Accurate and robust segmentation of small organs in whole-body MRI is difficult due to anatomical variation and class imbalance. Recent deep network based approaches have demonstrated promising performance on abdominal multi-organ segmentations. However, the performance on small organs is still suboptimal as these occupy only small regions of the whole-body volumes with unclear boundaries and variable shapes. A coarse-to-fine, hierarchical strategy is a common approach to alleviate this problem, however, this might miss useful contextual information. We propose a two-stage approach with weighting schemes based on auto-context and spatial atlas priors. Our experiments show that the proposed approach can boost the segmentation accuracy of multiple small organs in whole-body MRI scans.
Nagoya University（名古屋大学）；Aichi Cancer Center Hospital（爱知县癌症中心医院）
Deep learning-based methods achieved impressive results for the segmentation of medical images. With the development of 3D fully convolutional networks (FCNs), it has become feasible to produce improved results for multi-organ segmentation of 3D computed tomography (CT) images. The results of multi-organ segmentation using deep learning-based methods not only depend on the choice of networks architecture, but also strongly rely on the choice of loss function. In this paper, we present a discussion on the influence of Dice-based loss functions for multi-class organ segmentation using a dataset …
École Polytechnique de Montréal（蒙特利尔理工学院）；Montreal Institute for Learning Algorithms（蒙特利尔学习算法研究所）；Imagia Inc.（Imagia公司）；Université de Montréal（蒙特利尔大学）；CHUM Research Center（CHUM研究中心）
In this paper, we introduce a simple, yet powerful pipeline for medical image segmentation that combines Fully Convolutional Networks (FCNs) with Fully Convolutional Residual Networks (FC-ResNets). We propose and examine a design that takes particular advantage of recent advances in the understanding of both Convolutional Neural Networks as well as ResNets. Our approach focuses upon the importance of a trainable pre-processing when using FC-ResNets and we show that a low-capacity FCN model can serve as a pre-processor to normalize medical input data. In our image segmentation pipeline, we use …
Nagoya University（名古屋大学）；Aichi Cancer Center（爱知癌症中心）
Recent advances in 3D fully convolutional networks (FCN) have made it feasible to produce dense voxel-wise predictions of full volumetric images. In this work, we show that a multi-class 3D FCN trained on manually labeled CT scans of seven abdominal structures (artery, vein, liver, spleen, stomach, gallbladder, and pancreas) can achieve competitive segmentation results, while avoiding the need for handcrafting features or training organ-specific models. To this end, we propose a two-stage, coarse-to-fine approach that trains an FCN model to roughly delineate the organs of interest in the first…
Graduate School of Informatics, Nagoya University（名古屋大学信息学院研究生院）；Graduate School of Information Science, Nagoya University（名古屋大学信息科学研究生院）；School of Information Science, Aichi Institute of Technology（爱知工业大学信息科学学院）；Aichi Cancer Center（爱知癌症中心）；Nagoya University Graduate School of Medicine（名古屋大学医学院）；Department of Computing, Imperial College London（帝国理工学院计算机系）；Strategy Office, Information and Communications, Nagoya University（名古屋大学信息与通信战略办公室）
This paper presents a fully automated atlas-based pancreas segmentation method from CT volumes utilizing 3D fully convolutional network (FCN) feature-based pancreas localization. Segmentation of the pancreas is difficult because it has larger inter-patient spatial variations than other organs. Previous pancreas segmentation methods failed to deal with such variations. We propose a fully automated pancreas segmentation method that contains novel localization and segmentation. Since the pancreas neighbors many other organs, its position and size are strongly related to the positions of the surro…
Nagoya University（名古屋大学）；Gifu University（岐阜大学）；Nagoya University Graduate School of Medicine（名古屋大学医学研究生院）；Aichi Cancer Center（爱知癌症中心）
Recent advances in 3D fully convolutional networks (FCN) have made it feasible to produce dense voxel-wise predictions of volumetric images. In this work, we show that a multi-class 3D FCN trained on manually labeled CT scans of several anatomical structures (ranging from the large organs to thin vessels) can achieve competitive segmentation results, while avoiding the need for handcrafting features or training class-specific models. To this end, we propose a two-stage, coarse-to-fine approach that will first use a 3D FCN to roughly define a candidate region, which will then be used as input t…
Nagoya University（名古屋大学）；German Cancer Research Center (DKFZ)（德国癌症研究中心）；University Hospital Erlangen（埃尔朗根大学医院）；Paracelsus Medical University（帕拉塞尔苏斯医科大学）
Automatic multi-organ segmentation of the dual energy computed tomography (DECT) data can be beneficial for biomedical research and clinical applications. However, it is a challenging task. Recent advances in deep learning showed the feasibility to use 3-D fully convolutional networks (FCN) for voxel-wise dense predictions in single energy computed tomography (SECT). In this paper, we proposed a 3D FCN based method for automatic multi-organ segmentation in DECT. The work was based on a cascaded FCN and a general model for the major organs trained on a large set of SECT data. We preprocessed th…
Graduate School of Information Science Nagoya University（名古屋大学信息科学研究生院）；Graduate School of Informatics Nagoya University（名古屋大学信息学研究生院）；Research Center for Medical Bigdata National Institute of Informatics（国立信息学研究所医疗大数据研究中心）
