Automatic airway segmentation from Computed Tomography using robust and efficient 3-D convolutional neural networks
Erasmus MC（伊拉斯姆斯医学中心）；Erasmus MC-Sophia Children Hospital（伊拉斯姆斯医学中心索菲亚儿童医院）；University of Copenhagen（哥本哈根大学）；Copenhagen University Hospital（哥本哈根大学医院）；Herlev-Gentofte Hospital（海莱乌-根措夫特医院）
A. Garcia-Uceda, R. Selvan, Z. Saghir, H. A. W. M. Tiddens, M. de Bruijne
备注：
Changes have been made to reflect the minor revision and publication in Scientific Reports Nature
This paper presents a fully automatic and end-to-end optimised airway segmentation method for thoracic computed tomography, based on the U-Net architecture. We use a simple and low-memory 3D U-Net as backbone, which allows the method to process large 3D image patches, often comprising full lungs, in a single pass through the network. This makes the method simple, robust and efficient. We validated the proposed method on three datasets with very different characteristics and various airway abnormalities: i) a dataset of pediatric patients including subjects with cystic fibrosis, ii) a subset of the Danish Lung Cancer Screening Trial, including subjects with chronic obstructive pulmonary disease, and iii) the EXACT'09 public dataset. We compared our method with other state-of-the-art airway segmentation methods, including relevant learning-based methods in the literature evaluated on the EXACT'09 data. We show that our method can extract highly complete airway trees with few false positive errors, on scans from both healthy and diseased subjects, and also that the method generalizes well across different datasets. On the EXACT'09 test set, our method achieved the second highest sensitivity score among all methods that reported good specificity.
Airway segmentation in computed tomography images can be used to analyze pulmonary diseases, however, manual segmentation is labor intensive and relies on expert knowledge. This manuscript details our contribution to MICCAI's 2022 Airway Tree Modelling challenge, a competition of fully automated methods for airway segmentation. We employed a previously developed deep learning architecture based on a modified EfficientDet (MEDSeg), training from scratch for binary airway segmentation using the provided annotations. Our method achieved 90.72 Dice in internal validation, 95.52 Dice on external va…
Eindhoven University of Technology（埃因霍温理工大学）；Erasmus MC - University Medical Center Rotterdam（伊拉斯谟医学中心-鹿特丹大学医学中心）；Erasmus MC - Sophia Children’s Hospital（伊拉斯谟医学中心-索菲亚儿童医院）；University of Copenhagen（哥本哈根大学）
Measuring airways in chest computed tomography (CT) scans is important for characterizing diseases such as cystic fibrosis, yet very time-consuming to perform manually. Machine learning algorithms offer an alternative, but need large sets of annotated scans for good performance. We investigate whether crowdsourcing can be used to gather airway annotations. We generate image slices at known locations of airways in 24 subjects and request the crowd workers to outline the airway lumen and airway wall. After combining multiple crowd workers, we compare the measurements to those made by the experts…
Accurate, automatic and complete extraction of pulmonary airway in medical images plays an important role in analyzing thoracic CT volumes such as lung cancer detection, chronic obstructive pulmonary disease (COPD), and bronchoscopic-assisted surgery navigation. However, this task remains challenges, due to the complex tree-like structure of the airways. In this technical report, we use two-stage fully convolutional networks (FCNs) to automatically segment pulmonary airway in thoracic CT scans from multi-sites. Specifically, we firstly adopt a 3D FCN with U-shape network architecture to segmen…
Delft University of Technology（代尔夫特理工大学）；Erasmus Medical Center - Sophia Children’s Hospital（伊拉斯谟医学中心-索菲亚儿童医院）；Erasmus Medical Center（伊拉斯谟医学中心）；University of Copenhagen（哥本哈根大学）
Measuring airways in chest computed tomography (CT) images is important for characterizing diseases such as cystic fibrosis, yet very time-consuming to perform manually. Machine learning algorithms offer an alternative, but need large sets of annotated data to perform well. We investigate whether crowdsourcing can be used to gather airway annotations which can serve directly for measuring the airways, or as training data for the algorithms. We generate image slices at known locations of airways and request untrained crowd workers to outline the airway lumen and airway wall. Our results show th…
MEDPSeg: Hierarchical polymorphic multitask learning for the segmentation of ground-glass opacities, consolidation, and pulmonary structures on computed tomography
School of Electrical and Computer Engineering, Universidade Estadual de Campinas（坎皮纳斯州立大学电气与计算机工程学院）；University of Iowa（爱荷华大学）
Fast and automatic algorithm to segment Brain (intracranial region) from computed tomography (CT) head images using combination of HU thresholding, identification of intracranial voxels through ray intersection with cranium, special binary erosion and connected components per slice.
