Segmentation of objects of interest is one of the central tasks in medical image analysis, which is indispensable for quantitative analysis. When developing machine-learning based methods for automated segmentation, manual annotations are usually used as the ground truth toward which the models learn to mimic. While the bulky parts of the segmentation targets are relatively easy to label, the peripheral areas are often difficult to handle due to ambiguous boundaries and the partial volume effect, etc., and are likely to be labeled with uncertainty. This uncertainty in labeling may, in turn, result in unsatisfactory performance of the trained models. In this paper, we propose superpixel-based label softening to tackle the above issue. Generated by unsupervised over-segmentation, each superpixel is expected to represent a locally homogeneous area. If a superpixel intersects with the annotation boundary, we consider a high probability of uncertain labeling within this area. Driven by this intuition, we soften labels in this area based on signed distances to the annotation boundary and assign probability values within [0, 1] to them, in comparison with the original "hard", binary labels of either 0 or 1. The softened labels are then used to train the segmentation models together with the hard labels. Experimental results on a brain MRI dataset and an optical coherence tomography dataset demonstrate that this conceptually simple and implementation-wise easy method achieves overall superior segmentation performances to baseline and comparison methods for both 3D and 2D medical images.
Supervoxel methods such as Simple Linear Iterative Clustering (SLIC) are an effective technique for partitioning an image or volume into locally similar regions, and are a common building block for the development of detection, segmentation and analysis methods. We introduce maskSLIC an extension of SLIC to create supervoxels within regions-of-interest, and demonstrate,on examples from 2-dimensions to 4-dimensions, that maskSLIC overcomes issues that affect SLIC within an irregular mask. We highlight the benefits of this method through examples, and show that it is able to better represent und…
Pattern Recognition Lab, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU)（埃尔朗根-纽伦堡大学模式识别实验室）；Institute of Pathology, University Hospital Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU)（埃尔朗根-纽伦堡大学埃尔朗根医院病理学研究所）；Comprehensive Cancer Center Erlangen-EMN (CCC ER-EMN)（埃尔朗根-欧洲大都会区综合癌症中心）；Department Artificial Intelligence in Biomedical Engineering, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU)（埃尔朗根-纽伦堡大学生物医学工程人工智能系）；Department of Gynecology and Obstetrics, University Hospital Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU)（埃尔朗根-纽伦堡大学埃尔朗根医院妇产科）
Supervised deep learning has shown state-of-the-art performance for medical image segmentation across different applications, including histopathology and cancer research; however, the manual annotation of such data is extremely laborious. In this work, we explore the use of superpixel approaches to compute a pre-segmentation of HER2 stained images for breast cancer diagnosis that facilitates faster manual annotation and correction in a second step. Four methods are compared: Standard Simple Linear Iterative Clustering (SLIC) as a baseline, a domain adapted SLIC, and superpixels based on featu…
Imperial College London（帝国理工学院）；BioMedIA Group, Department of Computing（计算系BioMedIA小组）
Few-shot semantic segmentation (FSS) has great potential for medical imaging applications. Most of the existing FSS techniques require abundant annotated semantic classes for training. However, these methods may not be applicable for medical images due to the lack of annotations. To address this problem we make several contributions: (1) A novel self-supervised FSS framework for medical images in order to eliminate the requirement for annotations during training. Additionally, superpixel-based pseudo-labels are generated to provide supervision; (2) An adaptive local prototype pooling module pl…
ShanghaiTech University（上海科技大学）；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）
Learning segmentation from noisy labels is an important task for medical image analysis due to the difficulty in acquiring highquality annotations. Most existing methods neglect the pixel correlation and structural prior in segmentation, often producing noisy predictions around object boundaries. To address this, we adopt a superpixel representation and develop a robust iterative learning strategy that combines noise-aware training of segmentation network and noisy label refinement, both guided by the superpixels. This design enables us to exploit the structural constraints in segmentation lab…
National Engineering School of Sousse（苏塞国家工程学院）；University of Dundee（邓迪大学）
