MTGAN: Mask and Texture-Driven Generative Adversarial Network for Lung Nodule Segmentation

Wei Chen, Qiuli Wang, Kun Wang, Dan Yang, Xiaohong Zhang, Chen Liu, Yucong Li

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Auto-TLDR; Mask and Texture-driven Generative Adversarial Network for Lung Nodule Segmentation

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Accurate segmentation for lung nodules in lung computed tomography (CT) scans plays a key role in the early diagnosis of lung cancer. Many existing methods, especially UNet, have made significant progress in lung nodule segmentation. However, due to the complex shapes of lung nodules and the similarity of visual characteristics between nodules and lung tissues, an accurate segmentation with few false positives of lung nodules is still a challenging problem. Considering the fact that both boundary and texture information of lung nodules are important for obtaining an accurate segmentation result, we propose a novel Mask and Texture-driven Generative Adversarial Network (MTGAN) with a joint multi-scale L1 loss for lung nodule segmentation, which takes full advantages of U-Net and adversarial training. The proposed MTGAN leverages adversarial learning strategy guided by the boundary and texture information of lung nodules to generate more accurate segmentation results with lesser false positives. We validate our model with the LIDC–IDRI dataset, and experimental results show that our method achieves excellent segmentation results for a variety of lung nodules, especially for juxtapleural nodules and low-dense nodules. Without any bells and whistles, the proposed MTGAN achieves significant segmentation performance with the Dice similarity coefficient (DSC) of 85.24% on the LIDC–IDRI dataset.

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End-To-End Multi-Task Learning for Lung Nodule Segmentation and Diagnosis

Wei Chen, Qiuli Wang, Dan Yang, Xiaohong Zhang, Chen Liu, Yucong Li

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Auto-TLDR; A novel multi-task framework for lung nodule diagnosis based on deep learning and medical features

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Computer-Aided Diagnosis (CAD) systems for lung nodule diagnosis based on deep learning have attracted much attention in recent years. However, most existing methods ignore the relationships between the segmentation and classification tasks, which leads to unstable performances. To address this problem, we propose a novel multi-task framework, which can provide lung nodule segmentation mask, malignancy prediction, and medical features for interpretable diagnosis at the same time. Our framework mainly contains two sub-network: (1) Multi-Channel Segmentation Sub-network (MSN) for lung nodule segmentation, and (2) Joint Classification Sub-network (JCN) for interpretable lung nodule diagnosis. In the proposed framework, we use U-Net down-sampling processes for extracting low-level deep learning features, which are shared by two sub-networks. The JCN forces the down-sampling processes to learn better lowlevel deep features, which lead to a better construct of segmentation masks. Meanwhile, two additional channels constructed by OTSU and super-pixel (SLIC) methods, are utilized as the guideline of the feature extraction. The proposed framework takes advantages of deep learning methods and classical methods, which can significantly improve the performances of all tasks. We evaluate the proposed framework on public dataset LIDCIDRI. Our framework achieves a promising Dice score of 86.43% in segmentation, 87.07% in malignancy level prediction, and convincing results in interpretable medical feature predictions.

BG-Net: Boundary-Guided Network for Lung Segmentation on Clinical CT Images

Rui Xu, Yi Wang, Tiantian Liu, Xinchen Ye, Lin Lin, Yen-Wei Chen, Shoji Kido, Noriyuki Tomiyama

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Auto-TLDR; Boundary-Guided Network for Lung Segmentation on CT Images

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Lung segmentation on CT images is a crucial step for a computer-aided diagnosis system of lung diseases. The existing deep learning based lung segmentation methods are less efficient to segment lungs on clinical CT images, especially that the segmentation on lung boundaries is not accurate enough due to complex pulmonary opacities in practical clinics. In this paper, we propose a boundary-guided network (BG-Net) to address this problem. It contains two auxiliary branches that separately segment lungs and extract the lung boundaries, and an aggregation branch that efficiently exploits lung boundary cues to guide the network for more accurate lung segmentation on clinical CT images. We evaluate the proposed method on a private dataset collected from the Osaka university hospital and four public datasets including StructSeg, HUG, VESSEL12, and a Novel Coronavirus 2019 (COVID-19) dataset. Experimental results show that the proposed method can segment lungs more accurately and outperform several other deep learning based methods.

A Benchmark Dataset for Segmenting Liver, Vasculature and Lesions from Large-Scale Computed Tomography Data

Bo Wang, Zhengqing Xu, Wei Xu, Qingsen Yan, Liang Zhang, Zheng You

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Auto-TLDR; The Biggest Treatment-Oriented Liver Cancer Dataset for Segmentation

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How to build a high-performance liver-related computer assisted diagnosis system is an open question of great interest. However, the performance of the state-of-art algorithm is always limited by the amount of data and quality of the label. To address this problem, we propose the biggest treatment-oriented liver cancer dataset for liver surgery and treatment planning. This dataset provides 216 cases (totally about 268K frames) scanned images in contrast-enhanced computed tomography (CT). We labeled all the CT images with the liver, liver vasculature and liver tumor segmentation ground truth for train and tune segmentation algorithms in advance. Based on that, we evaluate several recent and state-of-the-art segmentation algorithms, including 7 deep learning methods, on CT sequences. All results are compared to reference segmentations five error metrics that highlight different aspects of segmentation accuracy. In general, compared with previous datasets, our dataset is really a challenging dataset. To our knowledge, the proposed dataset and benchmark allow for the first time systematic exploration of such issues, and will be made available to allow for further research in this field.

Unsupervised Detection of Pulmonary Opacities for Computer-Aided Diagnosis of COVID-19 on CT Images

Rui Xu, Xiao Cao, Yufeng Wang, Yen-Wei Chen, Xinchen Ye, Lin Lin, Wenchao Zhu, Chao Chen, Fangyi Xu, Yong Zhou, Hongjie Hu, Shoji Kido, Noriyuki Tomiyama

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Auto-TLDR; A computer-aided diagnosis of COVID-19 from CT images using unsupervised pulmonary opacity detection

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COVID-19 emerged towards the end of 2019 which was identified as a global pandemic by the world heath organization (WHO). With the rapid spread of COVID-19, the number of infected and suspected patients has increased dramatically. Chest computed tomography (CT) has been recognized as an efficient tool for the diagnosis of COVID-19. However, the huge CT data make it difficult for radiologist to fully exploit them on the diagnosis. In this paper, we propose a computer-aided diagnosis system that can automatically analyze CT images to distinguish the COVID-19 against to community-acquired pneumonia (CAP). The proposed system is based on an unsupervised pulmonary opacity detection method that locates opacity regions by a detector unsupervisedly trained from CT images with normal lung tissues. Radiomics based features are extracted insides the opacity regions, and fed into classifiers for classification. We evaluate the proposed CAD system by using 200 CT images collected from different patients in several hospitals. The accuracy, precision, recall, f1-score and AUC achieved are 95.5%, 100%, 91%, 95.1% and 95.9% respectively, exhibiting the promising capacity on the differential diagnosis of COVID-19 from CT images.

Deep Recurrent-Convolutional Model for AutomatedSegmentation of Craniomaxillofacial CT Scans

Francesca Murabito, Simone Palazzo, Federica Salanitri Proietto, Francesco Rundo, Ulas Bagci, Daniela Giordano, Rosalia Leonardi, Concetto Spampinato

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Auto-TLDR; Automated Segmentation of Anatomical Structures in Craniomaxillofacial CT Scans using Fully Convolutional Deep Networks

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In this paper we define a deep learning architecture for automated segmentation of anatomical structures in Craniomaxillofacial (CMF) CT scans that leverages the recent success of encoder-decoder models for semantic segmentation of natural images. In particular, we propose a fully convolutional deep network that combines the advantages of recent fully convolutional models, such as Tiramisu, with squeeze-and-excitation blocks for feature recalibration, integrated with convolutional LSTMs to model spatio-temporal correlations between consecutive slices. The proposed segmentation network shows superior performance and generalization capabilities (to different structures and imaging modalities) than state of the art methods on automated segmentation of CMF structures (e.g., mandibles and airways) in several standard benchmarks (e.g., MICCAI datasets) and on new datasets proposed herein, effectively facing shape variability.

