Automated brain tissue segmentation into white matter (WM), gray matter (GM), and cerebro-spinal fluid (CSF) from magnetic resonance images (MRI) is helpful in the diagnosis of neuro-disorders such as epilepsy, Alzheimer's, multiple sclerosis, etc. However, thin GM structures at the periphery of cortex and smooth transitions on tissue boundaries such as between GM and WM, or WM and CSF pose difficulty in building a reliable segmentation tool. This paper proposes a Fully Convolutional Neural Network (FCN) tool, that is a hybrid of two widely used deep learning segmentation architectures SegNet and U-Net, for improved brain tissue segmentation. We propose a skip connection inspired from U-Net, in the SegNet architetcure, to incorporate fine multiscale information for better tissue boundary identification. We show that the proposed U-SegNet architecture, improves segmentation performance, as measured by average dice ratio, to 89.74% on the widely used IBSR dataset consisting of T-1 weighted MRI volumes of 18 subjects.
ACS-SegNet: An Attention-Based CNN-SegFormer Segmentation Network for Tissue Segmentation in Histopathology
Research Center for Medical Image Analysis(医学图像分析研究中心);Artificial Intelligence, Department of Medicine, Faculty of Medicine(人工智能,医学系,医学学院);Dentistry, Danube Private University Department of Pathophysiology(牙科,丹ube私立大学病理学系);Allergy Research, Center of Pathophysiology, Infectiology(过敏研究,病理学中心,感染学);Immunology, Medical University of Vienna Comprehensive Center for AI in Medicine (CAIM), Medical University of Vienna(免疫学,维也纳医学大学人工智能医学中心(CAIM),维也纳医学大学)
Brain extraction or skull stripping of magnetic resonance images (MRI) is an essential step in neuroimaging studies, the accuracy of which can severely affect subsequent image processing procedures. Current automatic brain extraction methods demonstrate good results on human brains, but are often far from satisfactory on nonhuman primates, which are a necessary part of neuroscience research. To overcome the challenges of brain extraction in nonhuman primates, we propose a fully-automated brain extraction pipeline combining deep Bayesian convolutional neural network (CNN) and fully connected th…
Automatic segmentation of brain Magnetic Resonance Imaging (MRI) images is one of the vital steps for quantitative analysis of brain for further inspection. In this paper, NeuroNet has been adopted to segment the brain tissues (white matter (WM), grey matter (GM) and cerebrospinal fluid (CSF)) which uses Residual Network (ResNet) in encoder and Fully Convolution Network (FCN) in the decoder. To achieve the best performance, various hyper-parameters have been tuned, while, network parameters (kernel and bias) were initialized using the NeuroNet pre-trained model. Different pre-processing pipeli…
Magnetic Resonance Imaging (MRI) is widely used in the pathological and functional studies of the brain, such as epilepsy, tumor diagnosis, etc. Automated accurate brain tissue segmentation like cerebro-spinal fluid (CSF), gray matter (GM), white matter (WM) is the basis of these studies and many researchers are seeking it to the best. Based on the truth that multi-channel segmentation network with its own ground truth achieves up to average dice ratio 0.98, we propose a novel method that we add a fourth channel with the ground truth of the most similar image's obtained by CBIR from the databa…
Accurate segmentation of MR brain tissue is a crucial step for diagnosis, surgical planning, and treatment of brain abnormalities. Automatic and reliable segmenta-tion methods are required to assist doctor. Over the last few years, deep learning especially deep convolutional neural networks (CNNs) have emerged as one of the most prominent approaches for image recognition problems in various do-mains. But the improvement of deep networks always needs inspiration, which is rare for the ordinary. Until now,there have been reasonable MR brain tissue segmentation methods,all of which can achieve pr…
Tsinghua University(清华大学);Beijing Sanbo Brain Hospital(北京三博脑科医院);The First Affiliated Hospital of Harbin Medical University(哈尔滨医科大学附属第一医院)
