Kidney cortex segmentation in 2D CT with U-Nets ensemble aggregation

Abstract Purpose This work presents our contribution to one of the data challenges organized by the French Radiology Society during the Journees Francophones de Radiologie . This challenge consisted in segmenting the kidney cortex from coronal computed tomography (CT) images, cropped around the cortex. Materials and methods We chose to train an ensemble of fully-convolutional networks and to aggregate their prediction at test time to perform the segmentation. An image database was made available in 3 batches. A first training batch of 250 images with segmentation masks was provided by the challenge organizers one month before the conference. An additional training batch of 247 pairs was shared when the conference began. Participants were ranked using a Dice score. Results The segmentation results of our algorithm match the renal cortex with a good precision. Our strategy yielded a Dice score of 0.867, ranking us first in the data challenge. Conclusion The proposed solution provides robust and accurate automatic segmentations of the renal cortex in CT images although the precision of the provided reference segmentations seemed to set a low upper bound on the numerical performance. However, this process should be applied in 3D to quantify the renal cortex volume, which would require a marked labelling effort to train the networks.