End-to-end learning of brain tissue segmentation from imperfect labeling
The Mind Research Network（心智研究网络）；University of New Mexico（新墨西哥大学）；New College of Florida（新佛罗里达学院）；Moscow Institute of Physics and Technology（莫斯科物理技术学院）
Alex Fedorov, Jeremy Johnson, Eswar Damaraju, Alexei Ozerin, Vince Calhoun, Sergey Plis
备注：
Published as a conference paper at IJCNN 2017 Preprint version
Segmenting a structural magnetic resonance imaging (MRI) scan is an important pre-processing step for analytic procedures and subsequent inferences about longitudinal tissue changes. Manual segmentation defines the current gold standard in quality but is prohibitively expensive. Automatic approaches are computationally intensive, incredibly slow at scale, and error prone due to usually involving many potentially faulty intermediate steps. In order to streamline the segmentation, we introduce a deep learning model that is based on volumetric dilated convolutions, subsequently reducing both processing time and errors. Compared to its competitors, the model has a reduced set of parameters and thus is easier to train and much faster to execute. The contrast in performance between the dilated network and its competitors becomes obvious when both are tested on a large dataset of unprocessed human brain volumes. The dilated network consistently outperforms not only another state-of-the-art deep learning approach, the up convolutional network, but also the ground truth on which it was trained. Not only can the incredible speed of our model make large scale analyses much easier but we also believe it has great potential in a clinical setting where, with little to no substantial delay, a patient and provider can go over test results.
Columbia University（哥伦比亚大学）；Stevens Institute of Technology（史蒂文斯理工学院）；Imperial College London（帝国理工学院）；Institut Polytechnique de Paris（巴黎理工学院）
Automatically identifying the structural substrates underlying cardiac abnormalities can potentially provide real-time guidance for interventional procedures. With the knowledge of cardiac tissue substrates, the treatment of complex arrhythmias such as atrial fibrillation and ventricular tachycardia can be further optimized by detecting arrhythmia substrates to target for treatment (i.e., adipose) and identifying critical structures to avoid. Optical coherence tomography (OCT) is a real-time imaging modality that aids in addressing this need. Existing approaches for cardiac image analysis main…
Ultrasound image quality has continually been improving. However, when needles or other metallic objects are operating inside the tissue, the resulting reverberation artifacts can severely corrupt the surrounding image quality. Such effects are challenging for existing computer vision algorithms for medical image analysis. Needle reverberation artifacts can be hard to identify at times and affect various pixel values to different degrees. The boundaries of such artifacts are ambiguous, leading to disagreement among human experts labeling the artifacts. We propose a weakly- and semi-supervised,…
Extracting accurate foreground objects from a scene is an essential step for many video applications. Traditional background subtraction algorithms can generate coarse estimates, but generating high quality masks requires professional softwares with significant human interventions, e.g., providing trimaps or labeling key frames. We propose an automatic foreground extraction method in applications where a static but imperfect background is available. Examples include filming and surveillance where the background can be captured before the objects enter the scene or after they leave the scene. O…
University of British Columbia（不列颠哥伦比亚大学）；British Columbia Cancer Research Centre（不列颠哥伦比亚省癌症研究中心）
This paper addresses the problem of quantifying biomarkers in multi-stained tissues, based on color and spatial information. A deep learning based method that can automatically localize and quantify the cells expressing biomarker(s) in a whole slide image is proposed. The deep learning network is a fully convolutional network (FCN) whose input is the true RGB color image of a tissue and output is a map of the different biomarkers. The FCN relies on a convolutional neural network (CNN) that classifies each cell separately according to the biomarker it expresses. In this study, images of immunoh…
