Automatic deep learning system for COVID-19 infection quantification in chest CT

The paper proposes an automatic deep learning system for COVID-19 infection areas segmentation in chest CT scans. CT imaging proved its ability to detect the COVID-19 disease even for asymptotic patients, which make it a trustworthy alternative for PCR. Coronavirus disease spread globally and PCR screening is the adopted diagnostic testing method for COVID-19 detection. However, PCR is criticized due its low sensitivity ratios, also, it is time-consuming and manual complicated process. The proposed framework includes different steps; it starts to prepare the region of interest by segmenting the lung organ, which then undergoes edge enhancing diffusion filtering (EED) to improve the infection areas contrast and intensity homogeneity. The proposed FCN is implemented using U-net architecture with modified residual block to include concatenation skip connection. The block improves the learning of gradient values by forwarding the infection area features through the network. The proposed system is evaluated using different measures and achieved dice overlapping score of 0.961 and 0.780 for lung and infection areas segmentation, respectively. The proposed system is trained and tested using many 2D CT slices extracted from diverse datasets from different sources, which demonstrate the system generalization and effectiveness. The use of more datasets from different sources helps to enhance the system accuracy and generalization, which can be accomplished based on the data availability in in the future.