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.

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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.

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.

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.

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 Comparison of Neural Network Approaches for Melanoma Classification

Maria Frasca, Michele Nappi, Michele Risi, Genoveffa Tortora, Alessia Auriemma Citarella

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Auto-TLDR; Classification of Melanoma Using Deep Neural Network Methodologies

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Melanoma is the deadliest form of skin cancer and it is diagnosed mainly visually, starting from initial clinical screening and followed by dermoscopic analysis, biopsy and histopathological examination. A dermatologist’s recognition of melanoma may be subject to errors and may take some time to diagnose it. In this regard, deep learning can be useful in the study and classification of skin cancer. In particular, by classifying images with Deep Neural Network methodologies, it is possible to obtain comparable or even superior results compared to those of dermatologists. In this paper, we propose a methodology for the classification of melanoma by adopting different deep learning techniques applied to a common dataset, composed of images from the ISIC dataset and consisting of different types of skin diseases, including melanoma on which we applied a specific pre-processing phase. In particular, a comparison of the results is performed in order to select the best effective neural network to be applied to the problem of recognition and classification of melanoma. Moreover, we also evaluate the impact of the pre- processing phase on the final classification. Different metrics such as accuracy, sensitivity, and specificity have been selected to assess the goodness of the adopted neural networks and compare them also with the manual classification of dermatologists.

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.

Early Wildfire Smoke Detection in Videos

Taanya Gupta, Hengyue Liu, Bir Bhanu

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Auto-TLDR; Semi-supervised Spatio-Temporal Video Object Segmentation for Automatic Detection of Smoke in Videos during Forest Fire

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Recent advances in unmanned aerial vehicles and camera technology have proven useful for the detection of smoke that emerges above the trees during a forest fire. Automatic detection of smoke in videos is of great interest to Fire department. To date, in most parts of the world, the fire is not detected in its early stage and generally it turns catastrophic. This paper introduces a novel technique that integrates spatial and temporal features in a deep learning framework using semi-supervised spatio-temporal video object segmentation and dense optical flow. However, detecting this smoke in the presence of haze and without the labeled data is difficult. Considering the visibility of haze in the sky, a dark channel pre-processing method is used that reduces the amount of haze in video frames and consequently improves the detection results. Online training is performed on a video at the time of testing that reduces the need for ground-truth data. Tests using the publicly available video datasets show that the proposed algorithms outperform previous work and they are robust across different wildfire-threatened locations.

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.

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.

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 $0.73\pm0.06$.

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.

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.

A Systematic Investigation on Deep Architectures for Automatic Skin Lesions Classification

Pierluigi Carcagni, Marco Leo, Andrea Cuna, Giuseppe Celeste, Cosimo Distante

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Auto-TLDR; RegNet: Deep Investigation of Convolutional Neural Networks for Automatic Classification of Skin Lesions

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Computer vision-based techniques are more and more employed in healthcare and medical fields nowadays in order, principally, to be as a support to the experienced medical staff to help them to make a quick and correct diagnosis. One of the hot topics in this arena concerns the automatic classification of skin lesions. Several promising works exist about it, mainly leveraging Convolutional Neural Networks (CNN), but proposed pipeline mainly rely on complex data preprocessing and there is no systematic investigation about how available deep models can actually reach the accuracy needed for real applications. In order to overcome these drawbacks, in this work, an end-to-end pipeline is introduced and some of the most recent Convolutional Neural Networks (CNNs) architectures are included in it and compared on the largest common benchmark dataset recently introduced. To this aim, for the first time in this application context, a new network design paradigm, namely RegNet, has been exploited to get the best models among a population of configurations. The paper introduces a threefold level of contribution and novelty with respect the previous literature: the deep investigation of several CNN architectures driving to a consistent improvement of the lesions recognition accuracy, the exploitation of a new network design paradigm able to study the behavior of populations of models and a deep discussion about pro and cons of each analyzed method paving the path towards new research lines.

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.

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.

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.

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.

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.

