Lung segmentation in chest radiographs using anatomical atlases with nonrigid registration

BS-Net: Learning COVID-19 pneumonia severity on a large chest X-ray dataset

In this work we design an end-to-end deep learning architecture for predicting, on Chest X-rays images (CXR), a multi-regional score conveying the degree of lung compromise in COVID-19 patients. Such semi-quantitative scoring system, namely Brixia score, is applied in serial monitoring of such patients, showing significant prognostic value, in one of the hospitals that experienced one of the highest pandemic peaks in Italy. To solve such a challenging visual task, we adopt a weakly supervised learning strategy structured to handle different tasks (segmentation, spatial alignment, and score estimation) trained with a "from-the-part-to-the-whole" procedure involving different datasets. In particular, we exploit a clinical dataset of almost 5,000 CXR annotated images collected in the same hospital. Our BS-Net demonstrates self-attentive behavior and a high degree of accuracy in all processing stages. Through inter-rater agreement tests and a gold standard comparison, we show that our solution outperforms single human annotators in rating accuracy and consistency, thus supporting the possibility of using this tool in contexts of computer-assisted monitoring. Highly resolved (super-pixel level) explainability maps are also generated, with an original technique, to visually help the understanding of the network activity on the lung areas. We also consider other scores proposed in literature and provide a comparison with a recently proposed non-specific approach. We eventually test the performance robustness of our model on an assorted public COVID-19 dataset, for which we also provide Brixia score annotations, observing good direct generalization and fine-tuning capabilities that highlight the portability of BS-Net in other clinical settings. The CXR dataset along with the source code and the trained model are publicly released for research purposes.

Multilevel Deep-Aggregated Boosted Network to Recognize COVID-19 Infection from Large-Scale Heterogeneous Radiographic Data

In the present epidemic of the coronavirus disease 2019 (COVID-19), radiological imaging modalities, such as X-ray and computed tomography (CT), have been identified as effective diagnostic tools. However, the subjective assessment of radiographic examination is a time-consuming task and demands expert radiologists. Recent advancements in artificial intelligence have enhanced the diagnostic power of computer-aided diagnosis (CAD) tools and assisted medical specialists in making efficient diagnostic decisions. In this work, we propose an optimal multilevel deep-aggregated boosted network to recognize COVID-19 infection from heterogeneous radiographic data, including X-ray and CT images. Our method leverages multilevel deep-aggregated features and multistage training via a mutually beneficial approach to maximize the overall CAD performance. To improve the interpretation of CAD predictions, these multilevel deep features are visualized as additional outputs that can assist radiologists in validating the CAD results. A total of six publicly available datasets were fused to build a single large-scale heterogeneous radiographic collection that was used to analyze the performance of the proposed technique and other baseline methods. To preserve generality of our method, we selected different patient data for training, validation, and testing, and consequently, the data of same patient were not included in training, validation, and testing subsets. In addition, fivefold cross-validation was performed in all the experiments for a fair evaluation. Our method exhibits promising performance values of 95.38%, 95.57%, 92.53%, 98.14%, 93.16%, and 98.55% in terms of average accuracy, F-measure, specificity, sensitivity, precision, and area under the curve, respectively and outperforms various state-of-the-art methods.

Extreme Learning Machine based Differentiation of Pulmonary Tuberculosis in Chest Radiographs using Integrated Local Feature Descriptors

BACKGROUND AND OBJECTIVE

Computer aided diagnostics of Pulmonary Tuberculosis in chest radiographs relies on the differentiation of subtle and non-specific alterations in the images. In this study, an attempt has been made to identify and classify Tuberculosis conditions from healthy subjects in chest radiographs using integrated local feature descriptors and variants of extreme learning machine.

METHODS

Lung fields in the chest images are segmented using Reaction Diffusion Level Set method. Local feature descriptors such as Median Robust Extended Local Binary Patterns and Gradient Local Ternary Patterns are extracted. Extreme Learning Machine (ELM) and Online Sequential ELM (OSELM) classifiers are employed to identify Tuberculosis conditions and, their performances are analysed using standard metrics.

RESULTS

Results show that the adopted segmentation method is able to delineate lung fields in both healthy and Tuberculosis images. Extracted features are statistically significant even in images with inter and intra subject variability. Sigmoid activation function yields accuracy and sensitivity values greater than 98% for both the classifiers. Highest sensitivity is observed with OSELM for minimal significant features in detecting Tuberculosis images.

CONCLUSION

As ELM based method is able to differentiate the subtle changes in inter and intra subject variations of chest X-ray images, the proposed methodology seems to be useful for computer-based detection of Pulmonary Tuberculosis.

COVID-19 in CXR: From Detection and Severity Scoring to Patient Disease Monitoring

This work estimates the severity of pneumonia in COVID-19 patients and reports the findings of a longitudinal study of disease progression. It presents a deep learning model for simultaneous detection and localization of pneumonia in chest Xray (CXR) images, which is shown to generalize to COVID-19 pneumonia. The localization maps are utilized to calculate a "Pneumonia Ratio" which indicates disease severity. The assessment of disease severity serves to build a temporal disease extent profile for hospitalized patients. To validate the model's applicability to the patient monitoring task, we developed a validation strategy which involves a synthesis of Digital Reconstructed Radiographs (DRRs - synthetic Xray) from serial CT scans; we then compared the disease progression profiles that were generated from the DRRs to those that were generated from CT volumes.

2D Statistical Lung Shape Analysis Using Chest Radiographs: Modelling and Segmentation

Accurate information of the lung shape analysis and its anatomical variations is very noticeable in medical imaging. The normal variations of the lung shape can be interpreted as a normal lung. In contrast, abnormal variations of the lung shape can be a result of one of the pulmonary diseases. The goal of this study is twofold: (1) represent two lung shape models which are different at the reference points in registration process considering to show their impact on estimating the inter-patient 2D lung shape variations and (2) using the obtained models in lung field segmentation by utilizing active shape model (ASM) technique. The represented models which showed the inter-patient 2D lung shape variations in two different forms are fully compared and evaluated. The results show that the models along with standard principal component analysis (PCA) can be able to explain more than 95% of total variations in all cases using only first 7 principal component (PC) modes for both lungs. Both models are used in ASM-based segmentation technique for lung field segmentation. The segmentation results are evaluated using leave-one-out cross validation technique. According to the experimental results, the proposed method has average dice similarity coefficient of 97.1% and 96.1% for the right and the left lung, respectively. The results show that the proposed segmentation method is more stable and accurate than other model-based techniques to inter-patient lung field segmentation.

Deformable adversarial registration network with multiple loss constraints

Deformable medical image registration has the necessary value of theoretical research and clinical application. Traditional methods cannot meet clinical application standards in terms of registration accuracy and efficiency. This article proposes a deformable generate adversarial registration framework, which avoids the dependence on ground-truth deformation. The proposed residual registration network based on Nested U-Net has excellent feature extraction ability and robustness. Multiple constraints that incorporate the potential information of anatomical segmentation extracted by the discriminator can help the model adapt to different modal registration tasks. Through interpatient X-ray chest registration, the deep-supervised training method, and the proposed loss constraint are proved to improve the model's performance and training stability. The experimental results show that our model, compared with state-of-the-art methods, provides a more accurate spatial alignment relationship between different patients' lung organs while ensuring the displacement field's authenticity. Finally, we explored the relationship between the accuracy and validity of the model.