University of Copenhagen（哥本哈根大学）；Rigshospitalet, University Hospital of Copenhagen（哥本哈根大学医院）；Erasmus MC（伊拉斯谟医学中心）
Segmenting tree structures is common in several image processing applications. In medical image analysis, reliable segmentations of airways, vessels, neurons and other tree structures can enable important clinical applications. We present a framework for tracking tree structures comprising of elongated branches using probabilistic state-space models and Bayesian smoothing. Unlike most existing methods that proceed with sequential tracking of branches, we present an exploratory method, that is less sensitive to local anomalies in the data due to acquisition noise and/or interfering structures. …
Deep convolutional neural networks for image segmentation do not learn the label structure explicitly and may produce segmentations with an incorrect structure, e.g., with disconnected cylindrical structures in the segmentation of tree-like structures such as airways or blood vessels. In this paper, we propose a novel label refinement method to correct such errors from an initial segmentation, implicitly incorporating information about label structure. This method features two novel parts: 1) a model that generates synthetic structural errors, and 2) a label appearance simulation network that …
South China University of Technology（华南理工大学）；Fudan University（复旦大学）；University of Notre Dame（圣母大学）；Guangdong Cardiovascular Institute（广东省心血管病研究所）
Type-B Aortic Dissection (TBAD) is one of the most serious cardiovascular events characterized by a growing yearly incidence,and the severity of disease prognosis. Currently, computed tomography angiography (CTA) has been widely adopted for the diagnosis and prognosis of TBAD. Accurate segmentation of true lumen (TL), false lumen (FL), and false lumen thrombus (FLT) in CTA are crucial for the precise quantification of anatomical features. However, existing works only focus on only TL and FL without considering FLT. In this paper, we propose ImageTBAD, the first 3D computed tomography angiograp…
Sichuan University - Pittsburgh Institute（四川大学-匹兹堡学院）
Airway segmentation from chest computed tomography scans has played an essential role in the pulmonary disease diagnosis. The computer-assisted airway segmentation based on the U-net architecture is more efficient and accurate compared to the manual segmentation. In this paper we employ the U$^2$-net trained by the Dice loss function to model the airway tree from the multi-site CT scans based on 299 training CT scans provided by the ATM'22. The derived saliency probability map from the training is applied to the validation data to extract the corresponding airway trees. The observation shows t…
Automatic Left Ventricular Cavity Segmentation via Deep Spatial Sequential Network in 4D Computed Tomography Studies
School of Biomedical Engineering, Shanghai Jiao Tong University（上海交通大学生物医学工程学院）；School of Computer Science, University of Sydney（悉尼大学计算机学院）；Ruijin Hospital, Shanghai Jiaotong University School of Medicine（上海交通大学医学院附属瑞金医院）
Radboud University Medical Center（拉德堡德大学医学中心）；Radboud Institute for Health Sciences（拉德堡德健康科学研究所）
Early detection improves prognosis in pancreatic ductal adenocarcinoma (PDAC) but is challenging as lesions are often small and poorly defined on contrast-enhanced computed tomography scans (CE-CT). Deep learning can facilitate PDAC diagnosis, however current models still fail to identify small (<2cm) lesions. In this study, state-of-the-art deep learning models were used to develop an automatic framework for PDAC detection, focusing on small lesions. Additionally, the impact of integrating surrounding anatomy was investigated. CE-CT scans from a cohort of 119 pathology-proven PDAC patients an…
Shanghai Jiao Tong University（上海交通大学）；Imperial College London（帝国理工学院）
Airway segmentation on CT scans is critical for pulmonary disease diagnosis and endobronchial navigation. Manual extraction of airway requires strenuous efforts due to the complicated structure and various appearance of airway. For automatic airway extraction, convolutional neural networks (CNNs) based methods have recently become the state-of-the-art approach. However, there still remains a challenge for CNNs to perceive the tree-like pattern and comprehend the connectivity of airway. To address this, we propose a voxel-connectivity aware approach named AirwayNet for accurate airway segmentat…
University of Coimbra（科英布拉大学）；Erasmus MC（伊拉斯姆斯大学医学中心）；KU Leuven（鲁汶大学）；University of Porto（波尔图大学）；Centro Hospitalar e Universitário São João（圣若昂大学医院中心）；University Hospitals UZ Leuven（鲁汶大学医院）