Merged 1D-2D Deep Convolutional Neural Networks for Nerve Detection in Ultrasound Images

Mohammad Alkhatib, Adel Hafiane, Pierre Vieyres

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Auto-TLDR; A Deep Neural Network for Deep Neural Networks to Detect Median Nerve in Ultrasound-Guided Regional Anesthesia

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Ultrasound-Guided Regional Anesthesia (UGRA) becomes a standard procedure in surgical operations and contributes to pain management. It offers the advantages of the targeted nerve detection and provides the visualization of regions of interest such as anatomical structures. However, nerve detection is one of the most challenging tasks that anesthetists can encounter in the UGRA procedure. A computer-aided system that can detect automatically the nerve region would facilitate the anesthetist's daily routine and allow them to concentrate more on the anesthetic delivery. In this paper, we propose a new method based on merging deep learning models from different data to detect the median nerve. The merged architecture consists of two branches, one being one dimensional (1D) convolutional neural networks (CNN) branch and another 2D CNN branch. The merged architecture aims to learn the high-level features from 1D handcrafted noise-robust features and 2D ultrasound images. The obtained results show the validity and high accuracy of the proposed approach and its robustness.

Learning Defects in Old Movies from Manually Assisted Restoration

Arthur Renaudeau, Travis Seng, Axel Carlier, Jean-Denis Durou, Fabien Pierre, Francois Lauze, Jean-François Aujol

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Auto-TLDR; U-Net: Detecting Defects in Old Movies by Inpainting Techniques

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We propose to detect defects in old movies, as the first step of a larger framework of old movies restoration by inpainting techniques. The specificity of our work is to learn a film restorer's expertise from a pair of sequences, composed of a movie with defects, and the same movie which was semi-automatically restored with the help of a specialized software. In order to detect those defects with minimal human interaction and further reduce the time spent for a restoration, we feed a U-Net with consecutive defective frames as input to detect the unexpected variations of pixel intensity over space and time. Since the output of the network is a mask of defect location, we first have to create the dataset of mask frames on the basis of restored frames from the software used by the film restorer, instead of classical synthetic ground truth, which is not available. These masks are estimated by computing the absolute difference between restored frames and defectuous frames, combined with thresholding and morphological closing. Our network succeeds in automatically detecting real defects with more precision than the manual selection with an all-encompassing shape, including some the expert restorer could have missed for lack of time.

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.

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.

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.

EM-Net: Deep Learning for Electron Microscopy Image Segmentation

Afshin Khadangi, Thomas Boudier, Vijay Rajagopal

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Auto-TLDR; EM-net: Deep Convolutional Neural Network for Electron Microscopy Image Segmentation

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Recent high-throughput electron microscopy techniques such as focused ion-beam scanning electron microscopy (FIB-SEM) provide thousands of serial sections which assist the biologists in studying sub-cellular structures at high resolution and large volume. Low contrast of such images hinder image segmentation and 3D visualisation of these datasets. With recent advances in computer vision and deep learning, such datasets can be segmented and reconstructed in 3D with greater ease and speed than with previous approaches. However, these methods still rely on thousands of ground-truth samples for training and electron microscopy datasets require significant amounts of time for carefully curated manual annotations. We address these bottlenecks with EM-net, a scalable deep convolutional neural network for EM image segmentation. We have evaluated EM-net using two datasets, one of which belongs to an ongoing competition on EM stack segmentation since 2012. We show that EM-net variants achieve better performances than current deep learning methods using small- and medium-sized ground-truth datasets. We also show that the ensemble of top EM-net base classifiers outperforms other methods across a wide variety of evaluation metrics.

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.

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.

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.

Polarimetric Image Augmentation

Marc Blanchon, Fabrice Meriaudeau, Olivier Morel, Ralph Seulin, Desire Sidibe

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Auto-TLDR; Polarimetric Augmentation for Deep Learning in Robotics Applications

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This paper deals with new augmentation methods for an unconventional imaging modality sensitive to the physics of the observed scene called polarimetry. In nature, polarized light is obtained by reflection or scattering. Robotics applications in urban environments are subject to many obstacles that can be specular and therefore provide polarized light. These areas are prone to segmentation errors using standard modalities but could be solved using information carried by the polarized light. Deep Convolutional Neural Networks (DCNNs) have shown excellent segmentation results, but require a significant amount of data to achieve best performances. The lack of data is usually overcomed by using augmentation methods. However, unlike RGB images, polarization images are not only scalar (intensity) images and standard augmentation techniques cannot be applied straightforwardly. We propose enhancing deep learning models through a regularized augmentation procedure applied to polarimetric data in order to characterize scenes more effectively under challenging conditions. We subsequently observe an average of 18.1% improvement in IoU between not augmented and regularized training procedures on real world data.

