We present a novel approach to automatically segment magnetic resonance (MR) images of the human brain into anatomical regions. Our methodology is based on a deep artificial neural network that assigns each voxel in an MR image of the brain to its corresponding anatomical region. The inputs of the network capture information at different scales around the voxel of interest: 3D and orthogonal 2D intensity patches capture the local spatial context while large, compressed 2D orthogonal patches and distances to the regional centroids enforce global spatial consistency. Contrary to commonly used segmentation methods, our technique does not require any non-linear registration of the MR images. To benchmark our model, we used the dataset provided for the MICCAI 2012 challenge on multi-atlas labelling, which consists of 35 manually segmented MR images of the brain. We obtained competitive results (mean dice coefficient 0.725, error rate 0.163) showing the potential of our approach. To our knowledge, our technique is the first to tackle the anatomical segmentation of the whole brain using deep neural networks.
Research Institute for Signals, Systems and Computational Intelligence, sinc(i)（信号、系统与计算智能研究所）；CONICET（国家科学技术研究委员会）；Universidad Nacional del Litoral（国立滨海大学）
In this work we address the problem of landmark-based segmentation for anatomical structures. We propose HybridGNet, an encoder-decoder neural architecture which combines standard convolutions for image feature encoding, with graph convolutional neural networks to decode plausible representations of anatomical structures. We benchmark the proposed architecture considering other standard landmark and pixel-based models for anatomical segmentation in chest x-ray images, and found that HybridGNet is more robust to image occlusions. We also show that it can be used to construct landmark-based segm…
Anatomical Consistency Distillation and Inconsistency Synthesis for Brain Tumor Segmentation with Missing Modalities
University of Science and Technology of China（中国科学技术大学）；Tianjin University（天津大学）；Beijing Tiantan Hospital, Capital Medical University（首都医科大学附属北京天坛医院）；Hefei Comprehensive National Science Center（合肥综合性国家科学中心）
National Institute of Dental and Craniofacial Research (NIDCR), National Institutes of Health (NIH)（美国国立卫生研究院（NIH）国立牙科与颅面研究所（NIDCR））；University of South Dakota Sanford School of Medicine（南达科他大学桑福德医学院）；University of Central Florida（中佛罗里达大学）
In this paper, we propose a novel deep learning framework for anatomy segmentation and automatic landmark- ing. Specifically, we focus on the challenging problem of mandible segmentation from cone-beam computed tomography (CBCT) scans and identification of 9 anatomical landmarks of the mandible on the geodesic space. The overall approach employs three inter-related steps. In step 1, we propose a deep neu- ral network architecture with carefully designed regularization, and network hyper-parameters to perform image segmentation without the need for data augmentation and complex post- processing…
Technical University of Munich（慕尼黑工业大学）；University Medical Center Freiburg（弗莱堡大学医学中心）
With the advent of deep learning algorithms, fully automated radiological image analysis is within reach. In spine imaging, several atlas- and shape-based as well as deep learning segmentation algorithms have been proposed, allowing for subsequent automated analysis of morphology and pathology. The first Large Scale Vertebrae Segmentation Challenge (VerSe 2019) showed that these perform well on normal anatomy, but fail in variants not frequently present in the training dataset. Building on that experience, we report on the largely increased VerSe 2020 dataset and results from the second iterat…
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）
Convolutional networks (ConvNets) have achieved promising accuracy for various anatomical segmentation tasks. Despite the success, these methods can be sensitive to data appearance variations. Considering the large variability of scans caused by artifacts, pathologies, and scanning setups, robust ConvNets are vital for clinical applications, while have not been fully explored. In this paper, we propose to mitigate the challenge by enabling ConvNets' awareness of the underlying anatomical invariances among imaging scans. Specifically, we introduce a fully convolutional Constraint Adoption Modul…
Towards Unifying Anatomy Segmentation: Automated Generation of a Full-body CT Dataset via Knowledge Aggregation and Anatomical Guidelines