Accurate segmentation of MR brain tissue is a crucial step for diagnosis,surgical planning, and treatment of brain abnormalities. However,it is a time-consuming task to be performed by medical experts. So, automatic and reliable segmentation methods are required. How to choose appropriate training dataset from limited labeled dataset rather than the whole also has great significance in saving training time. In addition, medical data labeled is too rare and expensive to obtain extensively, so choosing appropriate unlabeled dataset instead of all the datasets to annotate, which can attain at lea…
Shanghai United Imaging Intelligence Co. Ltd(上海联影智能医疗科技有限公司);Southern Medical University(南方医科大学)
In brain tumor diagnosis and surgical planning, segmentation of tumor regions and accurate analysis of surrounding normal tissues are necessary for physicians. Pathological variability often renders difficulty to register a well-labeled normal atlas to such images and to automatic segment/label surrounding normal brain tissues. In this paper, we propose a new registration approach that first segments brain tumor using a U-Net and then simulates missed normal tissues within the tumor region using a partial convolutional network. Then, a standard normal brain atlas image is registered onto such …
University of Calcutta(加尔各答大学);West Bengal University of Technology(西孟加拉技术大学)
Tumor segmentation from magnetic resonance imaging (MRI) data is an important but time consuming manual task performed by medical experts. Automating this process is a challenging task because of the high diversity in the appearance of tumor tissues among different patients and in many cases similarity with the normal tissues. MRI is an advanced medical imaging technique providing rich information about the human soft-tissue anatomy. There are different brain tumor detection and segmentation methods to detect and segment a brain tumor from MRI images. These detection and segmentation approache…
University of Girona(赫罗纳大学);Computer Vision and Robotics Institute(计算机视觉与机器人研究所)
Accurate brain tissue segmentation in Magnetic Resonance Imaging (MRI) has attracted the attention of medical doctors and researchers since variations in tissue volume help in diagnosing and monitoring neurological diseases. Several proposals have been designed throughout the years comprising conventional machine learning strategies as well as convolutional neural networks (CNN) approaches. In particular, in this paper, we analyse a sub-group of deep learning methods producing dense predictions. This branch, referred in the literature as Fully CNN (FCNN), is of interest as these architectures …
University of Central Florida(中佛罗里达大学);Kyungpook National University(庆北国立大学)
Medical image segmentation being a substantial component of image processing plays a significant role to analyze gross anatomy, to locate an infirmity and to plan the surgical procedures. Segmentation of brain Magnetic Resonance Imaging (MRI) is of considerable importance for the accurate diagnosis. However, precise and accurate segmentation of brain MRI is a challenging task. Here, we present an efficient framework for segmentation of brain MR images. For this purpose, Gabor transform method is used to compute features of brain MRI. Then, these features are classified by using four different …
University of Zurich(苏黎世大学);ETH Zurich(苏黎世联邦理工学院);Lausanne University Hospital(洛桑大学医院);University of Lausanne(洛桑大学);Technical University of Munich(慕尼黑工业大学);Brain Research Institute, University of Zurich(苏黎世大学脑研究所);University of Debrecen(德布勒森大学)
It is critical to quantitatively analyse the developing human fetal brain in order to fully understand neurodevelopment in both normal fetuses and those with congenital disorders. To facilitate this analysis, automatic multi-tissue fetal brain segmentation algorithms are needed, which in turn requires open databases of segmented fetal brains. Here we introduce a publicly available database of 50 manually segmented pathological and non-pathological fetal magnetic resonance brain volume reconstructions across a range of gestational ages (20 to 33 weeks) into 7 different tissue categories (extern…
