This paper describes our method for our participation in the FeTA challenge2021 (team name: TRABIT). The performance of convolutional neural networks for medical image segmentation is thought to correlate positively with the number of training data. The FeTA challenge does not restrict participants to using only the provided training data but also allows for using other publicly available sources. Yet, open access fetal brain data remains limited. An advantageous strategy could thus be to expand the training data to cover broader perinatal brain imaging sources. Perinatal brain MRIs, other than the FeTA challenge data, that are currently publicly available, span normal and pathological fetal atlases as well as neonatal scans. However, perinatal brain MRIs segmented in different datasets typically come with different annotation protocols. This makes it challenging to combine those datasets to train a deep neural network. We recently proposed a family of loss functions, the label-set loss functions, for partially supervised learning. Label-set loss functions allow to train deep neural networks with partially segmented images, i.e. segmentations in which some classes may be grouped into super-classes. We propose to use label-set loss functions to improve the segmentation performance of a state-of-the-art deep learning pipeline for multi-class fetal brain segmentation by merging several publicly available datasets. To promote generalisability, our approach does not introduce any additional hyper-parameters tuning.
University Hospitals Leuven（鲁汶大学医院）；University Hospitals Tanta（坦塔大学医院）；University College London（伦敦大学学院）
Deep neural networks have increased the accuracy of automatic segmentation, however, their accuracy depends on the availability of a large number of fully segmented images. Methods to train deep neural networks using images for which some, but not all, regions of interest are segmented are necessary to make better use of partially annotated datasets. In this paper, we propose the first axiomatic definition of label-set loss functions that are the loss functions that can handle partially segmented images. We prove that there is one and only one method to convert a classical loss function for fu…
Fetal cortical plate segmentation is essential in quantitative analysis of fetal brain maturation and cortical folding. Manual segmentation of the cortical plate, or manual refinement of automatic segmentations is tedious and time-consuming. Automatic segmentation of the cortical plate, on the other hand, is challenged by the relatively low resolution of the reconstructed fetal brain MRI scans compared to the thin structure of the cortical plate, partial voluming, and the wide range of variations in the morphology of the cortical plate as the brain matures during gestation. To reduce the burde…
Imperial College London（伦敦帝国学院）；King’s College London（伦敦国王学院）；FAU Erlangen-Nürnberg（埃尔朗根-纽伦堡大学）；Technical University of Munich（慕尼黑工业大学）
Fetal Magnetic Resonance Imaging (MRI) is used in prenatal diagnosis and to assess early brain development. Accurate segmentation of the different brain tissues is a vital step in several brain analysis tasks, such as cortical surface reconstruction and tissue thickness measurements. Fetal MRI scans, however, are prone to motion artifacts that can affect the correctness of both manual and automatic segmentation techniques. In this paper, we propose a novel network structure that can simultaneously generate conditional atlases and predict brain tissue segmentation, called CAS-Net. The condition…
The availability of training data for supervision is a frequently encountered bottleneck of medical image analysis methods. While typically established by a clinical expert rater, the increase in acquired imaging data renders traditional pixel-wise segmentations less feasible. In this paper, we examine the use of a crowdsourcing platform for the distribution of super-pixel weak annotation tasks and collect such annotations from a crowd of non-expert raters. The crowd annotations are subsequently used for training a fully convolutional neural network to address the problem of fetal brain segmen…
When Multi-Task Learning Meets Partial Supervision: A Computer Vision Review
King’s College London（伦敦国王学院）；University of Luxembourg（卢森堡大学）；Tongji University（同济大学）；Shanghai Institute of Intelligent Science and Technology, Tongji University（同济大学上海智能科学与技术研究院）
Graduate School of Medicine, Osaka University（大阪大学医学院）
Computer-aided diagnosis system for diffuse lung diseases (DLDs) is necessary for the objective assessment of the lung diseases. In this paper, we develop semantic segmentation model for 5 kinds of DLDs. DLDs considered in this work are consolidation, ground glass opacity, honeycombing, emphysema, and normal. Convolutional neural network (CNN) is one of the most promising technique for semantic segmentation among machine learning algorithms. While creating annotated dataset for semantic segmentation is laborious and time consuming, creating partially annotated dataset, in which only one chosen…
Recent advances in deep learning have achieved promising performance for medical image analysis, while in most cases ground-truth annotations from human experts are necessary to train the deep model. In practice, such annotations are expensive to collect and can be scarce for medical imaging applications. Therefore, there is significant interest in learning representations from unlabelled raw data. In this paper, we propose a self-supervised learning approach to learn meaningful and transferable representations from medical imaging video without any type of human annotation. We assume that in …
Mask-HybridGNet: Graph-based segmentation with emergent anatomical correspondence from pixel-level supervision
