Automatic semantic segmentation of kidney cysts in MR images of patients affected by autosomal-dominant polycystic kidney disease

Purpose For patients affected by autosomal-dominant polycystic kidney disease (ADPKD), successful differentiation of cysts is useful for automatic classification of patient phenotypes, clinical decision-making, and disease progression. The objective was to develop and evaluate a fully automated semantic segmentation method to differentiate and analyze renal cysts in patients with ADPKD. Methods An automated deep learning approach using a convolutional neural network was trained, validated, and tested on a set of 60 MR T2-weighted images. A three-fold cross-validation approach was used to train three models on distinct training and validation sets (n = 40). An ensemble model was then built and tested on the hold out cases (n = 20), with each of the cases compared to manual segmentations performed by two readers. Segmentation agreement between readers and the automated method was assessed. Results The automated approach was found to perform at the level of interobserver variability. The automated approach had a Dice coefficient (mean +/- standard deviation) of 0.86 +/- 0.10 vs Reader-1 and 0.84 +/- 0.11 vs. Reader-2. Interobserver Dice was 0.86 +/- 0.08. In terms of total cyst volume (TCV), the automated approach had a percent difference of 3.9 +/- 19.1% vs Reader-1 and 8.0 +/- 24.1% vs Reader-2, whereas interobserver variability was - 2.0 +/- 16.4%. Conclusion This study developed and validated a fully automated approach for performing semantic segmentation of kidney cysts in MR images of patients affected by ADPKD. This approach will be useful for exploring additional imaging biomarkers of ADPKD and automatically classifying phenotypes.