DuMeta++: Spatiotemporal Dual Meta-Learning for Generalizable Few-Shot Brain Tissue Segmentation Across Diverse Ages
School of Mathematics and Statistics, Xi’an Jiaotong University(西安交通大学数学与统计学院);Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi’an Jiaotong University(教育部生物医学信息工程重点实验室,西安交通大学生命科学与技术学院)
Department of Computer Science, University of North Carolina at Chapel Hill, USA(北卡罗来纳大学教堂山分校计算机科学系);Department of Computer Science, University of Salzburg, Austria(萨尔茨堡大学计算机科学系);Kitware Inc., USA(Kitware公司);Center for Biomedical Image Computing and Analytics, Perelman School of Medicine, University of Pennsylvania, USA(宾夕法尼亚大学佩雷尔曼医学院生物医学图像计算与分析中心);Department of Computer Science, Technical University of Munich, Germany(慕尼黑工业大学计算机科学系);Institute of Neuroimaging and Informatics, University of Southern California, USA(南加州大学神经影像与信息学研究所);David Geffen School of Medicine, UCLA Medical Center, USA(加州大学洛杉矶分校医学中心大卫·格芬医学院)
Brain extraction from images is a common pre-processing step. Many approaches exist, but they are frequently only designed to perform brain extraction from images without strong pathologies. Extracting the brain from images with strong pathologies, for example, the presence of a tumor or of a traumatic brain injury, is challenging. In such cases, tissue appearance may deviate from normal tissue and violates algorithmic assumptions for these approaches; hence, the brain may not be correctly extracted. This paper proposes a brain extraction approach which can explicitly account for pathologies b…
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)
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 proc…
mViSE: A Visual Search Engine for Analyzing Multiplex IHC Brain Tissue Images
Cullen College of Engineering, University of Houston(休斯顿大学塞勒恩工程学院);The University of Texas McGovern Medical School(德克萨斯大学麦格芬医学学院);National Institute of Neurological Disorders and Stroke(国家神经疾病与中风研究所)
One-shot segmentation of brain tissues is typically a dual-model iterative learning: a registration model (reg-model) warps a carefully-labeled atlas onto unlabeled images to initialize their pseudo masks for training a segmentation model (seg-model); the seg-model revises the pseudo masks to enhance the reg-model for a better warping in the next iteration. However, there is a key weakness in such dual-model iteration that the spatial misalignment inevitably caused by the reg-model could misguide the seg-model, which makes it converge on an inferior segmentation performance eventually. In this…
Advanced Brain Tissue Imaging with Data-Consistent Diffusion Priors in Laminographic X-Ray Nanoimaging
École Polytechnique Fédérale de Lausanne(洛桑联邦理工学院);Paul Scherrer Institute(保罗·谢勒研究所);The Francis Crick Institute(弗朗西斯·克里克研究所);Mineral Resource CSIRO(澳大利亚联邦科学与工业研究组织矿产资源部);ESRF, The European Synchrotron(欧洲同步辐射光源)
Harvard Medical School(哈佛医学院);Northeastern University(东北大学)
The most recent fast and accurate image segmentation methods are built upon fully convolutional deep neural networks. In this paper, we propose new deep learning strategies for DenseNets to improve segmenting images with subtle differences in intensity values and features. We aim to segment brain tissue on infant brain MRI at about 6 months of age where white matter and gray matter of the developing brain show similar T1 and T2 relaxation times, thus appear to have similar intensity values on both T1- and T2-weighted MRI scans. Brain tissue segmentation at this age is, therefore, very challeng…
Denoising Diffusion Models for 3D Healthy Brain Tissue Inpainting
University Hospital Basel(巴塞尔大学医院);Helmholtz Center Munich(慕尼黑亥姆霍兹中心);Helmholtz AI(亥姆霍兹人工智能);Technical University of Munich(慕尼黑工业大学);University of Basel(巴塞尔大学);University of Zurich(苏黎世大学);Klinikum rechts der Isar(伊斯河畔医院);TranslaTUM - Central Institute for Translational Cancer Research(慕尼黑工业大学转化肿瘤学中央研究所(TranslaTUM))
University Medical Center Utrecht(乌得勒支大学医学中心);Wilhelmina Children’s Hospital(威廉明娜儿童医院);Utrecht University(乌得勒支大学)