Institute for Anthropomatics and Robotics, Karlsruhe Institute of Technology（卡尔斯鲁厄理工学院人机交互与机器人学研究所）；Institute for AI in Medicine, University Hospital Essen（埃森大学医院医学人工智能研究所）；Steinbuch Center for Computing, Karlsruhe Institute of Technology (KIT)（卡尔斯鲁厄理工学院（KIT）施泰因布赫计算中心）；Department of Medical Physics in Radiation Oncology, German Cancer Research Center (DKFZ)（德国癌症研究中心（DKFZ）放射肿瘤学医学物理科）；Heidelberg Institute of Radiation Oncology (HIRO)（海德堡放射肿瘤学研究所（HIRO））；National Center for Radiation Research in Oncology (NCRO)（国家肿瘤放射研究中心（NCRO））；Helmholtz Information and Data Science School for Health (HIDSS4Health)（亥姆霍兹健康信息与数据科学学院（HIDSS4Health））；Department of Diagnostic and Interventional Radiology and Neuroradiology, University Hospital Essen（埃森大学医院诊断与介入放射学及神经放射学系）
Indian Institute of Technology, Mandi（印度理工学院曼迪分校）；Indian Institute of Technology, Jodhpur（印度理工学院焦特布尔分校）
The segregation of brain fiber tractography data into distinct and anatomically meaningful clusters can help to comprehend the complex brain structure and early investigation and management of various neural disorders. We propose a novel stacked bidirectional long short-term memory(LSTM) based segmentation network, (BrainSegNet) for human brain fiber tractography data classification. We perform a two-level hierarchical classification a) White vs Grey matter (Macro) and b) White matter clusters (Micro). BrainSegNet is trained over three brain tractography data having over 250,000 fibers each. O…
Accuracy segmentation of brain structures could be helpful for glioma and radiotherapy planning. However, due to the visual and anatomical differences between different modalities, the accurate segmentation of brain structures becomes challenging. To address this problem, we first construct a residual block based U-shape network with a deep encoder and shallow decoder, which can trade off the framework performance and efficiency. Then, we introduce the Tversky loss to address the issue of the class imbalance between different foreground and the background classes. Finally, a model ensemble str…
Nanjing University of Aeronautics and Astronautics（南京航空航天大学）
Background: A universal unanswered question in neuroscience and machine learning is whether computers can decode the patterns of the human brain. Multi-Voxels Pattern Analysis (MVPA) is a critical tool for addressing this question. However, there are two challenges in the previous MVPA methods, which include decreasing sparsity and noise in the extracted features and increasing the performance of prediction. Methods: In overcoming mentioned challenges, this paper proposes Anatomical Pattern Analysis (APA) for decoding visual stimuli in the human brain. This framework develops a novel anatomica…
This work is an endeavor to develop a deep learning methodology for automated anatomical labeling of a given region of interest (ROI) in brain computed tomography (CT) scans. We combine both local and global context to obtain a representation of the ROI. We then use Relation Networks (RNs) to predict the corresponding anatomy of the ROI based on its relationship score for each class. Further, we propose a novel strategy employing nearest neighbors approach for training RNs. We train RNs to learn the relationship of the target ROI with the joint representation of its nearest neighbors in each c…
Segmentation of brain structures from magnetic resonance (MR) scans plays an important role in the quantification of brain morphology. Since 3D deep learning models suffer from high computational cost, 2D deep learning methods are favored for their computational efficiency. However, existing 2D deep learning methods are not equipped to effectively capture 3D spatial contextual information that is needed to achieve accurate brain structure segmentation. In order to overcome this limitation, we develop an Anatomical Context-Encoding Network (ACEnet) to incorporate 3D spatial and anatomical conte…
We consider the problem of segmenting a biomedical image into anatomical regions of interest. We specifically address the frequent scenario where we have no paired training data that contains images and their manual segmentations. Instead, we employ unpaired segmentation images to build an anatomical prior. Critically these segmentations can be derived from imaging data from a different dataset and imaging modality than the current task. We introduce a generative probabilistic model that employs the learned prior through a convolutional neural network to compute segmentations in an unsupervise…
Research institute for signals, systems and computational intelligence, sinc(i)（信号、系统与计算智能研究所（sinc(i)））；FICH-UNL（拉普拉塔国立大学工程学院）；CONICET（阿根廷国家科学与技术研究理事会）
