This research embarked on a comparative exploration of the holistic segmentation capabilities of Convolutional Neural Networks (CNNs) in both 2D and 3D formats, focusing on cystic fibrosis (CF) lesions. The study utilized data from two CF reference centers, covering five major CF structural changes. Initially, it compared the 2D and 3D models, highlighting the 3D model's superior capability in capturing complex features like mucus plugs and consolidations. To improve the 2D model's performance, a loss adapted to fine structures segmentation was implemented and evaluated, significantly enhancing its accuracy, though not surpassing the 3D model's performance. The models underwent further validation through external evaluation against pulmonary function tests (PFTs), confirming the robustness of the findings. Moreover, this study went beyond comparing metrics; it also included comprehensive assessments of the models' interpretability and reliability, providing valuable insights for their clinical application.
With lung cancer being the most fatal cancer worldwide, it is important to detect the disease early. A potentially effective way of detecting early cancer lesions developing along the airway walls (epithelium) is bronchoscopy. To this end, developments in bronchoscopy offer three promising noninvasive modalities for imaging bronchial lesions: white-light bronchoscopy (WLB), autofluorescence bronchoscopy (AFB), and narrow-band imaging (NBI). While these modalities give complementary views of the airway epithelium, the physician must manually inspect each video stream produced by a given modalit…
Saratoga High School（萨拉托加高中）；Stanford University（斯坦福大学）
Chest X-rays of coronavirus disease 2019 (COVID-19) patients are frequently obtained to determine the extent of lung disease and are a valuable source of data for creating artificial intelligence models. Most work to date assessing disease severity on chest imaging has focused on segmenting computed tomography (CT) images; however, given that CTs are performed much less frequently than chest X-rays for COVID-19 patients, automated lung lesion segmentation on chest X-rays could be clinically valuable. There currently exists a universal shortage of chest X-rays with ground truth COVID-19 lung le…
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）
Geisel School of Medicine at Dartmouth（达特茅斯盖泽尔医学院）；Dartmouth College（达特茅斯学院）；Dartmouth-Hitchcock Medical Center（达特茅斯-希区柯克医学中心）
In this paper, we demonstrate the feasibility and performance of deep residual neural networks for volumetric segmentation of irreversibly damaged brain tissue lesions on T1-weighted MRI scans for chronic stroke patients. A total of 239 T1-weighted MRI scans of chronic ischemic stroke patients from a public dataset were retrospectively analyzed by 3D deep convolutional segmentation models with residual learning, using a novel zoom-in&out strategy. Dice similarity coefficient (DSC), Average symmetric surface distance (ASSD), and Hausdorff distance (HD) of the identified lesions were measured by…
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）
The paper presents and comparatively analyses several deep learning approaches to automatically detect tuberculosis related lesions in lung CTs, in the context of the ImageClef 2020 Tuberculosis task. Three classes of methods, different with respect to the way the volumetric data is given as input to neural network-based classifiers are discussed and evaluated. All these come with a rich experimental analysis comprising a variety of neural network architectures, various segmentation algorithms and data augmentation schemes. The reported work belongs to the SenticLab.UAIC team, which obtained t…
Deep Learning-Based Airway Segmentation in Systemic Lupus Erythematosus Patients with Interstitial Lung Disease (SLE-ILD): A Comparative High-Resolution CT Analysis
Department of Radiology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College（放射科，北京地坛医院，中国医学科学院与北京联合医学院）；Research and Development Center (RDC), Canon Medical Systems (China)（研发部（RDC），佳能医疗系统（中国））；Canon Medical Systems (China)（佳能医疗系统（中国））
SegHeD: Segmentation of Heterogeneous Data for Multiple Sclerosis Lesions with Anatomical Constraints