Automated COVID-19 Detection from Chest X-Ray Images: A High-Resolution Network (HRNet) Approach

The pandemic, originated by novel coronavirus 2019 (COVID-19), continuing its devastating effect on the health, well-being, and economy of the global population. A critical step to restrain this pandemic is the early detection of COVID-19 in the human body to constraint the exposure and control the spread of the virus. Chest X-Rays are one of the non-invasive tools to detect this disease as the manual PCR diagnosis process is quite tedious and time-consuming. Our intensive background studies show that, the works till now are not efficient to produce an unbiased detection result. In this work, we proposed an automated COVID-19 classification method, utilizing available COVID and non-COVID X-Ray datasets, along with High-Resolution Network (HRNet) for feature extraction embedding with the UNet for segmentation purposes. To evaluate the proposed method, several baseline experiments have been performed employing numerous deep learning architectures. With extensive experiment, we got a significant result of 99.26% accuracy, 98.53% sensitivity, and 98.82% specificity with HRNet which surpasses the performances of the existing models. Finally, we conclude that our proposed methodology ensures unbiased high accuracy, which increases the probability of incorporating X-Ray images into the diagnosis of the disease.

A self-supervised feature-standardization-block for cross-domain lung disease classification

With the advance of deep learning technology, convolutional neural network (CNN) has been wildly used and achieved the state-of-the-art performances in the area of medical image classification. However, most existing medical image classification methods conduct their experiments on only one public dataset. When applying a well-trained model to a different dataset selected from different sources, the model usually shows large performance degradation and needs to be fine-tuned before it can be applied to the new dataset. The goal of this work is trying to solve the cross-domain image classification problem without using data from target domain. In this work, we designed a self-supervised plug-and-play feature-standardization-block (FSB) which consisting of image normalization (INB), contrast enhancement (CEB) and boundary detection blocks (BDB), to extract cross-domain robust feature maps for deep learning framework, and applied the network for chest x-ray-based lung diseases classification. Three classic deep networks, i.e. VGG, Xception and DenseNet and four chest x-ray lung diseases datasets were employed for evaluating the performance. The experimental result showed that when employing feature-standardization-block, all three networks showed better domain adaption performance. The image normalization, contrast enhancement and boundary detection blocks achieved in average 2%, 2% and 5% accuracy improvement, respectively. By combining all three blocks, feature-standardization-block achieved in average 6% accuracy improvement.

Light-weighted ensemble network with multilevel activation visualization for robust diagnosis of COVID19 pneumonia from large-scale chest radiographic database

Currently, the coronavirus disease 2019 (COVID19) pandemic has killed more than one million people worldwide. In the present outbreak, radiological imaging modalities such as computed tomography (CT) and X-rays are being used to diagnose this disease, particularly in the early stage. However, the assessment of radiographic images includes a subjective evaluation that is time-consuming and requires substantial clinical skills. Nevertheless, the recent evolution in artificial intelligence (AI) has further strengthened the ability of computer-aided diagnosis tools and supported medical professionals in making effective diagnostic decisions. Therefore, in this study, the strength of various AI algorithms was analyzed to diagnose COVID19 infection from large-scale radiographic datasets. Based on this analysis, a light-weighted deep network is proposed, which is the first ensemble design (based on MobileNet, ShuffleNet, and FCNet) in medical domain (particularly for COVID19 diagnosis) that encompasses the reduced number of trainable parameters (a total of 3.16 million parameters) and outperforms the various existing models. Moreover, the addition of a multilevel activation visualization layer in the proposed network further visualizes the lesion patterns as multilevel class activation maps (ML-CAMs) along with the diagnostic result (either COVID19 positive or negative). Such additional output as ML-CAMs provides a visual insight of the computer decision and may assist radiologists in validating it, particularly in uncertain situations Additionally, a novel hierarchical training procedure was adopted to perform the training of the proposed network. It proceeds the network training by the adaptive number of epochs based on the validation dataset rather than using the fixed number of epochs. The quantitative results show the better performance of the proposed training method over the conventional end-to-end training procedure.

A large collection of CT-scan and X-ray datasets (based on six publicly available datasets) was used to evaluate the performance of the proposed model and other baseline methods. The experimental results of the proposed network exhibit a promising performance in terms of diagnostic decision. An average F1 score (F1) of 94.60% and 95.94% and area under the curve (AUC) of 97.50% and 97.99% are achieved for the CT-scan and X-ray datasets, respectively. Finally, the detailed comparative analysis reveals that the proposed model outperforms the various state-of-the-art methods in terms of both quantitative and computational performance.

Enhanced Diagnosis of Pneumothorax with an Improved Real-Time Augmentation for Imbalanced Chest X-rays Data Based on DCNN

Pneumothorax is a common pulmonary disease that can lead to dyspnea and can be life-threatening. X-ray examination is the main means to diagnose this disease. Computer-aided diagnosis of pneumothorax on chest X-ray, as a prerequisite for a timely cure, has been widely studied, but it is still not satisfactory to achieve highly accurate results. In this paper, an image classification algorithm based on the deep convolutional neural network (DCNN) is proposed for high-resolution medical image analysis of pneumothorax X-rays, which features a Network In Network (NIN) for cleaning the data, random histogram equalization data augmentation processing, and a DCNN. The experimental results indicate that the proposed method can effectively increase the correct diagnosis rate of pneumothorax, and the Area under Curve (AUC) of the test verified in the experiment is 0.9844 on ZJU-2 test data and 0.9906 on the ChestX-ray14, respectively. In addition, a large number of atmospheric pleura samples are visualized and analyzed based on the experimental results and in-depth learning characteristics of the algorithm. The analysis results verify the validity of feature extraction for the network. Combined with the results of these two aspects, the proposed X-ray image processing algorithm can effectively improve the classification accuracy of pneumothorax photographs.

GraphCovidNet: A graph neural network based model for detecting COVID-19 from CT scans and X-rays of chest

COVID-19, a viral infection originated from Wuhan, China has spread across the world and it has currently affected over 115 million people. Although vaccination process has already started, reaching sufficient availability will take time. Considering the impact of this widespread disease, many research attempts have been made by the computer scientists to screen the COVID-19 from Chest X-Rays (CXRs) or Computed Tomography (CT) scans. To this end, we have proposed GraphCovidNet, a Graph Isomorphic Network (GIN) based model which is used to detect COVID-19 from CT-scans and CXRs of the affected patients. Our proposed model only accepts input data in the form of graph as we follow a GIN based architecture. Initially, pre-processing is performed to convert an image data into an undirected graph to consider only the edges instead of the whole image. Our proposed GraphCovidNet model is evaluated on four standard datasets: SARS-COV-2 Ct-Scan dataset, COVID-CT dataset, combination of covid-chestxray-dataset, Chest X-Ray Images (Pneumonia) dataset and CMSC-678-ML-Project dataset. The model shows an impressive accuracy of 99% for all the datasets and its prediction capability becomes 100% accurate for the binary classification problem of detecting COVID-19 scans. Source code of this work can be found at GitHub-link .