Deep convolutional neural networks (CNN) proved to be highly accurate to perform anatomical segmentation of medical images. However, some of the most popular CNN architectures for image segmentation still rely on post-processing strategies (e.g. Conditional Random Fields) to incorporate connectivity constraints into the resulting masks. These post-processing steps are based on the assumption that objects are usually continuous and therefore nearby pixels should be assigned the same object label. Even if it is a valid assumption in general, these methods do not offer a straightforward way to in…
Effective, robust, and automatic tools for brain tumor segmentation are needed for the extraction of information useful in treatment planning from magnetic resonance (MR) images. Context-aware artificial intelligence is an emerging concept for the development of deep learning applications for computer-aided medical image analysis. In this work, it is investigated whether the addition of contextual information from the brain anatomy in the form of white matter, gray matter, and cerebrospinal fluid masks and probability maps improves U-Net-based brain tumor segmentation. The BraTS2020 dataset wa…
University of Sherbrooke（舍布鲁克大学）；University of Bourgogne Franche-Comte（勃艮第-弗朗什孔泰大学）；CASIS inc.（CASIS公司）；University of Lyon（里昂大学）
Convolutional neural networks (CNN) have had unprecedented success in medical imaging and, in particular, in medical image segmentation. However, despite the fact that segmentation results are closer than ever to the inter-expert variability, CNNs are not immune to producing anatomically inaccurate segmentations, even when built upon a shape prior. In this paper, we present a framework for producing cardiac image segmentation maps that are guaranteed to respect pre-defined anatomical criteria, while remaining within the inter-expert variability. The idea behind our method is to use a well-trai…
Ecole de technologie supérieure（高等技术学院）；Shandong University（山东大学）
Despite their outstanding accuracy, semi-supervised segmentation methods based on deep neural networks can still yield predictions that are considered anatomically impossible by clinicians, for instance, containing holes or disconnected regions. To solve this problem, we present a Context-aware Virtual Adversarial Training (CaVAT) method for generating anatomically plausible segmentation. Unlike approaches focusing solely on accuracy, our method also considers complex topological constraints like connectivity which cannot be easily modeled in a differentiable loss function. We use adversarial …
Accurate segmentation of anatomical structures in chest radiographs is essential for many computer-aided diagnosis tasks. In this paper we investigate the latest fully-convolutional architectures for the task of multi-class segmentation of the lungs field, heart and clavicles in a chest radiograph. In addition, we explore the influence of using different loss functions in the training process of a neural network for semantic segmentation. We evaluate all models on a common benchmark of 247 X-ray images from the JSRT database and ground-truth segmentation masks from the SCR dataset. Our best pe…
The 4D Human Embryonic Brain Atlas: spatiotemporal atlas generation for rapid anatomical changes
Erasmus MC（埃拉斯姆斯医学院）；University Medical Center Groningen（格罗宁根大学医学中心）；Amsterdam UMC location University of Amsterdam（阿姆斯特丹大学阿姆斯特丹医学中心分部）；Amsterdam Reproduction and Development research institute（阿姆斯特丹生殖与发育研究所）
Institute for Signals, Systems and Computational Intelligence, sinc(i) CONICET-UNL（信号、系统与计算智能研究所，sinc(i) 阿根廷国家科学与技术研究理事会-国立利托拉尔大学）；Imperial College London（伦敦帝国理工学院）
We introduce Post-DAE, a post-processing method based on denoising autoencoders (DAE) to improve the anatomical plausibility of arbitrary biomedical image segmentation algorithms. Some of the most popular segmentation methods (e.g. based on convolutional neural networks or random forest classifiers) incorporate additional post-processing steps to ensure that the resulting masks fulfill expected connectivity constraints. These methods operate under the hypothesis that contiguous pixels with similar aspect should belong to the same class. Even if valid in general, this assumption does not consid…
We propose a 2D Encoder-Decoder based deep learning architecture for semantic segmentation, that incorporates anatomical priors by imitating the encoder component of an autoencoder in latent space. The autoencoder is additionally enhanced by means of hierarchical features, extracted by an U-Net module. Our suggested architecture is trained in an end-to-end manner and is evaluated on the example of pelvic bone segmentation in MRI. A comparison to the standard U-Net architecture shows promising improvements.
