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Register a new userMultiple resolution residual network for automatic thoracic organs-at-risk segmentation from CT
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We implemented and evaluated a multiple resolution residual network (MRRN) for multiple normal organs-at-risk (OAR) segmentation from computed tomography (CT) images for thoracic radiotherapy treatment (RT) planning. Our approach simultaneously combines feature streams computed at multiple image resolutions and feature levels through residual connections. The feature streams at each level are updated as the images are passed through various feature levels. We trained our approach using 206 thoracic CT scans of lung cancer patients with 35 scans held out for validation to segment the left and right lungs, heart, esophagus, and spinal cord. This approach was tested on 60 CT scans from the open-source AAPM Thoracic Auto-Segmentation Challenge dataset. Performance was measured using the Dice Similarity Coefficient (DSC). Our approach outperformed the best-performing method in the grand challenge for hard-to-segment structures like the esophagus and achieved comparable results for all other structures. Median DSC using our method was 0.97 (interquartile range [IQR]: 0.97-0.98) for the left and right lungs, 0.93 (IQR: 0.93-0.95) for the heart, 0.78 (IQR: 0.76-0.80) for the esophagus, and 0.88 (IQR: 0.86-0.89) for the spinal cord.
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Nasopharyngeal Carcinoma (NPC) is a leading form of Head-and-Neck (HAN) cancer in the Arctic, China, Southeast Asia, and the Middle East/North Africa. Accurate segmentation of Organs-at-Risk (OAR) from Computed Tomography (CT) images with uncertainty information is critical for effective planning of radiation therapy for NPC treatment. Despite the stateof-the-art performance achieved by Convolutional Neural Networks (CNNs) for automatic segmentation of OARs, existing methods do not provide uncertainty estimation of the segmentation results for treatment planning, and their accuracy is still limited by several factors, including the low contrast of soft tissues in CT, highly imbalanced sizes of OARs and large inter-slice spacing. To address these problems, we propose a novel framework for accurate OAR segmentation with reliable uncertainty estimation. First, we propose a Segmental Linear Function (SLF) to transform the intensity of CT images to make multiple organs more distinguishable than existing methods based on a simple window width/level that often gives a better visibility of one organ while hiding the others. Second, to deal with the large inter-slice spacing, we introduce a novel 2.5D network (named as 3D-SepNet) specially designed for dealing with clinic HAN CT scans with anisotropic spacing. Thirdly, existing hardness-aware loss function often deal with class-level hardness, but our proposed attention to hard voxels (ATH) uses a voxel-level hardness strategy, which is more suitable to dealing with some hard regions despite that its corresponding class may be easy. Our code is now available at https://github.com/HiLab-git/SepNet.
A 3D deep learning model (OARnet) is developed and used to delineate 28 H&N OARs on CT images. OARnet utilizes a densely connected network to detect the OAR bounding-box, then delineates the OAR within the box. It reuses information from any layer to subsequent layers and uses skip connections to combine information from different dense block levels to progressively improve delineation accuracy. Training uses up to 28 expert manual delineated (MD) OARs from 165 CTs. Dice similarity coefficient (DSC) and the 95th percentile Hausdorff distance (HD95) with respect to MD is assessed for 70 other CTs. Mean, maximum, and root-mean-square dose differences with respect to MD are assessed for 56 of the 70 CTs. OARnet is compared with UaNet, AnatomyNet, and Multi-Atlas Segmentation (MAS). Wilcoxon signed-rank tests using 95% confidence intervals are used to assess significance. Wilcoxon signed ranked tests show that, compared with UaNet, OARnet improves (p<0.05) the DSC (23/28 OARs) and HD95 (17/28). OARnet outperforms both AnatomyNet and MAS for DSC (28/28) and HD95 (27/28). Compared with UaNet, OARnet improves median DSC up to 0.05 and HD95 up to 1.5mm. Compared with AnatomyNet and MAS, OARnet improves median (DSC, HD95) by up to (0.08, 2.7mm) and (0.17, 6.3mm). Dosimetrically, OARnet outperforms UaNet (Dmax 7/28; Dmean 10/28), AnatomyNet (Dmax 21/28; Dmean 24/28), and MAS (Dmax 22/28; Dmean 21/28). The DenseNet architecture is optimized using a hybrid approach that performs OAR-specific bounding box detection followed by feature recognition. Compared with other auto-delineation methods, OARnet is better than or equal to UaNet for all but one geometric (Temporal Lobe L, HD95) and one dosimetric (Eye L, mean dose) endpoint for the 28 H&N OARs, and is better than or equal to both AnatomyNet and MAS for all OARs.
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.
In radiotherapy planning, manual contouring is labor-intensive and time-consuming. Accurate and robust automated segmentation models improve the efficiency and treatment outcome. We aim to develop a novel hybrid deep learning approach, combining convolutional neural networks (CNNs) and the self-attention mechanism, for rapid and accurate multi-organ segmentation on head and neck computed tomography (CT) images. Head and neck CT images with manual contours of 115 patients were retrospectively collected and used. We set the training/validation/testing ratio to 81/9/25 and used the 10-fold cross-validation strategy to select the best model parameters. The proposed hybrid model segmented ten organs-at-risk (OARs) altogether for each case. The performance of the model was evaluated by three metrics, i.e., the Dice Similarity Coefficient (DSC), Hausdorff distance 95% (HD95), and mean surface distance (MSD). We also tested the performance of the model on the Head and Neck 2015 challenge dataset and compared it against several state-of-the-art automated segmentation algorithms. The proposed method generated contours that closely resemble the ground truth for ten OARs. Our results of the new Weaving Attention U-net demonstrate superior or similar performance on the segmentation of head and neck CT images.
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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