SpatialFinder: a human-in-the-loop vision-language framework for prioritizing high-value regions in spatial transcriptomics

Sequencing an entire spatial transcriptomics slide can cost thousands of dollars per assay, making routine use impractical. Focusing on smaller regions of interest (ROIs) based on adjacent H&E slides offers a practical alternative, but there is (i) no reliable way to identify the most informative areas from standard H&E images alone; and (ii) limited solutions for clinicians to prioritize the microenvironment of their own interests. Here we introduce SpatialFinder, a framework that combines a biomedical vision-language model (VLM) with a human-in-the-loop optimization pipeline to predict gene expression heterogeneity and rank high-value ROIs across routine H&E tissue slides. Evaluated across four Visium HD tissue types, SpatialFinder consistently outperforms VLM-only baselines for both diversity- and tumor-targeted ROI ranking, achieving Spearman’s ρ up to 0.89 and Overlap@10% up to 78.8%, an absolute 24.9 percentage-point gain over the strongest VLM. These results demonstrate the potential of human-AI collaboration to make spatial transcriptomics more cost-effective and clinically actionable.