COLI-NET: Fully Automated COVID-19 Lung and Infection Pneumonia Lesion Detection and Segmentation from Chest CT Images

Shiri, I.; Arabi, H.; Salimi, Y.; Sanaat, A. H.; Akhavanalaf, A.; Hajianfar, G.; Askari, D.; Moradi, S.; Mansouri, Z.; Pakbin, M.; Sandoughdaran, S.; Abdollahi, H.; Radmard, A. R.; Rezaei-Kalantari, K.; Ghelich Oghli, M.; Zaidi, H.

Background We present a deep learning (DL)-based automated whole lung and COVID-19 pneumonia infectious lesions (COLI-Net) detection and segmentation from chest CT images. Methods We prepared 2358 ( 347259, 2D slices) and 180 (17341, 2D slices) volumetric CT images along with their corresponding manual segmentation of lungs and lesions, respectively, in the framework of a multi-center/multi-scanner study. All images were cropped, resized and the intensity values clipped and normalized. A residual network (ResNet) with non-square Dice loss function built upon TensorFlow was employed. The accuracy of lung and COVID-19 lesions segmentation was evaluated on an external RT-PCR positive COVID-19 dataset (7333, 2D slices) collected at five different centers. To evaluate the segmentation performance, we calculated different quantitative metrics, including radiomic features. Results The mean Dice coefficients were 0.98&0.011 (95% CI, 0.98-0.99) and 0.91&0.038 (95% CI, 0.90-0.91) for lung and lesions segmentation, respectively. The mean relative Hounsfield unit differences were 0.03&0.84% (95% CI, -0.12-0.18) and -0.18&3.4% (95% CI, -0.8 - 0.44) for the lung and lesions, respectively. The relative volume difference for lung and lesions were 0.38&1.2% (95% CI, 0.16-0.59) and 0.81&6.6% (95% CI, -0.39-2), respectively. Most radiomic features had a mean relative error less than 5% with the highest mean relative error achieved for the lung for the Range first-order feature (-6.95%) and least axis length shape feature (8.68%) for lesions. Conclusion We set out to develop an automated deep learning-guided three-dimensional whole lung and infected regions segmentation in COVID-19 patients in order to develop fast, consistent, robust and human error immune framework for lung and pneumonia lesion detection and quantification. Keywords: X-ray CT, COVID-19, pneumonia, deep learning, segmentation.