Improved Semantic Segmentation of Tuberculosis-Consistent Findings in Chest X-rays Using Augmented Training of Modality-Specific U-Net Models with Weak Localizations

Deep learning (DL) has drawn tremendous attention for object localization and recognition in both natural and medical images. U-Net segmentation models have demonstrated superior performance compared to conventional hand-crafted feature-based methods. Medical image modality-specific DL models are better at transferring domain knowledge to a relevant target task than those pretrained on stock photography images. This character helps improve model adaptation, generalization, and class-specific region of interest (ROI) localization. In this study, we train chest X-ray (CXR) modality-specific U-Nets and other state-of-the-art U-Net models for semantic segmentation of tuberculosis (TB)-consistent findings. Automated segmentation of such manifestations could help radiologists reduce errors and supplement decision-making while improving patient care and productivity. Our approach uses the publicly available TBX11K CXR dataset with weak TB annotations, typically provided as bounding boxes, to train a set of U-Net models. Next, we improve the results by augmenting the training data with weak localization, postprocessed into an ROI mask, from a DL classifier trained to classify CXRs as showing normal lungs or suspected TB manifestations. Test data are individually derived from the TBX11K CXR training distribution and other cross-institutional collections, including the Shenzhen TB and Montgomery TB CXR datasets. We observe that our augmented training strategy helped the CXR modality-specific U-Net models achieve superior performance with test data derived from the TBX11K CXR training distribution and cross-institutional collections (p < 0.05). We believe that this is the first study to i) use CXR modality-specific U-Nets for semantic segmentation of TB-consistent ROIs and ii) evaluate the segmentation performance while augmenting the training data with weak TB-consistent localizations.

Tuberculosis Diagnostics and Localization in Chest X-Rays via Deep Learning Models

For decades, tuberculosis (TB), a potentially serious infectious lung disease, continues to be a leading cause of worldwide death. Proven to be conveniently efficient and cost-effective, chest X-ray (CXR) has become the preliminary medical imaging tool for detecting TB. Arguably, the quality of TB diagnosis will improve vastly with automated CXRs for TB detection and the localization of suspected areas, which may manifest TB. The current line of research aims to develop an efficient computer-aided detection system that will support doctors (and radiologists) to become well-informed when making TB diagnosis from patients' CXRs. Here, an integrated process to improve TB diagnostics via convolutional neural networks (CNNs) and localization in CXRs via deep-learning models is proposed. Three key steps in the TB diagnostics process include (a) modifying CNN model structures, (b) model fine-tuning via artificial bee colony algorithm, and (c) the implementation of linear average–based ensemble method. Comparisons of the overall performance are made across all three steps among the experimented deep CNN models on two publicly available CXR datasets, namely, the Shenzhen Hospital CXR dataset and the National Institutes of Health CXR dataset. Validated performance includes detecting CXR abnormalities and differentiating among seven TB-related manifestations (consolidation, effusion, fibrosis, infiltration, mass, nodule, and pleural thickening). Importantly, class activation mapping is employed to inform a visual interpretation of the diagnostic result by localizing the detected lung abnormality manifestation on CXR. Compared to the state-of-the-art, the resulting approach showcases an outstanding performance both in the lung abnormality detection and the specific TB-related manifestation diagnosis vis-à-vis the localization in CXRs.

Coronavirus disease (COVID-19) detection in Chest X-Ray images using majority voting based classifier ensemble

Novel coronavirus disease (nCOVID-19) is the most challenging problem for the world. The disease is caused by severe acute respiratory syndrome coronavirus-2 (SARS-COV-2), leading to high morbidity and mortality worldwide. The study reveals that infected patients exhibit distinct radiographic visual characteristics along with fever, dry cough, fatigue, dyspnea, etc. Chest X-Ray (CXR) is one of the important, non-invasive clinical adjuncts that play an essential role in the detection of such visual responses associated with SARS-COV-2 infection. However, the limited availability of expert radiologists to interpret the CXR images and subtle appearance of disease radiographic responses remains the biggest bottlenecks in manual diagnosis. In this study, we present an automatic COVID screening (ACoS) system that uses radiomic texture descriptors extracted from CXR images to identify the normal, suspected, and nCOVID-19 infected patients. The proposed system uses two-phase classification approach (normal vs. abnormal and nCOVID-19 vs. pneumonia) using majority vote based classifier ensemble of five benchmark supervised classification algorithms. The training-testing and validation of the ACoS system are performed using 2088 (696 normal, 696 pneumonia and 696 nCOVID-19) and 258 (86 images of each category) CXR images, respectively. The obtained validation results for phase-I (accuracy (ACC) = 98.062%, area under curve (AUC) = 0.956) and phase-II (ACC = 91.329% and AUC = 0.831) show the promising performance of the proposed system. Further, the Friedman post-hoc multiple comparisons and z-test statistics reveals that the results of ACoS system are statistically significant. Finally, the obtained performance is compared with the existing state-of-the-art methods.

Convexity preserving level set for left ventricle segmentation

In clinical applications of cardiac left ventricle (LV) segmentation, the segmented LV is desired to include the cavity, trabeculae, and papillary muscles, which form a convex shape. However, the intensities of trabeculae and papillary muscles are similar to myocardium. Consequently, segmentation algorithms may easily misclassify trabeculae and papillary muscles as myocardium. In this paper, we propose a level set method with a convexity preserving mechanism to ensure the convexity of the segmented LV. In the proposed level set method, the curvature of the level set contours is used to control their convexity, such that the level set contour is finally deformed as a convex shape. The experimental results and the comparison with other level set methods show the advantage of our method in terms of segmentation accuracy. Compared with the state-of-the-art methods using deep-learning, our method is able to achieve comparable segmentation accuracy without the need for training, while the deep-learning based method requires a large set of training data and high-quality manual segmentation. Therefore, our method can be conveniently used in situation where training data and their manual segmentation are not available.

MSU-Net: Multi-Scale U-Net for 2D Medical Image Segmentation

Aiming at the limitation of the convolution kernel with a fixed receptive field and unknown prior to optimal network width in U-Net, multi-scale U-Net (MSU-Net) is proposed by us for medical image segmentation. First, multiple convolution sequence is used to extract more semantic features from the images. Second, the convolution kernel with different receptive fields is used to make features more diverse. The problem of unknown network width is alleviated by efficient integration of convolution kernel with different receptive fields. In addition, the multi-scale block is extended to other variants of the original U-Net to verify its universality. Five different medical image segmentation datasets are used to evaluate MSU-Net. A variety of imaging modalities are included in these datasets, such as electron microscopy, dermoscope, ultrasound, etc. Intersection over Union (IoU) of MSU-Net on each dataset are 0.771, 0.867, 0.708, 0.900, and 0.702, respectively. Experimental results show that MSU-Net achieves the best performance on different datasets. Our implementation is available at https://github.com/CN-zdy/MSU_Net.

