WORD: A large scale dataset, benchmark and clinical applicable study for abdominal organ segmentation from CT image
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）；Sichuan Cancer Hospital and Institute（四川省肿瘤医院（四川省肿瘤研究所））；Sichuan Cancer Center（四川省癌症中心）；Sichuan University（四川大学）；West China Hospital（华西医院）；Johns Hopkins University（约翰斯·霍普金斯大学）；SenseTime Research（商汤科技研究院）；Rutgers University（罗格斯大学）
Xiangde Luo, Wenjun Liao, Jianghong Xiao, Jieneng Chen, Tao Song, Xiaofan Zhang, Kang Li, Dimitris N. Metaxas, Guotai Wang, Shaoting Zhang
备注：
Accepted to Medical Image Analysis, dataset at: https://github.com/HiLab-git/WORD (we corrected the results or description in this version.)
Whole abdominal organ segmentation is important in diagnosing abdomen lesions, radiotherapy, and follow-up. However, oncologists' delineating all abdominal organs from 3D volumes is time-consuming and very expensive. Deep learning-based medical image segmentation has shown the potential to reduce manual delineation efforts, but it still requires a large-scale fine annotated dataset for training, and there is a lack of large-scale datasets covering the whole abdomen region with accurate and detailed annotations for the whole abdominal organ segmentation. In this work, we establish a new large-scale \textit{W}hole abdominal \textit{OR}gan \textit{D}ataset (\textit{WORD}) for algorithm research and clinical application development. This dataset contains 150 abdominal CT volumes (30495 slices). Each volume has 16 organs with fine pixel-level annotations and scribble-based sparse annotations, which may be the largest dataset with whole abdominal organ annotation. Several state-of-the-art segmentation methods are evaluated on this dataset. And we also invited three experienced oncologists to revise the model predictions to measure the gap between the deep learning method and oncologists. Afterwards, we investigate the inference-efficient learning on the WORD, as the high-resolution image requires large GPU memory and a long inference time in the test stage. We further evaluate the scribble-based annotation-efficient learning on this dataset, as the pixel-wise manual annotation is time-consuming and expensive. The work provided a new benchmark for the abdominal multi-organ segmentation task, and these experiments can serve as the baseline for future research and clinical application development.
Armed Forces Yangju Hospital（杨州武装部队医院）；Seoul National University（首尔国立大学）
For more clinical applications of deep learning models for medical image segmentation, high demands on labeled data and computational resources must be addressed. This study proposes a coarse-to-fine framework with two teacher models and a student model that combines knowledge distillation and cross teaching, a consistency regularization based on pseudo-labels, for efficient semi-supervised learning. The proposed method is demonstrated on the abdominal multi-organ segmentation task in CT images under the MICCAI FLARE 2022 challenge, with mean Dice scores of 0.8429 and 0.8520 in the validation …
State of Abdominal CT Datasets: A Critical Review of Bias, Clinical Relevance, and Real-world Applicability
Data Science and Machine Learning Lab (DML), Department of Computer Engineering, Sharif University of Technology（数据科学与机器学习实验室（DML），计算机工程系，谢里夫大学）；Data-Driven and Digital Health (D3M), The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai（数据驱动与数字健康（D3M），查尔斯·布朗弗曼个性化医学研究所，辛辛那提医学院）；Shahid Beheshti University of Medical Sciences（沙希德·贝赫什提医学科学大学）；Tehran University of Medical Sciences Cancer Research Institute（德黑兰医学院医学科学癌症研究所）
The Chinese University of Hong Kong（香港中文大学）；University of Leicester（莱斯特大学）
