CrossMoDA 2021 challenge: Benchmark of Cross-Modality Domain Adaptation techniques for Vestibular Schwannoma and Cochlea Segmentation
King’s College London（伦敦国王学院）；University of Pennsylvania（宾夕法尼亚大学）；NVIDIA（英伟达）；Imperial College London（伦敦帝国理工学院）
Reuben Dorent, Aaron Kujawa, Marina Ivory, Spyridon Bakas, Nicola Rieke, Samuel Joutard, Ben Glocker, Jorge Cardoso, Marc Modat, Kayhan Batmanghelich, Arseniy B… 展开作者
Reuben Dorent, Aaron Kujawa, Marina Ivory, Spyridon Bakas, Nicola Rieke, Samuel Joutard, Ben Glocker, Jorge Cardoso, Marc Modat, Kayhan Batmanghelich, Arseniy Belkov, Maria Baldeon Calisto, Jae Won Choi, Benoit M. Dawant, Hexin Dong, Sergio Escalera, Yubo Fan, Lasse Hansen, Mattias P. Heinrich, Smriti Joshi, Victoriya Kashtanova, Hyeon Gyu Kim, Satoshi Kondo, Christian N. Kruse, Susana K. Lai-Yuen, Hao Li, Han Liu, Buntheng Ly, Ipek Oguz, Hyungseob Shin, Boris Shirokikh, Zixian Su, Guotai Wang, Jianghao Wu, Yanwu Xu, Kai Yao, Li Zhang, Sebastien Ourselin, Jonathan Shapey, Tom Vercauteren
Domain Adaptation (DA) has recently raised strong interests in the medical imaging community. While a large variety of DA techniques has been proposed for image segmentation, most of these techniques have been validated either on private datasets or on small publicly available datasets. Moreover, these datasets mostly addressed single-class problems. To tackle these limitations, the Cross-Modality Domain Adaptation (crossMoDA) challenge was organised in conjunction with the 24th International Conference on Medical Image Computing and Computer Assisted Intervention (MICCAI 2021). CrossMoDA is the first large and multi-class benchmark for unsupervised cross-modality DA. The challenge's goal is to segment two key brain structures involved in the follow-up and treatment planning of vestibular schwannoma (VS): the VS and the cochleas. Currently, the diagnosis and surveillance in patients with VS are performed using contrast-enhanced T1 (ceT1) MRI. However, there is growing interest in using non-contrast sequences such as high-resolution T2 (hrT2) MRI. Therefore, we created an unsupervised cross-modality segmentation benchmark. The training set provides annotated ceT1 (N=105) and unpaired non-annotated hrT2 (N=105). The aim was to automatically perform unilateral VS and bilateral cochlea segmentation on hrT2 as provided in the testing set (N=137). A total of 16 teams submitted their algorithm for the evaluation phase. The level of performance reached by the top-performing teams is strikingly high (best median Dice - VS:88.4%; Cochleas:85.7%) and close to full supervision (median Dice - VS:92.5%; Cochleas:87.7%). All top-performing methods made use of an image-to-image translation approach to transform the source-domain images into pseudo-target-domain images. A segmentation network was then trained using these generated images and the manual annotations provided for the source image.