A Review on Deep Learning Techniques for the Diagnosis of Novel Coronavirus (COVID-19)

Novel coronavirus (COVID-19) outbreak, has raised a calamitous situation all over the world and has become one of the most acute and severe ailments in the past hundred years. The prevalence rate of COVID-19 is rapidly rising every day throughout the globe. Although no vaccines for this pandemic have been discovered yet, deep learning techniques proved themselves to be a powerful tool in the arsenal used by clinicians for the automatic diagnosis of COVID-19. This paper aims to overview the recently developed systems based on deep learning techniques using different medical imaging modalities like Computer Tomography (CT) and X-ray. This review specifically discusses the systems developed for COVID-19 diagnosis using deep learning techniques and provides insights on well-known data sets used to train these networks. It also highlights the data partitioning techniques and various performance measures developed by researchers in this field. A taxonomy is drawn to categorize the recent works for proper insight. Finally, we conclude by addressing the challenges associated with the use of deep learning methods for COVID-19 detection and probable future trends in this research area. The aim of this paper is to facilitate experts (medical or otherwise) and technicians in understanding the ways deep learning techniques are used in this regard and how they can be potentially further utilized to combat the outbreak of COVID-19.

Bayesian Learning of Shifted-Scaled Dirichlet Mixture Models and Its Application to Early COVID-19 Detection in Chest X-ray Images

Early diagnosis and assessment of fatal diseases and acute infections on chest X-ray (CXR) imaging may have important therapeutic implications and reduce mortality. In fact, many respiratory diseases have a serious impact on the health and lives of people. However, certain types of infections may include high variations in terms of contrast, size and shape which impose a real challenge on classification process. This paper introduces a new statistical framework to discriminate patients who are either negative or positive for certain kinds of virus and pneumonia. We tackle the current problem via a fully Bayesian approach based on a flexible statistical model named shifted-scaled Dirichlet mixture models (SSDMM). This mixture model is encouraged by its effectiveness and robustness recently obtained in various image processing applications. Unlike frequentist learning methods, our developed Bayesian framework has the advantage of taking into account the uncertainty to accurately estimate the model parameters as well as the ability to solve the problem of overfitting. We investigate here a Markov Chain Monte Carlo (MCMC) estimator, which is a computer–driven sampling method, for learning the developed model. The current work shows excellent results when dealing with the challenging problem of biomedical image classification. Indeed, extensive experiments have been carried out on real datasets and the results prove the merits of our Bayesian framework.

Deep learning assistance for tuberculosis diagnosis with chest radiography in low-resource settings

Tuberculosis (TB) is a major health issue with high mortality rates worldwide. Recently, tremendous researches of artificial intelligence (AI) have been conducted targeting at TB to reduce the diagnostic burden. However, most researches are conducted in the developed urban areas. The feasibility of applying AI in low-resource settings remains unexplored. In this study, we apply an automated detection (AI) system to screen a large population in an underdeveloped area and evaluate feasibility and contribution of applying AI to help local radiologists detect and diagnose TB using chest X-ray (CXR) images. First, we divide image data into one training dataset including 2627 TB-positive cases and 7375 TB-negative cases and one testing dataset containing 276 TB-positive cases and 619 TB-negative cases, respectively. Next, in building AI system, the experiment includes image labeling and preprocessing, model training and testing. A segmentation model named TB-UNet is also built to detect diseased regions, which uses ResNeXt as the encoder of U-Net. We use AI-generated confidence score to predict the likelihood of each testing case being TB-positive. Then, we conduct two experiments to compare results between the AI system and radiologists with and without AI assistance. Study results show that AI system yields TB detection accuracy of 85%, which is much higher than detection accuracy of radiologists (62%) without AI assistance. In addition, with AI assistance, the TB diagnostic sensitivity of local radiologists is improved by 11.8%. Therefore, this study demonstrates that AI has great potential to help detection, prevention, and control of TB in low-resource settings, particularly in areas with more scant doctors and higher rates of the infected population.

Online Learning of Finite and Infinite Gamma Mixture Models for COVID-19 Detection in Medical Images

The accurate detection of abnormalities in medical images (like X-ray and CT scans) is a challenging problem due to images’ blurred boundary contours, different sizes, variable shapes, and uneven density. In this paper, we tackle this problem via a new effective online variational learning model for both mixtures of finite and infinite Gamma distributions. The proposed approach takes advantage of the Gamma distribution flexibility, the online learning scalability, and the variational inference efficiency. Three different batch and online learning methods based on robust texture-based feature extraction are proposed. Our work is evaluated and validated on several real challenging data sets for different kinds of pneumonia infection detection. The obtained results are very promising given that we approach the classification problem in an unsupervised manner. They also confirm the superiority of the Gamma mixture model compared to the Gaussian mixture model for medical images’ classification.

EMCNet: Automated COVID-19 diagnosis from X-ray images using convolutional neural network and ensemble of machine learning classifiers

Recently, coronavirus disease (COVID-19) has caused a serious effect on the healthcare system and the overall global economy. Doctors, researchers, and experts are focusing on alternative ways for the rapid detection of COVID-19, such as the development of automatic COVID-19 detection systems. In this paper, an automated detection scheme named EMCNet was proposed to identify COVID-19 patients by evaluating chest X-ray images. A convolutional neural network was developed focusing on the simplicity of the model to extract deep and high-level features from X-ray images of patients infected with COVID-19. With the extracted features, binary machine learning classifiers (random forest, support vector machine, decision tree, and AdaBoost) were developed for the detection of COVID-19. Finally, these classifiers' outputs were combined to develop an ensemble of classifiers, which ensures better results for the dataset of various sizes and resolutions. In comparison with other recent deep learning-based systems, EMCNet showed better performance with 98.91% accuracy, 100% precision, 97.82% recall, and 98.89% F1-score. The system could maintain its great importance on the automatic detection of COVID-19 through instant detection and low false negative rate.

Comprehensive Computer-Aided Decision Support Framework to Diagnose Tuberculosis From Chest X-Ray Images: Data Mining Study

Background

Tuberculosis (TB) is one of the most infectious diseases that can be fatal. Its early diagnosis and treatment can significantly reduce the mortality rate. In the literature, several computer-aided diagnosis (CAD) tools have been proposed for the efficient diagnosis of TB from chest radiograph (CXR) images. However, the majority of previous studies adopted conventional handcrafted feature-based algorithms. In addition, some recent CAD tools utilized the strength of deep learning methods to further enhance diagnostic performance. Nevertheless, all these existing methods can only classify a given CXR image into binary class (either TB positive or TB negative) without providing further descriptive information.

Objective

The main objective of this study is to propose a comprehensive CAD framework for the effective diagnosis of TB by providing visual as well as descriptive information from the previous patients’ database.

Methods

To accomplish our objective, first we propose a fusion-based deep classification network for the CAD decision that exhibits promising performance over the various state-of-the-art methods. Furthermore, a multilevel similarity measure algorithm is devised based on multiscale information fusion to retrieve the best-matched cases from the previous database.

