Scribble2Label: Scribble-Supervised Cell Segmentation via Self-Generating Pseudo-Labels with Consistency

Abstract

Segmentation is a fundamental process in microscopic cell image analysis. With the advent of recent advances in deep learning, more accurate and high-throughput cell segmentation has become feasible. However, most existing deep learning-based cell segmentation algorithms require fully annotated ground-truth cell labels, which are time-consuming and labor-intensive to generate. In this paper, we introduce Scribble2Label, a novel weakly-supervised cell segmentation framework that exploits only a handful of scribble annotations without full segmentation labels. The core idea is to combine pseudo-labeling and label filtering to generate reliable labels from weak supervision. For this, we leverage the consistency of predictions by iteratively averaging the predictions to improve pseudo labels. We demonstrate the performance of Scribble2Label by comparing it to several state-of-the-art cell segmentation methods with various cell image modalities, including bright-field, fluorescence, and electron microscopy. We also show that our method performs robustly across different levels of scribble details, which confirms that only a few scribble annotations are required in real-use cases.