A visual–omics foundation model to bridge histopathology image with transcriptomics

Artificial intelligence has revolutionized computational biology. Recent developments in omics technologies, including single-cell RNA sequencing (scRNA-seq) and spatial transcriptomics (ST), provide detailed genomic data alongside tissue histology. However, current computational models focus on either omics or image analysis, lacking their integration. To address this, we developed OmiCLIP, a visual-omics foundation model linking hematoxylin and eosin (H&E) images and transcriptomics using tissue patches from Visium data. We transformed transcriptomic data into “sentences” by concatenating top-expressed gene symbols from each patch. We curated a dataset of 2.2 million paired tissue images and transcriptomic data across 32 organs to train OmiCLIP integrating histology and transcriptomics. Building on OmiCLIP, our Loki platform offers five key functions: tissue alignment, annotation via bulk RNA-seq or marker genes, cell type decomposition, image–transcriptomics retrieval, and ST gene expression prediction from H&E images. Compared with 22 state-of-the-art models on 5 simulations, 19 public, and 4 in-house experimental datasets, Loki demonstrated consistent accuracy and robustness.