The optic nerve head represents the intraocular section of the optic nerve (ONH), which is prone to damage by intraocular pressure. The advent of optical coherence tomography (OCT) has enabled the evaluation of novel optic nerve head parameters, namely the depth and curvature of the lamina cribrosa (LC). Together with the Bruch's membrane opening minimum-rim-width, these seem to be promising optic nerve head parameters for diagnosis and monitoring of retinal diseases such as glaucoma. Nonetheless, these optical coherence tomography derived biomarkers are mostly extracted through manual segment…
Washington University in St. Louis（圣路易斯华盛顿大学）；Washington University School of Medicine（华盛顿大学医学院）；Cardiovascular Research Foundation（心血管研究基金会）
Optical coherence tomography (OCT) can provide high-resolution cross-sectional images for analyzing superficial plaques in coronary arteries. Commonly, plaque characterization using intra-coronary OCT images is performed manually by expert observers. This manual analysis is time consuming and its accuracy heavily relies on the experience of human observers. Traditional machine learning based methods, such as the least squares support vector machine and random forest methods, have been recently employed to automatically characterize plaque regions in OCT images. Several processing steps, includ…
Velammal College of Engg and Tech（维拉马尔工程技术学院）；Thiagarajar College of Engg（蒂亚加拉贾工程技术学院）
The research work presented in this paper is to achieve the tissue classification and automatically diagnosis the abnormal tumor region present in Computed Tomography (CT) images using the wavelet based statistical texture analysis method. Comparative studies of texture analysis method are performed for the proposed wavelet based texture analysis method and Spatial Gray Level Dependence Method (SGLDM). Our proposed system consists of four phases i) Discrete Wavelet Decomposition (ii) Feature extraction (iii) Feature selection (iv) Analysis of extracted texture features by classifier. A wavelet…
Airway Segmentation Network for Enhanced Tubular Feature Extraction
School of Optical-electrical and Computer Engineering（光学电子与计算机工程学院）；University of Shanghai for Science and Technology（上海理工大学）；School of Information Technology（信息技术学院）；Jiangsu Open University（江苏开放大学）
Institute of Medical Robotics, Shanghai Jiao Tong University（上海交通大学医疗机器人研究所）；Institute of Image Processing and Pattern Recognition, Shanghai Jiao Tong University（上海交通大学图像处理与模式识别研究所）
Purpose: Bronchoscopic intervention is a widely-used clinical technique for pulmonary diseases, which requires an accurate and topological complete airway map for its localization and guidance. The airway map could be extracted from chest computed tomography (CT) scans automatically by airway segmentation methods. Due to the complex tree-like structure of the airway, preserving its topology completeness while maintaining the segmentation accuracy is a challenging task. Methods: In this paper, a long-term slice propagation (LTSP) method is proposed for accurate airway segmentation from patholog…
With the introduction of spectral-domain optical coherence tomography (SDOCT), much larger image datasets are routinely acquired compared to what was possible using the previous generation of time-domain OCT. Thus, there is a critical need for the development of 3D segmentation methods for processing these data. We present here a novel 3D automatic segmentation method for retinal OCT volume data. Briefly, to segment a boundary surface, two OCT volume datasets are obtained by using a 3D smoothing filter and a 3D differential filter. Their linear combination is then calculated to generate new vo…
National Heart and Lung Institute, Faculty of Medicine, Imperial College London（帝国理工学院医学院国家心肺研究所）；Department of Bioengineering, Faculty of Engineering, Imperial College London（帝国理工学院工程系生物工程系）；Royal Brompton Hospital（皇家布朗普顿医院）
Various structures in human physiology follow a treelike morphology, which often expresses complexity at very fine scales. Examples of such structures are intrathoracic airways, retinal blood vessels, and hepatic blood vessels. Large collections of 2D and 3D images have been made available by medical imaging modalities such as magnetic resonance imaging (MRI), computed tomography (CT), Optical coherence tomography (OCT) and ultrasound in which the spatial arrangement can be observed. Segmentation of these structures in medical imaging is of great importance since the analysis of the structure …
INESC TEC（INESC TEC科技与创新研究所）；Faculdade de Ciências da Universidade do Porto（波尔图大学理学院）；Champalimaud Clinical Center（尚帕利莫临床中心）；Hospital Pedro Hispano（佩德罗·伊斯帕诺医院）；Nova Medical School（诺瓦医学院）
