UniStain: A unified and organ-aware virtual H&E staining framework for label-free autofluorescence images

While hematoxylin and eosin (H&E) staining remains the gold standard for pathological diagnosis, its chemical-dependent workflow presents significant limitations, such as time-consuming protocols, hazardous reagent disposal and batch-to-batch variability in stain quality. We present UniStain, a breakthrough virtual staining framework that leverages label-free autofluorescence (AF) imaging and prompt-based deep learning to overcome these challenges. Unlike existing single-organ approaches that require multiple specialized models, our architecture enables versatile multi-tissue staining through a single model, significantly reducing computational overhead. The proposed crosspatch self-attention guidance (CPSG) mechanism addresses critical whole-slide image challenges by maintaining style consistency across adjacent patches and eliminating stitching artifacts. To support comprehensive evaluation, we curate and release the first multi-organ AF/H&E dataset with human tissue samples. Additionally, we introduce downstream clinical validation tasks including image retrieval and cancer subtyping analysis, thereby establishing a robust evaluation framework for virtual staining models. Quantitative assessments (image quality metrics, visual Turing tests) and downstream analyses demonstrate UniStain's superior performance compared to existing image translation methods, achieving state-of-the-art results while eliminating chemical staining requirements. The dataset and code of UniStain can be found at https://github.com/TABLAB-HKUST/UniStain.