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Register a new userAutomated detection and quantification of COVID-19 airspace disease on chest radiographs: A novel approach achieving radiologist-level performance using a CNN trained on digital reconstructed radiographs (DRRs) from CT-based ground-truth
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Purpose: To leverage volumetric quantification of airspace disease (AD) derived from a superior modality (CT) serving as ground truth, projected onto digitally reconstructed radiographs (DRRs) to: 1) train a convolutional neural network to quantify airspace disease on paired CXRs; and 2) compare the DRR-trained CNN to expert human readers in the CXR evaluation of patients with confirmed COVID-19. Materials and Methods: We retrospectively selected a cohort of 86 COVID-19 patients (with positive RT-PCR), from March-May 2020 at a tertiary hospital in the northeastern USA, who underwent chest CT and CXR within 48 hrs. The ground truth volumetric percentage of COVID-19 related AD (POv) was established by manual AD segmentation on CT. The resulting 3D masks were projected into 2D anterior-posterior digitally reconstructed radiographs (DRR) to compute area-based AD percentage (POa). A convolutional neural network (CNN) was trained with DRR images generated from a larger-scale CT dataset of COVID-19 and non-COVID-19 patients, automatically segmenting lungs, AD and quantifying POa on CXR. CNN POa results were compared to POa quantified on CXR by two expert readers and to the POv ground-truth, by computing correlations and mean absolute errors. Results: Bootstrap mean absolute error (MAE) and correlations between POa and POv were 11.98% [11.05%-12.47%] and 0.77 [0.70-0.82] for average of expert readers, and 9.56%-9.78% [8.83%-10.22%] and 0.78-0.81 [0.73-0.85] for the CNN, respectively. Conclusion: Our CNN trained with DRR using CT-derived airspace quantification achieved expert radiologist level of accuracy in the quantification of airspace disease on CXR, in patients with positive RT-PCR for COVID-19.
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Automated infection measurement and COVID-19 diagnosis based on Chest X-ray (CXR) imaging is important for faster examination. We propose a novel approach, called DRR4Covid, to learn automated COVID-19 diagnosis and infection segmentation on CXRs from digitally reconstructed radiographs (DRRs). DRR4Covid comprises of an infection-aware DRR generator, a classification and/or segmentation network, and a domain adaptation module. The infection-aware DRR generator is able to produce DRRs with adjustable strength of radiological signs of COVID-19 infection, and generate pixel-level infection annotations that match the DRRs precisely. The domain adaptation module is introduced to reduce the domain discrepancy between DRRs and CXRs by training networks on unlabeled real CXRs and labeled DRRs together.We provide a simple but effective implementation of DRR4Covid by using a domain adaptation module based on Maximum Mean Discrepancy (MMD), and a FCN-based network with a classification header and a segmentation header. Extensive experiment results have confirmed the efficacy of our method; specifically, quantifying the performance by accuracy, AUC and F1-score, our network without using any annotations from CXRs has achieved a classification score of (0.954, 0.989, 0.953) and a segmentation score of (0.957, 0.981, 0.956) on a test set with 794 normal cases and 794 positive cases. Besides, we estimate the sensitive of X-ray images in detecting COVID-19 infection by adjusting the strength of radiological signs of COVID-19 infection in synthetic DRRs. The estimated detection limit of the proportion of infected voxels in the lungs is 19.43%, and the estimated lower bound of the contribution rate of infected voxels is 20.0% for significant radiological signs of COVID-19 infection. Our codes will be made publicly available at https://github.com/PengyiZhang/DRR4Covid.