The deep inferior epigastric artery perforator (DIEAP) flap is the most common free flap used for breast reconstruction after a mastectomy. It makes use of the skin and fat of the lower abdomen to build a new breast mound either at the same time of the mastectomy or in a second surgery. This operation requires preoperative imaging studies to evaluate the branches - the perforators - that irrigate the tissue that will be used to reconstruct the breast mound. These branches will support tissue viability after the microsurgical ligation of the inferior epigastric vessels to the receptor vessels i…
University of Oxford（牛津大学）；Big Data Institute（大数据研究所）
Diabetic retinopathy (DR) is a complication of diabetes, and one of the major causes of vision impairment in the global population. As the early-stage manifestation of DR is usually very mild and hard to detect, an accurate diagnosis via eye-screening is clinically important to prevent vision loss at later stages. In this work, we propose an ensemble method to automatically grade DR using ultra-wide optical coherence tomography angiography (UW-OCTA) images available from Diabetic Retinopathy Analysis Challenge (DRAC) 2022. First, we adopt the state-of-the-art classification networks, i.e., Res…
University of Pittsburgh School of Medicine（匹兹堡大学医学院）；VA Pittsburgh Healthcare System（匹兹堡退伍军人医疗系统）
Purpose: To develop and validate a computer tool for automatic and simultaneous segmentation of body composition depicted on computed tomography (CT) scans for the following tissues: visceral adipose (VAT), subcutaneous adipose (SAT), intermuscular adipose (IMAT), skeletal muscle (SM), and bone. Approach: A cohort of 100 CT scans acquired from The Cancer Imaging Archive (TCIA) was used - 50 whole-body positron emission tomography (PET)-CTs, 25 chest, and 25 abdominal. Five different body compositions were manually annotated (VAT, SAT, IMAT, SM, and bone). A training-while-annotating strategy w…
Northeastern University（东北大学）；Shenyang University of Technology（沈阳工业大学）；The Chinese University of Hong Kong（香港中文大学）；Second Affiliated Hospital of Dalian Medical University（大连医科大学附属第二医院）；Central Hospital Affiliated to Shenyang Medical College（沈阳医学院附属中心医院）
Accurate airway extraction from computed tomography (CT) images is a critical step for planning navigation bronchoscopy and quantitative assessment of airway-related chronic obstructive pulmonary disease (COPD). The existing methods are challenging to sufficiently segment the airway, especially the high-generation airway, with the constraint of the limited label and cannot meet the clinical use in COPD. We propose a novel two-stage 3D contextual transformer-based U-Net for airway segmentation using CT images. The method consists of two stages, performing initial and refined airway segmentation…
OCTolyzer: Fully automatic toolkit for segmentation and feature extracting in optical coherence tomography and scanning laser ophthalmoscopy data
University of Edinburgh（爱丁堡大学）；Institute for Regeneration and Repair（再生与修复研究所）；Glasgow Caledonian University（格拉斯哥卡利多尼亚大学）；British Heart Foundation Centre for Cardiovascular Science（英国心脏基金会心血管科学中心）；Clinical Research Facility and Imaging（临床研究设施与影像中心）；Centre for Clinical Brain Sciences（临床脑科学中心）；School of Informatics（信息学院）；Institute for Adaptive and Neural Computation（自适应与神经计算研究所）；School of Mathematics（数学学院）
University College London（伦敦大学学院）；KU Leuven（鲁汶大学）；University Hospitals Leuven（鲁汶大学医院）；University of Antwerp（安特卫普大学）
Several chronic lung diseases, like idiopathic pulmonary fibrosis (IPF) are characterised by abnormal dilatation of the airways. Quantification of airway features on computed tomography (CT) can help characterise disease progression. Physics based airway measurement algorithms have been developed, but have met with limited success in part due to the sheer diversity of airway morphology seen in clinical practice. Supervised learning methods are also not feasible due to the high cost of obtaining precise airway annotations. We propose synthesising airways by style transfer using perceptual losse…
Massachusetts Institute of Technology（麻省理工学院）；Friedrich-Alexander-Universität Erlangen-Nürnberg（埃尔朗根-纽伦堡弗里德里希-亚历山大大学）；Tufts Medical Center（塔夫茨医疗中心）
Recent advances in optical coherence tomography such as the development of high speed ultrahigh resolution scanners and corresponding signal processing techniques may reveal new potential biomarkers in retinal diseases. Newly visible features are, for example, small hyperreflective specks in age-related macular degeneration. Identifying these new markers is crucial to investigate potential association with disease progression and treatment outcomes. Therefore, it is necessary to reliably detect these features in 3D volumetric scans. Because manual labeling of entire volumes is infeasible a nee…
Kamnoetvidya Science Academy（甘烹碧科学学院）；National Electronics and Computer Technology Center（泰国国家电子和计算机技术中心）；Vidyasirimedhi Institute of Science and Technology（瓦莱拉克科学技术研究院）
