS 2022 challenge is held by using the dataset. In this report, we present our solution for the AMOS 2022 challenge. We employ residual U-Net with deep super vision as our base model. The experimental results show that the mean scores of Dice similarity coefficient and normalized surface dice are 0.8504 and 0.8476 for CT only task and CT/MRI task, respectively.
Université Côte d’Azur（蔚蓝海岸大学）；Inria（法国国家信息与自动化研究所）；Centre Antoine Lacassagne（安托万·拉卡桑中心）
Planning of radiotherapy involves accurate segmentation of a large number of organs at risk, i.e. organs for which irradiation doses should be minimized to avoid important side effects of the therapy. We propose a deep learning method for segmentation of organs at risk inside the brain region, from Magnetic Resonance (MR) images. Our system performs segmentation of eight structures: eye, lens, optic nerve, optic chiasm, pituitary gland, hippocampus, brainstem and brain. We propose an efficient algorithm to train neural networks for an end-to-end segmentation of multiple and non-exclusive class…
Multi-organ segmentation: a progressive exploration of learning paradigms under scarce annotation
School of Basic Medical Science, Fudan University（复旦大学基础医学院）；Digital Medical Research Center（数字医学研究中心）；Shanghai Key Lab of Medical Image Computing and Computer Assisted Intervention（上海市医学影像计算与计算机辅助介入重点实验室）
Accurate segmentation of multiple organs of the head, neck, chest, and abdomen from medical images is an essential step in computer-aided diagnosis, surgical navigation, and radiation therapy. In the past few years, with a data-driven feature extraction approach and end-to-end training, automatic deep learning-based multi-organ segmentation method has far outperformed traditional methods and become a new research topic. This review systematically summarizes the latest research in this field. For the first time, from the perspective of full and imperfect annotation, we comprehensively compile 1…
Automatic segmentation of organs-at-risk (OAR) in computed tomography (CT) is an essential part of planning effective treatment strategies to combat lung and esophageal cancer. Accurate segmentation of organs surrounding tumours helps account for the variation in position and morphology inherent across patients, thereby facilitating adaptive and computer-assisted radiotherapy. Although manual delineation of OARs is still highly prevalent, it is prone to errors due to complex variations in the shape and position of organs across patients, and low soft tissue contrast between neighbouring organs…
UMIT – Private University for Health Sciences, Medical Informatics and Technology（UMIT——健康科学、医学信息学与技术私立大学）
The segmentation of organs at risk (OAR) is a required precondition for the cancer treatment with image guided radiation therapy. The automation of the segmentation task is therefore of high clinical relevance. Deep Learning (DL) based medical image segmentation is currently the most successful approach, but suffers from the over-presence of the background class and the anatomically given organ size difference, which is most severe in the head and neck (HAN) area. To tackle the HAN area specific class imbalance problem we first optimize the patch-size of the currently best performing general p…
School of Electronic and Information Engineering, South China University of Technology（华南理工大学电子与信息学院）；Sun Yat-sen University Cancer Center（中山大学肿瘤防治中心）
Nasopharyngeal carcinoma (NPC) is a kind of malignant tumor. Accurate and automatic segmentation of organs at risk (OAR) of computed tomography (CT) images is clinically significant. In recent years, deep learning models represented by U-Net have been widely applied in medical image segmentation tasks, which can help doctors with reduction of workload and get accurate results more quickly. In OAR segmentation of NPC, the sizes of OAR are variable, especially, some of them are small. Traditional deep neural networks underperform during segmentation due to the lack use of global and multi-size i…
Memorial Sloan Kettering Cancer Center（纪念斯隆-凯特琳癌症中心）
Our contribution is a unified cross-modality feature disentagling approach for multi-domain image translation and multiple organ segmentation. Using CT as the labeled source domain, our approach learns to segment multi-modal (T1-weighted and T2-weighted) MRI having no labeled data. Our approach uses a variational auto-encoder (VAE) to disentangle the image content from style. The VAE constrains the style feature encoding to match a universal prior (Gaussian) that is assumed to span the styles of all the source and target modalities. The extracted image style is converted into a latent style sc…
PromptForSegCXR: Prompt-Driven Multi-Organ and Multi-Disease Segmentation in Chest X-rays using a Multi-stage Fusion Mechanism
1 ,5Department of Computer Science \& Engineering,\ University of Engineering \& Technology, Rajshahi-6204, Bangladesh；2 Department of Electrical；Electronic Engineering,\ University of Engineering；Bachelor of Surgery,\ Suhrawardy Medical College , Sher-E-Bangla Nagar, Dhaka-1207；6 Department of Biomedical Engineering,\ University of Engineering
University of California Irvine（加州大学尔湾分校）；School of Medicine（医学院）；Shanghai Jiao Tong University（上海交通大学）
