Weakly supervised segmentation from extreme points

Abstract: Annotation of medical images has been a major bottleneck for the development of accurate and robust machine learning models. Annotation is costly and time-consuming and typically requires expert knowledge, especially in the medical domain. Here, we propose to use minimal user interaction in the form of extreme point clicks in order to train a segmentation model that can, in turn, be used to speed up the annotation of medical images. We use extreme points in each dimension of a 3D medical image to constrain an initial segmentation based on the random walker algorithm. This segmentation is then used as a weak supervisory signal to train a fully convolutional network that can segment the organ of interest based on the provided user clicks. We show that the network's predictions can be refined through several iterations of training and prediction using the same weakly annotated data. Ultimately, our method has the potential to speed up the generation process of new training datasets for the development of new machine learning and deep learning-based models for, but not exclusively, medical image analysis.