Since, cancer is curable when diagnosed at an early stage, lung cancer screening plays an important role in preventive care. Although both low dose computed tomography (LDCT) and computed tomography (CT) scans provide more medical information than normal chest x-rays, there is very limited access to these technologies in rural areas. Recently, there is a trend in using computer-aided diagnosis (CADx) to assist in screening and diagnosing of cancer from biomedical images. In this study, the 121-layer convolutional neural network also known as DenseNet-121 by G. Huang et. al., along with the tra…
In this research project, we put forward an advanced method for airway segmentation based on the existent convolutional neural network (CNN) and graph neural network (GNN). The method is originated from the vessel segmentation, but we ameliorate it and enable the novel model to perform better for datasets from computed tomography (CT) scans. Current methods for airway segmentation are considering the regular grid only. No matter what the detailed model is, including the 3-dimensional CNN or 2-dimensional CNN in three directions, the overall graph structures are not taken into consideration. In…
National Chiao-Tung University（国立交通大学）；National Cheng Kung University Hospital（国立成功大学附属医院）；College of Medicine, National Cheng Kung University（国立成功大学医学院）
This study was conducted to develop a computer-aided detection (CAD) system for triaging patients with pulmonary embolism (PE). The purpose of the system was to reduce the death rate during the waiting period. Computed tomography pulmonary angiography (CTPA) is used for PE diagnosis. Because CTPA reports require a radiologist to review the case and suggest further management, this creates a waiting period during which patients may die. Our proposed CAD method was thus designed to triage patients with PE from those without PE. In contrast to related studies involving CAD systems that identify k…
School of Mechanical engineering and Automation, Fuzhou University（福州大学机械工程及自动化学院）；School of Physics and Information Engineering, Fuzhou University（福州大学物理与信息工程学院）；Thoracic Department, Fujian Medical University Union Hospital（福建医科大学附属协和医院胸外科）
Automatic airway segmentation from chest computed tomography (CT) scans plays an important role in pulmonary disease diagnosis and computer-assisted therapy. However, low contrast at peripheral branches and complex tree-like structures remain as two mainly challenges for airway segmentation. Recent research has illustrated that deep learning methods perform well in segmentation tasks. Motivated by these works, a coarse-to-fine segmentation framework is proposed to obtain a complete airway tree. Our framework segments the overall airway and small branches via the multi-information fusion convol…
Pulmonary lobe segmentation in computed tomography scans is essential for regional assessment of pulmonary diseases. Recent works based on convolution neural networks have achieved good performance for this task. However, they are still limited in capturing structured relationships due to the nature of convolution. The shape of the pulmonary lobes affect each other and their borders relate to the appearance of other structures, such as vessels, airways, and the pleural wall. We argue that such structural relationships play a critical role in the accurate delineation of pulmonary lobes when the…
With the mushrooming use of computed tomography (CT) images in clinical decision making, management of CT data becomes increasingly difficult. From the patient identification perspective, using the standard DICOM tag to track patient information is challenged by issues such as misspelling, lost file, site variation, etc. In this paper, we explore the feasibility of leveraging the faces in 3D CT images as biometric features. Specifically, we propose an automatic processing pipeline that first detects facial landmarks in 3D for ROI extraction and then generates aligned 2D depth images, which are…
School of Advanced Technologies in Medicine（医学先进技术学院）；Isfahan University of Medical Sciences（伊斯法罕医科大学）
Age-related Macular Degeneration (AMD) and Diabetic Macular Edema (DME) are the major causes of vision loss in developed countries. Alteration of retinal layer structure and appearance of exudate are the most significant signs of these diseases. With the aim of automatic classification of DME, AMD and normal subjects from Optical Coherence Tomography (OCT) images, we proposed a classification algorithm. The two important issues intended in this approach are, not utilizing retinal layer segmentation which by itself is a challenging task and attempting to identify diseases in their early stages,…