Domain adaptation is crucial for transferring the knowledge from the source labeled CT dataset to the target unlabeled MR dataset in abdominal multi-organ segmentation. Meanwhile, it is highly desirable to avoid the high annotation cost related to the target dataset and protect the source dataset privacy. Therefore, we propose an effective source-free unsupervised domain adaptation method for cross-modality abdominal multi-organ segmentation without source dataset access. The proposed framework comprises two stages. In the first stage, the feature map statistics-guided model adaptation combine…
Nanjing University of Science and Technology（南京理工大学）；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）；Lenovo Research（联想研究院）；Nanjing University of Information Science and Technology（南京信息工程大学）；Shenzhen Haichuang Medical CO., LTD.（深圳海创医疗有限公司）；Jiangsu University of Technology（江苏理工学院）；Beihang University（北京航空航天大学）；Beijing Infervision Technology CO. LTD.（北京推想科技有限公司）；Tianjin University of Technology（天津理工大学）；Norwegian University of Science and Technology（挪威科技大学）；Nanjing University（南京大学）；Suzhou LungCare Medical Technology Co., Ltd（苏州朗润医疗科技有限公司）；King Abdullah University of Science and Technology（阿卜杜拉国王科技大学）
With the unprecedented developments in deep learning, automatic segmentation of main abdominal organs seems to be a solved problem as state-of-the-art (SOTA) methods have achieved comparable results with inter-rater variability on many benchmark datasets. However, most of the existing abdominal datasets only contain single-center, single-phase, single-vendor, or single-disease cases, and it is unclear whether the excellent performance can generalize on diverse datasets. This paper presents a large and diverse abdominal CT organ segmentation dataset, termed AbdomenCT-1K, with more than 1000 (1K…
A Multi-Center Benchmark for Abdominal Disease Diagnosis and Report Generation from Non-Contrast CT
Ain Shams University（艾因夏姆斯大学）；The Hong Kong University of Science and Technology（香港科技大学）；University of Catania（卡塔尼亚大学）；Universitat de Barcelona（巴塞罗那大学）
Human body is a complex dynamic system composed of various sub-dynamic parts. Especially, thoracic and abdominal organs have complex internal shape variations with different frequencies by various reasons such as respiration with fast motion and peristalsis with slower motion. CT protocols for abdominal lesions are multi-phase scans for various tumor detection to use different vascular contrast, however, they are not aligned well enough to visually check the same area. In this paper, we propose a time-efficient and accurate deformable registration algorithm for multi-phase CT scans considering…
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…
CT-IDP: Segmentation-Derived Quantitative Phenotypes for Interpretable Abdominal CT Disease Classification
Center for Virtual Imaging Trials, Carl E. Ravin Advanced Imaging Laboratories（虚拟成像试验中心，卡尔·E·拉文先进成像实验室）；Department of Radiology, Duke University School of Medicine（杜克大学医学学院放射科）；Electrical and Computer Engineering, Pratt School of Engineering, Duke University（杜克大学普拉特工程学院电气与计算机工程系）；Medical Physics Graduate Program, Duke University（杜克大学医学物理研究生项目）
Deformable registration of two-dimensional/three-dimensional (2D/3D) images of abdominal organs is a complicated task because the abdominal organs deform significantly and their contours are not detected in two-dimensional X-ray images. We propose a supervised deep learning framework that achieves 2D/3D deformable image registration between 3D volumes and single-viewpoint 2D projected images. The proposed method learns the translation from the target 2D projection images and the initial 3D volume to 3D displacement fields. In experiments, we registered 3D-computed tomography (CT) volumes to di…
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.
