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Register a new userCANet: Context Aware Network for 3D Brain Glioma Segmentation
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Added by
Zhihua Liu
Publication date
2020
fields
Informatics Engineering
and research's language is
English
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Automated segmentation of brain glioma plays an active role in diagnosis decision, progression monitoring and surgery planning. Based on deep neural networks, previous studies have shown promising technologies for brain glioma segmentation. However, these approaches lack powerful strategies to incorporate contextual information of tumor cells and their surrounding, which has been proven as a fundamental cue to deal with local ambiguity. In this work, we propose a novel approach named Context-Aware Network (CANet) for brain glioma segmentation. CANet captures high dimensional and discriminative features with contexts from both the convolutional space and feature interaction graphs. We further propose context guided attentive conditional random fields which can selectively aggregate features. We evaluate our method using publicly accessible brain glioma segmentation datasets BRATS2017, BRATS2018 and BRATS2019. The experimental results show that the proposed algorithm has better or competitive performance against several State-of-The-Art approaches under different segmentation metrics on the training and validation sets.
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In this paper, we propose a novel two-stage context-aware network named CANet for shadow removal, in which the contextual information from non-shadow regions is transferred to shadow regions at the embedded feature spaces. At Stage-I, we propose a contextual patch matching (CPM) module to generate a set of potential matching pairs of shadow and non-shadow patches. Combined with the potential contextual relationships between shadow and non-shadow regions, our well-designed contextual feature transfer (CFT) mechanism can transfer contextual information from non-shadow to shadow regions at different scales. With the reconstructed feature maps, we remove shadows at L and A/B channels separately. At Stage-II, we use an encoder-decoder to refine current results and generate the final shadow removal results. We evaluate our proposed CANet on two benchmark datasets and some real-world shadow images with complex scenes. Extensive experimental results strongly demonstrate the efficacy of our proposed CANet and exhibit superior performance to state-of-the-arts.
In this paper, we propose a similarity-aware fusion network (SAFNet) to adaptively fuse 2D images and 3D point clouds for 3D semantic segmentation. Existing fusion-based methods achieve remarkable performances by integrating information from multiple modalities. However, they heavily rely on the correspondence between 2D pixels and 3D points by projection and can only perform the information fusion in a fixed manner, and thus their performances cannot be easily migrated to a more realistic scenario where the collected data often lack strict pair-wise features for prediction. To address this, we employ a late fusion strategy where we first learn the geometric and contextual similarities between the input and back-projected (from 2D pixels) point clouds and utilize them to guide the fusion of two modalities to further exploit complementary information. Specifically, we employ a geometric similarity module (GSM) to directly compare the spatial coordinate distributions of pair-wise 3D neighborhoods, and a contextual similarity module (CSM) to aggregate and compare spatial contextual information of corresponding central points. The two proposed modules can effectively measure how much image features can help predictions, enabling the network to adaptively adjust the contributions of two modalities to the final prediction of each point. Experimental results on the ScanNetV2 benchmark demonstrate that SAFNet significantly outperforms existing state-of-the-art fusion-based approaches across various data integrity.
Zero padding is widely used in convolutional neural networks to prevent the size of feature maps diminishing too fast. However, it has been claimed to disturb the statistics at the border. As an alternative, we propose a context-aware (CA) padding approach to extend the image. We reformulate the padding problem as an image extrapolation problem and illustrate the effects on the semantic segmentation task. Using context-aware padding, the ResNet-based segmentation model achieves higher mean Intersection-Over-Union than the traditional zero padding on the Cityscapes and the dataset of DeepGlobe satellite imaging challenge. Furthermore, our padding does not bring noticeable overhead during training and testing.
In recent years, sparse voxel-based methods have become the state-of-the-arts for 3D semantic segmentation of indoor scenes, thanks to the powerful 3D CNNs. Nevertheless, being oblivious to the underlying geometry, voxel-based methods suffer from ambiguous features on spatially close objects and struggle with handling complex and irregular geometries due to the lack of geodesic information. In view of this, we present Voxel-Mesh Network (VMNet), a novel 3D deep architecture that operates on the voxel and mesh representations leveraging both the Euclidean and geodesic information. Intuitively, the Euclidean information extracted from voxels can offer contextual cues representing interactions between nearby objects, while the geodesic information extracted from meshes can help separate objects that are spatially close but have disconnected surfaces. To incorporate such information from the two domains, we design an intra-domain attentive module for effective feature aggregation and an inter-domain attentive module for adaptive feature fusion. Experimental results validate the effectiveness of VMNet: specifically, on the challenging ScanNet dataset for large-scale segmentation of indoor scenes, it outperforms the state-of-the-art SparseConvNet and MinkowskiNet (74.6% vs 72.5% and 73.6% in mIoU) with a simpler network structure (17M vs 30M and 38M parameters). Code release: https://github.com/hzykent/VMNet
Detailed whole brain segmentation is an essential quantitative technique, which provides a non-invasive way of measuring brain regions from a structural magnetic resonance imaging (MRI). Recently, deep convolution neural network (CNN) has been applied to whole brain segmentation. However, restricted by current GPU memory, 2D based methods, downsampling based 3D CNN methods, and patch-based high-resolution 3D CNN methods have been the de facto standard solutions. 3D patch-based high resolution methods typically yield superior performance among CNN approaches on detailed whole brain segmentation (>100 labels), however, whose performance are still commonly inferior compared with multi-atlas segmentation methods (MAS) due to the following challenges: (1) a single network is typically used to learn both spatial and contextual information for the patches, (2) limited manually traced whole brain volumes are available (typically less than 50) for training a network. In this work, we propose the spatially localized atlas network tiles (SLANT) method to distribute multiple independent 3D fully convolutional networks (FCN) for high-resolution whole brain segmentation. To address the first challenge, multiple spatially distributed networks were used in the SLANT method, in which each network learned contextual information for a fixed spatial location. To address the second challenge, auxiliary labels on 5111 initially unlabeled scans were created by multi-atlas segmentation for training. Since the method integrated multiple traditional medical image processing methods with deep learning, we developed a containerized pipeline to deploy the end-to-end solution. From the results, the proposed method achieved superior performance compared with multi-atlas segmentation methods, while reducing the computational time from >30 hours to 15 minutes (https://github.com/MASILab/SLANTbrainSeg).
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