Electrical Engineering And Systems Science

Radiotherapy is the main treatment modality for nasopharynx cancer. Delineation of Gross Target Volume (GTV) from medical images such as CT and MRI images is a prerequisite for radiotherapy. As manual delineation is time-consuming and laborious, automatic segmentation of GTV has a potential to improve this process. Currently, most of the deep learning-based automatic delineation methods of GTV are mainly performed on medical images like CT images. However, it is challenged by the low contrast between the pathology regions and surrounding soft tissues, small target region, and anisotropic resolution of clinical CT images. To deal with these problems, we propose a 2.5D Convolutional Neural Network (CNN) to handle the difference of inplane and through-plane resolution. Furthermore, we propose a spatial attention module to enable the network to focus on small target, and use channel attention to further improve the segmentation performance. Moreover, we use multi-scale sampling method for training so that the networks can learn features at different scales, which are combined with a multi-model ensemble method to improve the robustness of segmentation results. We also estimate the uncertainty of segmentation results based on our model ensemble, which is of great importance for indicating the reliability of automatic segmentation results for radiotherapy planning.

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 this https URL.

This paper presents a method for automatic segmentation, localization, and identification of vertebrae in arbitrary 3D CT images. Many previous works do not perform the three tasks simultaneously even though requiring a priori knowledge of which part of the anatomy is visible in the 3D CT images. Our method tackles all these tasks in a single multi-stage framework without any assumptions. In the first stage, we train a 3D Fully Convolutional Networks to find the bounding boxes of the cervical, thoracic, and lumbar vertebrae. In the second stage, we train an iterative 3D Fully Convolutional Networks to segment individual vertebrae in the bounding box. The input to the second networks have an auxiliary channel in addition to the 3D CT images. Given the segmented vertebra regions in the auxiliary channel, the networks output the next vertebra. The proposed method is evaluated in terms of segmentation, localization, and identification accuracy with two public datasets of 15 3D CT images from the MICCAI CSI 2014 workshop challenge and 302 3D CT images with various pathologies introduced in [1]. Our method achieved a mean Dice score of 96%, a mean localization error of 8.3 mm, and a mean identification rate of 84%. In summary, our method achieved better performance than all existing works in all the three metrics.

Segmentation of additive manufacturing (AM) defects in X-ray Computed Tomography (XCT) images is challenging, due to the poor contrast, small sizes and variation in appearance of defects. Automatic segmentation can, however, provide quality control for additive manufacturing. Over recent years, three-dimensional convolutional neural networks (3D CNNs) have performed well in the volumetric segmentation of medical images. In this work, we leverage techniques from the medical imaging domain and propose training a 3D U-Net model to automatically segment defects in XCT images of AM samples. This work not only contributes to the use of machine learning for AM defect detection but also demonstrates for the first time 3D volumetric segmentation in AM. We train and test with three variants of the 3D U-Net on an AM dataset, achieving a mean intersection of union (IOU) value of 88.4%.

Purpose: Body composition is known to be associated with many diseases including diabetes, cancers and cardiovascular diseases. In this paper, we developed a fully automatic body tissue decomposition procedure to segment three major compartments that are related to body composition analysis - subcutaneous adipose tissue (SAT), visceral adipose tissue (VAT) and muscle. Three additional compartments - the ventral cavity, lung and bones were also segmented during the segmentation process to assist segmentation of the major compartments. Methods: A convolutional neural network (CNN) model with densely connected layers was developed to perform ventral cavity segmentation. An image processing workflow was developed to segment the ventral cavity in any patient's CT using the CNN model, then further segment the body tissue into multiple compartments using hysteresis thresholding followed by morphological operations. It is important to segment ventral cavity firstly to allow accurate separation of compartments with similar Hounsfield unit (HU) inside and outside the ventral cavity. Results: The ventral cavity segmentation CNN model was trained and tested with manually labelled ventral cavities in 60 CTs. Dice scores (mean +/- standard deviation) for ventral cavity segmentation were 0.966+/-0.012. Tested on CT datasets with intravenous (IV) and oral contrast, the Dice scores were 0.96+/-0.02, 0.94+/-0.06, 0.96+/-0.04, 0.95+/-0.04 and 0.99+/-0.01 for bone, VAT, SAT, muscle and lung, respectively. The respective Dice scores were 0.97+/-0.02, 0.94+/-0.07, 0.93+/-0.06, 0.91+/-0.04 and 0.99+/-0.01 for non-contrast CT datasets. Conclusion: A body tissue decomposition procedure was developed to automatically segment multiple compartments of the ventral body. The proposed method enables fully automated quantification of 3D ventral body composition metrics from CT images.