Automatic methods to segment the vestibular schwannoma (VS) tumors and the cochlea from magnetic resonance imaging (MRI) are critical to VS treatment planning. Although supervised methods have achieved satisfactory performance in VS segmentation, they require full annotations by experts, which is laborious and time-consuming. In this work, we aim to tackle the VS and cochlea segmentation problem in an unsupervised domain adaptation setting. Our proposed method leverages both the image-level domain alignment to minimize the domain divergence and semi-supervised training to further boost the per…
Magnetic resonance images (MRIs) are widely used to quantify vestibular schwannoma and the cochlea. Recently, deep learning methods have shown state-of-the-art performance for segmenting these structures. However, training segmentation models may require manual labels in target domain, which is expensive and time-consuming. To overcome this problem, domain adaptation is an effective way to leverage information from source domain to obtain accurate segmentations without requiring manual labels in target domain. In this paper, we propose an unsupervised learning framework to segment the VS and c…
School of Information Science and Technology, ShanghaiTech University（上海科技大学信息科学与技术学院）；College of Computer Science, Sichuan University（四川大学计算机学院）；Shanghai Engineering Research Center of Intelligent Vision and Imaging（上海智能视觉与成像工程技术研究中心）；Institute of High Performance Computing (IHPC), Agency for Science, Technology and Research (A*STAR)（新加坡科技研究局高性能计算研究所）
Mohamed bin Zayed University of Artificial Intelligence（穆罕默德·本·扎耶德人工智能大学）
Vestibular schwannoma (VS) is a non-cancerous tumor located next to the ear that can cause hearing loss. Most brain MRI images acquired from patients are contrast-enhanced T1 (ceT1), with a growing interest in high-resolution T2 images (hrT2) to replace ceT1, which involves the use of a contrast agent. As hrT2 images are currently scarce, it is less likely to train robust machine learning models to segment VS or other brain structures. In this work, we propose a weakly supervised machine learning approach that learns from only ceT1 scans and adapts to segment two structures from hrT2 scans: th…
With the advances of deep learning, many medical image segmentation studies achieve human-level performance when in fully supervised condition. However, it is extremely expensive to acquire annotation on every data in medical fields, especially on magnetic resonance images (MRI) that comprise many different contrasts. Unsupervised methods can alleviate this problem; however, the performance drop is inevitable compared to fully supervised methods. In this work, we propose a self-training based unsupervised-learning framework that performs automatic segmentation of Vestibular Schwannoma (VS) and…
Automatic segmentation of vestibular schwannoma (VS) and cochlea from magnetic resonance imaging can facilitate VS treatment planning. Unsupervised segmentation methods have shown promising results without requiring the time-consuming and laborious manual labeling process. In this paper, we present an approach for VS and cochlea segmentation in an unsupervised domain adaptation setting. Specifically, we first develop a cross-site cross-modality unpaired image translation strategy to enrich the diversity of the synthesized data. Then, we devise a rule-based offline augmentation technique to fur…
Radboud University Medical Center（拉德堡德大学医学中心）；The Netherlands Cancer Institute（荷兰癌症研究所）；Nanjing University of Information Science and Technology（南京信息工程大学）
Domain adaptation has been widely adopted to transfer styles across multi-vendors and multi-centers, as well as to complement the missing modalities. In this challenge, we proposed an unsupervised domain adaptation framework for cross-modality vestibular schwannoma (VS) and cochlea segmentation and Koos grade prediction. We learn the shared representation from both ceT1 and hrT2 images and recover another modality from the latent representation, and we also utilize proxy tasks of VS segmentation and brain parcellation to restrict the consistency of image structures in domain adaptation. After …
Automatic methods to segment the vestibular schwannoma (VS) tumors and the cochlea from magnetic resonance imaging (MRI) are critical to VS treatment planning. Although supervised methods have achieved satisfactory performance in VS segmentation, they require full annotations by experts, which is laborious and time-consuming. In this work, we aim to tackle the VS and cochlea segmentation problem in an unsupervised domain adaptation setting. Our proposed method leverages both the image-level domain alignment to minimize the domain divergence and semi-supervised training to further boost the per…
