This paper gives a detailed description of the pipelines used for the 2nd edition of the MICCAI 2021 Challenge on Multiple Sclerosis Lesion Segmentation. An overview of the data preprocessing steps applied is provided along with a brief description of the pipelines used, in terms of the architecture and the hyperparameters. Our code for this work can be found at: https://github.com/ivadomed/ms-challenge-2021.
Heidelberg University（海德堡大学）；University Medical Center Mannheim（曼海姆大学医学中心）
At present, lesion segmentation is still performed manually (or semi-automatically) by medical experts. To facilitate this process, we contribute a fully-automatic lesion segmentation pipeline. This work proposes a method as a part of the LiTS (Liver Tumor Segmentation Challenge) competition for ISBI 17 and MICCAI 17 comparing methods for automatics egmentation of liver lesions in CT scans. By utilizing cascaded, densely connected 2D U-Nets and a Tversky-coefficient based loss function, our framework achieves very good shape extractions with high detection sensitivity, with competitive scores …
Transfer learning and joint learning approaches are extensively used to improve the performance of Convolutional Neural Networks (CNNs). In medical imaging applications in which the target dataset is typically very small, transfer learning improves feature learning while joint learning has shown effectiveness in improving the network's generalization and robustness. In this work, we study the combination of these two approaches for the problem of liver lesion segmentation and classification. For this purpose, 332 abdominal CT slices containing lesion segmentation and classification of three le…
SYNAPSE-Net: A Unified Framework with Lesion-Aware Hierarchical Gating for Robust Segmentation of Heterogeneous Brain Lesions
Department of Biomedical Engineering, Bangladesh University of Engineering and Technology（生物医学工程系，孟加拉国工程与技术大学）；Department of Computer Science and Engineering, Bangladesh University of Engineering and Technology（计算机科学与工程系，孟加拉国工程与技术大学）；Department of Electrical and Electronic Engineering, Bangladesh University of Engineering and Technology（电气与电子工程系，孟加拉国工程与技术大学）
King’s College London（伦敦国王学院）；Shanghai Jiao Tong University（上海交通大学）
Accurate stroke lesion segmentation plays a pivotal role in stroke rehabilitation research, to provide lesion shape and size information which can be used for quantification of the extent of the stroke and to assess treatment efficacy. Recently, automatic segmentation algorithms using deep learning techniques have been developed and achieved promising results. In this report, we present our stroke lesion segmentation model based on nnU-Net framework, and apply it to the Anatomical Tracings of Lesions After Stroke (ATLAS v2.0) dataset. Furthermore, we describe an effective post-processing strat…
Automatic segmentation of tumor lesions is a critical initial processing step for quantitative PET/CT analysis. However, numerous tumor lesion with different shapes, sizes, and uptake intensity may be distributed in different anatomical contexts throughout the body, and there is also significant uptake in healthy organs. Therefore, building a systemic PET/CT tumor lesion segmentation model is a challenging task. In this paper, we propose a novel training strategy to build deep learning models capable of systemic tumor segmentation. Our method is validated on the training set of the AutoPET 202…
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…
Philips Medical Systems Technologies Ltd.（飞利浦医疗系统技术有限公司）
Purpose: The goal of this study was to assess the potential added benefit of accounting for partial volume effects (PVE) in an automatic coronary lumen segmentation algorithm from coronary computed tomography angiography (CCTA). Materials and methods: We assessed the potential added value of PVE integration as a part of the automatic coronary lumen segmentation algorithm by means of segmentation accuracy using the MICCAI 2012 challenge framework and by means of flow simulation overall accuracy, sensitivity, specificity, negative and positive predictive values and the receiver operated characte…
Univ. Bordeaux（波尔多大学）；Bordeaux INP（波尔多国立理工学院）；CNRS（法国国家科学研究中心）；Universitat Politècnica de València（瓦伦西亚理工大学）；INSERM（法国国家健康与医学研究院）；Neurocentre Magendie（马让迪神经中心）
The detection of new multiple sclerosis (MS) lesions is an important marker of the evolution of the disease. The applicability of learning-based methods could automate this task efficiently. However, the lack of annotated longitudinal data with new-appearing lesions is a limiting factor for the training of robust and generalizing models. In this work, we describe a deep-learning-based pipeline addressing the challenging task of detecting and segmenting new MS lesions. First, we propose to use transfer-learning from a model trained on a segmentation task using single time-points. Therefore, we …
We present an automatic method for joint liver lesion segmentation and classification using a hierarchical fine-tuning framework. Our dataset is small, containing 332 2-D CT examinations with lesion annotated into 3 lesion types: cysts, hemangiomas, and metastases. Using a cascaded U-net that performs segmentation and classification simultaneously, we trained a strong lesion segmentation model on the dataset of MICCAI 2017 Liver Tumor Segmentation (LiTS) Challenge. We used the trained weights to fine-tune a slightly modified model to obtain improved lesion segmentation and classification, on t…