We introduce a dynamic multiscale tree (DMT) architecture that learns how to leverage the strengths of different existing classifiers for supervised multi-label image segmentation. Unlike previous works that simply aggregate or cascade classifiers for addressing image segmentation and labeling tasks, we propose to embed strong classifiers into a tree structure that allows bi-directional flow of information between its classifier nodes to gradually improve their performances. Our DMT is a generic classification model that inherently embeds different cascades of classifiers while enhancing learn…
National Institutes of Health Clinical Center（美国国立卫生研究院临床中心）
Automatic organ segmentation is an important yet challenging problem for medical image analysis. The pancreas is an abdominal organ with very high anatomical variability. This inhibits previous segmentation methods from achieving high accuracies, especially compared to other organs such as the liver, heart or kidneys. In this paper, we present a probabilistic bottom-up approach for pancreas segmentation in abdominal computed tomography (CT) scans, using multi-level deep convolutional networks (ConvNets). We propose and evaluate several variations of deep ConvNets in the context of hierarchical…
Center for Processing Speech and Images（语音和图像处理中心）；KU Leuven（比利时鲁汶大学）；Dept. ESAT（ESAT系（ESAT系））；ESAT（ESAT（比利时鲁汶大学的一个系/实验室））；KU Leuven, Belgium（比利时鲁汶大学）
Superpixel algorithms are a common pre-processing step for computer vision algorithms such as segmentation, object tracking and localization. Many superpixel methods only rely on colors features for segmentation, limiting performance in low-contrast regions and applicability to infrared or medical images where object boundaries have wide appearance variability. We study the inclusion of deep image features in the SLIC superpixel algorithm to exploit higher-level image representations. In addition, we devise a trainable superpixel algorithm, yielding an intermediate domain-specific image repres…
Technical University of Munich（慕尼黑工业大学）；Johns Hopkins University（约翰斯·霍普金斯大学）
Inpainting has recently been proposed as a successful deep learning technique for unsupervised medical image model discovery. The masks used for inpainting are generally independent of the dataset and are not tailored to perform on different given classes of anatomy. In this work, we introduce a method for generating shape-aware masks for inpainting, which aims at learning the statistical shape prior. We hypothesize that although the variation of masks improves the generalizability of inpainting models, the shape of the masks should follow the topology of the organs of interest. Hence, we prop…
ShanghaiTech University（上海科技大学）；Shanghai Institute of Microsystem and Information Technology, Chinese Academy of Sciences（中国科学院上海微系统与信息技术研究所）；University of Chinese Academy of Sciences（中国科学院大学）；Shanghai Jiao Tong University（上海交通大学）；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）；Institute for Infocomm Research, Agency for Science, Technology and Research (A*STAR)（新加坡科技研究局资讯通信研究院）；Southern University of Science and Technology（南方科技大学）；Cixi Institute of Biomedical Engineering, Chinese Academy of Sciences（中国科学院慈溪生物医学工程研究所）
Anomaly detection in medical images refers to the identification of abnormal images with only normal images in the training set. Most existing methods solve this problem with a self-reconstruction framework, which tends to learn an identity mapping and reduces the sensitivity to anomalies. To mitigate this problem, in this paper, we propose a novel Proxy-bridged Image Reconstruction Network (ProxyAno) for anomaly detection in medical images. Specifically, we use an intermediate proxy to bridge the input image and the reconstructed image. We study different proxy types, and we find that the sup…
Deep neural network-based medical image classifications often use "hard" labels for training, where the probability of the correct category is 1 and those of others are 0. However, these hard targets can drive the networks over-confident about their predictions and prone to overfit the training data, affecting model generalization and adaption. Studies have shown that label smoothing and softening can improve classification performance. Nevertheless, existing approaches are either non-data-driven or limited in applicability. In this paper, we present the Class-Correlation Learning Network (CCL…
SuperCL: Superpixel Guided Contrastive Learning for Medical Image Segmentation Pre-training
Institute of Medical Technology, Peking University Health Science Center, Peking University（北京大学医学部医学技术研究所）；Department of Biomedical Engineering, Peking University（北京大学生物医学工程系）；National Biomedical Imaging Center, Peking University（北京大学国家生物医学成像中心）；Institute of Biomedical Engineering, Shenzhen Bay Laboratory（深圳湾实验室生物医学工程研究所）；Institute of Biomedical Engineering, Peking University Shenzhen Graduate School（北京大学深圳研究生院生物医学工程研究所）
Fraunhofer Institute for Integrated Circuits IIS（弗劳恩霍夫集成电路研究所IIS）；Friedrich-Alexander-University, Erlangen-Nuremberg（埃尔朗根-纽伦堡弗里德里希-亚历山大大学）；University Hospital Erlangen, FAU Erlangen-Nuremberg（埃尔朗根-纽伦堡弗里德里希-亚历山大大学埃尔朗根大学医院）
