Pathological area segmentation in cardiac magnetic resonance (MR) images plays a vital role in the clinical diagnosis of cardiovascular diseases. Because of the irregular shape and small area, pathological segmentation has always been a challenging task. We propose an anatomy prior based framework, which combines the U-net segmentation network with the attention technique. Leveraging the fact that the pathology is inclusive, we propose a neighborhood penalty strategy to gauge the inclusion relationship between the myocardium and the myocardial infarction and no-reflow areas. This neighborhood penalty strategy can be applied to any two labels with inclusive relationships (such as the whole infarction and myocardium, etc.) to form a neighboring loss. The proposed framework is evaluated on the EMIDEC dataset. Results show that our framework is effective in pathological area segmentation.
University of Edinburgh（爱丁堡大学）；University of California（加利福尼亚大学）；Cedars-Sinai Medical Center（西达赛奈医疗中心）；University of Essex（埃塞克斯大学）；The Alan Turing Institute（艾伦·图灵研究所）
Automated pathology segmentation remains a valuable diagnostic tool in clinical practice. However, collecting training data is challenging. Semi-supervised approaches by combining labelled and unlabelled data can offer a solution to data scarcity. An approach to semi-supervised learning relies on reconstruction objectives (as self-supervision objectives) that learns in a joint fashion suitable representations for the task. Here, we propose Anatomy-Pathology Disentanglement Network (APD-Net), a pathology segmentation model that attempts to learn jointly for the first time: disentanglement of an…
Wayne State University（韦恩州立大学）；Henry Ford Health System（亨利·福特医疗系统）
Recently, interest in MR-only treatment planning using synthetic CTs (synCTs) has grown rapidly in radiation therapy. However, developing class solutions for medical images that contain atypical anatomy remains a major limitation. In this paper, we propose a novel spatial attention-guided generative adversarial network (attention-GAN) model to generate accurate synCTs using T1-weighted MRI images as the input to address atypical anatomy. Experimental results on fifteen brain cancer patients show that attention-GAN outperformed existing synCT models and achieved an average MAE of 85.22$\pm$12.0…
Vanderbilt University（范德堡大学）；Vanderbilt University Medical Center（范德堡大学医学中心）
Computer-assisted quantitative analysis on Giga-pixel pathology images has provided a new avenue in histology examination. The innovations have been largely focused on cancer pathology (i.e., tumor segmentation and characterization). In non-cancer pathology, the learning algorithms can be asked to examine more comprehensive tissue types simultaneously, as a multi-label setting. The prior arts typically needed to train multiple segmentation networks in order to match the domain-specific knowledge for heterogeneous tissue types (e.g., glomerular tuft, glomerular unit, proximal tubular, distal tu…
Bangladesh University of Engineering and Technology（孟加拉国工程技术大学）；Georgia Institute of Technology（佐治亚理工学院）
Thoracic disease detection from chest radiographs using deep learning methods has been an active area of research in the last decade. Most previous methods attempt to focus on the diseased organs of the image by identifying spatial regions responsible for significant contributions to the model's prediction. In contrast, expert radiologists first locate the prominent anatomical structures before determining if those regions are anomalous. Therefore, integrating anatomical knowledge within deep learning models could bring substantial improvement in automatic disease classification. Motivated by …
Pathology-Guided AI System for Accurate Segmentation and Diagnosis of Cervical Spondylosis
School of Biomedical Engineering, Shanghai Jiao Tong University（上海交通大学生物医学工程学院）；National Engineering Research Center of Advanced Magnetic Resonance Technologies for Diagnosis and Therapy (NERC-AMRT)（先进磁共振诊断与治疗技术国家工程研究中心）；Med-X Research Institute, Shanghai Jiao Tong University（Med-X研究院，上海交通大学）；Department of Spine Surgery, Renji Hospital, School of Medicine, Shanghai Jiao Tong University（上海交通大学医学院附属仁济医院脊柱外科部）；Department of Radiology, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine（上海交通大学医学院附属瑞金医院放射科）；Department of Radiology, Renji Hospital, School of Medicine, Shanghai Jiao Tong University（上海交通大学医学院附属仁济医院放射科）
College of Physics and Information Engineering, Fuzhou University（福州大学物理与信息工程学院）；School of Basic Medical Science, Fudan University（复旦大学基础医学院）