DARN: Deep Attentive Refinement Network for Liver Tumor Segmentation from 3D CT Volume

Yao Zhang, Jiang Tian, Cheng Zhong, Yang Zhang, Zhongchao Shi, Zhiqiang He

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Auto-TLDR; Deep Attentive Refinement Network for Liver Tumor Segmentation from 3D Computed Tomography Using Multi-Level Features

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Automatic liver tumor segmentation from 3D Computed Tomography (CT) is a necessary prerequisite in the interventions of hepatic abnormalities and surgery planning. However, accurate liver tumor segmentation remains challenging due to the large variability of tumor sizes and inhomogeneous texture. Recent advances based on Fully Convolutional Network (FCN) in liver tumor segmentation draw on success of learning discriminative multi-level features. In this paper, we propose a Deep Attentive Refinement Network (DARN) for improved liver tumor segmentation from CT volumes by fully exploiting both low and high level features embedded in different layers of FCN. Different from existing works, we exploit attention mechanism to leverage the relation of different levels of features encoded in different layers of FCN. Specifically, we introduce a Semantic Attention Refinement (SemRef) module to selectively emphasize global semantic information in low level features with the guidance of high level ones, and a Spatial Attention Refinement (SpaRef) module to adaptively enhance spatial details in high level features with the guidance of low level ones. We evaluate our network on the public MICCAI 2017 Liver Tumor Segmentation Challenge dataset (LiTS dataset) and it achieves state-of-the-art performance. The proposed refinement modules are an effective strategy to exploit multi-level features and has great potential to generalize to other medical image segmentation tasks.

BiLuNet: A Multi-Path Network for Semantic Segmentation on X-Ray Images

Van Luan Tran, Huei-Yung Lin, Rachel Liu, Chun-Han Tseng, Chun-Han Tseng

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Auto-TLDR; BiLuNet: Multi-path Convolutional Neural Network for Semantic Segmentation of Lumbar vertebrae, sacrum,

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Semantic segmentation and shape detection of lumbar vertebrae, sacrum, and femoral heads from clinical X-ray images are important and challenging tasks. In this paper, we propose a new multi-path convolutional neural network, BiLuNet, for semantic segmentation on X-ray images. The network is capable of medical image segmentation with very limited training data. With the shape fitting of the bones, we can identify the location of the target regions very accurately for lumbar vertebra inspection. We collected our dataset and annotated by doctors for model training and performance evaluation. Compared to the state-of-the-art methods, the proposed technique provides better mIoUs and higher success rates with the same training data. The experimental results have demonstrated the feasibility of our network to perform semantic segmentation for lumbar vertebrae, sacrum, and femoral heads.

Progressive Adversarial Semantic Segmentation

Abdullah-Al-Zubaer Imran, Demetri Terzopoulos

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Auto-TLDR; Progressive Adversarial Semantic Segmentation for End-to-End Medical Image Segmenting

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Medical image computing has advanced rapidly with the advent of deep learning techniques such as convolutional neural networks. Deep convolutional neural networks can perform exceedingly well given full supervision. However, the success of such fully-supervised models for various image analysis tasks (e.g., anatomy or lesion segmentation from medical images) is limited to the availability of massive amounts of labeled data. Given small sample sizes, such models are prohibitively data biased with large domain shift. To tackle this problem, we propose a novel end-to-end medical image segmentation model, namely Progressive Adversarial Semantic Segmentation (PASS), which can make improved segmentation predictions without requiring any domain-specific data during training time. Our extensive experimentation with 8 public diabetic retinopathy and chest X-ray datasets, confirms the effectiveness of PASS for accurate vascular and pulmonary segmentation, both for in-domain and cross-domain evaluations.

NephCNN: A Deep-Learning Framework for Vessel Segmentation in Nephrectomy Laparoscopic Videos

Alessandro Casella, Sara Moccia, Chiara Carlini, Emanuele Frontoni, Elena De Momi, Leonardo Mattos

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Auto-TLDR; Adversarial Fully Convolutional Neural Networks for kidney vessel segmentation from nephrectomy laparoscopic videos

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Objective: In the last years, Robot-assisted partial nephrectomy (RAPN) is establishing as elected treatment for renal cell carcinoma (RCC). Reduced field of view, field occlusions by surgical tools, and reduced maneuverability may potentially cause accidents, such as unwanted vessel resection with consequent bleeding. Surgical Data Science (SDS) can provide effective context-aware tools for supporting surgeons. However, currently no tools have been exploited for automatic vessels segmentation from nephrectomy laparoscopic videos. Herein, we propose a new approach based on adversarial Fully Convolutional Neural Networks (FCNNs) to kidney vessel segmentation from nephrectomy laparoscopic vision. Methods: The proposed approach enhances existing segmentation framework by (i) encoding 3D kernels for spatio-temporal features extraction to enforce pixel connectivity in time, and (ii) perform training in adversarial fashion, which constrains vessels shape. Results: We performed a preliminary study using 8 different RAPN videos (1871 frames), the first in the field, achieving a median Dice Similarity Coefficient of 71.76%. Conclusions: Results showed that the proposed approach could be a valuable solution with a view to assist surgeon during RAPN.

CAggNet: Crossing Aggregation Network for Medical Image Segmentation

Xu Cao, Yanghao Lin

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Auto-TLDR; Crossing Aggregation Network for Medical Image Segmentation

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In this paper, we present Crossing Aggregation Network (CAggNet), a novel densely connected semantic segmentation method for medical image analysis. The crossing aggregation network absorbs the idea of deep layer aggregation and makes significant innovations in layer connection and semantic information fusion. In this architecture, the traditional skip-connection structure of general U-Net is replaced by aggregations of multi-level down-sampling and up-sampling layers. This enables the network to fuse information interactively flows at different levels of layers in semantic segmentation. It also introduces weighted aggregation module to aggregate multi-scale output information. We have evaluated and compared our CAggNet with several advanced U-Net based methods in two public medical image datasets, including the 2018 Data Science Bowl nuclei detection dataset and the 2015 MICCAI gland segmentation competition dataset. Experimental results indicate that CAggNet improves medical object recognition and achieves a more accurate and efficient segmentation compared to existing improved U-Net and UNet++ structure.

FOANet: A Focus of Attention Network with Application to Myocardium Segmentation

Zhou Zhao, Elodie Puybareau, Nicolas Boutry, Thierry Geraud

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Auto-TLDR; FOANet: A Hybrid Loss Function for Myocardium Segmentation of Cardiac Magnetic Resonance Images

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In myocardium segmentation of cardiac magnetic resonance images, ambiguities often appear near the boundaries of the target domains due to tissue similarities. To address this issue, we propose a new architecture, called FOANet, which can be decomposed in three main steps: a localization step, a Gaussian-based contrast enhancement step, and a segmentation step. This architecture is supplied with a hybrid loss function that guides the FOANet to study the transformation relationship between the input image and the corresponding label in a threelevel hierarchy (pixel-, patch- and map-level), which is helpful to improve segmentation and recovery of the boundaries. We demonstrate the efficiency of our approach on two public datasets in terms of regional and boundary segmentations.

Triplet-Path Dilated Network for Detection and Segmentation of General Pathological Images

Jiaqi Luo, Zhicheng Zhao, Fei Su, Limei Guo

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Auto-TLDR; Triplet-path Network for One-Stage Object Detection and Segmentation in Pathological Images

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Deep learning has been widely applied in the field of medical image processing. However, compared with flourishing visual tasks in natural images, the progress achieved in pathological images is not remarkable, and detection and segmentation, which are among basic tasks of computer vision, are regarded as two independent tasks. In this paper, we make full use of existing datasets and construct a triplet-path network using dilated convolutions to cooperatively accomplish one-stage object detection and nuclei segmentation for general pathological images. First, in order to meet the requirement of detection and segmentation, a novel structure called triplet feature generation (TFG) is designed to extract high-resolution and multiscale features, where features from different layers can be properly integrated. Second, considering that pathological datasets are usually small, a location-aware and partially truncated loss function is proposed to improve the classification accuracy of datasets with few images and widely varying targets. We compare the performance of both object detection and instance segmentation with state-of-the-art methods. Experimental results demonstrate the effectiveness and efficiency of the proposed network on two datasets collected from multiple organs.