Kobe University Hospital（神户大学医院）；Research Center for Advanced Science and Technology, The University of Tokyo（东京大学先进科学技术研究中心）；Ichinomiyanishi Nishi Hospital（一宮西医院）；Osaka Red Cross Hospital（大阪红十字医院）
Background and Purpose: We aimed to develop and evaluate an automatic acute ischemic stroke-related (AIS) detection system involving a two-stage deep learning model. Methods: We included 238 cases from two different institutions. AIS-related findings were annotated on each of the 238 sets of head CT images by referring to head magnetic resonance imaging (MRI) images in which an MRI examination was performed within 24 h following the CT scan. These 238 annotated cases were divided into a training set including 189 cases and test set including 49 cases. Subsequently, a two-stage deep learning de…
Radboud University Medical Center（拉德堡德大学医学中心）；Polytechnic University of Turin（都灵理工大学）；Istituto Nazionale di Fisica Nucleare（国家核物理研究院）；Radboud University Nijmegen（拉德堡德大学）；Radboud University（拉德堡德大学）；The Chinese University of Hong Kong（香港中文大学）；University of Pisa（比萨大学）
Automatic detection of pulmonary nodules in thoracic computed tomography (CT) scans has been an active area of research for the last two decades. However, there have only been few studies that provide a comparative performance evaluation of different systems on a common database. We have therefore set up the LUNA16 challenge, an objective evaluation framework for automatic nodule detection algorithms using the largest publicly available reference database of chest CT scans, the LIDC-IDRI data set. In LUNA16, participants develop their algorithm and upload their predictions on 888 CT scans in o…
Institute for Systems and Computer Engineering, Technology and Science (INESC TEC)（系统与计算机工程、技术与科学研究所（INESC TEC））；Faculty of Engineering of the University of Porto (FEUP)（波尔图大学工程学院（FEUP））；University of Trás-os-Montes e Alto Douro (UTAD)（山后-上杜罗大学（UTAD））；Centro Hospitalar e Universitário de S. João（圣若昂大学医院中心）；Faculty of Medicine of the University of Porto (FMUP)（波尔图大学医学院（FMUP））
Lung cancer is the deadliest type of cancer worldwide and late detection is the major factor for the low survival rate of patients. Low dose computed tomography has been suggested as a potential screening tool but manual screening is costly, time-consuming and prone to variability. This has fueled the development of automatic methods for the detection, segmentation and characterisation of pulmonary nodules but its application to clinical routine is challenging. In this study, a new database for the development and testing of pulmonary nodule computer-aided strategies is presented which intends…
Institute of Medical Robotics, Shanghai Jiao Tong University（上海交通大学医学机器人研究所）；School of Computer Science and Technology, Guizhou University（贵州大学计算机科学与技术学院）；Shanghai Chest Hospital, Shanghai Jiao Tong University（上海交通大学附属胸科医院）；Université de Lyon, INSA Lyon, CREATIS, CNRS, INSERM（里昂大学、里昂国立应用科学学院、CREATIS实验室、法国国家科学研究中心、法国国家健康与医学研究院）
Training convolutional neural networks (CNNs) for segmentation of pulmonary airway, artery, and vein is challenging due to sparse supervisory signals caused by the severe class imbalance between tubular targets and background. We present a CNNs-based method for accurate airway and artery-vein segmentation in non-contrast computed tomography. It enjoys superior sensitivity to tenuous peripheral bronchioles, arterioles, and venules. The method first uses a feature recalibration module to make the best use of features learned from the neural networks. Spatial information of features is properly i…
Rongcheng College, Harbin University of Science and Technology（哈尔滨理工大学荣成学院）；Harbin University of Science and Technology（哈尔滨理工大学）；Hunan University of Technology and Business（湖南工商大学）
Background and objective: In this paper, a modified U-Net based framework is presented, which leverages techniques from Squeeze-and-Excitation (SE) block, Atrous Spatial Pyramid Pooling (ASPP) and residual learning for accurate and robust liver CT segmentation, and the effectiveness of the proposed method was tested on two public datasets LiTS17 and SLiver07. Methods: A new network architecture called SAR-U-Net was designed. Firstly, the SE block is introduced to adaptively extract image features after each convolution in the U-Net encoder, while suppressing irrelevant regions, and highlightin…
Stanford University（斯坦福大学）；National Institute of Standards and Technology (NIST)（美国国家标准与技术研究院）