Multi-sequence of cardiac magnetic resonance (CMR) images can provide complementary information for myocardial pathology (scar and edema). However, it is still challenging to fuse these underlying information for pathology segmentation effectively. This work presents an automatic cascade pathology segmentation framework based on multi-modality CMR images. It mainly consists of two neural networks: an anatomical structure segmentation network (ASSN) and a pathological region segmentation network (PRSN). Specifically, the ASSN aims to segment the anatomical structure where the pathology may exis…
GAPNet: Granularity Attention Network with Anatomy-Prior-Constraint for Carotid Artery Segmentation
Shandong Artificial Intelligence Institute, Qilu University of Technology (Shandong Academy of Sciences)（齐鲁工业大学（山东省科学院）山东省人工智能研究院）；School of Artificial Intelligence, Hebei University of Technology（河北工业大学人工智能学院）；School of Computer, Electronics and Information, Guangxi University（广西大学计算机与电子信息学院）；School of Intelligence Science and Technology, Nanjing University（南京大学智能科学与技术学院）；University Paris Dauphine, PSL Research University, CNRS, UMR 7534, CEREMADE（巴黎多芬大学（PSL研究大学）、法国国家科学研究中心UMR 7534、CEREMADE）
A large amount of manual segmentation is typically required to train a robust segmentation network so that it can segment objects of interest in a new imaging modality. The manual efforts can be alleviated if the manual segmentation in one imaging modality (e.g., CT) can be utilized to train a segmentation network in another imaging modality (e.g., CBCT/MRI/PET). In this work, we developed an anatomy-constrained contrastive synthetic segmentation network (AccSeg-Net) to train a segmentation network for a target imaging modality without using its ground truth. Specifically, we proposed to use a…
Yale University（耶鲁大学）；Yale School of Medicine（耶鲁大学医学院）；University of Science and Technology of China（中国科学技术大学）；Suzhou Institute for Advanced Research, University of Science and Technology of China（中国科学技术大学苏州高等研究院）；Chinese Academy of Sciences（中国科学院）
Multimodal image registration has many applications in diagnostic medical imaging and image-guided interventions, such as Transcatheter Arterial Chemoembolization (TACE) of liver cancer guided by intraprocedural CBCT and pre-operative MR. The ability to register peri-procedurally acquired diagnostic images into the intraprocedural environment can potentially improve the intra-procedural tumor targeting, which will significantly improve therapeutic outcomes. However, the intra-procedural CBCT often suffers from suboptimal image quality due to lack of signal calibration for Hounsfield unit, limi…
We propose an atlas-based method to segment the intracochlear anatomy (ICA) in the post-implantation CT (Post-CT) images of cochlear implant (CI) recipients that preserves the point-to-point correspondence between the meshes in the atlas and the segmented volumes. To solve this problem, which is challenging because of the strong artifacts produced by the implant, we use a pair of co-trained deep networks that generate dense deformation fields (DDFs) in opposite directions. One network is tasked with registering an atlas image to the Post-CT images and the other network is tasked with registeri…
The difficulty of detecting mitosis and its similarity to non-mitosis objects has remained a challenge in computational pathology. The lack of publicly available data has added more complexity. Deep learning algorithms have shown potentials in mitosis detection tasks. However, they face challenges when applied to pathology images with dense medium and diverse dataset. This paper introduces an optimized UV-Net architecture, developed to focus on mitosis details with high-resolution through feature preservation. Stain normalization methods are used to generalize the trained network. An F1 score …
Helmholtz AI（亥姆霍兹AI）；Helmholtz Center Munich（慕尼黑亥姆霍兹中心）；Klinikum Rechts der Isar（右岸医院）；Technical University of Munich (TUM)（慕尼黑工业大学）
In recent years, data-driven machine learning (ML) methods have revolutionized the computer vision community by providing novel efficient solutions to many unsolved (medical) image analysis problems. However, due to the increasing privacy concerns and data fragmentation on many different sites, existing medical data are not fully utilized, thus limiting the potential of ML. Federated learning (FL) enables multiple parties to collaboratively train a ML model without exchanging local data. However, data heterogeneity (non-IID) among the distributed clients is yet a challenge. To this end, we pro…