Purpose: To present a method that automatically segments and quantifies abnormal CT patterns commonly present in coronavirus disease 2019 (COVID-19), namely ground glass opacities and consolidations. Materials and Methods: In this retrospective study, the proposed method takes as input a non-contrasted chest CT and segments the lesions, lungs, and lobes in three dimensions, based on a dataset of 9749 chest CT volumes. The method outputs two combined measures of the severity of lung and lobe involvement, quantifying both the extent of COVID-19 abnormalities and presence of high opacities, based on deep learning and deep reinforcement learning. The first measure of (PO, PHO) is global, while the second of (LSS, LHOS) is lobewise. Evaluation of the algorithm is reported on CTs of 200 participants (100 COVID-19 confirmed patients and 100 healthy controls) from institutions from Canada, Europe and the United States collected between 2002-Present (April, 2020). Ground truth is established by manual annotations of lesions, lungs, and lobes. Correlation and regression analyses were performed to compare the prediction to the ground truth. Results: Pearson correlation coefficient between method prediction and ground truth for COVID-19 cases was calculated as 0.92 for PO (P < .001), 0.97 for PHO(P < .001), 0.91 for LSS (P < .001), 0.90 for LHOS (P < .001). 98 of 100 healthy controls had a predicted PO of less than 1%, 2 had between 1-2%. Automated processing time to compute the severity scores was 10 seconds per case compared to 30 minutes required for manual annotations. Conclusion: A new method segments regions of CT abnormalities associated with COVID-19 and computes (PO, PHO), as well as (LSS, LHOS) severity scores.
Dual-energy (DE) chest radiography provides the capability of selectively imaging two clinically relevant materials, namely soft tissues, and osseous structures, to better characterize a wide variety of thoracic pathology and potentially improve diagnosis in posteroanterior (PA) chest radiographs. However, DE imaging requires specialized hardware and a higher radiation dose than conventional radiography, and motion artifacts sometimes happen due to involuntary patient motion. In this work, we learn the mapping between conventional radiographs and bone suppressed radiographs. Specifically, we propose to utilize two variations of generative adversarial networks (GANs) for image-to-image translation between conventional and bone suppressed radiographs obtained by DE imaging technique. We compare the effectiveness of training with patient-wisely paired and unpaired radiographs. Experiments show both training strategies yield radio-realistic radiographs with suppressed bony structures and few motion artifacts on a hold-out test set. While training with paired images yields slightly better performance than that of unpaired images when measuring with two objective image quality metrics, namely Structural Similarity Index (SSIM) and Peak Signal-to-Noise Ratio (PSNR), training with unpaired images demonstrates better generalization ability on unseen anteroposterior (AP) radiographs than paired training.
The novel corona-virus disease (COVID-19) pandemic has caused a major outbreak in more than 200 countries around the world, leading to a severe impact on the health and life of many people globally. As of Aug 25th of 2020, more than 20 million people are infected, and more than 800,000 death are reported. Computed Tomography (CT) images can be used as a as an alternative to the time-consuming reverse transcription polymerase chain reaction (RT-PCR) test, to detect COVID-19. In this work we developed a deep learning framework to predict COVID-19 from CT images. We propose to use an attentional convolution network, which can focus on the infected areas of chest, enabling it to perform a more accurate prediction. We trained our model on a dataset of more than 2000 CT images, and report its performance in terms of various popular metrics, such as sensitivity, specificity, area under the curve, and also precision-recall curve, and achieve very promising results. We also provide a visualization of the attention maps of the model for several test images, and show that our model is attending to the infected regions as intended. In addition to developing a machine learning modeling framework, we also provide the manual annotation of the potentionally infected regions of chest, with the help of a board-certified radiologist, and make that publicly available for other researchers.
The novel COVID-19 is a global pandemic disease overgrowing worldwide. Computer-aided screening tools with greater sensitivity is imperative for disease diagnosis and prognosis as early as possible. It also can be a helpful tool in triage for testing and clinical supervision of COVID-19 patients. However, designing such an automated tool from non-invasive radiographic images is challenging as many manually annotated datasets are not publicly available yet, which is the essential core requirement of supervised learning schemes. This article proposes a 3D Convolutional Neural Network (CNN)-based classification approach considering both the inter- and intra-slice spatial voxel information. The proposed system is trained in an end-to-end manner on the 3D patches from the whole volumetric CT images to enlarge the number of training samples, performing the ablation studies on patch size determination. We integrate progressive resizing, segmentation, augmentations, and class-rebalancing to our 3D network. The segmentation is a critical prerequisite step for COVID-19 diagnosis enabling the classifier to learn prominent lung features while excluding the outer lung regions of the CT scans. We evaluate all the extensive experiments on a publicly available dataset, named MosMed, having binary- and multi-class chest CT image partitions. Our experimental results are very encouraging, yielding areas under the ROC curve of 0.914 and 0.893 for the binary- and multi-class tasks, respectively, applying 5-fold cross-validations. Our methods promising results delegate it as a favorable aiding tool for clinical practitioners and radiologists to assess COVID-19.
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