Detail-Revealing Deep Low-Dose CT Reconstruction

Xinchen Ye, Yuyao Xu, Rui Xu, Shoji Kido, Noriyuki Tomiyama

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Auto-TLDR; A Dual-branch Aggregation Network for Low-Dose CT Reconstruction

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Low-dose CT imaging emerges with low radiation risk due to the reduction of radiation dose, but brings negative impact on the imaging quality. This paper addresses the problem of low-dose CT reconstruction. Previous methods are unsatisfactory due to the inaccurate recovery of image details under the strong noise generated by the reduction of radiation dose, which directly affects the final diagnosis. To suppress the noise effectively while retain the structures well, we propose a detail-revealing dual-branch aggregation network to effectively reconstruct the degraded CT image. Specifically, the main reconstruction branch iteratively exploits and compensates the reconstruction errors to gradually refine the CT image, while the prior branch is to learn the structure details as prior knowledge to help recover the CT image. A sophisticated detail-revealing loss is designed to fuse the information from both branches and guide the learning to obtain better performance from pixel-wise and holistic perspectives respectively. Experimental results show that our method outperforms the state-of-art methods in both PSNR and SSIM metrics.

Automatic Semantic Segmentation of Structural Elements related to the Spinal Cord in the Lumbar Region by Using Convolutional Neural Networks

Jhon Jairo Sáenz Gamboa, Maria De La Iglesia-Vaya, Jon Ander Gómez

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Auto-TLDR; Semantic Segmentation of Lumbar Spine Using Convolutional Neural Networks

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This work addresses the problem of automatically segmenting the MR images corresponding to the lumbar spine. The purpose is to detect and delimit the different structural elements like vertebrae, intervertebral discs, nerves, blood vessels, etc. This task is known as semantic segmentation. The approach proposed in this work is based on convolutional neural networks whose output is a mask where each pixel from the input image is classified into one of the possible classes. Classes were defined by radiologists and correspond to structural elements and tissues. The proposed network architectures are variants of the U-Net. Several complementary blocks were used to define the variants: spatial attention models, deep supervision and multi-kernels at input, this last block type is based on the idea of inception. Those architectures which got the best results are described in this paper, and their results are discussed. Two of the proposed architectures outperform the standard U-Net used as baseline.

A Multi-Task Contextual Atrous Residual Network for Brain Tumor Detection & Segmentation

Ngan Le, Kashu Yamazaki, Quach Kha Gia, Thanh-Dat Truong, Marios Savvides

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Auto-TLDR; Contextual Brain Tumor Segmentation Using 3D atrous Residual Networks and Cascaded Structures

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In recent years, deep neural networks have achieved state-of-the-art performance in a variety of recognition and segmentation tasks in medical imaging including brain tumor segmentation. We investigate that segmenting brain tumor is facing to the imbalanced data problem where the number of pixels belonging to background class (non tumor pixel) is much larger than the number of pixels belonging to foreground class (tumor pixel). To address this problem, we propose a multi-task network which is formed as a cascaded structure and designed to share the feature maps. Our model consists of two targets, i.e., (i) effectively differentiating brain tumor regions and (ii) estimating brain tumor masks. The first task is performed by our proposed contextual brain tumor detection network, which plays the role of an attention gate and focuses on the region around brain tumor only while ignore the background (non tumor area). Instead of processing every pixel, our contextual brain tumor detection network only processes contextual regions around ground-truth instances and this strategy helps to produce meaningful regions proposals. The second task is built upon a 3D atrous residual network and under an encode-decode network in order to effectively segment both large and small objects (brain tumor). Our 3D atrous residual network is designed with a skip connection to enables the gradient from the deep layers to be directly propagated to shallow layers, thus, features of different depths are preserved and used for refining each other. In order to incorporate larger contextual information in volume MRI data, our network is designed by 3D atrous convolution with various kernel sizes, which enlarges the receptive field of filters. Our proposed network has been evaluated on various datasets including BRATS2015, BRATS2017 and BRATS2018 datasets with both validation set and testing set. Our performance has been benchmarked by both region-based metrics and surface-based metrics. We also have conducted comparisons against state-of-the-art approaches.

DA-RefineNet: Dual-Inputs Attention RefineNet for Whole Slide Image Segmentation

Ziqiang Li, Rentuo Tao, Qianrun Wu, Bin Li

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Auto-TLDR; DA-RefineNet: A dual-inputs attention network for whole slide image segmentation

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Automatic medical image segmentation techniques have wide applications for disease diagnosing, however, its much more challenging than natural optical image segmentation tasks due to the high-resolution of medical images and the corresponding huge computation cost. Sliding window was a commonly used technique for whole slide image (WSI) segmentation, however, for these methods that based on sliding window, the main drawback was lacking of global contextual information for supervision. In this paper, we proposed a dual-inputs attention network (denoted as DA-RefineNet) for WSI segmentation, where both local fine-grained information and global coarse information can be efficiently utilized. Sufficient comparative experiments were conducted to evaluate the effectiveness of the proposed method, the results proved that the proposed method can achieve better performance on WSI segmentation tasks compared to methods rely on single-input.

A Deep Learning Approach for the Segmentation of Myocardial Diseases

Khawala Brahim, Abdull Qayyum, Alain Lalande, Arnaud Boucher, Anis Sakly, Fabrice Meriaudeau

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Auto-TLDR; Segmentation of Myocardium Infarction Using Late GADEMRI and SegU-Net

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Cardiac left ventricular (LV) segmentation is of paramount essential step for both diagnosis and treatment of cardiac pathologies such as ischemia, myocardial infarction, arrhythmia and myocarditis. However, this segmentation is challenging due to high variability across patients and the potential lack of contrast between structures. In this work, we propose and evaluate a (2.5D) SegU-Net model based on the fusion of two deep learning techniques (U-Net and Seg-Net) for automated LGEMRI (Late gadolinium enhanced magnetic resonance imaging) myocardial disease (infarct core and no reflow region) quantification in a new multifield expert annotated dataset. Given that the scar tissue represents a small part of the whole MRI slices, we focused on myocardium area. Segmentation results show that this preprocessing step facilitate the learning procedure. In order to solve the class imbalance problem, we propose to apply the Jaccard loss and the Focal Loss as optimization loss function and to integrate a class weights strategy into the objective function. Late combination has been used to merge the output of the best trained models on a different set of hyperparameters. The final network segmentation performances will be useful for future comparison of new method to the current related work for this task. A total number of 2237 of slices (320 cases) were used for training/validation and 210 slices (35 cases) were used for testing. Experiments over our proposed dataset, using several evaluation metrics such Jaccard distance (IOU), Accuracy and Dice similarity coefficient (DSC), demonstrate efficiency performance in quantifying different zones of myocardium infarction across various patients. As compared to the second intra-observer study, our testing results showed that the SegUNet prediction model leads to these average dice coefficients over all segmented tissue classes, respectively : 'Background': 0.99999, 'Myocardium': 0.99434, 'Infarctus': 0.95587, 'Noreflow': 0.78187.

Do Not Treat Boundaries and Regions Differently: An Example on Heart Left Atrial Segmentation

Zhou Zhao, Elodie Puybareau, Nicolas Boutry, Thierry Geraud

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Auto-TLDR; Attention Full Convolutional Network for Atrial Segmentation using ResNet-101 Architecture

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Atrial fibrillation is the most common heart rhythm disease. Due to a lack of understanding in matter of underlying atrial structures, current treatments are still not satisfying. Recently, with the popularity of deep learning, many segmentation methods based on fully convolutional networks have been proposed to analyze atrial structures, especially from late gadolinium-enhanced magnetic resonance imaging. However, two problems still occur: 1) segmentation results include the atrial-like background; 2) boundaries are very hard to segment. Most segmentation approaches design a specific network that mainly focuses on the regions, to the detriment of the boundaries. Therefore, this paper proposes an attention full convolutional network framework based on the ResNet-101 architecture, which focuses on boundaries as much as on regions. The additional attention module is added to have the network pay more attention on regions and then to reduce the impact of the misleading similarity of neighboring tissues. We also use a hybrid loss composed of a region loss and a boundary loss to treat boundaries and regions at the same time. We demonstrate the efficiency of the proposed approach on the MICCAI 2018 Atrial Segmentation Challenge public dataset.