Fudan University（复旦大学）；University of Oxford（牛津大学）；Zhongshan Hospital, Fudan University（复旦大学附属中山医院）；Shanghai Medical School, Fudan University（复旦大学上海医学院）；Shanghai Institute of Medical Imaging（上海医学影像研究所）
Myocardial pathology segmentation (MyoPS) can be a prerequisite for the accurate diagnosis and treatment planning of myocardial infarction. However, achieving this segmentation is challenging, mainly due to the inadequate and indistinct information from an image. In this work, we develop an end-to-end deep neural network, referred to as MyoPS-Net, to flexibly combine five-sequence cardiac magnetic resonance (CMR) images for MyoPS. To extract precise and adequate information, we design an effective yet flexible architecture to extract and fuse cross-modal features. This architecture can tackle …
ASCON: Anatomy-aware Supervised Contrastive Learning Framework for Low-dose CT Denoising
Institute of Science and Technology for Brain-Inspired Intelligence, Fudan University（复旦大学类脑智能科学与技术研究院）；School of Cyber Science and Engineering, Sichuan University（四川大学网络空间安全学院）
Shanghai Jiao Tong University（上海交通大学）；Peking Union Medical College Hospital（北京协和医院）
The segmentation of coronary arteries by convolutional neural network is promising yet requires a large amount of labor-intensive manual annotations. Transferring knowledge from retinal vessels in widely-available public labeled fundus images (FIs) has a potential to reduce the annotation requirement for coronary artery segmentation in X-ray angiograms (XAs) due to their common tubular structures. However, it is challenged by the cross-anatomy domain shift due to the intrinsically different vesselness characteristics in different anatomical regions under even different imaging protocols. To so…
Z 2 Sky Technologies Inc.（Z 2 天工科技公司）；University of Rochester（罗切斯特大学）；Key Lab of Intelligent Information Processing of Chinese Academy of Sciences (CAS), Institute of Computing Technology, CAS（中国科学院计算技术研究所 中国科学院智能信息处理重点实验室）；University of Science and Technology of China（中国科学技术大学）；Suzhou Institute for Advance Research, University of Science and Technology of China（中国科学技术大学苏州高等研究院）
Spinal surgery planning necessitates automatic segmentation of vertebrae in cone-beam computed tomography (CBCT), an intraoperative imaging modality that is widely used in intervention. However, CBCT images are of low-quality and artifact-laden due to noise, poor tissue contrast, and the presence of metallic objects, causing vertebra segmentation, even manually, a demanding task. In contrast, there exists a wealth of artifact-free, high quality CT images with vertebra annotations. This motivates us to build a CBCT vertebra segmentation model using unpaired CT images with annotations. To overco…
Nanjing University of Information Science & Technology（南京信息工程大学）
Cerebrovascular accident, or commonly known as stroke, is an acute disease with extreme impact on patients and healthcare systems and is the second largest cause of death worldwide. Fast and precise stroke lesion detection and location is an extreme important process with regards to stroke diagnosis, treatment, and prognosis. Except from the manual segmentation approach, machine learning based segmentation methods are the most promising ones when considering efficiency and accuracy, and convolutional neural network based models are the first of its kind. However, most of these neural network m…
Magnetic Resonance Imaging (MRI) plays an important role in diagnosing the parotid tumor, where accurate segmentation of tumors is highly desired for determining appropriate treatment plans and avoiding unnecessary surgery. However, the task remains nontrivial and challenging due to ambiguous boundaries and various sizes of the tumor, as well as the presence of a large number of anatomical structures around the parotid gland that are similar to the tumor. To overcome these problems, we propose a novel anatomy-aware framework for automatic segmentation of parotid tumors from multimodal MRI. Fir…
Leveraging Pathology Foundation Models for Panoptic Segmentation of Melanoma in H&E Images
Tissue Image Analytics Centre, Department of Computer Science, University of Warwick, Coventry, United Kingdom（威斯敏斯特大学计算机科学系病理图像分析中心）；University Hospitals of Derby and Burton NHS Foundation Trust, United Kingdom（德比和伯顿国家健康服务基金会医院）；Department of Pathophysiology and Allergy Research, Center for Pathophysiology, Infectiology and Immunology, Medical University of Vienna, Austria（维也纳医学大学病理学与过敏研究系）；TissueGnostics GmbH, Vienna, Austria（维也纳TissueGnostics公司）
