Upgraded W-Net with Attention Gates and its Application in Unsupervised 3D Liver Segmentation
Otto von Guericke University（奥托·冯·格里克大学）；German Center for Neurodegenerative Disease（德国神经退行性疾病中心）；Center for Behavioral Brain Sciences（行为脑科学中心）；Leibniz Institute for Neurobiology（莱布尼茨神经生物学研究所）
Dhanunjaya Mitta, Soumick Chatterjee, Oliver Speck, Andreas Nürnberger
发表信息：
Proceedings of the 10th International Conference on Pattern Recognition Applications and Methods 2021 - Volume 1
Segmentation of biomedical images can assist radiologists to make a better diagnosis and take decisions faster by helping in the detection of abnormalities, such as tumors. Manual or semi-automated segmentation, however, can be a time-consuming task. Most deep learning based automated segmentation methods are supervised and rely on manually segmented ground-truth. A possible solution for the problem would be an unsupervised deep learning based approach for automated segmentation, which this research work tries to address. We use a W-Net architecture and modified it, such that it can be applied to 3D volumes. In addition, to suppress noise in the segmentation we added attention gates to the skip connections. The loss for the segmentation output was calculated using soft N-Cuts and for the reconstruction output using SSIM. Conditional Random Fields were used as a post-processing step to fine-tune the results. The proposed method has shown promising results, with a dice coefficient of 0.88 for the liver segmentation compared against manual segmentation.
Liver segmentation on images acquired using computed tomography (CT) and magnetic resonance imaging (MRI) plays an important role in clinical management of liver diseases. Compared to MRI, CT images of liver are more abundant and readily available. However, MRI can provide richer quantitative information of the liver compared to CT. Thus, it is desirable to achieve unsupervised domain adaptation for transferring the learned knowledge from the source domain containing labeled CT images to the target domain containing unlabeled MR images. In this work, we report a novel unsupervised domain adapt…
Yale University（耶鲁大学）；Yale School of Medicine（耶鲁大学医学院）
Deep neural networks have shown exceptional learning capability and generalizability in the source domain when massive labeled data is provided. However, the well-trained models often fail in the target domain due to the domain shift. Unsupervised domain adaptation aims to improve network performance when applying robust models trained on medical images from source domains to a new target domain. In this work, we present an approach based on the Wasserstein distance guided disentangled representation to achieve 3D multi-domain liver segmentation. Concretely, we embed images onto a shared conte…
Department of Biomedical Engineering, Yale University（耶鲁大学生物医学工程系）；Department of Radiology & Biomedical Imaging, Yale School of Medicine（耶鲁大学医学院放射科与生物医学成像系）；Department of Electrical Engineering, Yale University（耶鲁大学电气工程系）；Department of Statistics & Data Science, Yale University（耶鲁大学统计与数据科学系）；Yale School of Medicine（耶鲁大学医学院）；Yale University（耶鲁大学）
A deep learning model trained on some labeled data from a certain source domain generally performs poorly on data from different target domains due to domain shifts. Unsupervised domain adaptation methods address this problem by alleviating the domain shift between the labeled source data and the unlabeled target data. In this work, we achieve cross-modality domain adaptation, i.e. between CT and MRI images, via disentangled representations. Compared to learning a one-to-one mapping as the state-of-art CycleGAN, our model recovers a many-to-many mapping between domains to capture the complex c…
University of Georgia（佐治亚大学）；Shanghai Jiao Tong University（上海交通大学）
We introduce a neural network framework, utilizing adversarial learning to partition an image into two cuts, with one cut falling into a reference distribution provided by the user. This concept tackles the task of unsupervised anomaly segmentation, which has attracted increasing attention in recent years due to their broad applications in tasks with unlabelled data. This Adversarial-based Selective Cutting network (ASC-Net) bridges the two domains of cluster-based deep learning methods and adversarial-based anomaly/novelty detection algorithms. We evaluate this unsupervised learning model on …
Qatar University（卡塔尔大学）；Hamad Medical Corporation（哈马德医疗公司）