Segmentation of additive manufacturing (AM) defects in X-ray Computed Tomography (XCT) images is challenging, due to the poor contrast, small sizes and variation in appearance of defects. Automatic segmentation can, however, provide quality control for additive manufacturing. Over recent years, three-dimensional convolutional neural networks (3D CNNs) have performed well in the volumetric segmentation of medical images. In this work, we leverage techniques from the medical imaging domain and propose training a 3D U-Net model to automatically segment defects in XCT images of AM samples. This wo…
Radboud university medical center（拉德堡德大学医学中心）；Radboud Institute for Health Sciences（拉德堡德健康科学研究所）
Amidst the ongoing pandemic, several studies have shown that COVID-19 classification and grading using computed tomography (CT) images can be automated with convolutional neural networks (CNNs). Many of these studies focused on reporting initial results of algorithms that were assembled from commonly used components. The choice of these components was often pragmatic rather than systematic. For instance, several studies used 2D CNNs even though these might not be optimal for handling 3D CT volumes. This paper identifies a variety of components that increase the performance of CNN-based algorit…
ShanghaiTech University（上海科技大学）；University of Chinese Academy of Sciences（中国科学院大学）
Photoacoustic imaging (PAI) is a non-invasive imaging modality that detects the ultrasound signal generated from tissue with light excitation. Photoacoustic computed tomography (PACT) uses unfocused large-area light to illuminate the target with ultrasound transducer array for PA signal detection. Limited-view issue could cause a low-quality image in PACT due to the limitation of geometric condition. The model-based method is used to resolve this problem, which contains different regularization. To adapt fast and high-quality reconstruction of limited-view PA data, in this paper, a model-based…
Guangdong Provincial People’s Hospital（广东省人民医院）；University of Notre Dame（圣母大学）
Congenital heart disease (CHD) is the most common type of birth defect, which occurs 1 in every 110 births in the United States. CHD usually comes with severe variations in heart structure and great artery connections that can be classified into many types. Thus highly specialized domain knowledge and the time-consuming human process is needed to analyze the associated medical images. On the other hand, due to the complexity of CHD and the lack of dataset, little has been explored on the automatic diagnosis (classification) of CHDs. In this paper, we present ImageCHD, the first medical image d…
National Heart and Lung Institute, Imperial College London（帝国理工学院国家心肺研究所）；University of the Basque Country UPV/EHU（巴斯克大学（UPV/EHU））；TECNALIA, Basque Research and Technology Alliance (BRTA)（巴斯克研究与技术联盟（BRTA）泰克纳利亚研究中心）；Technical University of Munich（慕尼黑工业大学）；King Abdulaziz University（阿卜杜勒阿齐兹国王大学）；University of Alberta（阿尔伯塔大学）；The Systems Research Institute, Polish Academy of Sciences（波兰科学院系统研究所）；Royal Brompton Hospital（皇家布朗普顿医院）
Airway segmentation is crucial for the examination, diagnosis, and prognosis of lung diseases, while its manual delineation is unduly burdensome. To alleviate this time-consuming and potentially subjective manual procedure, researchers have proposed methods to automatically segment airways from computerized tomography (CT) images. However, some small-sized airway branches (e.g., bronchus and terminal bronchioles) significantly aggravate the difficulty of automatic segmentation by machine learning models. In particular, the variance of voxel values and the severe data imbalance in airway branch…
Myocardial Region-guided Feature Aggregation Net for Automatic Coronary artery Segmentation and Stenosis Assessment using Coronary Computed Tomography Angiography
School of Computer Science and Technology, Zhengzhou University of Light Industry（郑州轻工业大学计算机与通信工程学院）；School of Information Management and Engineering, Shanghai University of Finance and Economics（上海财经大学信息管理与工程学院）；Department of Applied Computing, Michigan Technological University（密歇根理工大学应用计算系）；Health Research Institute, Michigan Technological University（密歇根理工大学健康研究所）；Department of Computer Science, Kennesaw State University（肯尼索州立大学计算机科学系）
The University of Alabama（阿拉巴马大学）；University of California, Santa Cruz（加州大学圣克鲁兹分校）；New York University（纽约大学）；NYU Grossman School of Medicine（纽约大学格罗斯曼医学院）
The evaluation of infectious disease processes on radiologic images is an important and challenging task in medical image analysis. Pulmonary infections can often be best imaged and evaluated through computed tomography (CT) scans, which are often not available in low-resource environments and difficult to obtain for critically ill patients. On the other hand, X-ray, a different type of imaging procedure, is inexpensive, often available at the bedside and more widely available, but offers a simpler, two dimensional image. We show that by relying on a model that learns to generate CT images fro…