本文提出一种结合病理学基础模型Virchow2特征与Efficient-UNet的深度学习网络，用于黑色素瘤H&E图像五类组织分割，并在PUMA Grand Challenge中夺冠，验证了基础模型加速计算病理学流程的有效性。
School of Engineering, University of Edinburgh（爱丁堡大学工程学院）；Center for Cardiovascular Science, University of Edinburgh（爱丁堡大学心血管科学中心）；The Alan Turing Institute（艾伦·图灵研究所）
Automatic segmentation of multi-sequence (multi-modal) cardiac MR (CMR) images plays a significant role in diagnosis and management for a variety of cardiac diseases. However, the performance of relevant algorithms is significantly affected by the proper fusion of the multi-modal information. Furthermore, particular diseases, such as myocardial infarction, display irregular shapes on images and occupy small regions at random locations. These facts make pathology segmentation of multi-modal CMR images a challenging task. In this paper, we present the Max-Fusion U-Net that achieves improved path…
Institute of Network Technology（网络技术研究所）；School of Automation（自动化学院）；Beijing University of Posts and Telecommunications（北京邮电大学）
Automatic cell segmentation is an essential step in the pipeline of computer-aided diagnosis (CAD), such as the detection and grading of breast cancer. Accurate segmentation of cells can not only assist the pathologists to make a more precise diagnosis, but also save much time and labor. However, this task suffers from stain variation, cell inhomogeneous intensities, background clutters and cells from different tissues. To address these issues, we propose an Attention Enforced Network (AENet), which is built on spatial attention module and channel attention module, to integrate local features …
Full-Head Segmentation of MRI with Abnormal Brain Anatomy: Model and Data Release
The City College of New York（纽约市立学院）；New York University（纽约大学）；Georgetown University（乔治城大学）；University of North Carolina School of Medicine（北卡罗来纳大学医学院）；Soterix Medical
Segmentation has been a major task in neuroimaging. A large number of automated methods have been developed for segmenting healthy and diseased brain tissues. In recent years, deep learning techniques have attracted a lot of attention as a result of their high accuracy in different segmentation problems. We present a new deep learning based segmentation method, DeepMRSeg, that can be applied in a generic way to a variety of segmentation tasks. The proposed architecture combines recent advances in the field of biomedical image segmentation and computer vision. We use a modified UNet architectur…
Philips Research（飞利浦研究院）；Skolkovo Institute of Science and Technology（斯科尔科沃科技学院）
Domain Adaptation (DA) methods are widely used in medical image segmentation tasks to tackle the problem of differently distributed train (source) and test (target) data. We consider the supervised DA task with a limited number of annotated samples from the target domain. It corresponds to one of the most relevant clinical setups: building a sufficiently accurate model on the minimum possible amount of annotated data. Existing methods mostly fine-tune specific layers of the pretrained Convolutional Neural Network (CNN). However, there is no consensus on which layers are better to fine-tune, e.…
Brains with complex distortion of cerebral anatomy present several challenges to automatic tissue segmentation methods of T1-weighted MR images. First, the very high variability in the morphology of the tissues can be incompatible with the prior knowledge embedded within the algorithms. Second, the availability of MR images of distorted brains is very scarce, so the methods in the literature have not addressed such cases so far. In this work, we present the first evaluation of state-of-the-art automatic tissue segmentation pipelines on T1-weighted images of brains with different severity of co…
We present BrainPainter, a software that automatically generates images of highlighted brain structures given a list of numbers corresponding to the output colours of each region. Compared to existing visualisation software (i.e. Freesurfer, SPM, 3D Slicer), BrainPainter has three key advantages: (1) it does not require the input data to be in a specialised format, allowing BrainPainter to be used in combination with any neuroimaging analysis tools, (2) it can visualise both cortical and subcortical structures and (3) it can be used to generate movies showing dynamic processes, e.g. propagatio…
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…
