Abstract
Hematoxylin and Eosin staining (H&E) is widely used in clinical practice, but efficient and versatile image retrieval tools are lacking. We developed the H&E Retrieval Engine (HERE, https://hereapp.ccr.cancer.gov) to analyze patient cases based on image similarities to database records. Using H&E image regions as input, HERE searches 21.2 terabytes of whole-slide images from multiple tumor histopathology cohorts through a 12.1-gigabyte memory index, and returns top images containing regions similar to the query. HERE scans high-resolution images in the database using accurate artificial intelligence encoding and ultra-efficient hierarchical skip indexing. HERE demonstrated performance superior to existing image retrieval tools based on blinded pathologist scoring using benchmark queries that represent key image features of human tumors. By pairing spatial transcriptomics with H&E images, HERE also enables retrieving image features from gene transcriptomics input and identifies molecular pathways associated with tumor histologies.