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 the faster and GPU-memory saving 2D U-Nets. For other abdominal key organs, there were no significant differences, but we observe highly significant advantages for the 2D U-Net in terms of GPU computational efforts for all organs under study.
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…
Objective : Abdominal anatomy segmentation is crucial for numerous applications from computer-assisted diagnosis to image-guided surgery. In this context, we address fully-automated multi-organ segmentation from abdominal CT and MR images using deep learning. Methods: The proposed model extends standard conditional generative adversarial networks. Additionally to the discriminator which enforces the model to create realistic organ delineations, it embeds cascaded partially pre-trained convolutional encoder-decoders as generator. Encoder fine-tuning from a large amount of non-medical images all…
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…
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…
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…
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 …
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）
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-s…
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…
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…
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…
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）
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）
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…
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…
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）
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）
Segmentation of multiple organs-at-risk (OARs) is essential for radiation therapy treatment planning and other clinical applications. We developed an Automated deep Learning-based Abdominal Multi-Organ segmentation (ALAMO) framework based on 2D U-net and a densely connected network structure with tailored design in data augmentation and training procedures such as deep connection, auxiliary supervision, and multi-view. The model takes in multi-slice MR images and generates the output of segmentation results. Three-Tesla T1 VIBE (Volumetric Interpolated Breath-hold Examination) images of 102 su…
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）
Accurately estimating and correcting the motion artifacts are crucial for 3D image reconstruction of the abdominal and in-utero magnetic resonance imaging (MRI). The state-of-art methods are based on slice-to-volume registration (SVR) where multiple 2D image stacks are acquired in three orthogonal orientations. In this work, we present a novel reconstruction pipeline that only needs one orientation of 2D MRI scans and can reconstruct the full high-resolution image without masking or registration steps. The framework consists of two main stages: the respiratory motion estimation using a self-su…
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…
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）
Vanderbilt University（范德堡大学）；Sigma Technologies（12西格玛科技公司）；Vanderbilt University Medical Center（范德堡大学医学中心）
Segmentation of abdominal computed tomography(CT) provides spatial context, morphological properties, and a framework for tissue-specific radiomics to guide quantitative Radiological assessment. A 2015 MICCAI challenge spurred substantial innovation in multi-organ abdominal CT segmentation with both traditional and deep learning methods. Recent innovations in deep methods have driven performance toward levels for which clinical translation is appealing. However, continued cross-validation on open datasets presents the risk of indirect knowledge contamination and could result in circular reason…
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…
Hankuk University of Foreign Studies（韩国外国语大学）；Seoul National University Bundang Hospital（首尔国立大学盆唐医院）
Acute appendicitis characterized by a painful inflammation of the vermiform appendix is one of the most common surgical emergencies. Localizing the appendix is challenging due to its unclear anatomy amidst the complex colon-structure as observed in the conventional CT views, resulting in a time-consuming diagnosis. End-to-end learning of a convolutional neural network (CNN) is also not likely to be useful because of the negligible size of the appendix compared with the abdominal CT volume. With no prior computational approaches to the best of our knowledge, we propose the first computerized au…
Osaka University Graduate School of Medicine（大阪大学医学研究生院）
Multi-organ segmentation enables organ evaluation, accounts the relationship between multiple organs, and facilitates accurate diagnosis and treatment decisions. However, only few models can perform segmentation accurately because of the lack of datasets and computational resources. On AMOS2022 challenge, which is a large-scale, clinical, and diverse abdominal multiorgan segmentation benchmark, we trained a 3D-UNet model with large batch and patch sizes using multi-GPU distributed training. Segmentation performance tended to increase for models with large batch and patch sizes compared with th…
The University of Hong Kong（香港大学）；Imperial College London（帝国理工学院）