Medical image processing tasks such as segmentation often require capturing non-local information. As organs, bones, and tissues share common characteristics such as intensity, shape, and texture, the contextual information plays a critical role in correctly labeling them. Segmentation and labeling is now typically done with convolutional neural networks (CNNs) but the context of the CNN is limited by the receptive field which itself is limited by memory requirements and other properties. In this paper, we propose a new attention module, that we call Permutohedral Attention Module (PAM), to ef…
University of Stavanger（斯塔万格大学）；Erasmus MC Cancer Institute, University Medical Center（伊拉斯姆斯医学中心癌症研究所，大学医学中心）
Accurate segmentation of tissue in histopathological images can be very beneficial for defining regions of interest (ROI) for streamline of diagnostic and prognostic tasks. Still, adapting to different domains is essential for histopathology image analysis, as the visual characteristics of tissues can vary significantly across datasets. Yet, acquiring sufficient annotated data in the medical domain is cumbersome and time-consuming. The labeling effort can be significantly reduced by leveraging active learning, which enables the selective annotation of the most informative samples. Our proposed…
Segmentation is one of the most important tasks in MRI medical image analysis and is often the first and the most critical step in many clinical applications. In brain MRI analysis, head segmentation is commonly used for measuring and visualizing the brain's anatomical structures and is also a necessary step for other applications such as current-source reconstruction in electroencephalography and magnetoencephalography (EEG/MEG). Here we propose a deep learning framework that can segment brain, skull, and extra-cranial tissue using only T1-weighted MRI as input. In addition, we describe a rob…
StyleSeg V2: Towards Robust One-shot Segmentation of Brain Tissue via Optimization-free Registration Error Perception
Wuhan National Laboratory for Optoelectronics, Huazhong University of Science and Technology（华中科技大学武汉光电国家研究中心）；Wuhan United Imaging Healthcare Surgical Technology Co., Ltd.（武汉联影外科技术有限公司）
Sharif University of Technology（谢里夫理工大学）；Polytechnique Montreal（蒙特利尔理工学院）；Mila, Quebec AI Institute（米拉魁北克人工智能研究所）；University of Montreal（蒙特利尔大学）
Labeling vertebral discs from MRI scans is important for the proper diagnosis of spinal related diseases, including multiple sclerosis, amyotrophic lateral sclerosis, degenerative cervical myelopathy and cancer. Automatic labeling of the vertebral discs in MRI data is a difficult task because of the similarity between discs and bone area, the variability in the geometry of the spine and surrounding tissues across individuals, and the variability across scans (manufacturers, pulse sequence, image contrast, resolution and artefacts). In previous studies, vertebral disc labeling is often done aft…
University of Central Florida（中佛罗里达大学）；National Cancer Institute, National Institutes of Health（美国国立卫生研究院国家癌症研究所）；Frederick National Laboratory for Cancer Research（弗雷德里克国家癌症研究实验室）
Abdominal fat quantification is critical since multiple vital organs are located within this region. Although computed tomography (CT) is a highly sensitive modality to segment body fat, it involves ionizing radiations which makes magnetic resonance imaging (MRI) a preferable alternative for this purpose. Additionally, the superior soft tissue contrast in MRI could lead to more accurate results. Yet, it is highly labor intensive to segment fat in MRI scans. In this study, we propose an algorithm based on deep learning technique(s) to automatically quantify fat tissue from MR images through a c…
Guangdong Cardiovascular Institute（广东省心血管病研究所）；School of Computer Science and Engineering, South China University of Technology（华南理工大学计算机科学与工程学院）
Tissue-level semantic segmentation is a vital step in computational pathology. Fully-supervised models have already achieved outstanding performance with dense pixel-level annotations. However, drawing such labels on the giga-pixel whole slide images is extremely expensive and time-consuming. In this paper, we use only patch-level classification labels to achieve tissue semantic segmentation on histopathology images, finally reducing the annotation efforts. We proposed a two-step model including a classification and a segmentation phases. In the classification phase, we proposed a CAM-based mo…
Institute of Mathematics；Computer Sciences -- ICMC/USP -- Brazil a Ribeir\ a o Preto Medical School - HCFMRP/USP -- Brazil b；Department of Physical Therapy -- DFisio/UFSCar -- Brazil c；Institute of Computing -- IC/UFF -- Brazil d Fluminense Northwest Institute -- INFES/UFF -- Brazil e
