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Objectives To develop a pipeline for automated body composition analysis and skeletal muscle assessment with integrated quality control for large-scale application in opportunistic imaging. Methods First, a convolutional neural network for extraction of a single slice at the L3/L4 lumbar level was developed on CT scans of 240 patients applying the nnU-Net framework. Second, a 2D competitive dense fully convolutional U-Net for segmentation of visceral and subcutaneous adipose tissue (VAT, SAT), skeletal muscle (SM), and subsequent determination of fatty muscle fraction (FMF) was developed on single CT slices of 1143 patients. For both steps, automated quality control was integrated by a logistic regression model classifying the presence of L3/L4 and a linear regression model predicting the segmentation quality in terms of Dice score. To evaluate the performance of the entire pipeline end-to-end, body composition metrics, and FMF were compared to manual analyses including 364 patients from two centers. Results Excellent results were observed for slice extraction ( z -deviation = 2.46 ± 6.20 mm) and segmentation (Dice score for SM = 0.95 ± 0.04, VAT = 0.98 ± 0.02, SAT = 0.97 ± 0.04) on the dual-center test set excluding cases with artifacts due to metallic implants. No data were excluded for end-to-end performance analyses. With a restrictive setting of the integrated segmentation quality control, 39 of 364 patients were excluded containing 8 cases with metallic implants. This setting ensured a high agreement between manual and fully automated analyses with mean relative area deviations of ΔSM = 3.3 ± 4.1%, ΔVAT = 3.0 ± 4.7%, ΔSAT = 2.7 ± 4.3%, and ΔFMF = 4.3 ± 4.4%. Conclusions This study presents an end-to-end automated deep learning pipeline for large-scale opportunistic assessment of body composition metrics and sarcopenia biomarkers in clinical routine. Key Points • Body composition metrics and skeletal muscle quality can be opportunistically determined from routine abdominal CT scans. • A pipeline consisting of two convolutional neural networks allows an end-to-end automated analysis. • Machine-learning-based quality control ensures high agreement between manual and automatic analysis.

End-to-end automated body composition analyses with integrated quality control for opportunistic assessment of sarcopenia in CT