Abdominal magnetic resonance imaging (MRI) provides a straightforward way of characterizing tissue and locating lesions of patients as in standard diagnosis. However, abdominal MRI often suffers from respiratory motion artifacts, which leads to blurring and ghosting that significantly deteriorate the imaging quality. Conventional methods to reduce or eliminate these motion artifacts include breath holding, patient sedation, respiratory gating, and image post-processing, but these strategies inevitably involve extra scanning time and patient discomfort. In this paper, we propose a novel deep-le…
CT Synthesis with Conditional Diffusion Models for Abdominal Lymph Node Segmentation
Shanghai Jiao Tong University, Shanghai, China（上海交通大学）；Department of Surgical Oncology and General Surgery, Key Laboratory of Precision Diagnosis and Treatment of Gastrointestinal Tumors, Ministry of Education, The First Hospital of China Medical University, Shenyang, China（外科肿瘤科和普通外科，精准诊断与治疗胃肠肿瘤国家重点实验室，教育部，中国医科大学第一附属医院，沈阳，中国）；Department of Radiology, The First Hospital of China Medical University, Shenyang, China（放射科，中国医科大学第一附属医院，沈阳，中国）；Shanghai AI Laboratory, Shanghai, China（上海人工智能实验室，上海，中国）
SINTEF（挪威科学与工业研究基金会）；Norwegian University of Science and Technology (NTNU)（挪威科技大学）；St. Olavs hospital, Trondheim University Hospital（圣奥拉夫医院，特隆赫姆大学医院）；Oslo University Hospital（奥斯陆大学医院）
Purpose: This study aims to explore training strategies to improve convolutional neural network-based image-to-image deformable registration for abdominal imaging. Methods: Different training strategies, loss functions, and transfer learning schemes were considered. Furthermore, an augmentation layer which generates artificial training image pairs on-the-fly was proposed, in addition to a loss layer that enables dynamic loss weighting. Results: Guiding registration using segmentations in the training step proved beneficial for deep-learning-based image registration. Finetuning the pretrained m…
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）
Electron density maps must be accurately estimated to achieve valid dose calculation in MR-only radiotherapy. The goal of this study is to assess whether two deep learning models, the conditional generative adversarial network (cGAN) and the cycle-consistent generative adversarial network (cycleGAN), can generate accurate abdominal synthetic CT (sCT) images from 0.35T MR images for MR-only liver radiotherapy. A retrospective study was performed using CT images and 0.35T MR images of 12 patients with liver (n=8) and non-liver abdominal (n=4) cancer. CT images were deformably registered to the c…
Sparsity of annotated data is a major limitation in medical image processing tasks such as registration. Registered multimodal image data are essential for the diagnosis of medical conditions and the success of interventional medical procedures. To overcome the shortage of data, we present a method that allows the generation of annotated multimodal 4D datasets. We use a CycleGAN network architecture to generate multimodal synthetic data from the 4D extended cardiac-torso (XCAT) phantom and real patient data. Organ masks are provided by the XCAT phantom, therefore the generated dataset can serv…
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…
Graduate School of Informatics, Kyoto University（京都大学信息学研究科）；Graduate School of Medicine, Kyoto University（京都大学医学研究科）
Organ shape reconstruction based on a single-projection image during treatment has wide clinical scope, e.g., in image-guided radiotherapy and surgical guidance. We propose an image-to-graph convolutional network that achieves deformable registration of a 3D organ mesh for a single-viewpoint 2D projection image. This framework enables simultaneous training of two types of transformation: from the 2D projection image to a displacement map, and from the sampled per-vertex feature to a 3D displacement that satisfies the geometrical constraint of the mesh structure. Assuming application to radiati…
MSWAL: 3D Multi-class Segmentation of Whole Abdominal Lesions Dataset
Shanghai AI Lab（上海人工智能实验室）；University of Liverpool（利物浦大学）；Columbia university（哥伦比亚大学）；Monash University（墨尔本大学）；Xi'an Jiaotong-Liverpool University（西安交通大学利物浦大学）；MBZUAI（穆斯林人工智能研究所）；People's Hospital of Gong'an County（公安县人民医院）
本文提出首个 3D 全腹部病变多类分割数据集 MSWAL，覆盖七类常见病变，并提出 Inception nnU-Net 框架，在分割性能上显著优于现有方法。
Emory University（埃默里大学）；Johns Hopkins University（约翰斯·霍普金斯大学）；Memorial Sloan Kettering Cancer Center（纪念斯隆·凯特琳癌症中心）
In this work, we propose an adversarial attack-based data augmentation method to improve the deep-learning-based segmentation algorithm for the delineation of Organs-At-Risk (OAR) in abdominal Computed Tomography (CT) to facilitate radiation therapy. We introduce Adversarial Feature Attack for Medical Image (AFA-MI) augmentation, which forces the segmentation network to learn out-of-distribution statistics and improve generalization and robustness to noises. AFA-MI augmentation consists of three steps: 1) generate adversarial noises by Fast Gradient Sign Method (FGSM) on the intermediate featu…
A Study of Anatomical Priors for Deep Learning-Based Segmentation of Pheochromocytoma in Abdominal CT
Imaging Biomarkers and Computer-Aided Diagnosis Laboratory（影像生物标记与计算机辅助诊断实验室）；Clinical Center, NIH（国家卫生研究院临床中心）；Eunice Kennedy Shriver National Institute of Child Health and Human Development, NIH（欧尼丝·凯蒂·施里弗国家儿童健康与人类发展研究所，国家卫生研究院）；National Cancer Institute, NIH（国家癌症研究所，国家卫生研究院）；National Institute of Diabetes and Digestive and Kidney Diseases, NIH（国家糖尿病、消化系统与肾病研究所，国家卫生研究院）