Breast Anatomy Enriched Tumor Saliency Estimation

Fei Xu, Yingtao Zhang, Heng-Da Cheng, Jianrui Ding, Boyu Zhang, Chunping Ning, Ying Wang

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Auto-TLDR; Tumor Saliency Estimation for Breast Ultrasound using enriched breast anatomy knowledge

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Breast cancer investigation is of great significance and developing tumor detection methodologies is a critical need. However, it is a challenging task for breast cancer detection using breast ultrasound (BUS) images due to the complicated breast structure and poor quality of the images. In this paper, we propose a novel tumor saliency estimation (TSE) model guided by enriched breast anatomy knowledge to localize the tumor. First, the breast anatomy layers are generated by a deep neural network. Then we refine the layers by integrating a non-semantic breast anatomy model to solve the problems of incomplete mammary layers. Meanwhile, a new background map generation method weighted by the semantic probability and spatial distance is proposed to improve the performance. The experiment demonstrates that the proposed method with the new background map outperforms four state-of-the-art TSE models with increasing 10% of F_meansure on the public BUS dataset.

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.

Motion U-Net: Multi-Cue Encoder-Decoder Network for Motion Segmentation

Gani Rahmon, Filiz Bunyak, Kannappan Palaniappan

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Auto-TLDR; Motion U-Net: A Deep Learning Framework for Robust Moving Object Detection under Challenging Conditions

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Detection of moving objects is a critical first step in many computer vision applications. Several algorithms for motion and change detection were proposed. However, many of these approaches lack the ability to handle challenging real-world scenarios. Recently, deep learning approaches started to produce impressive solutions to computer vision tasks, particularly for detection and segmentation. Many existing deep learning networks proposed for moving object detection rely only on spatial appearance cues. In this paper, we propose a novel multi-cue and multi-stream network, Motion U-Net (MU-Net), which integrates motion, change, and appearance cues using a deep learning framework for robust moving object detection under challenging conditions. The proposed network consists of a two-stream encoder module followed by feature concatenation and a decoder module. Motion and change cues are computed through our tensor-based motion estimation and a multi-modal background subtraction modules. The proposed system was tested and evaluated on the change detection challenge datasets (CDnet-2014) and compared to state-of-the-art methods. On CDnet-2014 dataset, our approach reaches an average overall F-measure of 0.9852 and outperforms all current state-of-the-art methods. The network was also tested on the unseen SBI-2015 dataset and produced promising results.

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.

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.

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%.

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.

Inception Based Deep Learning Architecture for Tuberculosis Screening of Chest X-Rays

Dipayan Das, K.C. Santosh, Umapada Pal

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Auto-TLDR; End to End CNN-based Chest X-ray Screening for Tuberculosis positive patients in the severely resource constrained regions of the world

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The motivation for this work is the primary need of screening Tuberculosis (TB) positive patients in the severely resource constrained regions of the world. Chest X-ray (CXR) is considered to be a promising indicator for the onset of TB, but the lack of skilled radiologists in such regions degrades the situation. Therefore, several computer aided diagnosis (CAD) systems have been proposed to solve the decision making problem, which includes hand engineered feature extraction methods to deep learning or Convolutional Neural Network (CNN) based methods. Feature extraction, being a time and resource intensive process, often delays the process of mass screening. Hence an end to end CNN architecture is proposed in this work to solve the problem. Two benchmark CXR datasets have been used in this work, collected from Shenzhen (China) and Montgomery County (USA), on which the proposed methodology achieved a maximum abnormality detection accuracy (ACC) of 91.7\% (0.96 AUC) and 87.47\% (0.92 AUC) respectively. To the greatest of our knowledge, the obtained results are marginally superior to the state of the art results that have solely used deep learning methodologies on the aforementioned datasets.

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.