Results

The performance of the framework was evaluated based on 2 well-known CXR data sets made available by the US National Library of Medicine and the National Institutes of Health. Our classification model exhibited the best diagnostic performance (0.929, 0.937, 0.921, 0.928, and 0.965 for F1 score, average precision, average recall, accuracy, and area under the curve, respectively) and outperforms the performance of various state-of-the-art methods.

Conclusions

This paper presents a comprehensive CAD framework to diagnose TB from CXR images by retrieving the relevant cases and their clinical observations from the previous patients’ database. These retrieval results assist the radiologist in making an effective diagnostic decision related to the current medical condition of a patient. Moreover, the retrieval results can facilitate the radiologists in subjectively validating the CAD decision.

StackNet-DenVIS: a multi-layer perceptron stacked ensembling approach for COVID-19 detection using X-ray images

The highly contagious nature of Coronavirus disease 2019 (Covid-19) resulted in a global pandemic. Due to the relatively slow and taxing nature of conventional testing for Covid-19, a faster method needs to be in place. The current researches have suggested that visible irregularities found in the chest X-ray of Covid-19 positive patients are indicative of the presence of the disease. Hence, Deep Learning and Image Classification techniques can be employed to learn from these irregularities, and classify accordingly with high accuracy. This research presents an approach to create a classifier model named StackNet-DenVIS which is designed to act as a screening process before conducting the existing swab tests. Using a novel approach, which incorporates Transfer Learning and Stacked Generalization, the model aims to lower the False Negative rate of classification compensating for the 30% False Negative rate of the swab tests. A dataset gathered from multiple reliable sources consisting of 9953 Chest X-rays (868 Covid and 9085 Non-Covid) was used. Also, this research demonstrates handling data imbalance using various techniques involving Generative Adversarial Networks and sampling techniques. The accuracy, sensitivity, and specificity obtained on our proposed model were 95.07%, 99.40% and 94.61% respectively. To the best of our knowledge, the combination of accuracy and false negative rate obtained by this paper outperforms the current implementations. We must also highlight that our proposed architecture also considers other types of viral pneumonia. Given the unprecedented sensitivity of our model we are optimistic it contributes to a better Covid-19 detection.

Post-DAE: Anatomically Plausible Segmentation via Post-Processing With Denoising Autoencoders

We introduce Post-DAE, a post-processing method based on denoising autoencoders (DAE) to improve the anatomical plausibility of arbitrary biomedical image segmentation algorithms. Some of the most popular segmentation methods (e.g. based on convolutional neural networks or random forest classifiers) incorporate additional post-processing steps to ensure that the resulting masks fulfill expected connectivity constraints. These methods operate under the hypothesis that contiguous pixels with similar aspect should belong to the same class. Even if valid in general, this assumption does not consider more complex priors like topological restrictions or convexity, which cannot be easily incorporated into these methods. Post-DAE leverages the latest developments in manifold learning via denoising autoencoders. First, we learn a compact and non-linear embedding that represents the space of anatomically plausible segmentations. Then, given a segmentation mask obtained with an arbitrary method, we reconstruct its anatomically plausible version by projecting it onto the learnt manifold. The proposed method is trained using unpaired segmentation mask, what makes it independent of intensity information and image modality. We performed experiments in binary and multi-label segmentation of chest X-ray and cardiac magnetic resonance images. We show how erroneous and noisy segmentation masks can be improved using Post-DAE. With almost no additional computation cost, our method brings erroneous segmentations back to a feasible space.

Transfer-to-Transfer Learning Approach for Computer Aided Detection of COVID-19 in Chest Radiographs

The coronavirus disease 2019 (COVID-19) global pandemic has severely impacted lives across the globe. Respiratory disorders in COVID-19 patients are caused by lung opacities similar to viral pneumonia. A Computer-Aided Detection (CAD) system for the detection of COVID-19 using chest radiographs would provide a second opinion for radiologists. For this research, we utilize publicly available datasets that have been marked by radiologists into two-classes (COVID-19 and non-COVID-19). We address the class imbalance problem associated with the training dataset by proposing a novel transfer-to-transfer learning approach, where we break a highly imbalanced training dataset into a group of balanced mini-sets and apply transfer learning between these. We demonstrate the efficacy of the method using well-established deep convolutional neural networks. Our proposed training mechanism is more robust to limited training data and class imbalance. We study the performance of our algorithm(s) based on 10-fold cross validation and two hold-out validation experiments to demonstrate its efficacy. We achieved an overall sensitivity of 0.94 for the hold-out validation experiments containing 2265 and 2139 marked as COVID-19 chest radiographs, respectively. For the 10-fold cross validation experiment, we achieve an overall Area under the Receiver Operating Characteristic curve (AUC) value of 0.996 for COVID-19 detection. This paper serves as a proof-of-concept that an automated detection approach can be developed with a limited set of COVID-19 images, and in areas with scarcity of trained radiologists.

RTIP: A FULLY AUTOMATED ROOT TIP TRACKER FOR MEASURING PLANT GROWTH WITH INTERMITTENT PERTURBATIONS

RTip is a tool to quantify plant root growth velocity using high resolution microscopy image sequences at sub-pixel accuracy. The fully automated RTip tracker is designed for high-throughput analysis of plant phenotyping experiments with episodic perturbations. RTip is able to auto-skip past these manual intervention perturbation activity, i.e. when the root tip is not under the microscope, image is distorted or blurred. RTip provides the most accurate root growth velocity results with the lowest variance (i.e. localization jitter) compared to six tracking algorithms including the top performing unsupervised Discriminative Correlation Filter Tracker and the Deeper and Wider Siamese Network. RTip is the only tracker that is able to automatically detect and recover from (occlusion-like) varying duration perturbation events.

COVID-19 Control by Computer Vision Approaches: A Survey

The COVID-19 pandemic has triggered an urgent call to contribute to the fight against an immense threat to the human population. Computer Vision, as a subfield of artificial intelligence, has enjoyed recent success in solving various complex problems in health care and has the potential to contribute to the fight of controlling COVID-19. In response to this call, computer vision researchers are putting their knowledge base at test to devise effective ways to counter COVID-19 challenge and serve the global community. New contributions are being shared with every passing day. It motivated us to review the recent work, collect information about available research resources, and an indication of future research directions. We want to make it possible for computer vision researchers to find existing and future research directions. This survey article presents a preliminary review of the literature on research community efforts against COVID-19 pandemic.

Unveiling COVID-19 from CHEST X-Ray with Deep Learning: A Hurdles Race with Small Data

The possibility to use widespread and simple chest X-ray (CXR) imaging for early screening of COVID-19 patients is attracting much interest from both the clinical and the AI community. In this study we provide insights and also raise warnings on what is reasonable to expect by applying deep learning to COVID classification of CXR images. We provide a methodological guide and critical reading of an extensive set of statistical results that can be obtained using currently available datasets. In particular, we take the challenge posed by current small size COVID data and show how significant can be the bias introduced by transfer-learning using larger public non-COVID CXR datasets. We also contribute by providing results on a medium size COVID CXR dataset, just collected by one of the major emergency hospitals in Northern Italy during the peak of the COVID pandemic. These novel data allow us to contribute to validate the generalization capacity of preliminary results circulating in the scientific community. Our conclusions shed some light into the possibility to effectively discriminate COVID using CXR.

