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Register a new userFusionNet: Incorporating Shape and Texture for Abnormality Detection in 3D Abdominal CT Scans
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Added by
Fengze Liu
Publication date
2019
fields
Informatics Engineering
and research's language is
English
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Automatic abnormality detection in abdominal CT scans can help doctors improve the accuracy and efficiency in diagnosis. In this paper we aim at detecting pancreatic ductal adenocarcinoma (PDAC), the most common pancreatic cancer. Taking the fact that the existence of tumor can affect both the shape and the texture of pancreas, we design a system to extract the shape and texture feature at the same time for detecting PDAC. In this paper we propose a two-stage method for this 3D classification task. First, we segment the pancreas into a binary mask. Second, a FusionNet is proposed to take both the binary mask and CT image as input and perform a binary classification. The optimal architecture of the FusionNet is obtained by searching a pre-defined functional space. We show that the classification results using either shape or texture information are complementary, and by fusing them with the optimized architecture, the performance improves by a large margin. Our method achieves a specificity of 97% and a sensitivity of 92% on 200 normal scans and 136 scans with PDAC.
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This paper proposes a new convolutional neural network with multiscale processing for detecting ground-glass opacity (GGO) nodules in 3D computed tomography (CT) images, which is referred to as PiaNet for short. PiaNet consists of a feature-extraction module and a prediction module. The former module is constructed by introducing pyramid multiscale source connections into a contracting-expanding structure. The latter module includes a bounding-box regressor and a classifier that are employed to simultaneously recognize GGO nodules and estimate bounding boxes at multiple scales. To train the proposed PiaNet, a two-stage transfer learning strategy is developed. In the first stage, the feature-extraction module is embedded into a classifier network that is trained on a large data set of GGO and non-GGO patches, which are generated by performing data augmentation from a small number of annotated CT scans. In the second stage, the pretrained feature-extraction module is loaded into PiaNet, and then PiaNet is fine-tuned using the annotated CT scans. We evaluate the proposed PiaNet on the LIDC-IDRI data set. The experimental results demonstrate that our method outperforms state-of-the-art counterparts, including the Subsolid CAD and Aidence systems and S4ND and GA-SSD methods. PiaNet achieves a sensitivity of 91.75% with only one false positive per scan
Segmentation of mandibles in CT scans during virtual surgical planning is crucial for 3D surgical planning in order to obtain a detailed surface representation of the patients bone. Automatic segmentation of mandibles in CT scans is a challenging task due to large variation in their shape and size between individuals. In order to address this challenge we propose a convolutional neural network approach for mandible segmentation in CT scans by considering the continuum of anatomical structures through different planes. The proposed convolutional neural network adopts the architecture of the U-Net and then combines the resulting 2D segmentations from three different planes into a 3D segmentation. We implement such a segmentation approach on 11 neck CT scans and then evaluate the performance. We achieve an average dice coefficient of $ 0.89 $ on two testing mandible segmentation. Experimental results show that our proposed approach for mandible segmentation in CT scans exhibits high accuracy.
Tubular structure segmentation in medical images, e.g., segmenting vessels in CT scans, serves as a vital step in the use of computers to aid in screening early stages of related diseases. But automatic tubular structure segmentation in CT scans is a challenging problem, due to issues such as poor contrast, noise and complicated background. A tubular structure usually has a cylinder-like shape which can be well represented by its skeleton and cross-sectional radii (scales). Inspired by this, we propose a geometry-aware tubular structure segmentation method, Deep Distance Transform (DDT), which combines intuitions from the classical distance transform for skeletonization and modern deep segmentation networks. DDT first learns a multi-task network to predict a segmentation mask for a tubular structure and a distance map. Each value in the map represents the distance from each tubular structure voxel to the tubular structure surface. Then the segmentation mask is refined by leveraging the shape prior reconstructed from the distance map. We apply our DDT on six medical image datasets. The experiments show that (1) DDT can boost tubular structure segmentation performance significantly (e.g., over 13% improvement measured by DSC for pancreatic duct segmentation), and (2) DDT additionally provides a geometrical measurement for a tubular structure, which is important for clinical diagnosis (e.g., the cross-sectional scale of a pancreatic duct can be an indicator for pancreatic cancer).
Realistic color texture generation is an important step in RGB-D surface reconstruction, but remains challenging in practice due to inaccuracies in reconstructed geometry, misaligned camera poses, and view-dependent imaging artifacts. In this work, we present a novel approach for color texture generation using a conditional adversarial loss obtained from weakly-supervised views. Specifically, we propose an approach to produce photorealistic textures for approximate surfaces, even from misaligned images, by learning an objective function that is robust to these errors. The key idea of our approach is to learn a patch-based conditional discriminator which guides the texture optimization to be tolerant to misalignments. Our discriminator takes a synthesized view and a real image, and evaluates whether the synthesized one is realistic, under a broadened definition of realism. We train the discriminator by providing as `real examples pairs of input views and their misalign
This paper reports Deep LOGISMOS approach to 3D tumor segmentation by incorporating boundary information derived from deep contextual learning to LOGISMOS - layered optimal graph image segmentation of multiple objects and surfaces. Accurate and reliable tumor segmentation is essential to tumor growth analysis and treatment selection. A fully convolutional network (FCN), UNet, is first trained using three adjacent 2D patches centered at the tumor, providing contextual UNet segmentation and probability map for each 2D patch. The UNet segmentation is then refined by Gaussian Mixture Model (GMM) and morphological operations. The refined UNet segmentation is used to provide the initial shape boundary to build a segmentation graph. The cost for each node of the graph is determined by the UNet probability maps. Finally, a max-flow algorithm is employed to find the globally optimal solution thus obtaining the final segmentation. For evaluation, we applied the method to pancreatic tumor segmentation on a dataset of 51 CT scans, among which 30 scans were used for training and 21 for testing. With Deep LOGISMOS, DICE Similarity Coefficient (DSC) and Relative Volume Difference (RVD) reached 83.2+-7.8% and 18.6+-17.4% respectively, both are significantly improved (p<0.05) compared with contextual UNet and/or LOGISMOS alone.
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