The Koos grading scale is a classification system for vestibular schwannoma (VS) used to characterize the tumor and its effects on adjacent brain structures. The Koos classification captures many of the characteristics of treatment deci-sions and is often used to determine treatment plans. Although both contrast-enhanced T1 (ceT1) scanning and high-resolution T2 (hrT2) scanning can be used for Koos Classification, hrT2 scanning is gaining interest because of its higher safety and cost-effectiveness. However, in the absence of annotations for hrT2 scans, deep learning methods often inevitably s…
Longitudinal Vestibular Schwannoma Dataset with Consensus-based Human-in-the-loop Annotations
School of Biomedical Engineering and Imaging Sciences, King’s College London（生物医学工程与成像科学学院，伦敦国王学院）；King’s College Hospital NHS Foundation Trust（伦敦国王学院医院国家健康服务信托基金）；The Walton Centre NHS Foundation Trust（沃尔顿中心国家健康服务信托基金）
crossMoDA Challenge: Evolution of Cross-Modality Domain Adaptation Techniques for Vestibular Schwannoma and Cochlea Segmentation from 2021 to 2023
School of BMEIS, King's College London, London, United Kingdom（伦敦国王学院生物医学工程与信息科学学院）；Harvard University, USA（哈佛大学）；Elisabeth-TweeSteden Hospital, Tilburg, Netherlands（蒂尔堡埃利斯贝特-特维德登医院）；King's College Hospital, London, United Kingdom（伦敦国王学院医院）；Center for Data Science, Peking University, Beijing, China（北京大学数据科学中心）；Center for Data Science in Health and Medicine, Peking University, Beijing, China（北京大学健康与医学数据科学中心）；Department of Artificial Intelligence, Korea University, Seoul, Republic of Korea（韩国大学人工智能系）；Department of Radiology and Nuclear Medicine, Radboud University Medical Center, Geert Grooteplein 10, 6525 GA, Nijmegen, The Netherlands（拉德堡德大学医学中心放射科与核医学科）；Department of Radiology, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX, Amsterdam, The Netherlands（荷兰癌症研究所放射科）；Nanyang Technological University, Singapore（南洋理工大学）；Vanderbilt University, USA（范德比尔特大学）；Department of Automation, Shanghai Jiao Tong University, Shanghai, China（上海交通大学自动化系）；Mohamed bin Zayed University of Artificial Intelligence, Abu Dhabi, UAE（阿布扎克穆罕默德·本·扎耶德人工智能大学）；School of Computer Science and Technology, Huazhong University of Science and Technology, Wuhan, China（华中科技大学计算机科学与技术学院）；Center for Machine Vision and Security Research, Kennesaw State University, Marietta, MA 30060, USA（肯尼斯州立大学机器视觉与安全研究中心）；Muroran Institute of Technology, Hokkaido, Japan（北海道Muroran理工学院）；Niigata University of Health and Welfare, Niigata, Japan（Niigata健康与福利大学）；University of South Florida, Tampa, FL, USA（佛罗里达州立大学）；Infervision Advanced Research Institute, Beijing, China（北京Infervision高级研究 institutes）；Academy for Multidisciplinary Studies, Capital Normal University, Beijing, China（北京师范大学多学科研究学院）；School of Automation, Nanjing University of Information Science and Technology, Nanjing 210044, China（南京信息科学技术大学自动化学院）
College of Medicine, Seoul National University（首尔大学医学院）；Department of Radiology, Armed Forces Yangju Hospital（杨州国军医院放射科）
The purpose of this study is to apply and evaluate out-of-the-box deep learning frameworks for the crossMoDA challenge. We use the CUT model, a model for unpaired image-to-image translation based on patchwise contrastive learning and adversarial learning, for domain adaptation from contrast-enhanced T1 MR to high-resolution T2 MR. As data augmentation, we generate additional images with vestibular schwannomas with lower signal intensity. For the segmentation task, we use the nnU-Net framework. Our final submission achieved mean Dice scores of 0.8299 in the validation phase and 0.8253 in the te…
University of Electronic Science and Technology of China（电子科技大学）；King’s College London（伦敦国王学院）；University College London（伦敦大学学院）；National Hospital for Neurology and Neurosurgery（国家神经病学和神经外科医院）；NVIDIA（英伟达）；Queen Square Radiosurgery Centre (Gamma Knife)（女王广场放射外科中心（伽马刀））；Neuroimaging Analysis Centre, Queen Square（女王广场神经影像分析中心）
Automatic segmentation of vestibular schwannoma (VS) tumors from magnetic resonance imaging (MRI) would facilitate efficient and accurate volume measurement to guide patient management and improve clinical workflow. The accuracy and robustness is challenged by low contrast, small target region and low through-plane resolution. We introduce a 2.5D convolutional neural network (CNN) able to exploit the different in-plane and through-plane resolutions encountered in standard of care imaging protocols. We use an attention module to enable the CNN to focus on the small target and propose a supervis…
Huazhong University of Science and Technology（华中科技大学）；Kennesaw State University（肯尼索州立大学）