Classification of COVID-19 in chest X-ray images using DeTraC deep convolutional neural network

Chest X-ray is the first imaging technique that plays an important role in the diagnosis of COVID-19 disease. Due to the high availability of large-scale annotated image datasets, great success has been achieved using convolutional neural networks (CNN s) for image recognition and classification. However, due to the limited availability of annotated medical images, the classification of medical images remains the biggest challenge in medical diagnosis. Thanks to transfer learning, an effective mechanism that can provide a promising solution by transferring knowledge from generic object recognition tasks to domain-specific tasks. In this paper, we validate and a deep CNN, called Decompose, Transfer, and Compose (DeTraC), for the classification of COVID-19 chest X-ray images. DeTraC can deal with any irregularities in the image dataset by investigating its class boundaries using a class decomposition mechanism. The experimental results showed the capability of DeTraC in the detection of COVID-19 cases from a comprehensive image dataset collected from several hospitals around the world. High accuracy of 93.1% (with a sensitivity of 100%) was achieved by DeTraC in the detection of COVID-19 X-ray images from normal, and severe acute respiratory syndrome cases.

Contour-based lung shape analysis in order to tuberculosis detection: modeling and feature description

Statistical shape analysis of lung is a reliable alternative method for diagnosing pulmonary diseases such as tuberculosis (TB). The 2D contour-based lung shape analysis is investigated and developed using Fourier descriptors (FDs). The proposed 2D lung shape analysis is carried out in threefold: (1) represent the normal and the abnormal (i.e. pulmonary tuberculosis (PTB)) lung shape models using Fourier descriptors modeling (FDM) framework from chest X-ray (CXR) images, (2) estimate and compare the 2D inter-patient lung shape variations for the normal and abnormal lungs by applying principal component analysis (PCA) techniques, and (3) describe the optimal type of contour-based feature vectors to train a classifier in order to detect TB using one publicly available dataset-namely the Montgomery dataset. Since almost all of the previous works in lung shape analysis are content-based analysis, we proposed contour-based lung shape analysis for statistical modeling and feature description of PTB cases. The results show that the proposed approach is able to explain more than 95% of total variations in both of the normal and PTB cases using only 6 and 7 principal component modes for the right and the left lungs, respectively. In case of PTB detection, using 138 lung cases (80 normal and 58 PTB cases), we achieved the accuracy (ACC) and the area under the curve (AUC) of 82.03% and 88.75%, respectively. In comparison with existing state-of-art studies in the same dataset, the proposed approach is a very promising supplement for diagnosis of PTB disease. The method is robust and valuable for application in 2D automatic segmentation, classification, and atlas registration. Moreover, the approach could be used for any kind of pulmonary diseases. Graphical abstract Contour-based lung shape analysis in order to detect tuberculosis: modeling and feature description.

Computer-Aided System for the Detection of Multicategory Pulmonary Tuberculosis in Radiographs

The early screening and diagnosis of tuberculosis plays an important role in the control and treatment of tuberculosis infections. In this paper, an integrated computer-aided system based on deep learning is proposed for the detection of multiple categories of tuberculosis lesions in chest radiographs. In this system, the fully convolutional neural network method is used to segment the lung area from the entire chest radiograph for pulmonary tuberculosis detection. Different from the previous analysis of the whole chest radiograph, we focus on the specific tuberculosis lesion areas for the analysis and propose the first multicategory tuberculosis lesion detection method. In it, a learning scalable pyramid structure is introduced into the Faster Region-based Convolutional Network (Faster RCNN), which effectively improves the detection of small-area lesions, mines indistinguishable samples during the training process, and uses reinforcement learning to reduce the detection of false-positive lesions. To compare our method with the current tuberculosis detection system, we propose a classification rule for whole chest X-rays using a multicategory tuberculosis lesion detection model and achieve good performance on two public datasets (Montgomery: AUC = 0.977 and accuracy = 0.926; Shenzhen: AUC = 0.941 and accuracy = 0.902). Our proposed computer-aided system is superior to current systems that can be used to assist radiologists in diagnoses and public health providers in screening for tuberculosis in areas where tuberculosis is endemic.

Kidney segmentation from computed tomography images using deep neural network

BACKGROUND

The precise segmentation of kidneys and kidney tumors can help medical specialists to diagnose diseases and improve treatment planning, which is highly required in clinical practice. Manual segmentation of the kidneys is extremely time-consuming and prone to variability between different specialists due to their heterogeneity. Because of this hard work, computational techniques, such as deep convolutional neural networks, have become popular in kidney segmentation tasks to assist in the early diagnosis of kidney tumors. In this study, we propose an automatic method to delimit the kidneys in computed tomography (CT) images using image processing techniques and deep convolutional neural networks (CNNs) to minimize false positives.

METHODS

The proposed method has four main steps: (1) acquisition of the KiTS19 dataset, (2) scope reduction using AlexNet, (3) initial segmentation using U-Net 2D, and (4) false positive reduction using image processing to maintain the largest elements (kidneys).

RESULTS

The proposed method was evaluated in 210 CTs from the KiTS19 database and obtained the best result with an average Dice coefficient of 96.33%, an average Jaccard index of 93.02%, an average sensitivity of 97.42%, an average specificity of 99.94% and an average accuracy of 99.92%. In the KiTS19 challenge, it presented an average Dice coefficient of 93.03%.

CONCLUSION

In our method, we demonstrated that the kidney segmentation problem in CT can be solved efficiently using deep neural networks to define the scope of the problem and segment the kidneys with high precision and with the use of image processing techniques to reduce false positives.

Dense-Unet: a light model for lung fields segmentation in Chest X-Ray images

Automatic and accurate lung segmentation in chest X-ray (CXR) images is fundamental for computer-aided diagnosis systems since the lung is the region of interest in many diseases and also it can reveal useful information by its contours. While deep learning models have reached high performances in the segmentation of anatomical structures, the large number of training parameters is a concern since it increases memory usage and reduces the generalization of the model. To address this, a deep CNN model called Dense-Unet is proposed in which, by dense connectivity between various layers, information flow increases throughout the network. This lets us design a network with significantly fewer parameters while keeping the segmentation robust. To the best of our knowledge, Dense-Unet is the lightest deep model proposed for the segmentation of lung fields in CXR images. The model is evaluated on the JSRT and Montgomery datasets and experiments show that the performance of the proposed model is comparable with state-of-the-art methods.