MR images of fetuses allow clinicians to detect brain abnormalities in an early stage of development. The cornerstone of volumetric and morphologic analysis in fetal MRI is segmentation of the fetal brain into different tissue classes. Manual segmentation is cumbersome and time consuming, hence automatic segmentation could substantially simplify the procedure. However, automatic brain tissue segmentation in these scans is challenging owing to artifacts including intensity inhomogeneity, caused in particular by spontaneous fetal movements during the scan. Unlike methods that estimate the bias f…
Columbia University(哥伦比亚大学);Mortimer B. Zuckerman Mind Brain Behavior Institute(Mortimer B. Zuckerman 心智与脑行为研究所)
Brain tissue segmentation has demonstrated great utility in quantifying MRI data through Voxel-Based Morphometry and highlighting subtle structural changes associated with various conditions within the brain. However, manual segmentation is highly labor-intensive, and automated approaches have struggled due to properties inherent to MRI acquisition, leaving a great need for an effective segmentation tool. Despite the recent success of deep convolutional neural networks (CNNs) for brain tissue segmentation, many such solutions do not generalize well to new datasets, which is critical for a reli…
Automatic segmentation of brain MR images into white matter (WM), gray matter (GM), and cerebrospinal fluid (CSF) is critical for tissue volumetric analysis and cortical surface reconstruction. Due to dramatic structural and appearance changes associated with developmental and aging processes, existing brain tissue segmentation methods are only viable for specific age groups. Consequently, methods developed for one age group may fail for another. In this paper, we make the first attempt to segment brain tissues across the entire human lifespan (0-100 years of age) using a unified deep learning…
Department of Electrical Engineering, Indian Institute of Technology Madras (IITM)(电子工程系,印度理工学院Madras(IITM));Sudha Gopalakrishnan Brain Centre (SGBC), IITM(Sudha Gopalakrishnan脑中心(SGBC),IITM)
Brain Tissues Segmentation on MR Perfusion Images Using CUSUM Filter for Boundary Pixels
National Technical University of Ukraine “Igor Sikorsky Kyiv Polytechnic Institute”(乌克兰国立技术大学“伊戈尔·西科尔斯基基辅理工学院”);Taras Shevchenko National University of Kyiv(基辅塔拉斯·舍甫琴科国立大学)
Synthetic magnetic resonance images for domain adaptation: Application to fetal brain tissue segmentation
Lausanne University Hospital (CHUV)(洛桑大学医院(CHUV));University of Lausanne (UNIL)(洛桑大学(UNIL));CIBM Center for Biomedical Imaging(CIBM生物医学成像中心);University Children’s Hospital Zurich(苏黎世大学儿童医院);University of Zurich(苏黎世大学);Neuroscience Center Zurich(苏黎世神经科学中心)
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)
Imperial College London(伦敦帝国学院);King’s College London(伦敦国王学院);FAU Erlangen-Nürnberg(埃尔朗根-纽伦堡大学);Technical University of Munich(慕尼黑工业大学)
Fetal Magnetic Resonance Imaging (MRI) is used in prenatal diagnosis and to assess early brain development. Accurate segmentation of the different brain tissues is a vital step in several brain analysis tasks, such as cortical surface reconstruction and tissue thickness measurements. Fetal MRI scans, however, are prone to motion artifacts that can affect the correctness of both manual and automatic segmentation techniques. In this paper, we propose a novel network structure that can simultaneously generate conditional atlases and predict brain tissue segmentation, called CAS-Net. The condition…
International University of Business Agriculture and Technology(国际商业、农业与技术大学)
Tissue classification is one of the significant tasks in the field of biomedical image analysis. Magnetic Resonance Imaging (MRI) is of great importance in tissue classification especially in the areas of brain tissue classification which is able to recognize anatomical areas of interest such as surgical planning, monitoring therapy, clinical drug trials, image registration, stereotactic neurosurgery, radiotherapy etc. The task of this paper is to implement different unsupervised classification algorithms in ITK and perform tissue classification (white matter, gray matter, cerebrospinal fluid …