Fused 3-Stage Image Segmentation for Pleural Effusion Cell Clusters

Sike Ma, Meng Zhao, Hao Wang, Fan Shi, Xuguo Sun, Shengyong Chen, Hong-Ning Dai

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Auto-TLDR; Coarse Segmentation of Stained and Stained Unstained Cell Clusters in pleural effusion using 3-stage segmentation method

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The appearance of tumor cell clusters in pleural effusion is usually a vital sign of cancer metastasis. Segmentation, as an indispensable basis, is of crucial importance for diagnosing, chemical treatment, and prognosis in patients. However, accurate segmentation of unstained cell clusters containing more detailed features than the fluorescent staining images remains to be a challenging problem due to the complex background and the unclear boundary. Therefore, in this paper, we propose a fused 3-stage image segmentation algorithm, namely Coarse segmentation-Mapping-Fine segmentation (CMF) to achieve unstained cell clusters from whole slide images. Firstly, we establish a tumor cell cluster dataset consisting of 107 sets of images, with each set containing one unstained image, one stained image, and one ground-truth image. Then, according to the features of the unstained and stained cell clusters, we propose a three-stage segmentation method: 1) Coarse segmentation on stained images to extract suspicious cell regions-Region of Interest (ROI); 2) Mapping this ROI to the corresponding unstained image to get the ROI of the unstained image (UI-ROI); 3) Fine Segmentation using improved automatic fuzzy clustering framework (AFCF) on the UI-ROI to get precise cell cluster boundaries. Experimental results on 107 sets of images demonstrate that the proposed algorithm can achieve better performance on unstained cell clusters with an F1 score of 90.40%.

DE-Net: Dilated Encoder Network for Automated Tongue Segmentation

Hui Tang, Bin Wang, Jun Zhou, Yongsheng Gao

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Auto-TLDR; Automated Tongue Image Segmentation using De-Net

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Automated tongue recognition is a growing research field due to global demand for personal health care. Using mobile devices to take tongue pictures is convenient and of low cost for tongue recognition. It is particularly suitable for self-health evaluation of the public. However, images taken by mobile devices are easily affected by various imaging environment, which makes fine segmentation a more challenging task compared with those taken by specialized acquisition devices. Deep learning approaches are promising for tongue image segmentation because they have powerful feature learning and representation capability. However, the successive pooling operations in these methods lead to loss of information on image details, making them fail when segmenting low-quality images captured by mobile devices. To address this issue, we propose a dilated encoder network (DE-Net) to capture more high-level features and get high-resolution output for automated tongue image segmentation. In addition, we construct two tongue image datasets which contain images taken by specialized devices and mobile devices, respectively, to verify the effectiveness of the proposed method. Experimental results on both datasets demonstrate that the proposed method outperforms the state-of-the-art methods in tongue image segmentation.

Dual Encoder Fusion U-Net (DEFU-Net) for Cross-manufacturer Chest X-Ray Segmentation

Zhang Lipei, Aozhi Liu, Jing Xiao

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Auto-TLDR; Inception Convolutional Neural Network with Dilation for Chest X-Ray Segmentation

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A number of methods based on the deep learning have been applied to medical image segmentation and have achieved state-of-the-art performance. The most famous technique is U-Net which has been used to many medical datasets including the Chest X-ray. Due to the importance of chest x- ray data in studying COVID-19, there is a demand for state-of- art models capable of precisely segmenting chest x-rays. In this paper, we propose a dual encoder fusion U-Net framework for Chest X-rays based on Inception Convolutional Neural Network with dilation, Densely Connected Recurrent Convolutional Neural Network, which is named DEFU-Net. The densely connected recurrent path extends the network deeper for facilitating context feature extraction. In order to increase the width of network and enrich representation of features, the inception blocks with dilation have been used. The inception blocks can capture globally and locally spatial information with various receptive fields to avoid information loss caused by max-pooling. Meanwhile, the features fusion of two path by summation preserve the context and the spatial information for decoding part. We applied this model in Chest X-ray dataset from two different manufacturers (Montgomery and Shenzhen hospital). The DEFU-Net achieves the better performance than basic U-Net, residual U-Net, BCDU- Net, R2U-Net and attention R2U-Net. This model approaches state-of-the-art in this mixed dataset. The open source code for this proposed framework is public available.

Planar 3D Transfer Learning for End to End Unimodal MRI Unbalanced Data Segmentation

Martin Kolarik, Radim Burget, Carlos M. Travieso-Gonzalez, Jan Kocica

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Auto-TLDR; Planar 3D Res-U-Net Network for Unbalanced 3D Image Segmentation using Fluid Attenuation Inversion Recover

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We present a novel approach of 2D to 3D transfer learning based on mapping pre-trained 2D convolutional neural network weights into planar 3D kernels. The method is validated by proposed planar 3D res-u-net network with encoder transferred from the 2D VGG-16 which is applied for a single-stage unbalanced 3D image data segmentation. In particular, we evaluate the method on the MICCAI 2016 MS lesion segmentation challenge dataset utilizing solely Fluid Attenuation Inversion Recover (FLAIR) sequence without brain extraction for training and inference to simulate real medical praxis. The planar 3D res-u-net network performed the best both in sensitivity and Dice score amongst end to end methods processing raw MRI scans and achieved comparable Dice score to a state-of-the-art unimodal not end to end approach. Complete source code was released under the open-source license and this paper is in compliance with the Machine learning Reproducibility Checklist. By implementing practical transfer learning for 3D data representation we were able to successfully segment heavily unbalanced data without selective sampling and achieved more reliable results using less training data in single modality. From medical perspective, the unimodal approach gives an advantage in real praxis as it does not require co-registration nor additional scanning time during examination. Although modern medical imaging methods capture high resolution 3D anatomy scans suitable for computer aided detection system processing, deployment of automatic systems for interpretation of radiology imaging is still rather theoretical in many medical areas. Our work aims to bridge the gap offering solution for partial research questions.

Segmentation of Axillary and Supraclavicular Tumoral Lymph Nodes in PET/CT: A Hybrid CNN/Component-Tree Approach

Diana Lucia Farfan Cabrera, Nicolas Gogin, David Morland, Benoît Naegel, Dimitri Papathanassiou, Nicolas Passat

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Auto-TLDR; Coupling Convolutional Neural Networks and Component-Trees for Lymph node Segmentation from PET/CT Images

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The analysis of axillary and supraclavicular lymph nodes is a primary prognostic factor for the staging of breast cancer. However, due to the size of lymph nodes and the low resolution of PET data, their segmentation is challenging. We investigate the relevance of considering axillary and supraclavicular lymph node segmentation from PET/CT images by coupling Convolutional Neural Networks (CNNs) and Component-Trees (C-Trees). Building upon the U-Net architecture, we propose a framework that couples a multi-modal U-Net fed with PET and CT, coupled with a hierarchical model obtained from the PET that provides additional high-level region-based features as input channels. Our working hypotheses are twofold. First, we take advantage of both anatomical information from CT for detecting the nodes, and from functional information from PET for detecting the pathological ones. Second, we consider region-based attributes extracted from C-Tree analysis of 3D PET/CT images to improve the CNN segmentation. We carried out experiments on a dataset of 240 pathological lymph nodes from 52 patients scans, and compared our outputs with human expert-defined ground-truth, leading to promising results.

