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

A bstract 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 level 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. Existing fine-tuning approaches often require extensive retraining or are tailored to specific model architectures, limiting their adaptability and scalability in practical settings. 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 incorporates support for fine-tuning widely uaed segmentation models in the field of spatial omics, including recent published model Cellpose-SAM, while achieving high accuracy with very limited annotated data. 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.