Department of Neuro-Oncology, Massachusetts General Hospital(麻省总医院神经肿瘤科);MGH & BWH Center for Clinical Data Science(麻省总医院与布莱根妇女医院临床数据科学中心);Department of Radiology, Massachusetts General Hospital(麻省总医院放射科);Massachusetts General Hospital(麻省总医院);NVIDIA(英伟达)
Deep learning has quickly become the weapon of choice for brain lesion segmentation. However, few existing algorithms pre-configure any biological context of their chosen segmentation tissues, and instead rely on the neural network's optimizer to develop such associations de novo. We present a novel method for applying deep neural networks to the problem of glioma tissue segmentation that takes into account the structured nature of gliomas - edematous tissue surrounding mutually-exclusive regions of enhancing and non-enhancing tumor. We trained multiple deep neural networks with a 3D U-Net arc…
Brain tumor segmentation intends to delineate tumor tissues from healthy brain tissues. The tumor tissues include necrosis, peritumoral edema, and active tumor. In contrast, healthy brain tissues include white matter, gray matter, and cerebrospinal fluid. The MRI based brain tumor segmentation research is gaining popularity as; 1. It does not irradiate ionized radiation like X-ray or computed tomography imaging. 2. It produces detailed pictures of internal body structures. The MRI scans are input to deep learning-based approaches which are useful for automatic brain tumor segmentation. The fea…
King’s College London(伦敦国王学院);School of Biomedical Engineering & Imaging Sciences(生物医学工程与成像科学学院);King’s College Hospital NHS Foundation Trust(国王学院医院国民健康服务基金会信托);NVIDIA(英伟达);Dementia Research Centre, UCL Institute of Neurology, UCL(伦敦大学学院痴呆研究中心、伦敦大学学院神经学研究所、伦敦大学学院);Department of Medical Physics, UCL(伦敦大学学院医学物理系);Department of Neuroradiology(神经放射科);St. Thomas’ Hospital(圣托马斯医院)
Brain tissue segmentation from multimodal MRI is a key building block of many neuroimaging analysis pipelines. Established tissue segmentation approaches have, however, not been developed to cope with large anatomical changes resulting from pathology, such as white matter lesions or tumours, and often fail in these cases. In the meantime, with the advent of deep neural networks (DNNs), segmentation of brain lesions has matured significantly. However, few existing approaches allow for the joint segmentation of normal tissue and brain lesions. Developing a DNN for such a joint task is currently …
Tissue Segmentation of Thick-Slice Fetal Brain MR Scans with Guidance from High-Quality Isotropic Volumes
ShanghaiTech University(上海科技大学);Fudan University(复旦大学);Obstetrics and Gynecology Hospital of Fudan University(复旦大学附属妇产科医院);Northwestern Polytechnical University(西北工业大学);Shanghai United Imaging Intelligence company Ltd.(上海联影智能科技有限公司);Shanghai Clinical Research and Trial Center(上海临床研究中心)
Brain tissue segmentation from multimodal MRI is a key building block of many neuroscience analysis pipelines. It could also play an important role in many clinical imaging scenarios. Established tissue segmentation approaches have however not been developed to cope with large anatomical changes resulting from pathology. The effect of the presence of brain lesions, for example, on their performance is thus currently uncontrolled and practically unpredictable. Contrastingly, with the advent of deep neural networks (DNNs), segmentation of brain lesions has matured significantly and is achieving …
Comparative Study of Probabilistic Atlas and Deep Learning Approaches for Automatic Brain Tissue Segmentation from MRI Using N4 Bias Field Correction and Anisotropic Diffusion Pre-processing Techniques
University of Girona(赫罗纳大学);University of Burgundy(勃艮第大学);University of Cassino and Southern Lazio(卡西诺和南拉齐奥大学)
Conditional Fetal Brain Atlas Learning for Automatic Tissue Segmentation
Computational Imaging Research Lab(计算成像研究实验室);Department of Biomedical Imaging and Image-guided Therapy(生物医学成像与影像引导治疗部门);Medical University of Vienna(维也纳医科大学);Comprehensive Center for Artificial Intelligence in Medicine(医学人工智能综合中心);Division of General Radiology(普通放射学分会);Medical University Vienna(维也纳医科大学);Christian Doppler Laboratory for Mathematical Modelling and Simulation of Next-Generation Medical Ultrasound Devices(基督教·多普勒医学影像建模与模拟实验室)
