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

## TL;DR

CSRefiner is a lightweight framework that improves cell segmentation models using small datasets, enhancing accuracy for spatial transcriptomics.

## Contribution

CSRefiner introduces a versatile fine-tuning method that works with multiple models and requires minimal annotated data.

## Key findings

- CSRefiner achieves high accuracy with limited annotated data for cell segmentation.
- The framework is compatible with various mainstream segmentation models in spatial omics.
- It performs well across different staining types in whole-tissue analysis.

## Abstract

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 used segmentation models in the field of spatial omics, 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.