National University of Singapore（新加坡国立大学）；Singapore Eye Research Institute（新加坡眼科研究所）；Singapore National Eye Centre（新加坡国家眼科中心）；Singapore-MIT Alliance for Research and Technology（新加坡-麻省理工学院研究与技术联盟）；Yong Loo Lin School of Medicine, National University of Singapore（新加坡国立大学杨潞龄医学院）；Duke-NUS Graduate Medical School（杜克-新加坡国立大学医学院）；Nanyang Technological University Singapore（新加坡南洋理工大学）；Medical University of Vienna（维也纳医科大学）；Institute of Molecular and Clinical Ophthalmology, Basel（巴塞尔分子与临床眼科研究所）；Abyss Processing Pte Ltd（深渊处理私人有限公司）
Purpose: (1) To develop a deep learning algorithm to automatically segment structures of the optic nerve head (ONH) and macula in 3D wide-field optical coherence tomography (OCT) scans; (2) To assess whether 3D macula or ONH structures (or the combination of both) provide the best diagnostic power for glaucoma. Methods: A cross-sectional comparative study was performed which included wide-field swept-source OCT scans from 319 glaucoma subjects and 298 non-glaucoma subjects. All scans were compensated to improve deep-tissue visibility. We developed a deep learning algorithm to automatically lab…
National University of Singapore（新加坡国立大学）；Singapore Eye Research Institute（新加坡眼科研究所）；Singapore National Eye Centre（新加坡全国眼科中心）；Cardiff University（卡迪夫大学）；Newcastle Research and Innovation Institute（纽卡斯尔研究创新研究所）；National University Hospital（国立大学医院）
Accurate isolation and quantification of intraocular dimensions in the anterior segment (AS) of the eye using optical coherence tomography (OCT) images is important in the diagnosis and treatment of many eye diseases, especially angle closure glaucoma. In this study, we developed a deep convolutional neural network (DCNN) for the localization of the scleral spur, and the segmentation of anterior segment structures (iris, corneo-sclera shell, anterior chamber). With limited training data, the DCNN was able to detect the scleral spur on unseen ASOCT images as accurately as an experienced ophthal…
As a non-invasive optical imaging technique, optical coherence tomography (OCT) has proven promising for automatic fingerprint recognition system (AFRS) applications. Diverse approaches have been proposed for OCT-based fingerprint presentation attack detection (PAD). However, considering the complexity and variety of PA samples, it is extremely challenging to increase the generalization ability with the limited PA dataset. To solve the challenge, this paper presents a novel supervised learning-based PAD method, denoted as ISAPAD, which applies prior knowledge to guide network training and enha…
Image segmentation plays an important role in computer vision, object detection, traffic control, and video surveillance. Typically, it is a critical step in the 3D reconstruction of a specific organ in medical image processing which unveils the detailed tomography of organ, tumor, and nerve, and thus helping to improve the quality of surgical pathology. However, there may be high computational requirements in it. With the advent of GPUs, more complex and realistic models can be simulated, but the deployment of these facilities also requires a huge amount of capital. As a consequence, how to m…
University of California, Irvine（加州大学欧文分校）；Deep Voxel Inc.（深体素公司）
Pulmonary lobe segmentation is an important task for pulmonary disease related Computer Aided Diagnosis systems (CADs). Classical methods for lobe segmentation rely on successful detection of fissures and other anatomical information such as the location of blood vessels and airways. With the success of deep learning in recent years, Deep Convolutional Neural Network (DCNN) has been widely applied to analyze medical images like Computed Tomography (CT) and Magnetic Resonance Imaging (MRI), which, however, requires a large number of ground truth annotations. In this work, we release our manuall…
Australian Centre for Visual Technologies, The University of Adelaide（阿德莱德大学澳大利亚视觉技术中心）；School of Public Health, The University of Adelaide（阿德莱德大学公共卫生学院）；School of ITEE, The University of Queensland（昆士兰大学信息技术与电气工程学院）；Institute for Systems and Robotics, Instituto Superior Técnico（葡萄牙里斯本高等技术学院系统与机器人研究所）
We propose new methods for the prediction of 5-year mortality in elderly individuals using chest computed tomography (CT). The methods consist of a classifier that performs this prediction using a set of features extracted from the CT image and segmentation maps of multiple anatomic structures. We explore two approaches: 1) a unified framework based on deep learning, where features and classifier are automatically learned in a single optimisation process; and 2) a multi-stage framework based on the design and selection/extraction of hand-crafted radiomics features, followed by the classifier l…