Machine learning and computer vision techniques have grown rapidly in recent years due to their automation, suitability, and ability to generate astounding results. Hence, in this paper, we survey the key studies that are published between 2014 and 2022, showcasing the different machine learning algorithms researchers have used to segment the liver, hepatic tumors, and hepatic-vasculature structures. We divide the surveyed studies based on the tissue of interest (hepatic-parenchyma, hepatic-tumors, or hepatic-vessels), highlighting the studies that tackle more than one task simultaneously. Add…
Korea Advanced Institute of Science and Technology（韩国科学技术院）；University of Ulsan College of Medicine（蔚山大学医学院）；Asan Medical Center（峨山医学中心）
Medical image registration is one of the key processing steps for biomedical image analysis such as cancer diagnosis. Recently, deep learning based supervised and unsupervised image registration methods have been extensively studied due to its excellent performance in spite of ultra-fast computational time compared to the classical approaches. In this paper, we present a novel unsupervised medical image registration method that trains deep neural network for deformable registration of 3D volumes using a cycle-consistency. Thanks to the cycle consistency, the proposed deep neural networks can t…
Identifying Signatures of Image Phenotypes to Track Treatment Response in Liver Disease
Department of Biomedical Imaging and Image-guided Therapy, Medical University of Vienna, Austria（维也纳医科大学生物医学影像与影像引导治疗部门）；Institute of Clinical Epidemiology, Public Health, Health Economics, Medical Statistics and Informatics, Medical University of Innsbruck, Austria（因斯布鲁克医科大学临床流行病学、公共卫生、卫生经济学、医学统计与信息学研究所）；Novartis Pharmaceuticals Corporation, East Hanover, NJ, USA（诺华制药公司，东汉诺威，新泽西州，美国）；Novartis Pharma AG, Basel, Switzerland（诺华制药集团，巴塞尔，瑞士）；Comprehensive Center for Artificial Intelligence in Medicine, Medical University of Vienna, Austria（医学人工智能综合中心，维也纳医科大学，奥地利）；Division of Gastroenterology and Hepatology, Department of Medicine III, Medical University of Vienna, Austria（消化内科与肝病科，医学第三部，维也纳医科大学，奥地利）；Medical University of Vienna, Waehringer Guertel 18–20, 1090 Vienna, Austria（维也纳医科大学，瓦尔希林格特尔18–20号，1090维也纳，奥地利）
Synomaly Noise and Multi-Stage Diffusion: A Novel Approach for Unsupervised Anomaly Detection in Medical Images
Computer Aided Medical Procedures, Technical University of Munich, Munich, Germany（技术大学慕尼黑计算机辅助医疗程序）；Munich Center of Machine Learning, Munich, Germany（慕尼黑机器学习中心）；Department for Vascular and Endovascular Surgery, rechts der Isar University Hospital, Technical University of Munich, Munich, Germany（技术大学慕尼黑血管和内血管外科部门）
Radboud University Medical Center（拉德堡德大学医学中心）；Erasmus MC Cancer Institute（伊拉斯谟MC癌症研究所）；Facebook AI Research（Facebook人工智能研究院）
We focus on the problem of training convolutional neural networks on gigapixel histopathology images to predict image-level targets. For this purpose, we extend Neural Image Compression (NIC), an image compression framework that reduces the dimensionality of these images using an encoder network trained unsupervisedly. We propose to train this encoder using supervised multitask learning (MTL) instead. We applied the proposed MTL NIC to two histopathology datasets and three tasks. First, we obtained state-of-the-art results in the Tumor Proliferation Assessment Challenge of 2016 (TUPAC16). Seco…
College of Physics and Information Engineering, Fuzhou University（福州大学物理与信息工程学院）；School of Data Science, Fudan University（复旦大学大数据学院）；School of Biomedical Engineering, Shanghai Jiao Tong University（上海交通大学生物医学工程学院）
Multi-modality medical images can provide relevant or complementary information for a target (organ, tumor or tissue). Registering multi-modality images to a common space can fuse these comprehensive information, and bring convenience for clinical application. Recently, neural networks have been widely investigated to boost registration methods. However, it is still challenging to develop a multi-modality registration network due to the lack of robust criteria for network training. In this work, we propose a multi-modality registration network (MMRegNet), which can perform registration between…
Institute for Medical Imaging Technology, School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai 200030, China（中国上海200030，上海交通大学生物医学工程学院医学影像技术研究所）；Department of Radiology and Biomedical Research Imaging Center (BRIC), University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA（美国北卡罗来纳州教堂山27599，北卡罗来纳大学教堂山分校放射学与生物医学研究成像中心（BRIC））；North China Electric Power University, Beijing, China（中国北京华北电力大学）；Shanghai United Imaging Intelligence Co., Ltd, Shanghai, China（中国上海上海联影智能科技有限公司）；Shanghai Cancer Center, Fudan University, Shanghai, China（中国上海复旦大学附属肿瘤医院）