Accurate and robust abdominal multi-organ segmentation from CT imaging of different modalities is a challenging task due to complex inter- and intra-organ shape and appearance variations among abdominal organs. In this paper, we propose a probabilistic multi-organ segmentation network with hierarchical spatial-wise feature modulation to capture flexible organ semantic variants and inject the learnt variants into different scales of feature maps for guiding segmentation. More specifically, we design an input decomposition module via a conditional variational auto-encoder to learn organ-specific…
Fosun Aitrox Information Technology Co LTD（复星艾特罗克斯信息技术有限公司）
The contextual information, presented in abdominal CT scan, is relative consistent. In order to make full use of the overall 3D context, we develop a whole-volume-based coarse-to-fine framework for efficient and effective abdominal multi-organ segmentation. We propose a new efficientSegNet network, which is composed of basic encoder, slim decoder and efficient context block. For the decoder module, anisotropic convolution with a k*k*1 intra-slice convolution and a 1*1*k inter-slice convolution, is designed to reduce the computation burden. For the context block, we propose strip pooling module…
Swinburne University of Technology（斯威本科技大学）；Victoria University（维多利亚大学）；Kyung Hee University（庆熙大学）
Quantitative assessment of the abdominal region from clinically acquired CT scans requires the simultaneous segmentation of abdominal organs. Thanks to the availability of high-performance computational resources, deep learning-based methods have resulted in state-of-the-art performance for the segmentation of 3D abdominal CT scans. However, the complex characterization of organs with fuzzy boundaries prevents the deep learning methods from accurately segmenting these anatomical organs. Specifically, the voxels on the boundary of organs are more vulnerable to misprediction due to the highly-va…
DeepAAA: clinically applicable and generalizable detection of abdominal aortic aneurysm using deep learning
Nuance Communications Inc.（Nuance通信公司）；MGH and BWH Center for Clinical Data Science（麻省总医院与布莱根妇女医院临床数据科学中心）；Brigham and Women’s Hospital (BWH)（布莱根妇女医院）；Massachusetts General Hospital (MGH)（麻省总医院）
The University of Manchester（曼彻斯特大学）；The Christie NHS Foundation Trust（克里斯蒂NHS基金会信托）
Abdominal organ segmentation is a difficult and time-consuming task. To reduce the burden on clinical experts, fully-automated methods are highly desirable. Current approaches are dominated by Convolutional Neural Networks (CNNs) however the computational requirements and the need for large data sets limit their application in practice. By implementing a small and efficient custom 3D CNN, compiling the trained model and optimizing the computational graph: our approach produces high accuracy segmentations (Dice Similarity Coefficient (%): Liver: 97.3$\pm$1.3, Kidneys: 94.8$\pm$3.6, Spleen: 96.4…
A two-step concept for 3D segmentation on 5 abdominal organs inside volumetric CT images is presented. First each relevant organ's volume of interest is extracted as bounding box. The extracted volume acts as input for a second stage, wherein two compared U-Nets with different architectural dimensions re-construct an organ segmentation as label mask. In this work, we focus on comparing 2D U-Nets vs. 3D U-Net counterparts. Our initial results indicate Dice improvements of about 6\% at maximum. In this study to our surprise, liver and kidneys for instance were tackled significantly better using …
Devil is in Details: Locality-Aware 3D Abdominal CT Volume Generation for Self-Supervised Organ Segmentation
National Engineering Research Center for Multimedia Software（多媒体软件国家工程研究中心）；Hubei Key Laboratory of Multimedia and Network Communication Engineering（湖北省多媒体与网络通信工程重点实验室）；Institute of Artificial Intelligence（人工智能研究院）；School of Computer Science（计算机科学学院）
Dokuz Eylul University（多库兹·埃吕尔大学）；Ca’ Foscari University of Venice（威尼斯大学）；Ege University（爱琴海大学）；IMT Atlantique（大西洋国立高等工业技术学院）；Median Technologies（Median科技公司）；University of Duisburg-Essen（杜伊斯堡-埃森大学）；Otto von Guericke University（奥托·冯·格里克大学）；Middle East Technical University（中东技术大学）；Johns Hopkins University（约翰斯·霍普金斯大学）
