Edge-Based Self-supervision for Semi-supervised Few-Shot Microscopy Image Cell Segmentation

Youssef Dawoud, Katharina Ernst, Gustavo Carneiro, Vasileios Belagiannis

Abstract: Deep neural networks currently deliver promising results for microscopy image cell segmentation, but they require large-scale labelled databases, which is a costly and time-consuming process. In this work, we relax the labelling requirement by combining self-supervised with semi-supervised learning. We propose the prediction of edge-based maps for self-supervising the training of the unlabelled images, which is combined with the supervised training of a small number of labelled images for learning the segmentation task. In our experiments, we evaluate on a few-shot microscopy image cell segmentation benchmark and show that only a small number of annotated images, e.g. 10% of the original training set, is enough for our approach to reach similar performance as with the fully annotated databases on 1- to 10-shots. Our code and trained models is made publicly available https://github.com/Yussef93/EdgeSSFewShotMicroscopy .