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Framework for COVID-19 segmentation and classification based on deep learning of computed tomography lung images

ABSTRACT: Corona Virus Disease 2019 (COVID-19) has affected millions of people worldwide and caused more than 3.9 million deaths [1]. Increased attempts have been made to develop deep learning methods to diagnosis COVID-19 based on computed tomography (CT) lung images. It is a challenge to reproduce and obtain the CT lung data because it is not publicly available. This paper introduces a new generalized framework to segment and classify CT images and determine whether a patient is tested positive or negative for COVID-19 based on lung CT images. In this work, many different strategies are explored for the classification task. ResNet50 and VGG16 models are applied to classify CT lung images into COVID-19 positive or negative. Also, VGG16 and ReNet50 combined with U-Net, which is one of the most used architectures in deep learning for image segmentation, is employed to segment CT lung images before the classifying process to increase system performance. Moreover, the image size dependent normalization technique (ISDNT) and Wiener filter are utilized as the preprocessing techniques to enhance images and noise suppression. Additionally, transfer learning and data augmentation techniques are performed to solve the problem of COVID-19 CT lung images deficiency, therefore the over-fitting of deep models can be avoided. The proposed frameworks which compromises of, end-to-end, VGG16, ResNet50, and U-Net with VGG16 or ResNet50 are applied on the dataset which is sourced from COVID-19 lung CT images in Kaggle. The classification results show that using the preprocessed CT lung images as the input for U-Net hybrid with ResNet50 achieve the best performance. The proposed classification model achieves 98.98% accuracy(ACC), 98.87% area under the ROC curve (AUC), 98.89% sensitivity (Se), 97.99% precision (Pr), 97.88% F1- score, and 1.8974-seconds computational time.

SUBMITTER: Salama W

PROVIDER: S-EPMC9242681 | biostudies-literature |

REPOSITORIES: biostudies-literature

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Project description:PurposeThe novel coronavirus COVID-19, which spread globally in late December 2019, is a global health crisis. Chest computed tomography (CT) has played a pivotal role in providing useful information for clinicians to detect COVID-19. However, segmenting COVID-19-infected regions from chest CT results is challenging. Therefore, it is desirable to develop an efficient tool for automated segmentation of COVID-19 lesions using chest CT. Hence, we aimed to propose 2D deep-learning algorithms to automatically segment COVID-19-infected regions from chest CT slices and evaluate their performance.Material and methodsHerein, 3 known deep learning networks: U-Net, U-Net++, and Res-Unet, were trained from scratch for automated segmenting of COVID-19 lesions using chest CT images. The dataset consists of 20 labelled COVID-19 chest CT volumes. A total of 2112 images were used. The dataset was split into 80% for training and validation and 20% for testing the proposed models. Segmentation performance was assessed using Dice similarity coefficient, average symmetric surface distance (ASSD), mean absolute error (MAE), sensitivity, specificity, and precision.ResultsAll proposed models achieved good performance for COVID-19 lesion segmentation. Compared with Res-Unet, the U-Net and U-Net++ models provided better results, with a mean Dice value of 85.0%. Compared with all models, U-Net gained the highest segmentation performance, with 86.0% sensitivity and 2.22 mm ASSD. The U-Net model obtained 1%, 2%, and 0.66 mm improvement over the Res-Unet model in the Dice, sensitivity, and ASSD, respectively. Compared with Res-Unet, U-Net++ achieved 1%, 2%, 0.1 mm, and 0.23 mm improvement in the Dice, sensitivity, ASSD, and MAE, respectively.ConclusionsOur data indicated that the proposed models achieve an average Dice value greater than 84.0%. Two-dimensional deep learning models were able to accurately segment COVID-19 lesions from chest CT images, assisting the radiologists in faster screening and quantification of the lesion regions for further treatment. Nevertheless, further studies will be required to evaluate the clinical performance and robustness of the proposed models for COVID-19 semantic segmentation.

Project description:BackgroundPulmonary segments are valuable because they can provide more precise localization and intricate details of lung cancer than lung lobes. With advances in precision therapy, there is an increasing demand for the identification and visualization of pulmonary segments in computed tomography (CT) images to aid in the precise treatment of lung cancer. This study aimed to integrate multiple deep-learning models to accurately segment pulmonary segments in CT images using a bronchial tree (BT)-based approach.MethodsThe proposed segmentation method for pulmonary segments using the BT-based approach comprised the following five essential steps: (I) segmentation of the lung using a U-Net (R231) (public access) model; (II) segmentation of the lobes using a V-Net (self-developed) model; (III) segmentation of the airway using a combination of a differential geometric approach method and a BronchiNet (public access) model; (IV) labeling of the BT branches based on anatomical position; and (V) segmentation of the pulmonary segments based on the distance of each voxel to the labeled BT branches. This five-step process was applied to 14 high-resolution breath-hold CT images and compared against manual segmentations for evaluation.ResultsFor the lung segmentation, the lung mask had a mean dice similarity coefficient (DSC) of 0.98±0.03. For the lobe segmentation, the V-Net model had a mean DSC of 0.94±0.06. For the airway segmentation, the average total length of the segmented airway trees per image scan was 1,902.8±502.1 mm, and the average number of the maximum airway tree generations was 8.5±1.3. For the segmentation of the pulmonary segments, the proposed method had a DSC of 0.73±0.11 and a mean surface distance of 6.1±2.9 mm.ConclusionsThis study demonstrated the feasibility of combining multiple deep-learning models for the auxiliary segmentation of pulmonary segments on CT images using a BT-based approach. The results highlighted the potential of the BT-based method for the semi-automatic segmentation of the pulmonary segment.

Project description:ObjectiveWe aimed to develop a deep neural network for segmenting lung parenchyma with extensive pathological conditions on non-contrast chest computed tomography (CT) images.Materials and methodsThin-section non-contrast chest CT images from 203 patients (115 males, 88 females; age range, 31-89 years) between January 2017 and May 2017 were included in the study, of which 150 cases had extensive lung parenchymal disease involving more than 40% of the parenchymal area. Parenchymal diseases included interstitial lung disease (ILD), emphysema, nontuberculous mycobacterial lung disease, tuberculous destroyed lung, pneumonia, lung cancer, and other diseases. Five experienced radiologists manually drew the margin of the lungs, slice by slice, on CT images. The dataset used to develop the network consisted of 157 cases for training, 20 cases for development, and 26 cases for internal validation. Two-dimensional (2D) U-Net and three-dimensional (3D) U-Net models were used for the task. The network was trained to segment the lung parenchyma as a whole and segment the right and left lung separately. The University Hospitals of Geneva ILD dataset, which contained high-resolution CT images of ILD, was used for external validation.ResultsThe Dice similarity coefficients for internal validation were 99.6 ± 0.3% (2D U-Net whole lung model), 99.5 ± 0.3% (2D U-Net separate lung model), 99.4 ± 0.5% (3D U-Net whole lung model), and 99.4 ± 0.5% (3D U-Net separate lung model). The Dice similarity coefficients for the external validation dataset were 98.4 ± 1.0% (2D U-Net whole lung model) and 98.4 ± 1.0% (2D U-Net separate lung model). In 31 cases, where the extent of ILD was larger than 75% of the lung parenchymal area, the Dice similarity coefficients were 97.9 ± 1.3% (2D U-Net whole lung model) and 98.0 ± 1.2% (2D U-Net separate lung model).ConclusionThe deep neural network achieved excellent performance in automatically delineating the boundaries of lung parenchyma with extensive pathological conditions on non-contrast chest CT images.

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Framework for COVID-19 segmentation and classification based on deep learning of computed tomography lung images

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