Biomedical Image Technologies, ETSI Telecomunicación, Universidad Politécnica de Madrid, Madrid, Spain（生物医学影像技术，电信工程学院，马德里理工大学，马德里，西班牙）；IHU PRISM National Precision Medicine Center in Oncology, Cancer Data Science Unit, CentraleSupélec, Gustave Roussy, INSERM, Université Paris-Saclay, Gif-sur-Yvette, France（IHU PRISM国家精准医学中心（肿瘤学），癌症数据科学单元，中央圣艾尔布兰，格斯塔夫·罗西，国家医学研究所，巴黎-萨克雷大学，法国）
The Hebrew University of Jerusalem（耶路撒冷希伯来大学）；Tel Aviv Sourasky Medical Center（特拉维夫苏拉斯基医疗中心）；Tel Aviv University（特拉维夫大学）；Children’s Hospital of Eastern Ontario（东安大略儿童医院）；University of Ottawa（渥太华大学）
Deep learning methods have been shown to be effective for the automatic segmentation of structures and pathologies in medical imaging. However, they require large annotated datasets, whose manual segmentation is a tedious and time-consuming task, especially for large structures. We present a new method of partial annotations that uses a small set of consecutive annotated slices from each scan with an annotation effort that is equal to that of only few annotated cases. The training with partial annotations is performed by using only annotated blocks, incorporating information about slices outsi…
UPL-SFDA: Uncertainty-aware Pseudo Label Guided Source-Free Domain Adaptation for Medical Image Segmentation
School of Mechanical and Electrical Engineering, University of Electronic Science and Technology of China（电子科技大学机械与电气工程学院）；Shanghai AI laboratory（上海人工智能实验室）；Sichuan Provincial People’s Hospital, University of Electronic Science and Technology of China（电子科技大学附属四川省人民医院）；SenseTime Research（商汤科技研究院）；Zhejiang Laboratory（浙江实验室）；School of Biomedical Engineering & Imaging Sciences, King’s College London（伦敦国王学院生物医学工程与影像科学学院）
Institute of Biomedical Engineering, Department of Engineering Science, University of Oxford（牛津大学工程科学系生物医学工程研究所）；Nuffield Department of Obstetrics and Gynaecology, John Radcliffe Hospital, University of Oxford（牛津大学约翰拉德克利夫医院妇产科）；Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, University of Oxford（牛津大学李兆基健康信息与发现中心大数据研究所）
To improve the performance of most neuroimiage analysis pipelines, brain extraction is used as a fundamental first step in the image processing. But in the case of fetal brain development, there is a need for a reliable US-specific tool. In this work we propose a fully automated 3D CNN approach to fetal brain extraction from 3D US clinical volumes with minimal preprocessing. Our method accurately and reliably extracts the brain regardless of the large data variation inherent in this imaging modality. It also performs consistently throughout a gestational age range between 14 and 31 weeks, rega…
Due to the high human cost of annotation, it is non-trivial to curate a large-scale medical dataset that is fully labeled for all classes of interest. Instead, it would be convenient to collect multiple small partially labeled datasets from different matching sources, where the medical images may have only been annotated for a subset of classes of interest. This paper offers an empirical understanding of an under-explored problem, namely partially supervised multi-label classification (PSMLC), where a multi-label classifier is trained with only partially labeled medical images. In contrast to …
Beyond Instance-Level Self-Supervision in 3D Multi-Modal Medical Imaging
Fudan University, China（复旦大学）；University of Queensland, Australia（昆士兰大学）；Shanghai Academy of AI for Science, China（上海人工智能科学研究院）；Huashan Hospital, National Center for Neurological Disorders, Fudan University, China（华山医院，国家神经系统疾病中心，复旦大学）；Bioinformatics Institute (BII), Agency for Science, Technology and Research (A*STAR), Singapore（生物信息研究所（BII），科技研究局（A*STAR），新加坡）
McGill University（麦吉尔大学）；MILA (Québec Artificial Intelligence Institute)（MILA（魁北克人工智能研究所））；University of Edinburgh（爱丁堡大学）；The Alan Turing Institute（艾伦·图灵研究所）
We propose a hierarchically structured variational inference model for accurately disentangling observable evidence of disease (e.g. brain lesions or atrophy) from subject-specific anatomy in brain MRIs. With flexible, partially autoregressive priors, our model (1) addresses the subtle and fine-grained dependencies that typically exist between anatomical and pathological generating factors of an MRI to ensure the clinical validity of generated samples; (2) preserves and disentangles finer pathological details pertaining to a patient's disease state. Additionally, we experiment with an alternat…
University of Oxford（牛津大学）；UiT The Arctic University of Norway（挪威北极大学）；Sun Yat-sen University（中山大学）；Carnegie Mellon University（卡内基梅隆大学）；Mohamed bin Zayed University of Artificial Intelligence（穆罕默德·本·扎耶德人工智能大学）
The data-driven nature of deep learning (DL) models for semantic segmentation requires a large number of pixel-level annotations. However, large-scale and fully labeled medical datasets are often unavailable for practical tasks. Recently, partially supervised methods have been proposed to utilize images with incomplete labels in the medical domain. To bridge the methodological gaps in partially supervised learning (PSL) under data scarcity, we propose Vicinal Labels Under Uncertainty (VLUU), a simple yet efficient framework utilizing the human structure similarity for partially supervised medi…
University of Groningen（格罗宁根大学）；University of Twente（特文特大学）
Visual place recognition (VPR) is a fundamental task of computer vision for visual localization. Existing methods are trained using image pairs that either depict the same place or not. Such a binary indication does not consider continuous relations of similarity between images of the same place taken from different positions, determined by the continuous nature of camera pose. The binary similarity induces a noisy supervision signal into the training of VPR methods, which stall in local minima and require expensive hard mining algorithms to guarantee convergence. Motivated by the fact that tw…
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）