Imperial College London（伦敦帝国学院）；Data Science Institute, Imperial College London（伦敦帝国学院数据科学研究所）；Beijing Institute of Technology（北京理工大学）；UK Dementia Research Institute（英国痴呆症研究所）；Rosalind Franklin Institute（罗莎琳德·富兰克林研究所）
Acute ischemic stroke lesion segmentation in non-contrast CT images using 3D convolutional neural networks
Novosibirsk State University（新西伯利亚国立大学）；International Tomography Center SB RAS（西伯利亚分院国际断层扫描中心）；Sobolev Institute of Mathematics SB RAS（西伯利亚分院索博列夫数学研究所）
City College New York（纽约市立学院）；Memorial Sloan Kettering Cancer Center（纪念斯隆凯特琳癌症中心）
Purpose: Conventional automated segmentation of the head anatomy in MRI distinguishes different brain and non-brain tissues based on image intensities and prior tissue probability maps (TPM). This works well for normal head anatomies, but fails in the presence of unexpected lesions. Deep convolutional neural networks leverage instead spatial patterns and can learn to segment lesions, but often ignore prior probabilities. Approach: We add three sources of prior information to a three-dimensional convolutional network, namely, spatial priors with a TPM, morphological priors with conditional rand…
Brain tumor imaging has been part of the clinical routine for many years to perform non-invasive detection and grading of tumors. Tumor segmentation is a crucial step for managing primary brain tumors because it allows a volumetric analysis to have a longitudinal follow-up of tumor growth or shrinkage to monitor disease progression and therapy response. In addition, it facilitates further quantitative analysis such as radiomics. Deep learning models, in particular CNNs, have been a methodology of choice in many applications of medical image analysis including brain tumor segmentation. In this …
The University of Tokyo Hospital（东京大学医院）；Chiba University（千叶大学）
From birth to death, we all experience surprisingly ubiquitous changes over time due to aging. If we can predict aging in the digital domain, that is, the digital twin of the human body, we would be able to detect lesions in their very early stages, thereby enhancing the quality of life and extending the life span. We observed that none of the previously developed digital twins of the adult human body explicitly trained longitudinal conversion rules between volumetric medical images with deep generative models, potentially resulting in poor prediction performance of, for example, ventricular v…
SegBook: A Simple Baseline and Cookbook for Volumetric Medical Image Segmentation
Shanghai AI Laboratory（上海人工智能实验室）；Xiamen University（厦门大学）；East China Normal University（华东师范大学）；University of Cambridge（剑桥大学）；Stanford University（斯坦福大学）
Universidad de Buenos Aires（布宜诺斯艾利斯大学）；Universidad Nacional del Litoral（国立滨海大学）
Automatic segmentation of white matter hyperintensities in magnetic resonance images is of paramount clinical and research importance. Quantification of these lesions serve as a predictor for risk of stroke, dementia and mortality. During the last years, convolutional neural networks (CNN) specifically tailored for biomedical image segmentation have outperformed all previous techniques in this task. However, they are extremely data-dependent, and maintain a good performance only when data distribution between training and test datasets remains unchanged. When such distribution changes but we s…
Dose escalation radiotherapy allows increased control of prostate cancer (PCa) but requires segmentation of dominant index lesions (DIL), motivating the development of automated methods for fast, accurate, and consistent segmentation of PCa DIL. We evaluated five deep-learning networks on apparent diffusion coefficient (ADC) MRI from 500 lesions in 365 patients arising from internal training Dataset 1 (1.5Tesla GE MR with endorectal coil), external ProstateX Dataset 2 (3Tesla Siemens MR), and internal inter-rater Dataset 3 (3Tesla Philips MR). The networks include: multiple resolution residual…
University of Electronic Science and Technology of China（电子科技大学）；University of Maryland School of Medicine（马里兰大学医学院）；Rutgers, the State University of New Jersey（罗格斯大学（新泽西州立大学））