Background. The image-based identification of distinct tissues within dermatological wounds enhances patients' care since it requires no intrusive evaluations. This manuscript presents an approach, we named QTDU, that combines deep learning models with superpixel-driven segmentation methods for assessing the quality of tissues from dermatological ulcers. Method. QTDU consists of a three-stage pipeline for the obtaining of ulcer segmentation, tissues' labeling, and wounded area quantification. We set up our approach by using a real and annotated set of dermatological ulcers for training several…
Robust deep labeling of radiological emphysema subtypes using squeeze and excitation convolutional neural networks: The MESA Lung and SPIROMICS Studies
Ecole Polytechnique Montréal（蒙特利尔理工学院）；CHU Sainte-Justine Hospital Research Center（圣贾斯汀儿童医院研究中心）；University of Montreal（蒙特利尔大学）
The early detection, diagnosis and monitoring of liver cancer progression can be achieved with the precise delineation of metastatic tumours. However, accurate automated segmentation remains challenging due to the presence of noise, inhomogeneity and the high appearance variability of malignant tissue. In this paper, we propose an unsupervised metastatic liver tumour segmentation framework using a machine learning approach based on discriminant Grassmannian manifolds which learns the appearance of tumours with respect to normal tissue. First, the framework learns within-class and between-class…
Separating and labeling each instance of a nucleus (instance-aware segmentation) is the key challenge in segmenting single cell nuclei on fluorescence microscopy images. Deep Neural Networks can learn the implicit transformation of a nuclear image into a probability map indicating the class membership of each pixel (nucleus or background), but the use of post-processing steps to turn the probability map into a labeled object mask is error-prone. This especially accounts for nuclear images of tissue sections and nuclear images across varying tissue preparations. In this work, we aim to evaluate…
Guidelines for Cerebrovascular Segmentation: Managing Imperfect Annotations in the context of Semi-Supervised Learning
Université de Reims Champagne Ardenne（兰斯-香槟-阿登大学）；Univ Lyon（里昂大学）；INSA-Lyon（里昂国立应用科学学院）；Universite Claude Bernard Lyon 1（里昂第一大学）；IMT Atlantique（大西洋电信学院）；Inserm（法国国家健康与医学研究院）
ProBAG: Prototype-Guided Boundary-Aware Graph Diffusion for Weakly Supervised Histopathology Segmentation
AI VIETNAM Lab（AI越南实验室）；Washington University School of Medicine（华盛顿大学医学院）；Jeonbuk National University（全北国立大学）；Perelman School of Medicine, University of Pennsylvania（宾夕法尼亚大学佩雷尔曼医学院）
Panoptic Segmentation and Labelling of Lumbar Spine Vertebrae using Modified Attention Unet
A. K. Choudhury School of Information Technology, University of Calcutta（加尔各答大学A. K.乔杜里信息技术学院）；Rammohan College, University of Calcutta（加尔各答大学拉莫汉学院）；Indian Statistical Institute（印度统计研究所）
本研究提出基于改进注意力 U-Net 架构和新型掩码逻辑的方法，用于 3D 腰椎 MRI 数据的椎骨全景分割与标注，实现 99.5% 的高准确率，显著推进该领域最先进技术。
Breast region segmentation is an essential prerequisite in computerized analysis of mammograms. It aims at separating the breast tissue from the background of the mammogram and it includes two independent segmentations. The first segments the background region which usually contains annotations, labels and frames from the whole breast region, while the second removes the pectoral muscle portion (present in Medio Lateral Oblique (MLO) views) from the rest of the breast tissue. In this paper we propose hybridization of Connected Component Labeling (CCL), Fuzzy, and Straight line methods. Our pro…
University College London（伦敦大学学院）；Katholieke Universiteit Leuven（天主教鲁汶大学）；University College London Hospitals（伦敦大学学院医院）；Universitair Ziekenhuis Leuven（鲁汶大学医院）；Wellcome / EPSRC Centre for Surgical and Interventional Sciences, UCL, London, UK（惠康/英国工程与物理科学研究委员会外科与介入科学中心（伦敦大学学院））；Surgical Robot Vision Group, CMIC, Dept. Computer Science, University College London（伦敦大学学院计算机科学系CMIC外科机器人视觉小组）；Translational Imaging Group, CMIC, Dept. Med. Phys. Biomed. Eng., University College London（伦敦大学学院医学物理与生物医学工程系CMIC转化成像小组）
