Automated segmentation of five different body tissues on computed tomography using deep learning

Abstract Purpose To develop and validate a computer tool for automatic and simultaneous segmentation of five body tissues depicted on computed tomography (CT) scans: visceral adipose tissue (VAT), subcutaneous adipose tissue (SAT), intermuscular adipose tissue (IMAT), skeletal muscle (SM), and bone. Methods A cohort of 100 CT scans acquired on different subjects were collected from The Cancer Imaging Archive—50 whole‐body positron emission tomography‐CTs, 25 chest, and 25 abdominal. Five different body tissues (i.e., VAT, SAT, IMAT, SM, and bone) were manually annotated. A training‐while‐annotating strategy was used to improve the annotation efficiency. The 10‐fold cross‐validation method was used to develop and validate the performance of several convolutional neural networks (CNNs), including UNet, Recurrent Residual UNet (R2Unet), and UNet++. A grid‐based three‐dimensional patch sampling operation was used to train the CNN models. The CNN models were also trained and tested separately for each body tissue to see if they could achieve a better performance than segmenting them jointly. The paired sample t ‐test was used to statistically assess the performance differences among the involved CNN models Results When segmenting the five body tissues simultaneously, the Dice coefficients ranged from 0.826 to 0.840 for VAT, from 0.901 to 0.908 for SAT, from 0.574 to 0.611 for IMAT, from 0.874 to 0.889 for SM, and from 0.870 to 0.884 for bone, which were significantly higher than the Dice coefficients when segmenting the body tissues separately ( p < 0.05), namely, from 0.744 to 0.819 for VAT, from 0.856 to 0.896 for SAT, from 0.433 to 0.590 for IMAT, from 0.838 to 0.871 for SM, and from 0.803 to 0.870 for bone. Conclusion There were no significant differences among the CNN models in segmenting body tissues, but jointly segmenting body tissues achieved a better performance than segmenting them separately.