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Register a new userSemi-supervised Semantic Segmentation of Prostate and Organs-at-Risk on 3D Pelvic CT Images
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Zhuangzhuang Zhang
Publication date
2020
fields
Informatics Engineering
and research's language is
English
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Automated segmentation can assist radiotherapy treatment planning by saving manual contouring efforts and reducing intra-observer and inter-observer variations. The recent development of deep learning approaches has revoluted medical data processing, including semantic segmentation, by dramatically improving performance. However, training effective deep learning models usually require a large amount of high-quality labeled data, which are often costly to collect. We developed a novel semi-supervised adversarial deep learning approach for 3D pelvic CT image semantic segmentation. Unlike supervised deep learning methods, the new approach can utilize both annotated and un-annotated data for training. It generates un-annotated synthetic data by a data augmentation scheme using generative adversarial networks (GANs). We applied the new approach to segmenting multiple organs in male pelvic CT images, where CT images without annotations and GAN-synthesized un-annotated images were used in semi-supervised learning. Experimental results, evaluated by three metrics (Dice similarity coefficient, average Hausdorff distance, and average surface Hausdorff distance), showed that the new method achieved either comparable performance with substantially fewer annotated images or better performance with the same amount of annotated data, outperforming the existing state-of-the-art methods.
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Purpose: The research is to develop a novel CNN-based adversarial deep learning method to improve and expedite the multi-organ semantic segmentation of CT images, and to generate accurate contours on pelvic CT images. Methods: Planning CT and structure datasets for 120 patients with intact prostate cancer were retrospectively selected and divided for 10-fold cross-validation. The proposed adversarial multi-residual multi-scale pooling Markov Random Field (MRF) enhanced network (ARPM-net) implements an adversarial training scheme. A segmentation network and a discriminator network were trained jointly, and only the segmentation network was used for prediction. The segmentation network integrates a newly designed MRF block into a variation of multi-residual U-net. The discriminator takes the product of the original CT and the prediction/ground-truth as input and classifies the input into fake/real. The segmentation network and discriminator network can be trained jointly as a whole, or the discriminator can be used for fine-tuning after the segmentation network is coarsely trained. Multi-scale pooling layers were introduced to preserve spatial resolution during pooling using less memory compared to atrous convolution layers. An adaptive loss function was proposed to enhance the training on small or low contrast organs. The accuracy of modeled contours was measured with the Dice similarity coefficient (DSC), Average Hausdorff Distance (AHD), Average Surface Hausdorff Distance (ASHD), and relative Volume Difference (VD) using clinical contours as references to the ground-truth. The proposed ARPM-net method was compared to several stateof-the-art deep learning methods.
3D point cloud semantic segmentation is a challenging topic in the computer vision field. Most of the existing methods in literature require a large amount of fully labeled training data, but it is extremely time-consuming to obtain these training data by manually labeling massive point clouds. Addressing this problem, we propose a superpoint-guided semi-supervised segmentation network for 3D point clouds, which jointly utilizes a small portion of labeled scene point clouds and a large number of unlabeled point clouds for network training. The proposed network is iteratively updated with its predicted pseudo labels, where a superpoint generation module is introduced for extracting superpoints from 3D point clouds, and a pseudo-label optimization module is explored for automatically assigning pseudo labels to the unlabeled points under the constraint of the extracted superpoints. Additionally, there are some 3D points without pseudo-label supervision. We propose an edge prediction module to constrain features of edge points. A superpoint feature aggregation module and a superpoint feature consistency loss function are introduced to smooth superpoint features. Extensive experimental results on two 3D public datasets demonstrate that our method can achieve better performance than several state-of-the-art point cloud segmentation networks and several popular semi-supervised segmentation methods with few labeled scenes.
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.
Pixel-wise clean annotation is necessary for fully-supervised semantic segmentation, which is laborious and expensive to obtain. In this paper, we propose a weakly supervised 2D semantic segmentation model by incorporating sparse bounding box labels with available 3D information, which is much easier to obtain with advanced sensors. We manually labeled a subset of the 2D-3D Semantics(2D-3D-S) dataset with bounding boxes, and introduce our 2D-3D inference module to generate accurate pixel-wise segment proposal masks. Guided by 3D information, we first generate a point cloud of objects and calculate objectness probability score for each point. Then we project the point cloud with objectness probabilities back to 2D images followed by a refinement step to obtain segment proposals, which are treated as pseudo labels to train a semantic segmentation network. Our method works in a recursive manner to gradually refine the above-mentioned segment proposals. Extensive experimental results on the 2D-3D-S dataset show that the proposed method can generate accurate segment proposals when bounding box labels are available on only a small subset of training images. Performance comparison with recent state-of-the-art methods further illustrates the effectiveness of our method.
We present a novel semi-supervised semantic segmentation method which jointly achieves two desiderata of segmentation model regularities: the label-space consistency property between image augmentations and the feature-space contrastive property among different pixels. We leverage the pixel-level L2 loss and the pixel contrastive loss for the two purposes respectively. To address the computational efficiency issue and the false negative noise issue involved in the pixel contrastive loss, we further introduce and investigate several negative sampling techniques. Extensive experiments demonstrate the state-of-the-art performance of our method (PC2Seg) with the DeepLab-v3+ architecture, in several challenging semi-supervised settings derived from the VOC, Cityscapes, and COCO datasets.
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