Efficient end-to-end learning for cell segmentation with machine generated weak annotations

Abstract Automated cell segmentation from optical microscopy images is usually the first step in the pipeline of single-cell analysis. Recently, deep-learning based algorithms have shown superior performances for the cell segmentation tasks. However, a disadvantage of deep-learning is the requirement for a large amount of fully annotated training data, which is costly to generate. Weakly-supervised and self-supervised learning is an active research area, but often the model accuracy is inversely correlated with the amount of annotation information provided. Here we focus on a specific subtype of weak annotations, which can be generated programmably from experimental data, thus allowing for more annotation information content without sacrificing the annotation speed. We designed a new model architecture for end-to-end training using such incomplete annotations. We have benchmarked our method on a variety of publicly available datasets, covering both fluorescence and bright-field imaging modality. We additionally tested our method on a microscopy dataset generated by us, using machine-generated annotations. The results demonstrated that our models trained under weak supervision can achieve segmentation accuracy competitive to, and in some cases, surpassing, state-of-the-art models trained under full supervision. Therefore, our method can be a practical alternative to the established full-supervision methods.