Self-Supervised Learning for Annotation Efficient Biomedical Image Segmentation

Objective: The scarcity of high-quality annotated data is omnipresent in machine learning. Especially in biomedical segmentation applications, experts need to spend a lot of their time into annotating due to the complexity. Hence, methods to reduce such efforts are desired. Methods: Self-Supervised Learning (SSL) is an emerging field that increases performance when unannotated data is present. However, profound studies regarding segmentation tasks and small datasets are still absent. A comprehensive qualitative and quantitative evaluation is conducted, examining SSL's applicability with a focus on biomedical imaging. We consider various metrics and introduce multiple novel application-specific measures. All metrics and state-of-the-art methods are provided in a directly applicable software package (https://osf.io/gu2t8/). Results: We show that SSL can lead to performance improvements of up to 10%, which is especially notable for methods designed for segmentation tasks. Conclusion: SSL is a sensible approach to data-efficient learning, especially for biomedical applications, where generating annotations requires much effort. Additionally, our extensive evaluation pipeline is vital since there are significant differences between the various approaches. Significance: We provide biomedical practitioners with an overview of innovative data-efficient solutions and a novel toolbox for their own application of new approaches. Our pipeline for analyzing SSL methods is provided as a ready-to-use software package.