3D Medical Multi-Modal Segmentation Network Guided by Multi-Source Correlation Constraint

Tongxue Zhou, Stéphane Canu, Pierre Vera, Su Ruan

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Auto-TLDR; Multi-modality Segmentation with Correlation Constrained Network

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In the field of multimodal segmentation, the correlation between different modalities can be considered for improving the segmentation results. In this paper, we propose a multi-modality segmentation network with a correlation constraint. Our network includes N model-independent encoding paths with N image sources, a correlation constrain block, a feature fusion block, and a decoding path. The model-independent encoding path can capture modality-specific features from the N modalities. Since there exists a strong correlation between different modalities, we first propose a linear correlation block to learn the correlation between modalities, then a loss function is used to guide the network to learn the correlated features based on the correlation representation block. This block forces the network to learn the latent correlated features which are more relevant for segmentation. Considering that not all the features extracted from the encoders are useful for segmentation, we propose to use dual attention based fusion block to recalibrate the features along the modality and spatial paths, which can suppress less informative features and emphasize the useful ones. The fused feature representation is finally projected by the decoder to obtain the segmentation result. Our experiment results tested on BraTS-2018 dataset for brain tumor segmentation demonstrate the effectiveness of our proposed method.

A Transformer-Based Network for Anisotropic 3D Medical Image Segmentation

Guo Danfeng, Demetri Terzopoulos

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Auto-TLDR; A transformer-based model to tackle the anisotropy problem in 3D medical image analysis

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A critical challenge of applying neural networks to 3D medical image analysis is to deal with the anisotropy problem. The inter-slice contextual information contained in medical images is important, especially when the structural information of lesions is needed. However, such information often varies with cases because of variable slice spacing. Image anisotropy downgrades model performance especially when slice spacing varies significantly among training and testing datasets. ExsiWe proposed a transformer-based model to tackle the anisotropy problem. It is adaptable to different levels of anisotropy and is computationally efficient. Experiments are conducted on 3D lung cancer segmentation task. Our model achieves an average Dice score of approximately 0.87, which generally outperforms baseline models.

Semantic Segmentation of Breast Ultrasound Image with Pyramid Fuzzy Uncertainty Reduction and Direction Connectedness Feature

Kuan Huang, Yingtao Zhang, Heng-Da Cheng, Ping Xing, Boyu Zhang

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Auto-TLDR; Uncertainty-Based Deep Learning for Breast Ultrasound Image Segmentation

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Deep learning approaches have achieved impressive results in breast ultrasound (BUS) image segmentation. However, these methods did not solve uncertainty and noise in BUS images well. To address this issue, we present a novel deep learning structure for BUS image semantic segmentation by analyzing the uncertainty using a pyramid fuzzy block and generating a novel feature based on connectedness. Firstly, feature maps in the proposed network are down-sampled to different resolutions. Fuzzy transformation and uncertainty representation are applied to each resolution to obtain the uncertainty degree on different scales. Meanwhile, the BUS images contain layer structures. From top to bottom, there are skin layer, fat layer, mammary layer, muscle layer, and background area. A spatial recurrent neural network (RNN) is utilized to calculate the connectedness between each pixel and the pixels on the four boundaries in horizontal and vertical lines. The spatial-wise context feature can introduce the characteristic of layer structure to deep neural network. Finally, the original convolutional features are combined with connectedness feature according to the uncertainty degrees. The proposed methods are applied to two datasets: a BUS image benchmark with two categories (background and tumor) and a five-category BUS image dataset with fat layer, mammary layer, muscle layer, background, and tumor. The proposed method achieves the best results on both datasets compared with eight state-of-the-art deep learning-based approaches.

Learning to Segment Clustered Amoeboid Cells from Brightfield Microscopy Via Multi-Task Learning with Adaptive Weight Selection

Rituparna Sarkar, Suvadip Mukherjee, Elisabeth Labruyere, Jean-Christophe Olivo-Marin

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Auto-TLDR; Supervised Cell Segmentation from Microscopy Images using Multi-task Learning in a Multi-Task Learning Paradigm

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Detecting and segmenting individual cells from microscopy images is critical to various life science applications. Traditional cell segmentation tools are often ill-suited for applications in brightfield microscopy due to poor contrast and intensity heterogeneity, and only a small subset are applicable to segment cells in a cluster. In this regard, we introduce a novel supervised technique for cell segmentation in a multi-task learning paradigm. A combination of a multi-task loss, based on the region and cell boundary detection, is employed for an improved prediction efficiency of the network. The learning problem is posed in a novel min-max framework which enables adaptive estimation of the hyper-parameters in an automatic fashion. The region and cell boundary predictions are combined via morphological operations and active contour model to segment individual cells. The proposed methodology is particularly suited to segment touching cells from brightfield microscopy images without manual interventions. Quantitatively, we observe an overall Dice score of 0.93 on the validation set, which is an improvement of over 15.9% on a recent unsupervised method, and outperforms the popular supervised U-net algorithm by at least 5.8% on average.

OCT Image Segmentation Using NeuralArchitecture Search and SRGAN

Saba Heidari, Omid Dehzangi, Nasser M. Nasarabadi, Ali Rezai

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Auto-TLDR; Automatic Segmentation of Retinal Layers in Optical Coherence Tomography using Neural Architecture Search

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Alzheimer’s disease (AD) diagnosis is one of the major research areas in computational medicine. Optical coherence tomography (OCT) is a non-invasive, inexpensive, and timely efficient method that scans the human’s retina with depth. It has been hypothesized that the thickness of the retinal layers extracted from OCTs could be an efficient and effective biomarker for early diagnosis of AD. In this work, we aim to design a self-training model architecture for the task of segmenting the retinal layers in OCT scans. Neural architecture search (NAS) is a subfield of AutoML domain, which has a significant impact on improving the accuracy of machine vision tasks. We integrate the NAS algorithm with a Unet auto-encoder architecture as its backbone. Then, we employ our proposed model to segment the retinal nerve fiber layer in our preprocessed OCT images with the aim of AD diagnosis. In this work, we trained a super-resolution generative adversarial network on the raw OCT scans to improve the quality of the images before the modeling stage. In our architecture search strategy, different primitive operations suggested to find down- \& up-sampling Unet cell blocks and the binary gate method has been applied to make the search strategy more practical. Our architecture search method is empirically evaluated by training on the Unet and NAS-Unet from scratch. Specifically, the proposed NAS-Unet training significantly outperforms the baseline human-designed architecture by achieving 95.1\% in the mean Intersection over Union metric and 79.1\% in the Dice similarity coefficient.

Segmenting Kidney on Multiple Phase CT Images Using ULBNet

Yanling Chi, Yuyu Xu, Gang Feng, Jiawei Mao, Sihua Wu, Guibin Xu, Weimin Huang

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Auto-TLDR; A ULBNet network for kidney segmentation on multiple phase CT images

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Abstract—Segmentation of kidney on CT images is critical to computer-assisted surgical planning for kidney interventional therapy. Segmenting kidney manually is impractical in clinical, automatic segmentation is desirable. U-Net has been successful in medical image segmentation and is a promising candidate for the task. However, semantic gap still exists, especially when multiple phase images or multiple center images are involved. In this paper, we proposed an ULBNet to reduce the semantic gap and to improve segmentation performance. The proposed architecture includes new skip connections of local binary convolution (LBC). We also proposed a novel strategy of fast retraining a model for a new task without manually labelling required. We evaluated the network for kidney segmentation on multiple phase CT images. ULBNet resulted in an overall accuracy of 98.0% with comparison to Resunet 97.5%. Specifically, on the plain phase CT images, 98.1% resulted from ULBNet and 97.6% from Resunet; on the corticomedullay phase images, 97.8% from ULBNet and 97.2% from Resunet; on the nephrographic phase images, 97.6% from ULBNet and 97.4% from Resunet; on the excretory phase images, 98.1% from ULBNet and 97.4% from Resunet. The proposed network architecture performs better than Resunet on generalizing to multiple phase images.

