An important step in early brain development study is to perform automatic segmentation of infant brain magnetic resonance (MR) images into cerebrospinal fluid (CSF), gray matter (GM) and white matter (WM) regions. This task is especially challenging in the isointense stage (approximately 6-8 months of age) when GM and WM exhibit similar levels of intensities in MR images. Deep learning has shown its great promise in various image segmentation tasks. However, existing models do not have an efficient and effective way to aggregate global information. They also suffer from information loss during up-sampling operations. In this work, we address these problems by proposing a global aggregation block, which can be flexibly used for global information fusion. We build a novel model based on 3D U-Net to make fast and accurate voxel-wise dense prediction. We perform thorough experiments, and results indicate that our model outperforms previous best models significantly on 3D multimodality isointense infant brain MR image segmentation.
The U-Net @cite_42 architecture incorporates both local and global contextual information through the encoding-decoding process. In the past several years, many variants of U-Net have been developed and they achieved improved performance on biomedical image segmentation. For example, FusionNet @cite_27 , residual deconvolutional network (RDN) @cite_1 and residual symmetric U-Net @cite_2 addressed the 2D electron microscopy image segmentation task by building a U-Net-based network with additional short-range residual connections @cite_7 . In addition, U-Net was extended from 2D to 3D cases for volumetric biomedical images, leading to models like 3D U-Net @cite_11 , V-Net @cite_50 , and CC-3D-FCN @cite_9 . Meanwhile, DeepMedic @cite_3 explored another way to fuse both local and global contextual information by removing the decoder of U-Net and employing a dual pathway architecture. However, without the decoder, the spatial sizes of outputs become smaller as compared to U-Net-based models, which harms the inference efficiency since more patches need to be processed during inference. DeepMedic has been outperformed by U-Net-based models like CC-3D-FCN @cite_9 . In this work, we unified previous models and employed the 3D U-Net architecture with short-range residual connections as the basic framework.
@cite_7 @cite_9 @cite_42 @cite_1 @cite_3 @cite_27 @cite_50 @cite_2 @cite_11
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U-Net has been providing state-of-the-art performance in many medical image segmentation problems. Many modifications have been proposed for U-Net, such as attention U-Net, recurrent residual convolutional U-Net (R2-UNet), and U-Net with residual blocks or blocks with dense connections. However, all these modifications have an encoder-decoder structure with skip connections, and the number of paths for information flow is limited. We propose LadderNet in this paper, which can be viewed as a chain of multiple U-Nets. Instead of only one pair of encoder branch and decoder branch in U-Net, a LadderNet has multiple pairs of encoder-decoder branches, and has skip connections between every pair of adjacent decoder and decoder branches in each level. Inspired by the success of ResNet and R2-UNet, we use modified residual blocks where two convolutional layers in one block share the same weights. A LadderNet has more paths for information flow because of skip connections and residual blocks, and can be viewed as an ensemble of Fully Convolutional Networks (FCN). The equivalence to an ensemble of FCNs improves segmentation accuracy, while the shared weights within each residual block reduce parameter number. Semantic segmentation is essential for retinal disease detection. We tested LadderNet on two benchmark datasets for blood vessel segmentation in retinal images, and achieved superior performance over methods in the literature. The implementation is provided https: github.com juntang-zhuang LadderNet In this paper, we present UNet++, a new, more powerful architecture for medical image segmentation. Our architecture is essentially a deeply-supervised encoder-decoder network where the encoder and decoder sub-networks are connected through a series of nested, dense skip pathways. The re-designed skip pathways aim at reducing the semantic gap between the feature maps of the encoder and decoder sub-networks. We argue that the optimizer would deal with an easier learning task when the feature maps from the decoder and encoder networks are semantically similar. We have evaluated UNet++ in comparison with U-Net and wide U-Net architectures across multiple medical image segmentation tasks: nodule segmentation in the low-dose CT scans of chest, nuclei segmentation in the microscopy images, liver segmentation in abdominal CT scans, and polyp segmentation in colonoscopy videos. Our experiments demonstrate that UNet++ with deep supervision achieves an average IoU gain of 3.9 and 3.4 points over U-Net and wide U-Net, respectively. Deep learning (DL) based semantic segmentation methods have been providing state-of-the-art performance in the last few years. More specifically, these techniques have been successfully applied to medical image classification, segmentation, and detection tasks. One deep learning technique, U-Net, has become one of the most popular for these applications. In this paper, we propose a Recurrent Convolutional Neural Network (RCNN) based on U-Net as well as a Recurrent Residual Convolutional Neural Network (RRCNN) based on U-Net models, which are named RU-Net and R2U-Net respectively. The proposed models utilize the power of U-Net, Residual Network, as well as RCNN. There are several advantages of these proposed architectures for segmentation tasks. First, a residual unit helps when training deep architecture. Second, feature accumulation with recurrent residual convolutional layers ensures better feature representation for segmentation tasks. Third, it allows us to design better U-Net architecture with same number of network parameters with better performance for medical image segmentation. The proposed models are tested on three benchmark datasets such as blood vessel segmentation in retina images, skin cancer segmentation, and lung lesion segmentation. The experimental results show superior performance on segmentation tasks compared to equivalent models including U-Net and residual U-Net (ResU-Net). Recent work has made significant progress in improving spatial resolution for pixelwise labeling with Fully Convolutional Network (FCN) framework by employing Dilated Atrous convolution, utilizing multi-scale features and refining boundaries. In this paper, we explore the impact of global contextual information in semantic segmentation by introducing the Context Encoding Module, which captures the semantic context of scenes and selectively highlights class-dependent featuremaps. The proposed Context Encoding Module significantly improves semantic segmentation results with only marginal extra computation cost over FCN. Our approach has achieved new state-of-the-art results 51.7 mIoU on PASCAL-Context, 85.9 mIoU on PASCAL VOC 2012. Our single model achieves a final score of 0.5567 on ADE20K test set, which surpasses the winning entry of COCO-Place Challenge 2017. In addition, we also explore how the Context Encoding Module can improve the feature representation of relatively shallow networks for the image classification on CIFAR-10 dataset. Our 14 layer network has achieved an error rate of 3.45 , which is comparable with state-of-the-art approaches with over 10A— more layers. The source code for the complete system are publicly available1.