Fully automated body composition analysis in routine CT imaging using 3D semantic segmentation convolutional neural networks

Objectives Body tissue composition is a long-known biomarker with high diagnostic and prognostic value not only in cardiovascular, oncological, and orthopedic diseases but also in rehabilitation medicine or drug dosage. In this study, the aim was to develop a fully automated, reproducible, and quantitative 3D volumetry of body tissue composition from standard CT examinations of the abdomen in order to be able to offer such valuable biomarkers as part of routine clinical imaging. Methods Therefore, an in-house dataset of 40 CTs for training and 10 CTs for testing were fully annotated on every fifth axial slice with five different semantic body regions: abdominal cavity, bones, muscle, subcutaneous tissue, and thoracic cavity. Multi-resolution U-Net 3D neural networks were employed for segmenting these body regions, followed by subclassifying adipose tissue and muscle using known Hounsfield unit limits. Results The Sørensen Dice scores averaged over all semantic regions was 0.9553 and the intra-class correlation coefficients for subclassified tissues were above 0.99. Conclusions Our results show that fully automated body composition analysis on routine CT imaging can provide stable biomarkers across the whole abdomen and not just on L3 slices, which is historically the reference location for analyzing body composition in the clinical routine. Key Points • Our study enables fully automated body composition analysis on routine abdomen CT scans. • The best segmentation models for semantic body region segmentation achieved an averaged Sørensen Dice score of 0.9553. • Subclassified tissue volumes achieved intra-class correlation coefficients over 0.99.