CT-UNet: An Improved Neural Network Based on U-Net for Building Segmentation in Remote Sensing Images

Huanran Ye, Sheng Liu, Kun Jin, Haohao Cheng

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Auto-TLDR; Context-Transfer-UNet: A UNet-based Network for Building Segmentation in Remote Sensing Images

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With the proliferation of remote sensing images, how to segment buildings more accurately in remote sensing images is a critical challenge. First, the high resolution leads to blurred boundaries in the extracted building maps. Second, the similarity between buildings and background results in intra-class inconsistency. To address these two problems, we propose an UNet-based network named Context-Transfer-UNet (CT-UNet). Specifically, we design Dense Boundary Block (DBB). Dense Block utilizes reuse mechanism to refine features and increase recognition capabilities. Boundary Block introduces the low-level spatial information to solve the fuzzy boundary problem. Then, to handle intra-class inconsistency, we construct Spatial Channel Attention Block (SCAB). It combines context space information and selects more distinguishable features from space and channel. Finally, we propose a novel loss function to enhance the purpose of loss by adding evaluation indicator. Based on our proposed CT-UNet, we achieve 85.33% mean IoU on the Inria dataset and 91.00% mean IoU on the WHU dataset, which outperforms our baseline (U-Net ResNet-34) by 3.76% and Web-Net by 2.24%.

Machine-Learned Regularization and Polygonization of Building Segmentation Masks

Stefano Zorzi, Ksenia Bittner, Friedrich Fraundorfer

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Auto-TLDR; Automatic Regularization and Polygonization of Building Segmentation masks using Generative Adversarial Network

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We propose a machine learning based approach for automatic regularization and polygonization of building segmentation masks. Taking an image as input, we first predict building segmentation maps exploiting generic fully convolutional network (FCN). A generative adversarial network (GAN) is then involved to perform a regularization of building boundaries to make them more realistic, i.e., having more rectilinear outlines which construct right angles if required. This is achieved through the interplay between the discriminator which gives a probability of input image being true and generator that learns from discriminator’s response to create more realistic images. Finally, we train the backbone convolutional neural network (CNN) which is adapted to predict sparse outcomes corresponding to building corners out of regularized building segmentation results. Experiments on three building segmentation datasets demonstrate that the proposed method is not only capable of obtaining accurate results, but also of producing visually pleasing building outlines parameterized as polygons.

Segmentation of Intracranial Aneurysm Remnant in MRA Using Dual-Attention Atrous Net

Subhashis Banerjee, Ashis Kumar Dhara, Johan Wikström, Robin Strand

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Auto-TLDR; Dual-Attention Atrous Net for Segmentation of Intracranial Aneurysm Remnant from MRA Images

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Due to the advancement of non-invasive medical imaging modalities like Magnetic Resonance Angiography (MRA), an increasing number of Intracranial Aneurysm (IA) cases are being reported in recent years. The IAs are typically treated by so-called endovascular coiling, where blood flow in the IA is prevented by embolization with a platinum coil. Accurate quantification of the IA Remnant (IAR), i.e. the volume with blood flow present post treatment is the utmost important factor in choosing the right treatment planning. This is typically done by manually segmenting the aneurysm remnant from the MRA volume. Since manual segmentation of volumetric images is a labour-intensive and error-prone process, development of an automatic volumetric segmentation method is required. Segmentation of small structures such as IA, that may largely vary in size, shape, and location is considered extremely difficult. Similar intensity distribution of IAs and surrounding blood vessels makes it more challenging and susceptible to false positive. In this paper we propose a novel 3D CNN architecture called Dual-Attention Atrous Net (DAtt-ANet), which can efficiently segment IAR volumes from MRA images by reconciling features at different scales using the proposed Parallel Atrous Unit (PAU) along with the use of self-attention mechanism for extracting fine-grained features and intra-class correlation. The proposed DAtt-ANet model is trained and evaluated on a clinical MRA image dataset (prospective research project, approved by the local ethical committee) of IAR consisting of 46 subjects, annotated by an expert radiologist from our group. We compared the proposed DAtt-ANet with five state-of-the-art CNN models based on their segmentation performance. The proposed DAtt-ANet outperformed all other methods and was able to achieve a five-fold cross-validation DICE score of $0.73\pm0.06$.

Semi-Supervised Generative Adversarial Networks with a Pair of Complementary Generators for Retinopathy Screening

Yingpeng Xie, Qiwei Wan, Hai Xie, En-Leng Tan, Yanwu Xu, Baiying Lei

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Auto-TLDR; Generative Adversarial Networks for Retinopathy Diagnosis via Fundus Images

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Several typical types of retinopathy are major causes of blindness. However, early detection of retinopathy is quite not easy since few symptoms are observable in the early stage, attributing to the development of non-mydriatic retinal camera. These camera produces high-resolution retinal fundus images provide the possibility of Computer-Aided-Diagnosis (CAD) via deep learning to assist diagnosing retinopathy. Deep learning algorithms usually rely on a great number of labelled images which are expensive and time-consuming to obtain in the medical imaging area. Moreover, the random distribution of various lesions which often vary greatly in size also brings significant challenges to learn discriminative information from high-resolution fundus image. In this paper, we present generative adversarial networks simultaneously equipped with "good" generator and "bad" generator (GBGANs) to make up for the incomplete data distribution provided by limited fundus images. To improve the generative feasibility of generator, we introduce into pre-trained feature extractor to acquire condensed feature for each fundus image in advance. Experimental results on integrated three public iChallenge datasets show that the proposed GBGANs could fully utilize the available fundus images to identify retinopathy with little label cost.

BCAU-Net: A Novel Architecture with Binary Channel Attention Module for MRI Brain Segmentation

Yongpei Zhu, Zicong Zhou, Guojun Liao, Kehong Yuan

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Auto-TLDR; BCAU-Net: Binary Channel Attention U-Net for MRI brain segmentation

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Recently deep learning-based networks have achieved advanced performance in medical image segmentation. However, the development of deep learning is slow in magnetic resonance image (MRI) segmentation of normal brain tissues. In this paper, inspired by channel attention module, we propose a new architecture, Binary Channel Attention U-Net (BCAU-Net), by introducing a novel Binary Channel Attention Module (BCAM) into skip connection of U-Net, which can take full advantages of the channel information extracted from the encoding path and corresponding decoding path. To better aggregate multi-scale spatial information of the feature map, spatial pyramid pooling (SPP) modules with different pooling operations are used in BCAM instead of original average-pooling and max-pooling operations. We verify this model on two datasets including IBSR and MRBrainS18, and obtain better performance on MRI brain segmentation compared with other methods. We believe the proposed method can advance the performance in brain segmentation and clinical diagnosis.

One-Stage Multi-Task Detector for 3D Cardiac MR Imaging

Weizeng Lu, Xi Jia, Wei Chen, Nicolò Savioli, Antonio De Marvao, Linlin Shen, Declan O'Regan, Jinming Duan

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Auto-TLDR; Multi-task Learning for Real-Time, simultaneous landmark location and bounding box detection in 3D space

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Fast and accurate landmark location and bounding box detection are important steps in 3D medical imaging. In this paper, we propose a novel multi-task learning framework, for real-time, simultaneous landmark location and bounding box detection in 3D space. Our method extends the famous single-shot multibox detector (SSD) from single-task learning to multi-task learning and from 2D to 3D. Furthermore, we propose a post-processing approach to refine the network landmark output, by averaging the candidate landmarks. Owing to these settings, the proposed framework is fast and accurate. For 3D cardiac magnetic resonance (MR) images with size 224 × 224 × 64, our framework runs about 128 volumes per second (VPS) on GPU and achieves 6.75mm average point-to-point distance error for landmark location, which outperforms both state-of-the-art and baseline methods. We also show that segmenting the 3D image cropped with the bounding box results in both improved performance and efficiency.

