CSRefiner: A lightweight framework for fine-tuning cell segmentation models with small datasets

Recent advances in spatial omics technologies have enabled transcriptome profiling at subcellular resolution. By performing cell segmentation on nuclear or membrane staining images, researchers can acquire single-cell spatial gene expression data, which in turn enables subsequent biological interpretation. Although deep learning-based segmentation models achieve high overall accuracy, their performance remains suboptimal for whole-tissue analysis, particularly in ensuring consistent segmentation accuracy across diverse cell populations. Moreover, manual annotation of complete or multiple tissue sections imposes prohibitive time and cost constraints that significantly impede research progress. To address these challenges, we present CSRefiner, a lightweight and efficient fine-tuning framework for precise whole-tissue single-cell spatial expression analysis. Our approach adapts pre-trained segmentation models using only a minimal set of annotated image patches. This study demonstrates CSRefiner’s superior performance across various staining types and its compatibility with multiple mainstream models. Combining operational simplicity with robust accuracy, our framework offers a practical solution for real-world spatial transcriptomics applications.