Real-time tool segmentation from endoscopic videos is an essential part of many computer-assisted robotic surgical systems and of critical importance in robotic surgical data science. We propose two novel deep learning architectures for automatic segmentation of non-rigid surgical instruments. Both methods take advantage of automated deep-learning-based multi-scale feature extraction while trying to maintain an accurate segmentation quality at all resolutions. The two proposed methods encode the multi-scale constraint inside the network architecture. The first proposed architecture enforces it…
Segmentation of histological images is one of the most crucial tasks for many biomedical analyses including quantification of certain tissue type. However, challenges are posed by high variability and complexity of structural features in such images, in addition to imaging artifacts. Further, the conventional approach of manual thresholding is labor-intensive, and highly sensitive to inter- and intra-image intensity variations. An accurate and robust automated segmentation method is of high interest. We propose and evaluate an elegant convolutional neural network (CNN) designed for segmentatio…
Duke University（杜克大学）；Tsinghua University（清华大学）；Lund University（隆德大学）
Fast noninvasive probing of spatially varying decorrelating events, such as cerebral blood flow beneath the human skull, is an essential task in various scientific and clinical settings. One of the primary optical techniques used is diffuse correlation spectroscopy (DCS), whose classical implementation uses a single or few single-photon detectors, resulting in poor spatial localization accuracy and relatively low temporal resolution. Here, we propose a technique termed Classifying Rapid decorrelation Events via Parallelized single photon dEtection (CREPE)}, a new form of DCS that can probe and…
Automating the extraction and quantification of features from three-dimensional (3-D) image stacks is a critical task for advancing computer vision research. The union of 3-D image acquisition and analysis enables the quantification of biological resistance of a plant tissue to fungal infection through the analysis of attributes such as fungal penetration depth, fungal mass, and branching of the fungal network of connected cells. From an image processing perspective, these tasks reduce to segmentation of vessel-like structures and the extraction of features from their skeletonization. In order…
University at Buffalo, The State University of New York（纽约州立大学布法罗分校）
The recent state-of-the-art deep learning methods have significantly improved brain tumor segmentation. However, fully supervised training requires a large amount of manually labeled masks, which is highly time-consuming and needs domain expertise. Weakly supervised learning with scribbles provides a good trade-off between model accuracy and the effort of manual labeling. However, for segmenting the hierarchical brain tumor structures, manually labeling scribbles for each substructure could still be demanding. In this paper, we use only two kinds of weak labels, i.e., scribbles on whole tumor …
German Aerospace Center (DLR)（德国航空航天中心）；Technical University of Munich (TUM)（慕尼黑工业大学）
Accurate object segmentation is a crucial task in the context of robotic manipulation. However, creating sufficient annotated training data for neural networks is particularly time consuming and often requires manual labeling. To this end, we propose a simple, yet robust solution for learning to segment unknown objects grasped by a robot. Specifically, we exploit motion and temporal cues in RGB video sequences. Using optical flow estimation we first learn to predict segmentation masks of our given manipulator. Then, these annotations are used in combination with motion cues to automatically di…
LOTUS: Learning to Optimize Task-based US representations
Technical University of Munich（慕尼黑工业大学）；Sharif University of Technology（谢里夫理工大学）；Stanford University School of Medicine（斯坦福大学医学院）；Ecole Centrale Nantes（南特中央理工学院）；John Hopkins University（约翰斯·霍普金斯大学）
Massachusetts General Hospital（麻省总医院）；Zhejiang University（浙江大学）；University of Michigan（密歇根大学）；Beijing Institute of Technology（北京理工大学）
Tissue characterization has long been an important component of Computer Aided Diagnosis (CAD) systems for automatic lesion detection and further clinical planning. Motivated by the superior performance of deep learning methods on various computer vision problems, there has been increasing work applying deep learning to medical image analysis. However, the development of a robust and reliable deep learning model for computer-aided diagnosis is still highly challenging due to the combination of the high heterogeneity in the medical images and the relative lack of training samples. Specifically,…