A Lumen Segmentation Method in Ureteroscopy Images Based on a Deep Residual U-Net Architecture

Jorge Lazo, Marzullo Aldo, Sara Moccia, Michele Catellani, Benoit Rosa, Elena De Momi, Michel De Mathelin, Francesco Calimeri

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Auto-TLDR; A Deep Neural Network for Ureteroscopy with Residual Units

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Ureteroscopy is becoming the first surgical treatment option for the majority of urinary affections. This procedure is carried out using an endoscope which provides the surgeon with the visual and spatial information necessary to navigate inside the urinary tract. Having in mind the development of surgical assistance systems, that could enhance the performance of surgeon, the task of lumen segmentation is a fundamental part since this is the visual reference which marks the path that the endoscope should follow. This is something that has not been analyzed in ureteroscopy data before. However, this task presents several challenges given the image quality and the conditions itself of ureteroscopy procedures. In this paper, we study the implementation of a Deep Neural Network which exploits the advantage of residual units in an architecture based on U-Net. For the training of these networks, we analyze the use of two different color spaces: gray-scale and RGB data images. We found that training on gray-scale images gives the best results obtaining mean values of Dice Score, Precision, and Recall of 0.73, 0.58, and 0.92 respectively. The results obtained show that the use of residual U-Net could be a suitable model for further development for a computer-aided system for navigation and guidance through the urinary system.

Attention Based Multi-Instance Thyroid Cytopathological Diagnosis with Multi-Scale Feature Fusion

Shuhao Qiu, Yao Guo, Chuang Zhu, Wenli Zhou, Huang Chen

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Auto-TLDR; A weakly supervised multi-instance learning framework based on attention mechanism with multi-scale feature fusion for thyroid cytopathological diagnosis

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In recent years, deep learning has been popular in combining with cytopathology diagnosis. Using the whole slide images (WSI) scanned by electronic scanners at clinics, researchers have developed many algorithms to classify the slide (benign or malignant). However, the key area that support the diagnosis result can be relatively small in a thyroid WSI, and only the global label can be acquired, which make the direct use of the strongly supervised learning framework infeasible. What’s more, because the clinical diagnosis of the thyroid cells requires the use of visual features in different scales, a generic feature extraction way may not achieve good performance. In this paper, we propose a weakly supervised multi-instance learning framework based on attention mechanism with multi-scale feature fusion (MSF) using convolutional neural network (CNN) for thyroid cytopathological diagnosis. We take each WSI as a bag, each bag contains multiple instances which are the different regions of the WSI, our framework is trained to learn the key area automatically and make the classification. We also propose a feature fusion structure, merge the low-level features into the final feature map and add an instance-level attention module in it, which improves the classification accuracy. Our model is trained and tested on the collected clinical data, reaches the accuracy of 93.2%, which outperforms the other existing methods. We also tested our model on a public histopathology dataset and achieves better result than the state-of-the-art deep multi-instance method.

Transfer Learning through Weighted Loss Function and Group Normalization for Vessel Segmentation from Retinal Images

Abdullah Sarhan, Jon Rokne, Reda Alhajj, Andrew Crichton

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Auto-TLDR; Deep Learning for Segmentation of Blood Vessels in Retinal Images

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The vascular structure of blood vessels is important in diagnosing retinal conditions such as glaucoma and diabetic retinopathy. Accurate segmentation of these vessels can help in detecting retinal objects such as the optic disc and optic cup and hence determine if there are damages to these areas. Moreover, the structure of the vessels can help in diagnosing glaucoma. The rapid development of digital imaging and computer-vision techniques has increased the potential for developing approaches for segmenting retinal vessels. In this paper, we propose an approach for segmenting retinal vessels that uses deep learning along with transfer learning. We adapted the U-Net structure to use a customized InceptionV3 as the encoder and used multiple skip connections to form the decoder. Moreover, we used a weighted loss function to handle the issue of class imbalance in retinal images. Furthermore, we contributed a new dataset to this field. We tested our approach on six publicly available datasets and a newly created dataset. We achieved an average accuracy of 95.60\% and a Dice coefficient of 80.98\%. The results obtained from comprehensive experiments demonstrate the robustness of our approach to the segmentation of blood vessels in retinal images obtained from different sources. Our approach results in greater segmentation accuracy than other approaches.

Deep Multi-Stage Model for Automated Landmarking of Craniomaxillofacial CT Scans

Simone Palazzo, Giovanni Bellitto, Luca Prezzavento, Francesco Rundo, Ulas Bagci, Daniela Giordano, Rosalia Leonardi, Concetto Spampinato

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Auto-TLDR; Automated Landmarking of Craniomaxillofacial CT Images Using Deep Multi-Stage Architecture

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In this paper we define a deep multi-stage architecture for automated landmarking of craniomaxillofacial (CMF) CT images. Our model is composed of three subnetworks that first localize, on reduced-resolution images, areas where land-marks may be found and then refine the search, at full-resolution scale, through a hierarchical structure aiming at increasing the granularity of the investigated region. The multi-stage pipeline is designed to deal with full resolution data and does not require any additional pre-processing step to reduce search space, as opposed to existing methods that can be only adopted for searching landmarks located in well-defined anatomical structures (e.g.,mandibles). The automated landmarking system is tested on identifying landmarks located in several CMF regions, achieving an average error of 0.8 mm, significantly lower than expert readings. The proposed model also outperforms baselines and is on par with existing models that employ additional upstream segmentation, on state-of-the-art benchmarks.

MBD-GAN: Model-Based Image Deblurring with a Generative Adversarial Network

Li Song, Edmund Y. Lam

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Auto-TLDR; Model-Based Deblurring GAN for Inverse Imaging

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This paper presents a methodology to tackle inverse imaging problems by leveraging the synergistic power of imaging model and deep learning. The premise is that while learning-based techniques have quickly become the methods of choice in various applications, they often ignore the prior knowledge embedded in imaging models. Incorporating the latter has the potential to improve the image estimation. Specifically, we first provide a mathematical basis of using generative adversarial network (GAN) in inverse imaging through considering an optimization framework. Then, we develop the specific architecture that connects the generator and discriminator networks with the imaging model. While this technique can be applied to a variety of problems, from image reconstruction to super-resolution, we take image deblurring as the example here, where we show in detail the implementation and experimental results of what we call the model-based deblurring GAN (MBD-GAN).

Super-Resolution Guided Pore Detection for Fingerprint Recognition

Syeda Nyma Ferdous, Ali Dabouei, Jeremy Dawson, Nasser M. Nasarabadi

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Auto-TLDR; Super-Resolution Generative Adversarial Network for Fingerprint Recognition Using Pore Features

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Performance of fingerprint recognition algorithms substantially rely on fine features extracted from fingerprints. Apart from minutiae and ridge patterns, pore features have proven to be usable for fingerprint recognition. Although features from minutiae and ridge patterns are quite attainable from low-resolution images, using pore features is practical only if the fingerprint image is of high resolution which necessitates a model that enhances the image quality of the conventional 500 ppi legacy fingerprints preserving the fine details. To find a solution for recovering pore information from low-resolution fingerprints, we adopt a joint learning-based approach that combines both super-resolution and pore detection networks. Our modified single image Super-Resolution Generative Adversarial Network (SRGAN) framework helps to reliably reconstruct high-resolution fingerprint samples from low-resolution ones assisting the pore detection network to identify pores with a high accuracy. The network jointly learns a distinctive feature representation from a real low-resolution fingerprint sample and successfully synthesizes a high-resolution sample from it. To add discriminative information and uniqueness for all the subjects, we have integrated features extracted from a deep fingerprint verifier with the SRGAN quality discriminator. We also add ridge reconstruction loss, utilizing ridge patterns to make the best use of extracted features. Our proposed method solves the recognition problem by improving the quality of fingerprint images. High recognition accuracy of the synthesized samples that is close to the accuracy achieved using the original high-resolution images validate the effectiveness of our proposed model.

Robust Localization of Retinal Lesions Via Weakly-Supervised Learning

Ruohan Zhao, Qin Li, Jane You

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Auto-TLDR; Weakly Learning of Lesions in Fundus Images Using Multi-level Feature Maps and Classification Score

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Retinal fundus images reveal the condition of retina, blood vessels and optic nerve. Retinal imaging is becoming widely adopted in clinical work because any subtle changes to the structures at the back of the eyes can affect the eyes and indicate the overall health. Machine learning, in particular deep learning by convolutional neural network (CNN), has been increasingly adopted for computer-aided detection (CAD) of retinal lesions. However, a significant barrier to the high performance of CNN based CAD approach is caused by the lack of sufficient labeled ground-truth image samples for training. Unlike the fully-supervised learning which relies on pixel-level annotation of pathology in fundus images, this paper presents a new approach to discriminate the location of various lesions based on image-level labels via weakly learning. More specifically, our proposed method leverages multi-level feature maps and classification score to cope with both bright and red lesions in fundus images. To enhance capability of learning less discriminative parts of objects (e.g. small blobs of microaneurysms opposed to bulk of exudates), the classifier is regularized by refining images with corresponding labels. The experimental results of the performance evaluation and benchmarking at both image-level and pixel-level on the public DIARETDB1 dataset demonstrate the feasibility and excellent potentials of our method in practice.