University of Sherbrooke（舍布鲁克大学）；Université de Bourgogne Franche-Comté（勃艮第-弗朗什孔泰大学）；CArdiac Simulation & Imaging Software（心脏模拟与成像软件公司）；Université de Lyon（里昂大学）
Recent publications have shown that the segmentation accuracy of modern-day convolutional neural networks (CNN) applied on cardiac MRI can reach the inter-expert variability, a great achievement in this area of research. However, despite these successes, CNNs still produce anatomically inaccurate segmentations as they provide no guarantee on the anatomical plausibility of their outcome, even when using a shape prior. In this paper, we propose a cardiac MRI segmentation method which always produces anatomically plausible results. At the core of the method is an adversarial variational autoencod…
Metadata-Conditioned Generative Models to Synthesize Anatomically-Plausible 3D Brain MRIs
Stanford University（斯坦福大学）；University of Missouri（密苏里大学）；Missouri Institute of Mental Health（密苏里精神卫生研究所）；Weill Cornell Medicine（威尔康奈尔医学院）；SRI International（SRI国际研究所）
Segmentation of medical images is a challenging task owing to their complexity. A standard segmentation problem within Magnetic Resonance Imaging (MRI) is the task of labeling voxels according to their tissue type. Image segmentation provides volumetric quantification of liver area and thus helps in the diagnosis of disorders, such as Hepatitis, Cirrhosis, Jaundice, Hemochromatosis etc.This work deals with comparison of segmentation by applying Level Set Method,Fuzzy Level Information C-Means Clustering Algorithm and Gradient Vector Flow Snake Algorithm.The results are compared using the param…
Helmholtz-Zentrum Dresden-Rossendorf（亥姆霍兹德累斯顿罗森多夫研究中心）；University Hospital Carl Gustav Carus（卡尔·古斯塔夫·卡鲁斯大学医院）
Multimodal medical image fusion helps in combining contrasting features from two or more input imaging modalities to represent fused information in a single image. One of the pivotal clinical applications of medical image fusion is the merging of anatomical and functional modalities for fast diagnosis of malignant tissues. In this paper, we present a novel end-to-end unsupervised learning-based Convolutional Neural Network (CNN) for fusing the high and low frequency components of MRI-PET grayscale image pairs, publicly available at ADNI, by exploiting Structural Similarity Index (SSIM) as the …
WASABI: A Metric for Evaluating Morphometric Plausibility of Synthetic Brain MRIs
Department of Radiology, Weill Cornell Medicine, New York, NY, USA（放射科，韦尔·科恩医学中心，纽约，纽约州，美国）；Department of Psychiatry and Behavioral Sciences, Stanford University, Stanford, CA, USA（精神病学与行为科学系，斯坦福大学，斯坦福，加利福尼亚州，美国）；Department of Electrical and Computer Engineering, Cornell University, Ithaca, NY, USA（电气与计算机工程系，康奈尔大学，伊萨卡，纽约州，美国）
Institute for Signals, Systems and Computational Intelligence, sinc(i) CONICET-UNL（信号、系统与计算智能研究所，sinc(i) 阿根廷国家科学技术研究委员会-国立利托拉尔大学）；Hospital Italiano de Buenos Aires（布宜诺斯艾利斯意大利医院）；Universidad Tecnológica Nacional（国立技术大学）
Anatomical segmentation is a fundamental task in medical image computing, generally tackled with fully convolutional neural networks which produce dense segmentation masks. These models are often trained with loss functions such as cross-entropy or Dice, which assume pixels to be independent of each other, thus ignoring topological errors and anatomical inconsistencies. We address this limitation by moving from pixel-level to graph representations, which allow to naturally incorporate anatomical constraints by construction. To this end, we introduce HybridGNet, an encoder-decoder neural archit…
University of California, Los Angeles（加州大学洛杉矶分校）；RedNova Health
Label propagation is a popular technique for anatomical segmentation. In this work, we propose a novel deep framework for label propagation based on non-local label fusion. Our framework, named CompareNet, incorporates subnets for both extracting discriminating features, and learning the similarity measure, which lead to accurate segmentation. We also introduce the voxel-wise classification as an unary potential to the label fusion function, for alleviating the search failure issue of the existing non-local fusion strategies. Moreover, CompareNet is end-to-end trainable, and all the parameters…
Bruno Kessler Foundation（布鲁诺·凯斯勒基金会）；University of Trento（特伦托大学）；Indiana University（印第安纳大学）