In this work, we present a memory-efficient fully convolutional network (FCN) incorporated with several memory-optimized techniques to reduce the run-time GPU memory demand during training phase. In medical image segmentation tasks, subvolume cropping has become a common preprocessing. Subvolumes (or small patch volumes) were cropped to reduce GPU memory demand. However, small patch volumes capture less spatial context that leads to lower accuracy. As a pilot study, the purpose of this work is to propose a memory-efficient FCN which enables us to train the model on full size CT image directly …
School of Public health, Peking University（北京大学公共卫生学院）；School of Physics, Peking University（北京大学物理学院）；School of Computer Science, Peking University（北京大学计算机学院）
Eindhoven University of Technology（埃因霍温理工大学）；Philips Research（飞利浦研究院）
Fast and accurate catheter detection in cardiac catheterization using harmless 3D ultrasound (US) can improve the efficiency and outcome of the intervention. However, the low image quality of US requires extra training for sonographers to localize the catheter. In this paper, we propose a catheter detection method based on a pre-trained VGG network, which exploits 3D information through re-organized cross-sections to segment the catheter by a shared fully convolutional network (FCN), which is called a Direction-Fused FCN (DF-FCN). Based on the segmented image of DF-FCN, the catheter can be loc…
Nagoya University（名古屋大学）；Aichi Cancer Center（爱知县癌症中心）；National Institute of Informatics（国立信息学研究所）
Recent advances in deep learning, like 3D fully convolutional networks (FCNs), have improved the state-of-the-art in dense semantic segmentation of medical images. However, most network architectures require severely downsampling or cropping the images to meet the memory limitations of today's GPU cards while still considering enough context in the images for accurate segmentation. In this work, we propose a novel approach that utilizes auto-context to perform semantic segmentation at higher resolutions in a multi-scale pyramid of stacked 3D FCNs. We train and validate our models on a dataset …
Imperial College London（帝国理工学院）；TECNALIA, Basque Research & Technology Alliance（巴斯克研究与技术联盟TECNALIA）；University of the Basque Country（巴斯克大学）；Royal Brompton Hospital（皇家布朗普顿医院）
Automatic segmentation of multiple organs and tumors from 3D medical images such as magnetic resonance imaging (MRI) and computed tomography (CT) scans using deep learning methods can aid in diagnosing and treating cancer. However, organs often overlap and are complexly connected, characterized by extensive anatomical variation and low contrast. In addition, the diversity of tumor shape, location, and appearance, coupled with the dominance of background voxels, makes accurate 3D medical image segmentation difficult. In this paper, a novel large-kernel (LK) attention module is proposed to addre…
Isfahan University of Technology（伊斯法罕理工大学）；University of Michigan（密歇根大学）
The need for CT scan analysis is growing for pre-diagnosis and therapy of abdominal organs. Automatic organ segmentation of abdominal CT scan can help radiologists analyze the scans faster and segment organ images with fewer errors. However, existing methods are not efficient enough to perform the segmentation process for victims of accidents and emergencies situations. In this paper we propose an efficient liver segmentation with our 3D to 2D fully connected network (3D-2D-FCN). The segmented mask is enhanced by means of conditional random field on the organ's border. Consequently, we segment…
Nanjing University of Posts and Telecommunications（南京邮电大学）；Nanjing University of Science and Technology（南京理工大学）；Key Laboratory of Intelligent Perception and Systems for High-Dimensional Information of Ministry of Education（高维信息智能感知与系统教育部重点实验室）
In this paper, we propose an easily trained yet powerful representation learning approach with performance highly competitive to deep neural networks in a digital pathology image segmentation task. The method, called sparse coding driven deep decision tree ensembles that we abbreviate as ScD2TE, provides a new perspective on representation learning. We explore the possibility of stacking several layers based on non-differentiable pairwise modules and generate a densely concatenated architecture holding the characteristics of feature map reuse and end-to-end dense learning. Under this architect…
Technical University of Munich（慕尼黑工业大学）；Ulm University（乌尔姆大学）
The lack of sufficient annotated image data is a common issue in medical image segmentation. For some organs and densities, the annotation may be scarce, leading to poor model training convergence, while other organs have plenty of annotated data. In this work, we present MetaMedSeg, a gradient-based meta-learning algorithm that redefines the meta-learning task for the volumetric medical data with the goal to capture the variety between the slices. We also explore different weighting schemes for gradients aggregation, arguing that different tasks might have different complexity, and hence, con…
Shortage of fully annotated datasets has been a limiting factor in developing deep learning based image segmentation algorithms and the problem becomes more pronounced in multi-organ segmentation. In this paper, we propose a unified training strategy that enables a novel multi-scale deep neural network to be trained on multiple partially labeled datasets for multi-organ segmentation. In addition, a new network architecture for multi-scale feature abstraction is proposed to integrate pyramid input and feature analysis into a U-shape pyramid structure. To bridge the semantic gap caused by direct…
A Two-Stage Deep Learning Framework for Segmentation of Ten Gastrointestinal Organs from Coronal MR Enterography
Department of Biomedical Physics and Technology, University of Dhaka（达卡大学生物医学物理与技术系）；Department of Biomedical Engineering, Jashore University of Science and Technology（贾沙尔大学科学与技术学院生物医学工程系）；Department of Radiology, Hamad Medical Corporation（哈马德医疗集团放射科）；Department of Electrical Engineering, Qatar University（卡塔尔大学电气工程系）