PCANet: Pyramid Context-Aware Network for Retinal Vessel Segmentation

Yi Zhang, Yixuan Chen, Kai Zhang

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Auto-TLDR; PCANet: Adaptive Context-Aware Network for Automated Retinal Vessel Segmentation

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Automated retinal vessel segmentation plays an important role in the diagnosis of some diseases such as diabetes, arteriosclerosis and hypertension. Recent works attempt to improve segmentation performance by exploring either global or local contexts. However, the context demands are varying from regions in each image and different levels of network. To address these problems, we propose Pyramid Context-aware Network (PCANet), which can adaptively capture multi-scale context representations. Specifically, PCANet is composed of multiple Adaptive Context-aware (ACA) blocks arranged in parallel, each of which can adaptively obtain the context-aware features by estimating affinity coefficients at a specific scale under the guidance of global contextual dependencies. Meanwhile, we import ACA blocks with specific scales in different levels of the network to obtain a coarse-to-fine result. Furthermore, an integrated test-time augmentation method is developed to further boost the performance of PCANet. Finally, extensive experiments demonstrate the effectiveness of the proposed PCANet, and state-of-the-art performances are achieved with AUCs of 0.9866, 0.9886 and F1 Scores of 0.8274, 0.8371 on two public datasets, DRIVE and STARE, respectively.

Learn to Segment Retinal Lesions and Beyond

Qijie Wei, Xirong Li, Weihong Yu, Xiao Zhang, Yongpeng Zhang, Bojie Hu, Bin Mo, Di Gong, Ning Chen, Dayong Ding, Youxin Chen

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Auto-TLDR; Multi-task Lesion Segmentation and Disease Classification for Diabetic Retinopathy Grading

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Towards automated retinal screening, this paper makes an endeavor to simultaneously achieve pixel-level retinal lesion segmentation and image-level disease classification. Such a multi-task approach is crucial for accurate and clinically interpretable disease diagnosis. Prior art is insufficient due to three challenges, i.e., lesions lacking objective boundaries, clinical importance of lesions irrelevant to their size, and the lack of one-to-one correspondence between lesion and disease classes. This paper attacks the three challenges in the context of diabetic retinopathy (DR) grading. We propose Lesion-Net, a new variant of fully convolutional networks, with its expansive path re- designed to tackle the first challenge. A dual Dice loss that leverages both semantic segmentation and image classification losses is introduced to resolve the second challenge. Lastly, we build a multi-task network that employs Lesion-Net as a side- attention branch for both DR grading and result interpretation. A set of 12K fundus images is manually segmented by 45 ophthalmologists for 8 DR-related lesions, resulting in 290K manual segments in total. Extensive experiments on this large- scale dataset show that our proposed approach surpasses the prior art for multiple tasks including lesion segmentation, lesion classification and DR grading.

Cross-View Relation Networks for Mammogram Mass Detection

Ma Jiechao, Xiang Li, Hongwei Li, Ruixuan Wang, Bjoern Menze, Wei-Shi Zheng

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Auto-TLDR; Multi-view Modeling for Mass Detection in Mammogram

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In medical image analysis, multi-view modeling is crucial for pathology detection when the target lesion is presented in different views, e.g. mass lesions in breast. Currently mammogram is the most effective imaging modality for mass lesion detection of breast cancer at the early stage. The pathological information from the two paired views (i.e., medio-lateral oblique and cranio-caudal) are highly relational and complementary, which is crucial for diagnosis in clinical practice. Existing mass detection methods do not consider learning synergistic features from the two relational views. For the first time, we propose a novel mass detection framework to capture the latent relation information from the two paired views of a same mass in mammogram. We evaluate our model on a public mammogram dataset and a large-scale private dataset, demonstrating that the proposed method outperforms existing feature fusion approaches and state-of-the-art mass detection methods. We further analyze the performance gains from the relation modeling. Our quantitative and qualitative results suggest that jointly learning cross-view features boosts the detection performance of existing models, which is a promising avenue for mass detection task in mammogram.

Bridging the Gap between Natural and Medical Images through Deep Colorization

Lia Morra, Luca Piano, Fabrizio Lamberti, Tatiana Tommasi

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Auto-TLDR; Transfer Learning for Diagnosis on X-ray Images Using Color Adaptation

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Deep learning has thrived by training on large-scale datasets. However, in many applications, as for medical image diagnosis, getting massive amount of data is still prohibitive due to privacy, lack of acquisition homogeneity and annotation cost. In this scenario transfer learning from natural image collections is a standard practice that attempts to tackle shape, texture and color discrepancy all at once through pretrained model fine-tuning. In this work we propose to disentangle those challenges and design a dedicated network module that focuses on color adaptation. We combine learning from scratch of the color module with transfer learning of different classification backbones obtaining an end-to-end, easy-to-train architecture for diagnostic image recognition on X-ray images. Extensive experiments show how our approach is particularly efficient in case of data scarcity and provides a new path for further transferring the learned color information across multiple medical datasets.

Accurate Cell Segmentation in Digital Pathology Images Via Attention Enforced Networks

Zeyi Yao, Kaiqi Li, Guanhong Zhang, Yiwen Luo, Xiaoguang Zhou, Muyi Sun

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Auto-TLDR; AENet: Attention Enforced Network for Automatic Cell Segmentation

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Automatic cell segmentation is an essential step in the pipeline of computer-aided diagnosis (CAD), such as the detection and grading of breast cancer. Accurate segmentation of cells can not only assist the pathologists to make a more precise diagnosis, but also save much time and labor. However, this task suffers from stain variation, cell inhomogeneous intensities, background clutters and cells from different tissues. To address these issues, we propose an Attention Enforced Network (AENet), which is built on spatial attention module and channel attention module, to integrate local features with global dependencies and weight effective channels adaptively. Besides, we introduce a feature fusion branch to bridge high-level and low-level features. Finally, the marker controlled watershed algorithm is applied to post-process the predicted segmentation maps for reducing the fragmented regions. In the test stage, we present an individual color normalization method to deal with the stain variation problem. We evaluate this model on the MoNuSeg dataset. The quantitative comparisons against several prior methods demonstrate the priority of our approach.

Thermal Image Enhancement Using Generative Adversarial Network for Pedestrian Detection

Mohamed Amine Marnissi, Hajer Fradi, Anis Sahbani, Najoua Essoukri Ben Amara

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Auto-TLDR; Improving Visual Quality of Infrared Images for Pedestrian Detection Using Generative Adversarial Network

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Infrared imaging has recently played an important role in a wide range of applications including surveillance, robotics and night vision. However, infrared cameras often suffer from some limitations, essentially about low-contrast and blurred details. These problems contribute to the loss of observation of target objects in infrared images, which could limit the feasibility of different infrared imaging applications. In this paper, we mainly focus on the problem of pedestrian detection on thermal images. Particularly, we emphasis the need for enhancing the visual quality of images beforehand performing the detection step. % to ensure effective results. To address that, we propose a novel thermal enhancement architecture based on Generative Adversarial Network, and composed of two modules contrast enhancement and denoising modules with a post-processing step for edge restoration in order to improve the overall quality. The effectiveness of the proposed architecture is assessed by means of visual quality metrics and better results are obtained compared to the original thermal images and to the obtained results by other existing enhancement methods. These results have been conduced on a subset of KAIST dataset. Using the same dataset, the impact of the proposed enhancement architecture has been demonstrated on the detection results by obtaining better performance with a significant margin using YOLOv3 detector.