Thermal ablation is a minimally invasive procedure for treat-ing small or unresectable tumors. Although CT is widely used for guiding ablation procedures, the contrast of tumors against surrounding normal tissues in CT images is often poor, aggravating the difficulty in accurate thermal ablation. In this paper, we propose a fast MR-CT image registration method to overlay a pre-procedural MR (pMR) image onto an intra-procedural CT (iCT) image for guiding the thermal ablation of liver tumors. By first using a Cycle-GAN model with mutual information constraint to generate synthesized CT (sCT) ima…
University of Toronto（多伦多大学）；Sunnybrook Research Institute（桑尼布鲁克研究所）
Quantitative medical image computing (radiomics) has been widely applied to build prediction models from medical images. However, overfitting is a significant issue in conventional radiomics, where a large number of radiomic features are directly used to train and test models that predict genotypes or clinical outcomes. In order to tackle this problem, we propose an unsupervised learning pipeline composed of an autoencoder for representation learning of radiomic features and a Gaussian mixture model based on minimum message length criterion for clustering. By incorporating probabilistic modeli…
DINO-AD: Unsupervised Anomaly Detection with Frozen DINO-V3 Features
National Heart and Lung Institute, Imperial College London, London, UK（帝国理工学院伦敦心脏和肺研究所）；Department of Digital Twins for Healthcare, BMEIS, King’s College London, London, UK（King’s College London医疗数字双领域部门）；SonoScape Medical Corp.（SonoScape医疗公司）
University of Georgia（佐治亚大学）；Zhongnan Hospital of Wuhan University（武汉大学中南医院）；Shanghai Jiao Tong University（上海交通大学）
In this paper we consider the problem of unsupervised anomaly segmentation in medical images, which has attracted increasing attention in recent years due to the expensive pixel-level annotations from experts and the existence of a large amount of unannotated normal and abnormal image scans. We introduce a segmentation network that utilizes adversarial learning to partition an image into two cuts, with one of them falling into a reference distribution provided by the user. This Adversarial-based Selective Cutting network (ASC-Net) bridges the two domains of cluster-based deep segmentation and …
Tsinghua University（清华大学）；Brigham and Women’s Hospital（布莱根妇女医院）；Harvard Medical School（哈佛医学院）
Deformable image registration (DIR) is essential for many image-guided therapies. Recently, deep learning approaches have gained substantial popularity and success in DIR. Most deep learning approaches use the so-called mono-stream "high-to-low, low-to-high" network structure, and can achieve satisfactory overall registration results. However, accurate alignments for some severely deformed local regions, which are crucial for pinpointing surgical targets, are often overlooked. Consequently, these approaches are not sensitive to some hard-to-align regions, e.g., intra-patient registration of de…
Memorial Sloan Kettering Cancer Center（纪念斯隆凯特琳癌症中心）
We developed a new joint probabilistic segmentation and image distribution matching generative adversarial network (PSIGAN) for unsupervised domain adaptation (UDA) and multi-organ segmentation from magnetic resonance (MRI) images. Our UDA approach models the co-dependency between images and their segmentation as a joint probability distribution using a new structure discriminator. The structure discriminator computes structure of interest focused adversarial loss by combining the generated pseudo MRI with probabilistic segmentations produced by a simultaneously trained segmentation sub-networ…
PAII Inc.（PAII公司）；Johns Hopkins University（约翰斯·霍普金斯大学）；Vanderbilt University（范德堡大学）；Chang Gung Memorial Hospital（长庚纪念医院）；Ping An Technology（平安科技）
Multi-modal image registration is a challenging problem that is also an important clinical task for many real applications and scenarios. As a first step in analysis, deformable registration among different image modalities is often required in order to provide complementary visual information. During registration, semantic information is key to match homologous points and pixels. Nevertheless, many conventional registration methods are incapable in capturing high-level semantic anatomical dense correspondences. In this work, we propose a novel multi-task learning system, JSSR, based on an end…
Behind Every Domain There is a Shift: Adapting Distortion-aware Vision Transformers for Panoramic Semantic Segmentation
Karlsruhe Institute of Technology（卡尔斯鲁厄理工学院）；Hunan University（湖南大学）；University of Oxford（牛津大学）；Zhejiang University（浙江大学）；ByteDance Inc.（字节跳动公司）；Beihang University（北京航空航天大学）