Automatic outlining of different tissue types in digitized histological specimen provides a basis for follow-up analyses and can potentially guide subsequent medical decisions. The immense size of whole-slide-images (WSI), however, poses a challenge in terms of computation time. In this regard, the analysis of non-overlapping patches outperforms pixelwise segmentation approaches, but still leaves room for optimization. Furthermore, the division into patches, regardless of the biological structures they contain, is a drawback due to the loss of local dependencies. We propose to subdivide the WS…
Superpixel-Based QUBO for Scalable Quantum-Enhanced Medical Image Segmentation
American University of Beirut（贝鲁特美国大学）；Centre de Visió per Computador (CVC)（计算机视觉中心 (CVC)）；Ingenii Inc.（英格尼公司）；Hamad Bin Khalifa University（哈马德·本·哈利法大学）
The Hospital for Sick Children（病童医院）；University of Toronto（多伦多大学）；Vector Institute（Vector研究所）
Deep convolutional neural networks (CNNs) have become an essential tool in the medical imaging-based computer-aided diagnostic pipeline. However, training accurate and reliable CNNs requires large fine-grain annotated datasets. To alleviate this, weakly-supervised methods can be used to obtain local information from global labels. This work proposes the use of localized perturbations as a weakly-supervised solution to extract segmentation masks of brain tumours from a pretrained 3D classification model. Furthermore, we propose a novel optimal perturbation method that exploits 3D superpixels to…
BITS Pilani, Goa Campus（比特斯皮拉尼大学果阿校区）；Savitribai Phule Pune University（萨维特里巴伊·普莱浦那大学）
Superpixels are higher-order perceptual groups of pixels in an image, often carrying much more information than the raw pixels. There is an inherent relational structure to the relationship among different superpixels of an image such as adjacent superpixels are neighbours of each other. Our interest here is to treat these relative positions of various superpixels as relational information of an image. This relational information can convey higher-order spatial information about the image, such as the relationship between superpixels representing two eyes in an image of a cat. That is, two eye…
Medical Visual Prompting (MVP): A Unified Framework for Versatile and High-Quality Medical Image Segmentation
School of Automation, Guangdong University of Technology（广东工业大学自动化学院）；School of Computer Science and Technology, Guangdong University of Technology（广东工业大学计算机科学与技术学院）；School of Information Science and Technology, Guangdong University of Foreign Studies（广东外语外贸大学信息科学与技术学院）；Faculty of Science and Technology, University of Macau（澳门大学科技学院）；The First Affiliated Hospital of Sun Yat-Sen University（中山大学附属第一医院）；Sun Yat-sen University Cancer Center（中山大学肿瘤防治中心）；South China Hospital, Shenzhen University（深圳大学华南医院）
National Institutes of Health Clinical Center（美国国立卫生研究院临床中心）
Accurate and automatic organ segmentation from 3D radiological scans is an important yet challenging problem for medical image analysis. Specifically, the pancreas demonstrates very high inter-patient anatomical variability in both its shape and volume. In this paper, we present an automated system using 3D computed tomography (CT) volumes via a two-stage cascaded approach: pancreas localization and segmentation. For the first step, we localize the pancreas from the entire 3D CT scan, providing a reliable bounding box for the more refined segmentation step. We introduce a fully deep-learning a…
UCAD: Uncertainty-guided Contour-aware Displacement for semi-supervised medical image segmentation
University of Science and Technology of China（科学技术大学）；Suzhou Institute for Advanced Research（苏州先进研究院）；State Key Laboratory of Precision and Intelligent Chemistry（精密与智能化学国家重点实验室）
Durham University（杜伦大学）；University of Exeter（埃克塞特大学）；County Durham and Darlington NHS Foundation Trust（达勒姆郡和达灵顿国民保健服务基金会信托）
Medical segmentation is performed to determine the bounds of regions of interest (ROI) prior to surgery. By allowing the study of growth, structure, and behaviour of the ROI in the planning phase, critical information can be obtained, increasing the likelihood of a successful operation. Usually, segmentations are performed manually or via machine learning methods trained on manual annotations. In contrast, this paper proposes a fully automatic, unsupervised inpainting-based brain tumour segmentation system for T1-weighted MRI. First, a deep convolutional neural network (DCNN) is trained to rec…
National Heart and Lung Institute, Imperial College London（帝国理工学院国家心肺研究所）；Royal Brompton Hospital（皇家布朗普顿医院）；Centre for Cardiovascular Science, University of Edinburgh（爱丁堡大学心血管科学中心）；School of Computer Science and Electronic Engineering, University of Essex（埃塞克斯大学计算机科学与电子工程学院）
As a pragmatic data augmentation tool, data synthesis has generally returned dividends in performance for deep learning based medical image analysis. However, generating corresponding segmentation masks for synthetic medical images is laborious and subjective. To obtain paired synthetic medical images and segmentations, conditional generative models that use segmentation masks as synthesis conditions were proposed. However, these segmentation mask-conditioned generative models still relied on large, varied, and labeled training datasets, and they could only provide limited constraints on human…