Segmenting white matter bundles from human tractograms is a task of interest for several applications. Current methods for bundle segmentation consider either only prior knowledge about the relative anatomical position of a bundle, or only its geometrical properties. Our aim is to improve the results of segmentation by proposing a method that takes into account information about both the underlying anatomy and the geometry of bundles at the same time. To achieve this goal, we extend a state-of-the-art example-based method based on the Linear Assignment Problem (LAP) by including prior anatomic…
Comparative Study of Anatomical and Learned Features in AI Models for Structural Brain MRI
Center for Data Science, New York University（纽约大学数据科学中心）；NYU Grossman School of Medicine（纽约大学格罗斯曼医学院）；Courant Institute of Mathematical Sciences, NYU（纽约大学柯朗数学科学研究所）
University of Science and Technology of China（中国科学技术大学）
Segmentation of multiple anatomical structures is of great importance in medical image analysis. In this study, we proposed a $\mathcal{W}$-net to simultaneously segment both the optic disc (OD) and the exudates in retinal images based on the multi-task learning (MTL) scheme. We introduced a class-balanced loss and a multi-task weighted loss to alleviate the imbalanced problem and to improve the robustness and generalization property of the $\mathcal{W}$-net. We demonstrated the effectiveness of our approach by applying five-fold cross-validation experiments on two public datasets e\_ophtha\_E…
The Chinese University of Hong Kong（香港中文大学）；Siemens Healthcare（西门子医疗）
Accurate detection and segmentation of anatomical structures from ultrasound images are crucial for clinical diagnosis and biometric measurements. Although ultrasound imaging has been widely used with superiorities such as low cost and portability, the fuzzy border definition and existence of abounding artifacts pose great challenges for automatically detecting and segmenting the complex anatomical structures. In this paper, we propose a multi-domain regularized deep learning method to address this challenging problem. By leveraging the transfer learning from cross domains, the feature represe…
Anatomically Faithful Artifact Suppression in SENSE Accelerated Brain MRI
East China Normal University（华东师范大学）；Affiliated Hospital of Guizhou Medical University（贵州医科大学附属医院）；West China Hospital, Sichuan University（四川大学华西医院）；Chinese Academy of Medical Sciences（中国医学科学院）；RadioDynamic Medical（镭动医疗）；Lucile Packard Children’s Hospital（露西尔·帕卡德儿童医院）
Johns Hopkins University School of Medicine（约翰斯·霍普金斯大学医学院）；Johns Hopkins University（约翰斯·霍普金斯大学）；Johns Hopkins Hospital（约翰斯·霍普金斯医院）
Visualizing disease-induced scarring and fibrosis in the heart on cardiac magnetic resonance (CMR) imaging with contrast enhancement (LGE) is paramount in characterizing disease progression and quantifying pathophysiological substrates of arrhythmias. However, segmentation and scar/fibrosis identification from LGE-CMR is an intensive manual process prone to large inter-observer variability. Here, we present a novel fully-automated anatomically-informed deep learning solution for left ventricle (LV) and scar/fibrosis segmentation and clinical feature extraction from LGE-CMR. The technology invo…
University of South Carolina（南卡罗来纳大学）；PAII Inc.（PAII公司）；University of Rochester（罗切斯特大学）；Chang Gung Memorial Hospital（长庚纪念医院）；Ping An Technology（平安科技）
Accurate segmentation of anatomical structures is vital for medical image analysis. The state-of-the-art accuracy is typically achieved by supervised learning methods, where gathering the requisite expert-labeled image annotations in a scalable manner remains a main obstacle. Therefore, annotation-efficient methods that permit to produce accurate anatomical structure segmentation are highly desirable. In this work, we present Contour Transformer Network (CTN), a one-shot anatomy segmentation method with a naturally built-in human-in-the-loop mechanism. We formulate anatomy segmentation as a co…
Philips Research Paris（飞利浦巴黎研究院）；Institut Imagine, Université Paris Cité（巴黎西岱大学想象研究所）；Université Paris Cité（巴黎西岱大学）；Hôpital Necker Enfants-Malades, APHP（巴黎公共援助医院集团内克儿童病院）；Sorbonne Université（索邦大学）；CNRS, LIP6（法国国家科学研究中心LIP6实验室）；Technology Innovation Institute（技术创新研究所）
Anatomical structures such as blood vessels in contrast-enhanced CT (ceCT) images can be challenging to segment due to the variability in contrast medium diffusion. The combined use of ceCT and contrast-free (CT) CT images can improve the segmentation performances, but at the cost of a double radiation exposure. To limit the radiation dose, generative models could be used to synthesize one modality, instead of acquiring it. The CycleGAN approach has recently attracted particular attention because it alleviates the need for paired data that are difficult to obtain. Despite the great performance…