The Color Out of Space: Learning Self-Supervised Representations for Earth Observation Imagery

Stefano Vincenzi, Angelo Porrello, Pietro Buzzega, Marco Cipriano, Pietro Fronte, Roberto Cuccu, Carla Ippoliti, Annamaria Conte, Simone Calderara

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Auto-TLDR; Satellite Image Representation Learning for Remote Sensing

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The recent growth in the number of satellite images fosters the development of effective deep-learning techniques for Remote Sensing (RS). However, their full potential is untapped due to the lack of large annotated datasets. Such a problem is usually countered by fine-tuning a feature extractor that is previously trained on the ImageNet dataset. Unfortunately, the domain of natural images differs from the RS one, which hinders the final performance. In this work, we propose to learn meaningful representations from satellite imagery, leveraging its high-dimensionality spectral bands to reconstruct the visible colors. We conduct experiments on land cover classification (BigEarthNet) and West Nile Virus detection, showing that colorization is a solid pretext task for training a feature extractor. Furthermore, we qualitatively observe that guesses based on natural images and colorization rely on different parts of the input. This paves the way to an ensemble model that eventually outperforms both the above-mentioned techniques.

Fine-Tuning Convolutional Neural Networks: A Comprehensive Guide and Benchmark Analysis for Glaucoma Screening

Amed Mvoulana, Rostom Kachouri, Mohamed Akil

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Auto-TLDR; Fine-tuning Convolutional Neural Networks for Glaucoma Screening

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This work aimed at giving a comprehensive and in-detailed guide on the route to fine-tuning Convolutional Neural Networks (CNNs) for glaucoma screening. Transfer learning consists in a promising alternative to train CNNs from stratch, to avoid the huge data and resources requirements. After a thorough study of five state-of-the-art CNNs architectures, a complete and well-explained strategy for fine-tuning these networks is proposed, using hyperparameter grid-searching and two-phase training approach. Excellent performance is reached on model evaluation, with a 0.9772 AUROC validation rate, giving arise to reliable glaucoma diagosis-help systems. Also, a benchmark analysis is conducted across all fine-tuned models, studying them according to performance indices such as model complexity and size, AUROC density and inference time. This in-depth analysis allows a rigorous comparison between model characteristics, and is useful for giving practioners important trademarks for prospective applications and deployments.

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.

Supporting Skin Lesion Diagnosis with Content-Based Image Retrieval

Stefano Allegretti, Federico Bolelli, Federico Pollastri, Sabrina Longhitano, Giovanni Pellacani, Costantino Grana

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Auto-TLDR; Skin Images Retrieval Using Convolutional Neural Networks for Skin Lesion Classification and Segmentation

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Given the relevance of skin cancer, many attempts have been dedicated to the creation of automated devices that could assist both expert and beginner dermatologists towards fast and early diagnosis of skin lesions. In recent years, tasks such as skin lesion classification and segmentation have been extensively addressed with deep learning algorithms, which in some cases reach a diagnostic accuracy comparable to that of expert physicians. However, the general lack of interpretability and reliability severely hinders the ability of those approaches to actually support dermatologists in the diagnosis process. In this paper a novel skin images retrieval system is presented, which exploits features extracted by Convolutional Neural Networks to gather similar images from a publicly available dataset, in order to assist the diagnosis process of both expert and novice practitioners. In the proposed framework, Resnet-50 is initially trained for the classification of dermoscopic images; then, the feature extraction part is isolated, and an embedding network is build on top of it. The embedding learns an alternative representation, which allows to check image similarity by means of a distance measure. Experimental results reveal that the proposed method is able to select meaningful images, which can effectively boost the classification accuracy of human dermatologists.