The crossMoDA challenge aims to automatically segment the vestibular schwannoma (VS) tumor and cochlea regions of unlabeled high-resolution T2 scans by leveraging labeled contrast-enhanced T1 scans. The 2022 edition extends the segmentation task by including multi-institutional scans. In this work, we proposed an unpaired cross-modality segmentation framework using data augmentation and hybrid convolutional networks. Considering heterogeneous distributions and various image sizes for multi-institutional scans, we apply the min-max normalization for scaling the intensities of all scans between …
Nanyang Technological University（南洋理工大学）；National University of Singapore（新加坡国立大学）
Domain shift has been a long-standing issue for medical image segmentation. Recently, unsupervised domain adaptation (UDA) methods have achieved promising cross-modality segmentation performance by distilling knowledge from a label-rich source domain to a target domain without labels. In this work, we propose a multi-scale self-ensembling based UDA framework for automatic segmentation of two key brain structures i.e., Vestibular Schwannoma (VS) and Cochlea on high-resolution T2 images. First, a segmentation-enhanced contrastive unpaired image translation module is designed for image-level doma…
King’s College London（伦敦国王学院）；King’s College Hospital（国王学院医院）
Vestibular Schwannoma (VS) typically grows from the inner ear to the brain. It can be separated into two regions, intrameatal and extrameatal respectively corresponding to being inside or outside the inner ear canal. The growth of the extrameatal regions is a key factor that determines the disease management followed by the clinicians. In this work, a VS segmentation approach with subdivision into intra-/extra-meatal parts is presented. We annotated a dataset consisting of 227 T2 MRI instances, acquired longitudinally on 137 patients, excluding post-operative instances. We propose a staged app…
Management of vestibular schwannoma (VS) is based on tumour size as observed on T1 MRI scans with contrast agent injection. Current clinical practice is to measure the diameter of the tumour in its largest dimension. It has been shown that volumetric measurement is more accurate and more reliable as a measure of VS size. The reference approach to achieve such volumetry is to manually segment the tumour, which is a time intensive task. We suggest that semi-automated segmentation may be a clinically applicable solution to this problem and that it could replace linear measurements as the clinical…
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）；Wellcome/EPSRC Centre for Interventional and Surgical Sciences, University College London（伦敦大学学院威尔康姆/工程与物理科学研究委员会介入与外科科学中心）；National Hospital for Neurology and Neurosurgery, London（伦敦神经病学与神经外科国家医院）；UCL Ear Institute, University College London（伦敦大学学院UCL耳科研究所）
Although deep convolutional networks have reached state-of-the-art performance in many medical image segmentation tasks, they have typically demonstrated poor generalisation capability. To be able to generalise from one domain (e.g. one imaging modality) to another, domain adaptation has to be performed. While supervised methods may lead to good performance, they require to fully annotate additional data which may not be an option in practice. In contrast, unsupervised methods don't need additional annotations but are usually unstable and hard to train. In this work, we propose a novel weakly-…
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）；West China Hospital, Sichuan University（四川大学华西医院）
The success of Convolutional Neural Networks (CNNs) in 3D medical image segmentation relies on massive fully annotated 3D volumes for training that are time-consuming and labor-intensive to acquire. In this paper, we propose to annotate a segmentation target with only seven points in 3D medical images, and design a two-stage weakly supervised learning framework PA-Seg. In the first stage, we employ geodesic distance transform to expand the seed points to provide more supervision signal. To further deal with unannotated image regions during training, we propose two contextual regularization str…
Unsupervised domain adaptation is a type of domain adaptation and exploits labeled data from the source domain and unlabeled data from the target one. In the Cross-Modality Domain Adaptation for Medical Image Segmenta-tion challenge (crossMoDA2022), contrast enhanced T1 MRI volumes for brain are provided as the source domain data, and high-resolution T2 MRI volumes are provided as the target domain data. The crossMoDA2022 challenge contains two tasks, segmentation of vestibular schwannoma (VS) and cochlea, and clas-sification of VS with Koos grade. In this report, we presented our solution for…
COSMOS: Cross-Modality Unsupervised Domain Adaptation for 3D Medical Image Segmentation based on Target-aware Domain Translation and Iterative Self-Training