All Sizes Matter: Improving Volumetric Brain Segmentation on Small Lesions
Technical University of Munich（慕尼黑工业大学）；Klinikum rechts der Isar（伊萨尔河右岸医院）；Deutsches Konsortium für Translationale Krebsforschung (DKTK)（德国转化癌症研究联盟（DKTK））；Helmholtz Center Munich（慕尼黑亥姆霍兹中心）
Supervised machine learning algorithms, especially in the medical domain, are affected by considerable ambiguity in expert markings. In this study we address the case where the experts' opinion is obtained as a distribution over the possible values. We propose a soft version of the STAPLE algorithm for experts' markings fusion that can handle soft values. The algorithm was applied to obtain consensus from soft Multiple Sclerosis (MS) segmentation masks. Soft MS segmentations are constructed from manual binary delineations by including lesion surrounding voxels in the segmentation mask with a r…
UNISELF: A Unified Network with Instance Normalization and Self-Ensembled Lesion Fusion for Multiple Sclerosis Lesion Segmentation
Department of Electrical and Computer Engineering, Johns Hopkins University, Baltimore, MD 21218, USA（电气与计算机工程系，约翰霍普金斯大学）；Department of Electrical and Computer Engineering, Vanderbilt University, Nashville, TN 37215, USA（电气与计算机工程系，范德比尔特大学）；Department of Neurology, Johns Hopkins School of Medicine, Baltimore, MD 21287, USA（神经病学系，约翰霍普金斯医学院）；Department of Computer Science, Johns Hopkins University, Baltimore, MD 21218, USA（计算机科学系，约翰霍普金斯大学）；Department of Radiology, Uniformed Services University of the Health Sciences, Bethesda, MD, 20814, USA（放射学系，统一服务大学健康科学学院）
Philips Healthcare（飞利浦医疗）；Philips Research（飞利浦研究院）；Semmelweis University（塞梅尔魏斯大学）；Queen’s University（女王大学）；South Eastern Health and Social Care Trust（东南健康与社会护理信托基金）
We introduce a functional for the learning of an optimal database for patch-based image segmentation with application to coronary lumen segmentation from coronary computed tomography angiography (CCTA) data. The proposed functional consists of fidelity, sparseness and robustness to small-variations terms and their associated weights. Existing work address database optimization by prototype selection aiming to optimize the database by either adding or removing prototypes according to a set of predefined rules. In contrast, we formulate the database optimization task as an energy minimization pr…
QU-BraTS: MICCAI BraTS 2020 Challenge on Quantifying Uncertainty in Brain Tumor Segmentation - Analysis of Ranking Scores and Benchmarking Results
McGill University（麦吉尔大学）；University of Oxford（牛津大学）；University of Pennsylvania（宾夕法尼亚大学）；Perelman School of Medicine at the University of Pennsylvania（宾夕法尼亚大学佩雷尔曼医学院）；University of Bern（伯尔尼大学）；Bern University Hospital（伯尔尼大学医院）；University of Texas Southwestern Medical Center（德克萨斯大学西南医学中心）；Universidad de los Andes（洛斯安第斯大学）；Imperial College London（帝国理工学院）；Indian Statistical Institute（印度统计研究所）；University of Calcutta（加尔各答大学）；Uppsala University（乌普萨拉大学）；The University of Pittsburgh Medical Center（匹兹堡大学医学中心）；Inserm（法国国家健康与医学研究院）；University of Auckland（奥克兰大学）；Auckland City Hospital（奥克兰市医院）；Massachusetts General Hospital（麻省总医院）；Massachusetts Institute of Technology（麻省理工学院）；EPITA Research and Development Laboratory (LRDE)（EPITA研发实验室）；Old Dominion University（老道明大学）；University of Girona（赫罗纳大学）；University of Tehran（德黑兰大学）；University of Nottingham（诺丁汉大学）；NVIDIA（英伟达）；University of Virginia（弗吉尼亚大学）；Indian Institute of Technology - Jodhpur（印度理工学院焦特布尔分校）
The Brain Tumor Segmentation (BraTS) Challenge: Local Synthesis of Healthy Brain Tissue via Inpainting
Helmholtz AI, Germany（亥姆霍兹人工智能研究所）；Technical University of Munich, Germany（慕尼黑工业大学）；Helmholtz Munich, Germany（亥姆霍兹慕尼黑中心）；University of Zurich, Switzerland（苏黎世大学）；Klinikum Rechts der Isar, Munich, Germany（慕尼黑右岸医院）；SETLabs Research GmbH, Healthcare Technologies, Munich, Germany（SETLabs研究有限公司）；Ludwig Maximilian University, Munich, Germany（路德维希马克西米利安慕尼黑大学）
Anisotropic Hybrid Networks for liver tumor segmentation with uncertainty quantification
Univ. Grenoble Alpes（格勒诺布尔大学）；Inserm（法国国家健康与医学研究院）；Grenoble Institut Neurosciences（格勒诺布尔神经科学研究所）；Pixyl（Pixyl公司）；Research and Development Laboratory（研发实验室）；Inria（法国国家信息与自动化研究所）；CNRS（法国国家科学研究中心）；Grenoble INP（格勒诺布尔综合理工学院）；LJK（格勒诺布尔大学联合实验室（注：因LJK无明确对应中文通用名称，按原文保留英文缩写））
University of Minnesota（明尼苏达大学）；German Cancer Research Center (DKFZ)（德国癌症研究中心）；University of Heidelberg（海德堡大学）；PingAn Technology Co., Ltd（平安科技有限公司）；Shanghai United Imaging Intelligence Inc.（上海联影智能医疗科技有限公司）；Southern Medical University（南方医科大学）；Peking University First Hospital（北京大学第一医院）；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）
There is a large body of literature linking anatomic and geometric characteristics of kidney tumors to perioperative and oncologic outcomes. Semantic segmentation of these tumors and their host kidneys is a promising tool for quantitatively characterizing these lesions, but its adoption is limited due to the manual effort required to produce high-quality 3D segmentations of these structures. Recently, methods based on deep learning have shown excellent results in automatic 3D segmentation, but they require large datasets for training, and there remains little consensus on which methods perform…