Enhancing Semantic Segmentation of Aerial Images with Inhibitory Neurons

Ihsan Ullah, Sean Reilly, Michael Madden

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Auto-TLDR; Lateral Inhibition in Deep Neural Networks for Object Recognition and Semantic Segmentation

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In a Convolutional Neural Network, each neuron in the output feature map takes input from the neurons in its receptive field. This receptive field concept plays a vital role in today's deep neural networks. However, inspired by neuro-biological research, it has been proposed to add inhibitory neurons outside the receptive field, which may enhance the performance of neural network models. In this paper, we begin with deep network architectures such as VGG and ResNet, and propose an approach to add lateral inhibition in each output neuron to reduce its impact on its neighbours, both in fine-tuning pre-trained models and training from scratch. Our experiments show that notable improvements upon prior baseline deep models can be achieved. A key feature of our approach is that it is easy to add to baseline models; it can be adopted in any model containing convolution layers, and we demonstrate its value in applications including object recognition and semantic segmentation of aerial images, where we show state-of-the-art result on the Aeroscape dataset. On semantic segmentation tasks, our enhancement shows 17.43% higher mIoU than a single baseline model on a single source (the Aeroscape dataset), 13.43% higher performance than an ensemble model on the same single source, and 7.03% higher than an ensemble model on multiple sources (segmentation datasets). Our experiments illustrate the potential impact of using inhibitory neurons in deep learning models, and they also show better results than the baseline models that have standard convolutional layer.

BAT Optimized CNN Model Identifies Water Stress in Chickpea Plant Shoot Images

Shiva Azimi, Taranjit Kaur, Tapan Gandhi

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Auto-TLDR; BAT Optimized ResNet-18 for Stress Classification of chickpea shoot images under water deficiency

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Stress due to water deficiency in plants can significantly lower the agricultural yield. It can affect many visible plant traits such as size and surface area, the number of leaves and their color, etc. In recent years, computer vision-based plant phenomics has emerged as a promising tool for plant research and management. Such techniques have the advantage of being non-destructive, non-evasive, fast, and offer high levels of automation. Pulses like chickpeas play an important role in ensuring food security in poor countries owing to their high protein and nutrition content. In the present work, we have built a dataset comprising of two varieties of chickpea plant shoot images under different moisture stress conditions. Specifically, we propose a BAT optimized ResNet-18 model for classifying stress induced by water deficiency using chickpea shoot images. BAT algorithm identifies the optimal value of the mini-batch size to be used for training rather than employing the traditional manual approach of trial and error. Experimentation on two crop varieties (JG and Pusa) reveals that BAT optimized approach achieves an accuracy of 96% and 91% for JG and Pusa varieties that is better than the traditional method by 4%. The experimental results are also compared with state of the art CNN models like Alexnet, GoogleNet, and ResNet-50. The comparison results demonstrate that the proposed BAT optimized ResNet-18 model achieves higher performance than the comparison counterparts.

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.

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.

Attention Based Coupled Framework for Road and Pothole Segmentation

Shaik Masihullah, Ritu Garg, Prerana Mukherjee, Anupama Ray

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Auto-TLDR; Few Shot Learning for Road and Pothole Segmentation on KITTI and IDD

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In this paper, we propose a novel attention based coupled framework for road and pothole segmentation. In many developing countries as well as in rural areas, the drivable areas are neither well-defined, nor well-maintained. Under such circumstances, an Advance Driver Assistant System (ADAS) is needed to assess the drivable area and alert about the potholes ahead to ensure vehicle safety. Moreover, this information can also be used in structured environments for assessment and maintenance of road health. We demonstrate few shot learning approach for pothole detection to leverage accuracy even with fewer training samples. We report the exhaustive experimental results for road segmentation on KITTI and IDD datasets. We also present pothole segmentation on IDD.

Enhancing Deep Semantic Segmentation of RGB-D Data with Entangled Forests

Matteo Terreran, Elia Bonetto, Stefano Ghidoni

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Auto-TLDR; FuseNet: A Lighter Deep Learning Model for Semantic Segmentation

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Semantic segmentation is a problem which is getting more and more attention in the computer vision community. Nowadays, deep learning methods represent the state of the art to solve this problem, and the trend is to use deeper networks to get higher performance. The drawback with such models is a higher computational cost, which makes it difficult to integrate them on mobile robot platforms. In this work we want to explore how to obtain lighter deep learning models without compromising performance. To do so we will consider the features used in the Entangled Random Forest algorithm and we will study the best strategies to integrate these within FuseNet deep network. Such new features allow us to shrink the network size without loosing performance, obtaining hence a lighter model which achieves state-of-the-art performance on the semantic segmentation task and represents an interesting alternative for mobile robotics applications, where computational power and energy are limited.