Deep Learning-Based 3D and 2D Approaches for Skeletal Muscle Segmentation on CT Images

Automated segmentation of skeletal muscle from computed tomography (CT) images is essential for large-scale quantitative body composition analysis. However, manual segmentation is time-consuming and impractical for routine or high-throughput use. This study presents a systematic comparison of two-dimensional (2D) and three-dimensional (3D) deep learning architectures for segmenting skeletal muscle at the anatomically standardized level of the third lumbar vertebra (L3) in low-dose computed tomography (LDCT) scans. We implemented and evaluated the DeepLabv3+ (2D) and UNet3+ (3D) architectures on a curated dataset of 534 LDCT scans, applying preprocessing protocols, L3 slice selection, and region of interest extraction. The model performance was evaluated using a comprehensive set of evaluation metrics, including Dice similarity coefficient (DSC) and 95th percentile Hausdorff distance (HD95). DeepLabv3+ achieved the highest segmentation accuracy (DSC = 0.982 ± 0.010, HD95 = 1.04 ± 0.46 mm), while UNet3+ showed competitive performance (DSC = 0.967 ± 0.013, HD95 = 1.27 ± 0.58 mm) with 26 times fewer parameters (1.27 million vs. 33.6 million) and lower inference time. Both models exceeded or matched results reported in the recent CT-based muscle segmentation literature. This work offers practical insights into architecture selection for automated LDCT-based muscle segmentation workflows, with a focus on the L3 vertebral level, which remains the gold standard in muscle quantification protocols.