University of Copenhagen(哥本哈根大学);Erasmus Medical Center(伊拉斯谟医学中心)
Suppose one is faced with the challenge of tissue segmentation in MR images, without annotators at their center to provide labeled training data. One option is to go to another medical center for a trained classifier. Sadly, tissue classifiers do not generalize well across centers due to voxel intensity shifts caused by center-specific acquisition protocols. However, certain aspects of segmentations, such as spatial smoothness, remain relatively consistent and can be learned separately. Here we present a smoothness prior that is fit to segmentations produced at another medical center. This inf…
Automated Segmentation of Coronal Brain Tissue Slabs for 3D Neuropathology
Martinos Center for Biomedical Imaging, Massachusetts General Hospital and Harvard Medical School(马萨诸塞州总医院和哈佛医学院生物医学成像中心);Massachusetts Alzheimer’s Disease Research Center, Massachusetts General Hospital and Harvard Medical School(马萨诸塞州阿尔茨海默病研究中心,马萨诸塞州总医院和哈佛医学院);Department of Neurological Surgery, University of Washington School of Medicine(华盛顿大学医学院神经外科部门);Department of Laboratory Medicine and Pathology, University of Washington School of Medicine(华盛顿大学医学院实验室医学与病理学部门);Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology(麻省理工学院计算机科学与人工智能实验室);Hawkes Institute, University College London(伦敦大学学院霍克斯研究所)
Boston Children’s Hospital(波士顿儿童医院);Harvard Medical School(哈佛医学院)
Automatic fetal brain tissue segmentation can enhance the quantitative assessment of brain development at this critical stage. Deep learning methods represent the state of the art in medical image segmentation and have also achieved impressive results in brain segmentation. However, effective training of a deep learning model to perform this task requires a large number of training images to represent the rapid development of the transient fetal brain structures. On the other hand, manual multi-label segmentation of a large number of 3D images is prohibitive. To address this challenge, we segm…
Improving cross-domain brain tissue segmentation in fetal MRI with synthetic data
Lausanne University Hospital(洛桑大学医院);University of Lausanne (UNIL)(洛桑大学);CIBM Center for Biomedical Imaging(CIBM生物医学成像中心);King’s College London(伦敦国王学院);FAU Erlangen-Nuremberg(埃尔朗根-纽伦堡大学)
Segmentation of Gray Matters and White Matters from Brain MRI data
Department of Computer Science and Engineering(计算机科学与工程系);Waseda University(早稻田大学);Department of Neurosurgery(神经外科);Teraoka Memorial Hospital(寺田纪念医院);Department of Radiology(放射科);Nippon Medical School Hospital(日本医学大学医院);Tokyo Rosai Hospital(东京罗赛医院)
Ege University(埃格大学);National Institute on Aging, National Institutes of Health(美国国立卫生研究院国家老龄化研究所);Johns Hopkins University School of Medicine(约翰斯·霍普金斯大学医学院);University of Central Florida(中佛罗里达大学)
Magnetic resonance imaging (MRI) is the non-invasive modality of choice for body tissue composition analysis due to its excellent soft tissue contrast and lack of ionizing radiation. However, quantification of body composition requires an accurate segmentation of fat, muscle and other tissues from MR images, which remains a challenging goal due to the intensity overlap between them. In this study, we propose a fully automated, data-driven image segmentation platform that addresses multiple difficulties in segmenting MR images such as varying inhomogeneity, non-standardness, and noise, while pr…
Facebook Artificial Intelligence(脸书人工智能);University of Southern California(南加州大学);Massachusetts General Hospital(麻省总医院);Harvard Medical School(哈佛医学院)
Deformable registration of magnetic resonance images between patients with brain tumors and healthy subjects has been an important tool to specify tumor geometry through location alignment and facilitate pathological analysis. Since tumor region does not match with any ordinary brain tissue, it has been difficult to deformably register a patients brain to a normal one. Many patient images are associated with irregularly distributed lesions, resulting in further distortion of normal tissue structures and complicating registration's similarity measure. In this work, we follow a multi-step contex…