Segmentation of abdominal organs has been a comprehensive, yet unresolved, research field for many years. In the last decade, intensive developments in deep learning (DL) have introduced new state-of-the-art segmentation systems. In order to expand the knowledge on these topics, the CHAOS - Combined (CT-MR) Healthy Abdominal Organ Segmentation challenge has been organized in conjunction with IEEE International Symposium on Biomedical Imaging (ISBI), 2019, in Venice, Italy. CHAOS provides both abdominal CT and MR data from healthy subjects for single and multiple abdominal organ segmentation. F…
MRISegmentator-Abdomen: A Fully Automated Multi-Organ and Structure Segmentation Tool for T1-weighted Abdominal MRI
Radiology and Imaging Sciences（放射学与影像科学）；National Institutes of Health Clinical Center（国家卫生研究院临床中心）；Walter Reed National Military Medical Center（沃尔特·里德国家军事医学中心）；Biostatistics and Clinical Epidemiology Services（生物统计与临床流行病学服务）
Large curated datasets are necessary, but annotating medical images is a time-consuming, laborious, and expensive process. Therefore, recent supervised methods are focusing on utilizing a large amount of unlabeled data. However, to do so, is a challenging task. To address this problem, we propose a new 3D Cross-Pseudo Supervision (3D-CPS) method, a semi-supervised network architecture based on nnU-Net with the Cross-Pseudo Supervision method. We design a new nnU-Net based preprocessing. In addition, we set the semi-supervised loss weights to expand linearity with each epoch to prevent the mode…
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…
Multi-planar 2D-U-Net Segmentation of 3D-CT Abdominal Organs augmented by Spatial Occurrence Maps
Glasgow Caledonian University School of Science & Engineering（格拉斯哥卡里多尼亚大学科学与工程学院）；Jade University of Applied Sciences Department of Engineering & Medical Technology（雅德应用科学大学工程与医疗技术系）
Dynamic U-Net: Adaptively Calibrate Features for Abdominal Multi-organ Segmentation
Washington University School of Medicine（华盛顿大学医学院）；Institute for Informatics, Data Science and Biostatistics, Washington University School of Medicine（华盛顿大学医学院信息学、数据科学与生物统计学研究所）
Fully Automated Multi-Organ Segmentation in Abdominal Magnetic Resonance Imaging with Deep Neural Networks
University of California, Los Angeles（加州大学洛杉矶分校）；Cedars-Sinai Medical Center（西达赛奈医疗中心）；Capital Medical University（首都医科大学）；Fujian Medical University Union Hospital（福建医科大学附属协和医院）；University of Southern California（南加州大学）
Vanderbilt University（范德堡大学）；Vanderbilt University Medical Center（范德堡大学医学中心）
Non-contrast computed tomography (NCCT) is commonly acquired for lung cancer screening, assessment of general abdominal pain or suspected renal stones, trauma evaluation, and many other indications. However, the absence of contrast limits distinguishing organ in-between boundaries. In this paper, we propose a novel unsupervised approach that leverages pairwise contrast-enhanced CT (CECT) context to compute non-contrast segmentation without ground-truth label. Unlike generative adversarial approaches, we compute the pairwise morphological context with CECT to provide teacher guidance instead of…
Vanderbilt University（范德堡大学）；Vanderbilt University Medical Center（范德堡大学医学中心）
Performing coarse-to-fine abdominal multi-organ segmentation facilitates to extract high-resolution segmentation minimizing the lost of spatial contextual information. However, current coarse-to-refine approaches require a significant number of models to perform single organ refine segmentation corresponding to the extracted organ region of interest (ROI). We propose a coarse-to-fine pipeline, which starts from the extraction of the global prior context of multiple organs from 3D volumes using a low-resolution coarse network, followed by a fine phase that uses a single refined model to segment…
College of Science and Engineering, James Cook University（詹姆斯·库克大学理工学院）；McGill University（麦吉尔大学）；Element AI（Element AI公司）；College of Healthcare Sciences, James Cook University（詹姆斯·库克大学健康科学学院）
