Deep learning kidney segmentation with very limited training data using a cascaded convolution neural network

Abstract

Background Deep learning segmentation requires large datasets with ground truth. Image annotation is time consuming and leads to shortages of ground truth data for clinical imaging. This study is to investigate the feasibility of kidney segmentation using deep learning convolution neural network (CNN) models trained with MR images from only a few subjects. Methods A total of 60 subjects from two cohorts were included in this study. The first cohort of 20 subjects from publicly available data was used for training and testing. The second cohort of 40 subjects with renal masses from our institution was used for testing only. A few-shot deep learning approach using 3D augmentation was investigated. T1-weighted images in the first cohort were used for training and testing. Cascaded CNN networks were trained using images from one, three, and six subjects, respectively. Images for the remaining subjects were used for testing. Images in the second cohort were utilized for testing only. Dice and Jaccard coefficients were generated to evaluate the performance of CNN models. Statistical analyses for segmentation metrics among different approaches were performed. Results Our approach achieved mean Dice coefficients of 0.85 using a single training subject and 0.91 with six training subjects. Compared to a single Unet, the cascaded network significantly improved the results using a single training subject (Dice, 0.759 vs. 0.835; p<0.001) and three subjects (0.864 vs. 0.893; p = 0.015) in the first cohort, and the results for the second cohort (0.821 vs. 0.873; p = 0.008). Conclusion Our few-shot kidney segmentation approach using 3D augmentation achieved a good performance even using a single Unet. Furthermore, the cascaded network significantly improved the performance of segmentation and was superior to a single Unet in certain cases. Our approach provides a promising solution to segmentation in medical imaging when the number of ground truth masks is limited.