Computed Tomography (CT) plays an important role in monitoring radiation-induced Pulmonary Fibrosis (PF), where accurate segmentation of the PF lesions is highly desired for diagnosis and treatment follow-up. However, the task is challenged by ambiguous boundary, irregular shape, various position and size of the lesions, as well as the difficulty in acquiring a large set of annotated volumetric images for training. To overcome these problems, we propose a novel convolutional neural network called PF-Net and incorporate it into a semi-supervised learning framework based on Iterative Confidence-…
EURECOM（欧洲通信学院）；University of Brasília（巴西利亚大学）；Syrian-Lebanese Hospital（叙利亚-黎巴嫩医院）
Gliomas are the most common malignant brain tumors that are treated with chemoradiotherapy and surgery. Magnetic Resonance Imaging (MRI) is used by radiotherapists to manually segment brain lesions and to observe their development throughout the therapy. The manual image segmentation process is time-consuming and results tend to vary among different human raters. Therefore, there is a substantial demand for automatic image segmentation algorithms that produce a reliable and accurate segmentation of various brain tissue types. Recent advances in deep learning have led to convolutional neural ne…
SWDL: Stratum-Wise Difference Learning with Deep Laplacian Pyramid for Semi-Supervised 3D Intracranial Hemorrhage Segmentation
School of Computer Science and Engineering, Southeast University（东南大学计算机科学与工程学院）；Research Center for Medical Artificial Intelligence, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences（中国科学院深圳先进技术研究院医学人工智能研究中心）；Beijing Tiantan Hospital, Capital Medical University（首都医科大学北京天坛医院）
German Center for Neurodegenerative Diseases (DZNE)（德国神经退行性疾病研究中心）；A. A. Martinos Center for Biomedical Imaging, Massachusetts General Hospital（马萨诸塞州总医院A. A. Martinos生物医学影像中心）；Department of Radiology, Harvard Medical School（哈佛医学院放射学系）
Deep learning approaches for diffusion MRI have so far focused primarily on voxel-based segmentation of lesions or white-matter fiber tracts. A drawback of representing tracts as volumetric labels, rather than sets of streamlines, is that it precludes point-wise analyses of microstructural or geometric features along a tract. Traditional tractography pipelines, which do allow such analyses, can benefit from detailed whole-brain segmentations to guide tract reconstruction. Here, we introduce fast, deep learning-based segmentation of 170 anatomical regions directly on diffusion-weighted MR image…
DeepEdit: Deep Editable Learning for Interactive Segmentation of 3D Medical Images
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）；NVIDIA（英伟达）；Semmelweis University（塞麦尔维斯大学）；EBATINCA, S.L.（EBATINCA有限公司）；Beth Israel Deaconess Medical Center（贝斯以色列女执事医疗中心）；Isomics, Inc.（Isomics公司）
Umeå University（于默奥大学）；Eindhoven University of Technology（埃因霍温理工大学）
When using Convolutional Neural Networks (CNNs) for segmentation of organs and lesions in medical images, the conventional approach is to work with inputs and outputs either as single slice (2D) or whole volumes (3D). One common alternative, in this study denoted as pseudo-3D, is to use a stack of adjacent slices as input and produce a prediction for at least the central slice. This approach gives the network the possibility to capture 3D spatial information, with only a minor additional computational cost. In this study, we systematically evaluate the segmentation performance and computationa…
Institute of Medical Technology and Intelligent Systems, Hamburg University of Technology（汉堡工业大学医学技术与智能系统研究所）；jung diagnostics GmbH（jung diagnostics 有限公司）
Purpose. Brain Magnetic Resonance Images (MRIs) are essential for the diagnosis of neurological diseases. Recently, deep learning methods for unsupervised anomaly detection (UAD) have been proposed for the analysis of brain MRI. These methods rely on healthy brain MRIs and eliminate the requirement of pixel-wise annotated data compared to supervised deep learning. While a wide range of methods for UAD have been proposed, these methods are mostly 2D and only learn from MRI slices, disregarding that brain lesions are inherently 3D and the spatial context of MRI volumes remains unexploited. Metho…