Pyramid attention recurrent networks for real-time guidewire segmentation and tracking in intraoperative X-ray fluoroscopy

In endovascular and cardiovascular surgery, real-time and accurate segmentation and tracking of interventional instruments can aid in reducing radiation exposure, contrast agent and processing time. Nevertheless, this task often comes with the challenges of the elongated deformable structures with low contrast in noisy X-ray fluoroscopy. To address these issues, a novel efficient network architecture, termed pyramid attention recurrent networks (PAR-Net), is proposed for real-time guidewire segmentation and tracking. The proposed PAR-Net contains three major modules, namely pyramid attention module, recurrent residual module and pre-trained MobileNetV2 encoder. Specifically, a hybrid loss function of both reinforced focal loss and dice loss is proposed to better address the issues of class imbalance and misclassified examples. Quantitative and qualitative evaluations on clinical intraoperative images demonstrate that the proposed approach significantly outperforms simpler baselines as well as the best previously published result for this task, achieving the state-of-the-art performance.

Assessment of an ensemble of machine learning models toward abnormality detection in chest radiographs

Respiratory diseases account for a significant proportion of deaths and disabilities across the world. Chest X-ray (CXR) analysis remains a common diagnostic imaging modality for confirming intra-thoracic cardiopulmonary abnormalities. However, there remains an acute shortage of expert radiologists, particularly in under-resourced settings, resulting in severe interpretation delays. These issues can be mitigated by a computer-aided diagnostic (CADx) system to supplement decision-making and improve throughput while preserving and possibly improving the standard-of-care. Systems reported in the literature or popular media use handcrafted features and/or data-driven algorithms like deep learning (DL) to learn underlying data distributions. The remarkable success of convolutional neural networks (CNN) toward image recognition tasks has made them a promising choice for automated medical image analyses. However, CNNs suffer from high variance and may overfit due to their sensitivity to training data fluctuations. Ensemble learning helps to reduce this variance by combining predictions of multiple learning algorithms to construct complex, non-linear functions and improve robustness and generalization. This study aims to construct and assess the performance of an ensemble of machine learning (ML) models applied to the challenge of classifying normal and abnormal CXRs and significantly reducing the diagnostic load of radiologists and primary-care physicians.

Generalization of intensity distribution of medical images using GANs

The performance of a CNN based medical-image classification network depends on the intensities of the trained images. Therefore, it is necessary to generalize medical images of various intensities against degradation of performance. For lesion classification, features of generalized images should be carefully maintained. To maintain the performance of the medical image classification network and minimize the loss of features, we propose a method using a generative adversarial network (GAN) as a generator to adapt the arbitrary intensity distribution to the specific intensity distribution of the training set. We also select CycleGAN and UNIT to train unpaired medical image data sets. The following was done to evaluate each method’s performance: the similarities between the generalized image and the original were measured via the structural similarity index (SSIM) and histogram, and the original domain data set was passed to a classifier that trained only the original domain images for accuracy comparisons. The results show that the performance evaluation of the generalized images is better than that of the originals, confirming that our proposed method is a simple but powerful solution to the performance degradation of a classification network.

Lung X-ray Segmentation using Deep Convolutional Neural Networks on Contrast-Enhanced Binarized Images

Automatically locating the lung regions effectively and efficiently in digital chest X-ray (CXR) images is important in computer-aided diagnosis. In this paper, we propose an adaptive pre-processing approach for segmenting the lung regions from CXR images using convolutional neural networks-based (CNN-based) architectures. It is comprised of three steps. First, a contrast enhancement method specifically designed for CXR images is adopted. Second, adaptive image binarization is applied to CXR images to separate the image foreground and background. Third, CNN-based architectures are trained on the binarized images for image segmentation. The experimental results show that the proposed pre-processing approach is applicable and effective to various CNN-based architectures and can achieve comparable segmentation accuracy to that of state-of-the-art methods while greatly expediting the model training by up to 20.74 % and reducing storage space for CRX image datasets by down to 94.6 % on average.

A Generic Approach to Lung Field Segmentation From Chest Radiographs Using Deep Space and Shape Learning

Computer-aided diagnosis (CAD) techniques for lung field segmentation from chest radiographs (CXR) have been proposed for adult cohorts, but rarely for pediatric subjects. Statistical shape models (SSMs), the workhorse of most state-of-the-art CXR-based lung field segmentation methods, do not efficiently accommodate shape variation of the lung field during the pediatric developmental stages. The main contributions of our work are: 1) a generic lung field segmentation framework from CXR accommodating large shape variation for adult and pediatric cohorts; 2) a deep representation learning detection mechanism, ensemble space learning, for robust object localization; and 3) marginal shape deep learning for the shape deformation parameter estimation. Unlike the iterative approach of conventional SSMs, the proposed shape learning mechanism transforms the parameter space into marginal subspaces that are solvable efficiently using the recursive representation learning mechanism. Furthermore, our method is the first to include the challenging retro-cardiac region in the CXR-based lung segmentation for accurate lung capacity estimation. The framework is evaluated on 668 CXRs of patients between 3 month to 89 year of age. We obtain a mean Dice similarity coefficient of 0.96 ±0.03 (including the retro-cardiac region). For a given accuracy, the proposed approach is also found to be faster than conventional SSM-based iterative segmentation methods. The computational simplicity of the proposed generic framework could be similarly applied to the fast segmentation of other deformable objects.

Artificial Intelligence-Based Diagnosis of Cardiac and Related Diseases

Automatic chest anatomy segmentation plays a key role in computer-aided disease diagnosis, such as for cardiomegaly, pleural effusion, emphysema, and pneumothorax. Among these diseases, cardiomegaly is considered a perilous disease, involving a high risk of sudden cardiac death. It can be diagnosed early by an expert medical practitioner using a chest X-Ray (CXR) analysis. The cardiothoracic ratio (CTR) and transverse cardiac diameter (TCD) are the clinical criteria used to estimate the heart size for diagnosing cardiomegaly. Manual estimation of CTR and other diseases is a time-consuming process and requires significant work by the medical expert. Cardiomegaly and related diseases can be automatically estimated by accurate anatomical semantic segmentation of CXRs using artificial intelligence. Automatic segmentation of the lungs and heart from the CXRs is considered an intensive task owing to inferior quality images and intensity variations using nonideal imaging conditions. Although there are a few deep learning-based techniques for chest anatomy segmentation, most of them only consider single class lung segmentation with deep complex architectures that require a lot of trainable parameters. To address these issues, this study presents two multiclass residual mesh-based CXR segmentation networks, X-RayNet-1 and X-RayNet-2, which are specifically designed to provide fine segmentation performance with a few trainable parameters compared to conventional deep learning schemes. The proposed methods utilize semantic segmentation to support the diagnostic procedure of related diseases. To evaluate X-RayNet-1 and X-RayNet-2, experiments were performed with a publicly available Japanese Society of Radiological Technology (JSRT) dataset for multiclass segmentation of the lungs, heart, and clavicle bones; two other publicly available datasets, Montgomery County (MC) and Shenzhen X-Ray sets (SC), were evaluated for lung segmentation. The experimental results showed that X-RayNet-1 achieved fine performance for all datasets and X-RayNet-2 achieved competitive performance with a 75% parameter reduction.