Multi-organ segmentation is one of most successful applications of deep learning in medical image analysis. Deep convolutional neural nets (CNNs) have shown great promise in achieving clinically applicable image segmentation performance on CT or MRI images. State-of-the-art CNN segmentation models apply either 2D or 3D convolutions on input images, with pros and cons associated with each method: 2D convolution is fast, less memory-intensive but inadequate for extracting 3D contextual information from volumetric images, while the opposite is true for 3D convolution. To fit a 3D CNN model on CT …
Duke University School of Medicine（杜克大学医学院）；Duke University（杜克大学）；Universitat de Girona（赫罗纳大学）；Université de Bourgogne（勃艮第大学）；Università degli studi di Cassino（卡西诺大学）
Organ segmentation of medical images is a key step in virtual imaging trials. However, organ segmentation datasets are limited in terms of quality (because labels cover only a few organs) and quantity (since case numbers are limited). In this study, we explored the tradeoffs between quality and quantity. Our goal is to create a unified approach for multi-organ segmentation of body CT, which will facilitate the creation of large numbers of accurate virtual phantoms. Initially, we compared two segmentation architectures, 3D-Unet and DenseVNet, which were trained using XCAT data that is fully lab…
The University of Hong Kong（香港大学）；Shenzhen Research Institute of Big Data, The Chinese University of Hong Kong (Shenzhen)（香港中文大学（深圳）深圳大数据研究院）；Longgang Central Hospital of Shenzhen（深圳龙岗中心医院）；Longgang People Hospital of Shenzhen（深圳龙岗人民医院）
Despite the considerable progress in automatic abdominal multi-organ segmentation from CT/MRI scans in recent years, a comprehensive evaluation of the models' capabilities is hampered by the lack of a large-scale benchmark from diverse clinical scenarios. Constraint by the high cost of collecting and labeling 3D medical data, most of the deep learning models to date are driven by datasets with a limited number of organs of interest or samples, which still limits the power of modern deep models and makes it difficult to provide a fully comprehensive and fair estimate of various methods. To miti…
SRPR-Net: Semantic and Relational Prompt Refinement for Automated SAM-based Instance Segmentation
Ruijin-XJTLU Intelligent Medicine Institute, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine（瑞金-西交利物浦智能医学研究所，瑞金医院，上海交通大学医学院）；School of Biomedical Engineering, Shanghai Jiao Tong University（上海交通大学生物医学工程学院）
This paper presents a novel framework to integrate both semantic and instance contexts for panoptic segmentation. In existing works, it is common to use a shared backbone to extract features for both things (countable classes such as vehicles) and stuff (uncountable classes such as roads). This, however, fails to capture the rich relations among them, which can be utilized to enhance visual understanding and segmentation performance. To address this shortcoming, we propose a novel Panoptic, Instance, and Semantic Relations (PISR) module to exploit such contexts. First, we generate panoptic enc…
Institute of Computing Technology, Chinese Academy of Sciences（中国科学院计算技术研究所）；University of Chinese Academy of Sciences（中国科学院大学）；Horizon Robotics（地平线机器人）；Wuhan University（武汉大学）
Current Knowledge Distillation (KD) methods for semantic segmentation often guide the student to mimic the teacher's structured information generated from individual data samples. However, they ignore the global semantic relations among pixels across various images that are valuable for KD. This paper proposes a novel Cross-Image Relational KD (CIRKD), which focuses on transferring structured pixel-to-pixel and pixel-to-region relations among the whole images. The motivation is that a good teacher network could construct a well-structured feature space in terms of global pixel dependencies. CI…
Displacement Preserving Relational Distillation for Robust Medical Segmentation
Bowling Green State University（鲍灵格林州立大学）；The University of Findlay（芬德利大学）；University of Alabama at Birmingham（阿拉巴马大学伯明翰分校）；University of Toronto（多伦多大学）；University of Houston - Clear Lake（休斯顿大学清水湖分校）；UTHealth Houston（德克萨斯大学健康科学中心休斯顿分校）
Ludwig Maximilians University（路德维希-马克西米利安大学）；Technical University Munich（慕尼黑工业大学）
The wide range of research in deep learning-based medical image segmentation pushed the boundaries in a multitude of applications. A clinically relevant problem that received less attention is the handling of scans with irregular anatomy, e.g., after organ resection. State-of-the-art segmentation models often lead to organ hallucinations, i.e., false-positive predictions of organs, which cannot be alleviated by oversampling or post-processing. Motivated by the increasing need to develop robust deep learning models, we propose HALOS for abdominal organ segmentation in MR images that handles cas…
Mila - Québec AI Institute（米拉-魁北克人工智能研究所）；Meta AI (FAIR)（Meta人工智能（基础人工智能研究团队））；Shanghai Jiao Tong University（上海交通大学）；Université de Montréal（蒙特利尔大学）；HEC Montréal（蒙特利尔高等商学院）
