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With the injection of contrast material into blood vessels, multi-phase contrasted CT images can enhance the visibility of vessel networks in the human body. Reconstructing the 3D geometric morphology of liver vessels from the contrasted CT images can enable multiple liver preoperative surgical planning applications. Automatic reconstruction of liver vessel morphology remains a challenging problem due to the morphological complexity of liver vessels and the inconsistent vessel intensities among different multi-phase contrasted CT images. On the other side, high integrity is required for the 3D reconstruction to avoid decision making biases. In this paper, we propose a framework for liver vessel morphology reconstruction using both a fully convolutional neural network and a graph attention network. A fully convolutional neural network is first trained to produce the liver vessel centerline heatmap. An over-reconstructed liver vessel graph model is then traced based on the heatmap using an image processing based algorithm. We use a graph attention network to prune the false-positive branches by predicting the presence probability of each segmented branch in the initial reconstruction using the aggregated CNN features. We evaluated the proposed framework on an in-house dataset consisting of 418 multi-phase abdomen CT images with contrast. The proposed graph network pruning improves the overall reconstruction F1 score by 6.4% over the baseline. It also outperformed the other state-of-the-art curvilinear structure reconstruction algorithms.
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In this paper, we propose a phase attention residual network (PA-ResSeg) to model multi-phase features for accurate liver tumor segmentation, in which a phase attention (PA) is newly proposed to additionally exploit the images of arterial (ART) phase to facilitate the segmentation of portal venous (PV) phase. The PA block consists of an intra-phase attention (Intra-PA) module and an inter-phase attention (Inter-PA) module to capture channel-wise self-dependencies and cross-phase interdependencies, respectively. Thus it enables the network to learn more representative multi-phase features by refining the PV features according to the channel dependencies and recalibrating the ART features based on the learned interdependencies between phases. We propose a PA-based multi-scale fusion (MSF) architecture to embed the PA blocks in the network at multiple levels along the encoding path to fuse multi-scale features from multi-phase images. Moreover, a 3D boundary-enhanced loss (BE-loss) is proposed for training to make the network more sensitive to boundaries. To evaluate the performance of our proposed PA-ResSeg, we conducted experiments on a multi-phase CT dataset of focal liver lesions (MPCT-FLLs). Experimental results show the effectiveness of the proposed method by achieving a dice per case (DPC) of 0.77.87, a dice global (DG) of 0.8682, a volumetric overlap error (VOE) of 0.3328 and a relative volume difference (RVD) of 0.0443 on the MPCT-FLLs. Furthermore, to validate the effectiveness and robustness of PA-ResSeg, we conducted extra experiments on another multi-phase liver tumor dataset and obtained a DPC of 0.8290, a DG of 0.9132, a VOE of 0.2637 and a RVD of 0.0163. The proposed method shows its robustness and generalization capability in different datasets and different backbones.
3D to 2D retinal vessel segmentation is a challenging problem in Optical Coherence Tomography Angiography (OCTA) images. Accurate retinal vessel segmentation is important for the diagnosis and prevention of ophthalmic diseases. However, making full use of the 3D data of OCTA volumes is a vital factor for obtaining satisfactory segmentation results. In this paper, we propose a Progressive Attention-Enhanced Network (PAENet) based on attention mechanisms to extract rich feature representation. Specifically, the framework consists of two main parts, the three-dimensional feature learning path and the two-dimensional segmentation path. In the three-dimensional feature learning path, we design a novel Adaptive Pooling Module (APM) and propose a new Quadruple Attention Module (QAM). The APM captures dependencies along the projection direction of volumes and learns a series of pooling coefficients for feature fusion, which efficiently reduces feature dimension. In addition, the QAM reweights the features by capturing four-group cross-dimension dependencies, which makes maximum use of 4D feature tensors. In the two-dimensional segmentation path, to acquire more detailed information, we propose a Feature Fusion Module (FFM) to inject 3D information into the 2D path. Meanwhile, we adopt the Polarized Self-Attention (PSA) block to model the semantic interdependencies in spatial and channel dimensions respectively. Experimentally, our extensive experiments on the OCTA-500 dataset show that our proposed algorithm achieves state-of-the-art performance compared with previous methods.
Pulmonary vessel segmentation is important for clinical diagnosis of pulmonary diseases, while is also challenging due to the complicated structure. In this work, we present an effective framework and refinement process of pulmonary vessel segmentation from chest computed tomographic (CT) images. The key to our approach is a 2.5D segmentation network applied from three orthogonal axes, which presents a robust and fully automated pulmonary vessel segmentation result with lower network complexity and memory usage compared to 3D networks. The slice radius is introduced to convolve the adjacent information of the center slice and the multi-planar fusion optimizes the presentation of intra- and inter- slice features. Besides, the tree-like structure of the pulmonary vessel is extracted in the post-processing process, which is used for segmentation refining and pruning. In the evaluation experiments, three fusion methods are tested and the most promising one is compared with the state-of-the-art 2D and 3D structures on 300 cases of lung images randomly selected from LIDC dataset. Our method outperforms other network structures by a large margin and achieves by far the highest average DICE score of 0.9272 and precision of 0.9310, as per our knowledge from the pulmonary vessel segmentation models available in the literature.
Automatic segmentation of hepatic lesions in computed tomography (CT) images is a challenging task to perform due to heterogeneous, diffusive shape of tumors and complex background. To address the problem more and more researchers rely on assistance of deep convolutional neural networks (CNN) with 2D or 3D type architecture that have proven to be effective in a wide range of computer vision tasks, including medical image processing. In this technical report, we carry out research focused on more careful approach to the process of learning rather than on complex architecture of the CNN. We have chosen MICCAI 2017 LiTS dataset for training process and the public 3DIRCADb dataset for validation of our method. The proposed algorithm reached DICE score 78.8% on the 3DIRCADb dataset. The described method was then applied to the 2019 Kidney Tumor Segmentation (KiTS-2019) challenge, where our single submission achieved 96.38% for kidney and 67.38% for tumor Dice scores.
The ongoing global pandemic of Coronavirus Disease 2019 (COVID-19) poses a serious threat to public health and the economy. Rapid and accurate diagnosis of COVID-19 is crucial to prevent the further spread of the disease and reduce its mortality. Chest Computed tomography (CT) is an effective tool for the early diagnosis of lung diseases including pneumonia. However, detecting COVID-19 from CT is demanding and prone to human errors as some early-stage patients may have negative findings on images. Recently, many deep learning methods have achieved impressive performance in this regard. Despite their effectiveness, most of these methods underestimate the rich spatial information preserved in the 3D structure or suffer from the propagation of errors. To address this problem, we propose a Dual-Attention Residual Network (DARNet) to automatically identify COVID-19 from other common pneumonia (CP) and healthy people using 3D chest CT images. Specifically, we design a dual-attention module consisting of channel-wise attention and depth-wise attention mechanisms. The former is utilized to enhance channel independence, while the latter is developed to recalibrate the depth-level features. Then, we integrate them in a unified manner to extract and refine the features at different levels to further improve the diagnostic performance. We evaluate DARNet on a large public CT dataset and obtain superior performance. Besides, the ablation study and visualization analysis prove the effectiveness and interpretability of the proposed method.
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