Image-to-Images Translation for Multi-Task Organ Segmentation and Bone Suppression in Chest X-Ray Radiography

Chest X-ray radiography is one of the earliest medical imaging technologies and remains one of the most widely-used for diagnosis, screening, and treatment follow up of diseases related to lungs and heart. The literature in this field of research reports many interesting studies dealing with the challenging tasks of bone suppression and organ segmentation but performed separately, limiting any learning that comes with the consolidation of parameters that could optimize both processes. This study, and for the first time, introduces a multitask deep learning model that generates simultaneously the bone-suppressed image and the organ-segmented image, enhancing the accuracy of tasks, minimizing the number of parameters needed by the model and optimizing the processing time, all by exploiting the interplay between the network parameters to benefit the performance of both tasks. The architectural design of this model, which relies on a conditional generative adversarial network, reveals the process on how the wellestablished pix2pix network (image-to-image network) is modified to fit the need for multitasking and extending it to the new image-to-images architecture. The developed source code of this multitask model is shared publicly on Github as the first attempt for providing the two-task pix2pix extension, a supervised/paired/aligned/registered image-to-images translation which would be useful in many multitask applications. Dilated convolutions are also used to improve the results through a more effective receptive field assessment. The comparison with state-of-the-art al-gorithms along with ablation study and a demonstration video1 are provided to evaluate the efficacy and gauge the merits of the proposed approach.

Contour-aware multi-label chest X-ray organ segmentation

PURPOSE

Segmentation of organs from chest X-ray images is an essential task for an accurate and reliable diagnosis of lung diseases and chest organ morphometry. In this study, we investigated the benefits of augmenting state-of-the-art deep convolutional neural networks (CNNs) for image segmentation with organ contour information and evaluated the performance of such augmentation on segmentation of lung fields, heart, and clavicles from chest X-ray images.

METHODS

Three state-of-the-art CNNs were augmented, namely the UNet and LinkNet architecture with the ResNeXt feature extraction backbone, and the Tiramisu architecture with the DenseNet. All CNN architectures were trained on ground-truth segmentation masks and additionally on the corresponding contours. The contribution of such contour-based augmentation was evaluated against the contour-free architectures, and 20 existing algorithms for lung field segmentation.

RESULTS

The proposed contour-aware segmentation improved the segmentation performance, and when compared against existing algorithms on the same publicly available database of 247 chest X-ray images, the UNet architecture with the ResNeXt50 encoder combined with the contour-aware approach resulted in the best overall segmentation performance, achieving a Jaccard overlap coefficient of 0.971, 0.933, and 0.903 for the lung fields, heart, and clavicles, respectively.

CONCLUSION

In this study, we proposed to augment CNN architectures for CXR segmentation with organ contour information and were able to significantly improve segmentation accuracy and outperform all existing solution using a public chest X-ray database.

Modality-specific deep learning model ensembles toward improving TB detection in chest radiographs

The proposed study evaluates the efficacy of knowledge transfer gained through an ensemble of modality-specific deep learning models toward improving the state-of-the-art in Tuberculosis (TB) detection. A custom convolutional neural network (CNN) and selected popular pretrained CNNs are trained to learn modality-specific features from large-scale publicly available chest x-ray (CXR) collections including (i) RSNA dataset (normal = 8851, abnormal = 17833), (ii) Pediatric pneumonia dataset (normal = 1583, abnormal = 4273), and (iii) Indiana dataset (normal = 1726, abnormal = 2378). The knowledge acquired through modality-specific learning is transferred and fine-tuned for TB detection on the publicly available Shenzhen CXR collection (normal = 326, abnormal =336). The predictions of the best performing models are combined using different ensemble methods to demonstrate improved performance over any individual constituent model in classifying TB-infected and normal CXRs. The models are evaluated through cross-validation (n = 5) at the patient-level with an aim to prevent overfitting, improve robustness and generalization. It is observed that a stacked ensemble of the top-3 retrained models demonstrates promising performance (accuracy: 0.941; 95% confidence interval (CI): [0.899, 0.985], area under the curve (AUC): 0.995; 95% CI: [0.945, 1.00]). One-way ANOVA analyses show there are no statistically significant differences in accuracy (P = .759) and AUC (P = .831) among the ensemble methods. Knowledge transferred through modality-specific learning of relevant features helped improve the classification. The ensemble model resulted in reduced prediction variance and sensitivity to training data fluctuations. Results from their combined use are superior to the state-of-the-art.

MIMIC-CXR, a de-identified publicly available database of chest radiographs with free-text reports

Chest radiography is an extremely powerful imaging modality, allowing for a detailed inspection of a patient's chest, but requires specialized training for proper interpretation. With the advent of high performance general purpose computer vision algorithms, the accurate automated analysis of chest radiographs is becoming increasingly of interest to researchers. Here we describe MIMIC-CXR, a large dataset of 227,835 imaging studies for 65,379 patients presenting to the Beth Israel Deaconess Medical Center Emergency Department between 2011-2016. Each imaging study can contain one or more images, usually a frontal view and a lateral view. A total of 377,110 images are available in the dataset. Studies are made available with a semi-structured free-text radiology report that describes the radiological findings of the images, written by a practicing radiologist contemporaneously during routine clinical care. All images and reports have been de-identified to protect patient privacy. The dataset is made freely available to facilitate and encourage a wide range of research in computer vision, natural language processing, and clinical data mining.

Using deep-learning techniques for pulmonary-thoracic segmentations and improvement of pneumonia diagnosis in pediatric chest radiographs

PURPOSE

To evaluate the efficacy of a deep-learning model to segment the lung and thorax regions in pediatric chest X-rays (CXRs). Validating the diagnosis of bacterial or viral pneumonia could be improved after lung segmentation.

MATERIALS AND METHODS

A clinical-pediatric CXR set including 1351 patients was proposed to develop a deep-learning model for the pulmonary-thoracic segmentations. Model performance was evaluated by Jaccard's similarity coefficient (JSC) and Dice's coefficient (DC). Two adult CXR sets were used to assess the model's generalizability. According to the pulmonary-thoracic ratio, Pearson's correlation coefficient and the Bland-Altman plot were generated to demonstrate the correlation and agreement between manual and automatic segmentations. The receiver operating characteristic curves and areas under the curve (AUCs) were used to compare the pneumonia classification performance based on the lung-extracted images with that based on the original images.

RESULTS

The model achieved JSCs of 0.910 and 0.950, DCs of 0.948 and 0.974 for lung and thorax segmentations, respectively. Pearson's r = 0.96, P < .0001. In the Bland-Altman plot, the mean difference was 0.0025 with a 95% confidence interval of (-0.0451, 0.0501). For testing with two adult CXR sets, the JSCs were 0.903 and 0.888, respectively, while the DCs were 0.948 and 0.937, respectively. After lung segmentation, the AUC of a classifier to identify bacterial or viral pneumonia increased from 0.815 to 0.879.

CONCLUSION

We built a pediatric CXR dataset and exploited a deep-learning model for accurate pulmonary-thoracic segmentations. Lung segmentation can notably improve the diagnosis of bacterial or viral pneumonia.