Modeling spatial relationship in the data remains critical across many different tasks, such as image classification, semantic segmentation and protein structure understanding. Previous works often use a unified solution like relative positional encoding. However, there exists different kinds of spatial relations, including short-range, medium-range and long-range relations, and modeling them separately can better capture the focus of different tasks on the multi-range relations (e.g., short-range relations can be important in instance segmentation, while long-range relations should be upweigh…
Can We Go Beyond Visual Features? Neural Tissue Relation Modeling for Relational Graph Analysis in Non-Melanoma Skin Histology
Mohamed bin Zayed University of AI（Mohamed bin Zayed人工智能大学）；School of Information and Data Sciences（信息与数据科学学院）；Vellore Institute of Technology（维洛雷理工学院）；Loughborough University（洛桑大学）；MD Anderson Cancer Center, The University of Texas（MD安德森癌症中心，德克萨斯大学）
Temporal relational modeling in video is essential for human action understanding, such as action recognition and action segmentation. Although Graph Convolution Networks (GCNs) have shown promising advantages in relation reasoning on many tasks, it is still a challenge to apply graph convolution networks on long video sequences effectively. The main reason is that large number of nodes (i.e., video frames) makes GCNs hard to capture and model temporal relations in videos. To tackle this problem, in this paper, we introduce an effective GCN module, Dilated Temporal Graph Reasoning Module (DTGR…
Cooperative Medianet Innovation Center, Shanghai Jiao Tong University（上海交通大学媒体网络协同创新中心）
Annotating multiple organs in 3D medical images is time-consuming and costly. Meanwhile, there exist many single-organ datasets with one specific organ annotated. This paper investigates how to learn a multi-organ segmentation model leveraging a set of binary-labeled datasets. A novel Multi-teacher Single-student Knowledge Distillation (MS-KD) framework is proposed, where the teacher models are pre-trained single-organ segmentation networks, and the student model is a multi-organ segmentation network. Considering that each teacher focuses on different organs, a region-based supervision method,…
Beijing UCAS Space Technology Co., Ltd.（北京国科大空间技术有限公司）；University of Science and Technology of China（中国科学技术大学）；Institute of Computing Technology, CAS（中国科学院计算技术研究所）
Objective and Impact Statement: Accurate organ segmentation is critical for many clinical applications at different clinical sites, which may have their specific application requirements that concern different organs. Introduction: However, learning high-quality, site-specific organ segmentation models is challenging as it often needs on-site curation of a large number of annotated images. Security concerns further complicate the matter. Methods: The paper aims to tackle these challenges via a two-phase aggregation-then-adaptation approach. The first phase of federated aggregation learns a sin…
InferLink Corporation（InferLink公司）；Fred Hutch Cancer Research Center（弗雷德·哈钦森癌症研究中心）
The analysis of animal cross section images, such as cross sections of laboratory mice, is critical in assessing the effect of experimental drugs such as the biodistribution of candidate compounds in preclinical drug development stage. Tissue distribution of radiolabeled candidate therapeutic compounds can be quantified using techniques like Quantitative Whole-Body Autoradiography (QWBA).QWBA relies, among other aspects, on the accurate segmentation or identification of key organs of interest in the animal cross section image such as the brain, spine, heart, liver and others. We present a deep…
Deep Mutual Learning among Partially Labeled Datasets for Multi-Organ Segmentation
Digital Medical Research Center, School of Basic Medical Science, Fudan University（复旦大学基础医学院数字医学研究中心）；Shanghai Key Lab of Medical Image Computing and Computer Assisted Intervention（上海市医学影像计算与计算机辅助介入重点实验室）
IME-USP（圣保罗大学数学与统计研究所）；University of São Paulo（圣保罗大学）；Methodist University of Piracicaba（皮拉西卡巴卫理公会大学）；UNIMEP（皮拉西卡巴卫理公会大学）；Ecole Nationale Supérieure des Télécommunications（国立高等电信学院）
This paper proposes a novel algorithm for the problem of structural image segmentation through an interactive model-based approach. Interaction is expressed in the model creation, which is done according to user traces drawn over a given input image. Both model and input are then represented by means of attributed relational graphs derived on the fly. Appearance features are taken into account as object attributes and structural properties are expressed as relational attributes. To cope with possible topological differences between both graphs, a new structure called the deformation graph is i…
Most existing approaches to train a unified multi-organ segmentation model from several single-organ datasets require simultaneously access multiple datasets during training. In the real scenarios, due to privacy and ethics concerns, the training data of the organs of interest may not be publicly available. To this end, we investigate a data-free incremental organ segmentation scenario and propose a novel incremental training framework to solve it. We use the pretrained model instead of its own training data for privacy protection. Specifically, given a pretrained $K$ organ segmentation model …