Health professionals extensively use Two- Dimensional (2D) Ultrasound (US) videos and images to visualize and measure internal organs for various purposes including evaluation of muscle architectural changes. US images can be used to measure abdominal muscles dimensions for the diagnosis and creation of customized treatment plans for patients with Low Back Pain (LBP), however, they are difficult to interpret. Due to high variability, skilled professionals with specialized training are required to take measurements to avoid low intra-observer reliability. This variability stems from the challen…
Universal and Extensible Language-Vision Models for Organ Segmentation and Tumor Detection from Abdominal Computed Tomography
City University of Hong Kong（香港城市大学）；Johns Hopkins University（约翰斯·霍普金斯大学）；University of California, San Francisco（加州大学旧金山分校）；University of Illinois Urbana-Champaign（伊利诺伊大学厄巴纳-香槟分校）；Chinese University of Hong Kong（香港中文大学）；NVIDIA（英伟达）
Two-Stage Hybrid Supervision Framework for Fast, Low-resource, and Accurate Organ and Pan-cancer Segmentation in Abdomen CT
Beijing University of Posts and Telecommunications（北京邮电大学）；Dalian University of Technology（大连理工大学）；Guilin University of Electronic Technology（桂林电子科技大学）
AI-Driven Automated Tool for Abdominal CT Body Composition Analysis in Gastrointestinal Cancer Management
Peking University（北京大学）；Peking University Cancer Hospital and Institute（北京大学肿瘤医院暨肿瘤研究所）；Beijing International Center for Mathematical Research (BICMR), Peking University（北京大学北京国际数学研究中心）；Center for Machine Learning Research, Peking University（北京大学机器学习研究中心）；National Biomedical Imaging Center, Peking University（北京大学国家生物医学成像中心）
Accurate liver and lesion segmentation from computed tomography (CT) images are highly demanded in clinical practice for assisting the diagnosis and assessment of hepatic tumor disease. However, automatic liver and lesion segmentation from contrast-enhanced CT volumes is extremely challenging due to the diversity in contrast, resolution, and quality of images. Previous methods based on UNet for 2D slice-by-slice or 3D volume-by-volume segmentation either lack sufficient spatial contexts or suffer from high GPU computational cost, which limits the performance. To tackle these issues, we propose…
Self-supervised Recurrent Neural Network for 4D Abdominal and In-utero MR Imaging
School of Biomedical Engineering and Imaging Sciences, King’s College London（伦敦国王学院生物医学工程与成像科学学院）；Department of Women and Children’s Health, School of Life Course Sciences, King’s College London（伦敦国王学院生命历程科学学院妇幼健康系）
Robustness Evaluation of a Foundation Segmentation Model Under Simulated Domain Shifts in Abdominal CT: Implications for Health Digital Twin Deployment
Healthcare Informatics, University of Illinois Springfield（医疗信息学，伊利诺伊大学斯普林菲尔德分校）
Technical University of Munich（慕尼黑工业大学）；Sharif University of Technology（谢里夫理工大学）；Klinikum rechts der Isar（慕尼黑 Rechts der Isar 医院）；John Hopkins University（约翰·霍普金斯大学）
Abdominal aortic aneurysm (AAA) is a vascular disease in which a section of the aorta enlarges, weakening its walls and potentially rupturing the vessel. Abdominal ultrasound has been utilized for diagnostics, but due to its limited image quality and operator dependency, CT scans are usually required for monitoring and treatment planning. Recently, abdominal CT datasets have been successfully utilized to train deep neural networks for automatic aorta segmentation. Knowledge gathered from this solved task could therefore be leveraged to improve US segmentation for AAA diagnosis and monitoring. …
The manual ground truth of abdominal multi-organ is labor-intensive. In order to make full use of CT data, we developed a semi-supervised learning based dual-light UNet. In the training phase, it consists of two light UNets, which make full use of label and unlabeled data simultaneously by using consistent-based learning. Moreover, separable convolution and residual concatenation was introduced light UNet to reduce the computational cost. Further, a robust segmentation loss was applied to improve the performance. In the inference phase, only a light UNet is used, which required low time cost a…