Although the video compression ratio nowadays becomes higher, the video coders such as H.264/AVC, H.265/HEVC, H.266/VVC always suffer from the video artifacts. In this paper, we design a neural network to enhance the quality of the compressed frame by leveraging the block information, called B-DRRN (Deep Recursive Residual Network with Block information). Firstly, an extra network branch is designed for leveraging the block information of the coding unit (CU). Moreover, to avoid a great increase in the network size, Recursive Residual structure and sharing weight techniques are applied. We also conduct a new large-scale dataset with 209,152 training samples. Experimental results show that the proposed B-DRRN can reduce 6.16% BD-rate compared to the HEVC standard. After efficiently adding an extra network branch, this work can improve the performance of the main network without increasing any memory for storing.

We propose a simple extension of residual networks that works simultaneously in multiple resolutions. Our network design is inspired by the iterative back-projection algorithm but seeks the more difficult task of learning how to enhance images. Compared to similar approaches, we propose a novel solution to make back-projections run in multiple resolutions by using a data pipeline workflow. Features are updated at multiple scales in each layer of the network. The update dynamic through these layers includes interactions between different resolutions in a way that is causal in scale, and it is represented by a system of ODEs, as opposed to a single ODE in the case of ResNets. The system can be used as a generic multi-resolution approach to enhance images. We test it on several challenging tasks with special focus on super-resolution and raindrop removal. Our results are competitive with state-of-the-arts and show a strong ability of our system to learn both global and local image features.

Recent deep learning approaches focus on improving quantitative scores of dedicated benchmarks, and therefore only reduce the observation-related (aleatoric) uncertainty. However, the model-immanent (epistemic) uncertainty is less frequently systematically analyzed. In this work, we introduce a Bayesian variational framework to quantify the epistemic uncertainty. To this end, we solve the linear inverse problem of undersampled MRI reconstruction in a variational setting. The associated energy functional is composed of a data fidelity term and the total deep variation (TDV) as a learned parametric regularizer. To estimate the epistemic uncertainty we draw the parameters of the TDV regularizer from a multivariate Gaussian distribution, whose mean and covariance matrix are learned in a stochastic optimal control problem. In several numerical experiments, we demonstrate that our approach yields competitive results for undersampled MRI reconstruction. Moreover, we can accurately quantify the pixelwise epistemic uncertainty, which can serve radiologists as an additional resource to visualize reconstruction reliability.

In multi-view fluorescence microscopy, each angular acquisition needs to be aligned with care to obtain an optimal volumetric reconstruction. Here, instead, we propose a neat protocol based on auto-correlation inversion, that leads directly to the formation of inherently aligned tomographies. Our method generates sharp reconstructions, with the same accuracy reachable after sub-pixel alignment but with improved point-spread-function. The procedure can be performed simultaneously with deconvolution further increasing the reconstruction resolution.

The chest X-ray plays a key role in screening and diagnosis of many lung diseases including the COVID-19. More recently, many works construct deep neural networks (DNNs) for chest X-ray images to realize automated and efficient diagnosis of lung diseases. However, bias field caused by the improper medical image acquisition process widely exists in the chest X-ray images while the robustness of DNNs to the bias field is rarely explored, which definitely poses a threat to the X-ray-based automated diagnosis system. In this paper, we study this problem based on the recent adversarial attack and propose a brand new attack, i.e., the adversarial bias field attack where the bias field instead of the additive noise works as the adversarial perturbations for fooling the DNNs. This novel attack posts a key problem: how to locally tune the bias field to realize high attack success rate while maintaining its spatial smoothness to guarantee high realisticity. These two goals contradict each other and thus has made the attack significantly challenging. To overcome this challenge, we propose the adversarial-smooth bias field attack that can locally tune the bias field with joint smooth & adversarial constraints. As a result, the adversarial X-ray images can not only fool the DNNs effectively but also retain very high level of realisticity. We validate our method on real chest X-ray datasets with powerful DNNs, e.g., ResNet50, DenseNet121, and MobileNet, and show different properties to the state-of-the-art attacks in both image realisticity and attack transferability. Our method reveals the potential threat to the DNN-based X-ray automated diagnosis and can definitely benefit the development of bias-field-robust automated diagnosis system.