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      Central focused convolutional neural networks: Developing a data-driven model for lung nodule segmentation

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          Abstract

          Accurate lung nodule segmentation from computed tomography (CT) images is of great importance for image-driven lung cancer analysis. However, the heterogeneity of lung nodules and the presence of similar visual characteristics between nodules and their surroundings make it difficult for robust nodule segmentation. In this study, we propose a data-driven model, termed the Central Focused Convolutional Neural Networks (CF-CNN), to segment lung nodules from heterogeneous CT images. Our approach combines two key insights: 1) the proposed model captures a diverse set of nodule-sensitive features from both 3-D and 2-D CT images simultaneously; 2) when classifying an image voxel, the effects of its neighbor voxels can vary according to their spatial locations. We describe this phenomenon by proposing a novel central pooling layer retaining much information on voxel patch center, followed by a multi-scale patch learning strategy. Moreover, we design a weighted sampling to facilitate the model training, where training samples are selected according to their degree of segmentation difficulty. The proposed method has been extensively evaluated on the public LIDC dataset including 893 nodules and an independent dataset with 74 nodules from Guangdong General Hospital (GDGH). We showed that CF-CNN achieved superior segmentation performance with average dice scores of 82.15% and 80.02% for the two datasets respectively. Moreover, we compared our results with the inter-radiologists consistency on LIDC dataset, showing a difference in average dice score of only 1.98%.

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          Most cited references40

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          U-Net: Convolutional Networks for Biomedical Image Segmentation

          There is large consent that successful training of deep networks requires many thousand annotated training samples. In this paper, we present a network and training strategy that relies on the strong use of data augmentation to use the available annotated samples more efficiently. The architecture consists of a contracting path to capture context and a symmetric expanding path that enables precise localization. We show that such a network can be trained end-to-end from very few images and outperforms the prior best method (a sliding-window convolutional network) on the ISBI challenge for segmentation of neuronal structures in electron microscopic stacks. Using the same network trained on transmitted light microscopy images (phase contrast and DIC) we won the ISBI cell tracking challenge 2015 in these categories by a large margin. Moreover, the network is fast. Segmentation of a 512x512 image takes less than a second on a recent GPU. The full implementation (based on Caffe) and the trained networks are available at http://lmb.informatik.uni-freiburg.de/people/ronneber/u-net .
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            An experimental comparison of min-cut/max-flow algorithms for energy minimization in vision.

            After [15], [31], [19], [8], [25], [5], minimum cut/maximum flow algorithms on graphs emerged as an increasingly useful tool for exact or approximate energy minimization in low-level vision. The combinatorial optimization literature provides many min-cut/max-flow algorithms with different polynomial time complexity. Their practical efficiency, however, has to date been studied mainly outside the scope of computer vision. The goal of this paper is to provide an experimental comparison of the efficiency of min-cut/max flow algorithms for applications in vision. We compare the running times of several standard algorithms, as well as a new algorithm that we have recently developed. The algorithms we study include both Goldberg-Tarjan style "push-relabel" methods and algorithms based on Ford-Fulkerson style "augmenting paths." We benchmark these algorithms on a number of typical graphs in the contexts of image restoration, stereo, and segmentation. In many cases, our new algorithm works several times faster than any of the other methods, making near real-time performance possible. An implementation of our max-flow/min-cut algorithm is available upon request for research purposes.
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              Batch Normalization: Accelerating Deep Network Training by Reducing Internal Covariate Shift

              Training Deep Neural Networks is complicated by the fact that the distribution of each layer's inputs changes during training, as the parameters of the previous layers change. This slows down the training by requiring lower learning rates and careful parameter initialization, and makes it notoriously hard to train models with saturating nonlinearities. We refer to this phenomenon as internal covariate shift, and address the problem by normalizing layer inputs. Our method draws its strength from making normalization a part of the model architecture and performing the normalization for each training mini-batch. Batch Normalization allows us to use much higher learning rates and be less careful about initialization. It also acts as a regularizer, in some cases eliminating the need for Dropout. Applied to a state-of-the-art image classification model, Batch Normalization achieves the same accuracy with 14 times fewer training steps, and beats the original model by a significant margin. Using an ensemble of batch-normalized networks, we improve upon the best published result on ImageNet classification: reaching 4.9% top-5 validation error (and 4.8% test error), exceeding the accuracy of human raters.
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                Author and article information

                Journal
                9713490
                21159
                Med Image Anal
                Med Image Anal
                Medical image analysis
                1361-8415
                1361-8423
                20 October 2017
                30 June 2017
                August 2017
                30 October 2017
                : 40
                : 172-183
                Affiliations
                [a ]CAS Key Laboratory of Molecular Imaging, Institute of Automation, Chinese Academy of Sciences, Beijing 100190, China
                [b ]Stanford Center for Biomedical Informatics Research (BMIR), Department of Medicine, Stanford University, CA 94305, USA
                [c ]University of Chinese Academy of Sciences, Beijing 10 0 049, China
                [d ]Guangdong General Hospital, Guangzhou, Guangdong 510080, China
                [e ]Beijing Key Laboratory of Molecular Imaging, Beijing 100190, China
                Author notes
                [1]

                Contributed equally.

                Article
                NIHMS914253
                10.1016/j.media.2017.06.014
                5661888
                28688283
                0d86414d-0eb2-4945-9f9a-e3436c9228fa

                This is an open access article under the CC BY license. ( http://creativecommons.org/licenses/by/4.0/)

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                Categories
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                Radiology & Imaging
                lung nodule segmentation,convolutional neural networks,deep learning,computer-aided diagnosis

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