Robust chest CT image segmentation of COVID-19 lung infection based on limited data

Dominik Müller; Iñaki Soto-Rey; Frank Kramer

doi:10.1016/j.imu.2021.100681

Robust chest CT image segmentation of COVID-19 lung infection based on limited data

Inform Med Unlocked. 2021:25:100681. doi: 10.1016/j.imu.2021.100681. Epub 2021 Jul 27.

Authors

Dominik Müller¹, Iñaki Soto-Rey¹, Frank Kramer¹

Affiliation

¹ IT-Infrastructure for Translational Medical Research, Faculty of Applied Computer Science, Faculty of Medicine, University of Augsburg, Germany.

Abstract

Background: The coronavirus disease 2019 (COVID-19) affects billions of lives around the world and has a significant impact on public healthcare. For quantitative assessment and disease monitoring medical imaging like computed tomography offers great potential as alternative to RT-PCR methods. For this reason, automated image segmentation is highly desired as clinical decision support. However, publicly available COVID-19 imaging data is limited which leads to overfitting of traditional approaches.

Methods: To address this problem, we propose an innovative automated segmentation pipeline for COVID-19 infected regions, which is able to handle small datasets by utilization as variant databases. Our method focuses on on-the-fly generation of unique and random image patches for training by performing several preprocessing methods and exploiting extensive data augmentation. For further reduction of the overfitting risk, we implemented a standard 3D U-Net architecture instead of new or computational complex neural network architectures.

Results: Through a k-fold cross-validation on 20 CT scans as training and validation of COVID-19, we were able to develop a highly accurate as well as robust segmentation model for lungs and COVID-19 infected regions without overfitting on limited data. We performed an in-detail analysis and discussion on the robustness of our pipeline through a sensitivity analysis based on the cross-validation and impact on model generalizability of applied preprocessing techniques. Our method achieved Dice similarity coefficients for COVID-19 infection between predicted and annotated segmentation from radiologists of 0.804 on validation and 0.661 on a separate testing set consisting of 100 patients.

Conclusions: We demonstrated that the proposed method outperforms related approaches, advances the state-of-the-art for COVID-19 segmentation and improves robust medical image analysis based on limited data.

Keywords: Artificial intelligence; COVID-19; Computed tomography; Deep learning; Limited data; Segmentation.