Semantic segmentation of thigh muscle using 2.5D deep learning network trained with limited datasets

Purpose: We propose a 2.5D deep learning neural network (DLNN) to automatically classify thigh muscle into 11 classes and evaluate its classification accuracy over 2D and 3D DLNN when trained with limited datasets. Enables operator invariant quantitative assessment of the thigh muscle volume change with respect to the disease progression. Materials and methods: Retrospective datasets consist of 48 thigh volume (TV) cropped from CT DICOM images. Cropped volumes were aligned with femur axis and resample into 2mm voxel-spacing. Proposed 2.5D U-Net consists of three 2D U-Net trained with axial, coronal and sagittal muscle slices respectively. A voting algorithm was used to combine the output of U-Nets to create final segmentation. 2.5D U-Net was trained on PC with 38 TV and the remaining 10 TV were used to evaluate segmentation accuracy of 10 classes within Thigh. The segmentation result of both left and right thigh were de-cropped to original CT volume space. Finally, segmentation accuracies were compared between proposed DLNN and 2D,3D U-Net. Results:Average segmentation DSC score accuracy of all classes with 2.5D U-Net as 91.18% and Average Surface Distance (ASD) accuracy as 0.84 ± 0.27mm. We found, mean DSC score for 2D U-Net was 3.3% lower than the that of 2.5D U-Net and mean DSC score of 3D U-Net was 5.7% lower than that of 2.5D U-Net when trained with same datasets. Conclusion: We achieved a faster computationally efficient and automatic segmentation of thigh muscle into 11 classes with reasonable accuracy. Enables quantitative evaluation of muscle atrophy with disease progression.