{"doi":"10.1101/2024.11.10.622859","title":"<i>ROSIE</i> : AI generation of multiplex immunofluorescence staining from histopathology images","abstract":"Abstract Hematoxylin and eosin (H&amp;E) is a common and inexpensive histopathology assay. Though widely used and information-rich, it cannot directly inform about specific molecular markers, which require additional experiments to assess. To address this gap, we present ROSIE, a deep-learning framework that computationally imputes the expression and localization of dozens of proteins from H&amp;E images. Our model is trained on a dataset of over 1000 paired and aligned H&amp;E and multiplex immunofluorescence (mIF) samples from 20 tissues and disease conditions, spanning over 16 million cells. Validation of our in silico mIF staining method on held-out H&amp;E samples demonstrates that the predicted biomarkers are effective in identifying cell phenotypes, particularly distinguishing lymphocytes such as B cells and T cells, which are not readily discernible with H&amp;E staining alone. Additionally, ROSIE facilitates the robust identification of stromal and epithelial microenvironments and immune cell subtypes like tumor-infiltrating lymphocytes (TILs), which are important for understanding tumor-immune interactions and can help inform treatment strategies in cancer research.","journal":"bioRxiv (Cold Spring Harbor Laboratory)","year":2024,"id":484760,"datarank":0.48328314097436675,"base_score":2.1972245773362196,"endowment":2.1972245773362196,"self_citation_contribution":0.32958368660043297,"citation_network_contribution":0.1536994543739338,"self_endowment_contribution":0.32958368660043297,"citer_contribution":0.1536994543739338,"corpus_percentile":null,"corpus_rank":null,"citation_count":8,"citer_count":7,"citers_with_citation_signal":6,"citers_with_endowment":6,"datacite_reuse_total":0,"is_dataset":false,"is_dataset_confidence":0.9597,"is_data_producer":false,"deposit_databanks":null,"is_oa":true,"file_count":0,"downloads":0,"has_version_chain":false,"published_date":"2024-01-01","fair_score":null,"fair_percentile":null,"algorithm_id":"datarank_citation_only_1hop_v6","ranking_scope":"data_only","authors":[{"id":588524,"name":"Matthew Bieniosek","orcid":null,"position":1,"is_corresponding":false},{"id":453683,"name":"Zhenqin Wu","orcid":"0000-0002-0148-7055","position":2,"is_corresponding":false},{"id":984611,"name":"Nitya Thakkar","orcid":"0000-0002-5647-6775","position":3,"is_corresponding":false},{"id":351058,"name":"Gregory W. Charville","orcid":"0000-0002-2774-2704","position":4,"is_corresponding":false},{"id":95236,"name":"Ahmad Makky","orcid":"0000-0002-4205-1303","position":5,"is_corresponding":false},{"id":95250,"name":"Christian M. Schürch","orcid":"0000-0002-1792-1768","position":6,"is_corresponding":false},{"id":90056,"name":"Jeroen R. Huyghe","orcid":"0000-0001-6027-9806","position":7,"is_corresponding":false},{"id":218649,"name":"Ulrike Peters","orcid":"0000-0001-5666-9318","position":8,"is_corresponding":false},{"id":218624,"name":"Christopher I. Li","orcid":"0000-0003-1543-0743","position":9,"is_corresponding":false},{"id":1326935,"name":"Li Li","orcid":"0000-0001-8240-9472","position":10,"is_corresponding":false},{"id":1171069,"name":"Hannah Giba","orcid":null,"position":11,"is_corresponding":false},{"id":1170705,"name":"Vivek Behera","orcid":"0000-0001-6013-5706","position":12,"is_corresponding":false},{"id":326795,"name":"Arjun S. Raman","orcid":"0000-0002-7303-7272","position":13,"is_corresponding":false},{"id":562989,"name":"Alexandro E. Trevino","orcid":"0000-0002-9763-1540","position":14,"is_corresponding":false},{"id":294104,"name":"Aaron T. Mayer","orcid":"0000-0001-6429-0420","position":15,"is_corresponding":false},{"id":63151,"name":"James Zou","orcid":"0000-0001-8880-4764","position":16,"is_corresponding":false},{"id":1013918,"name":"Eric Q. Wu","orcid":"0000-0001-8379-3373","position":0,"is_corresponding":true}],"reference_count":37,"raw_metadata":{"citation_network_status":"fetched"},"created_at":"2026-07-19T02:07:42.971417Z","pmid":"39605711","pmcid":null,"fwci":null,"citation_percentile":null,"influential_citations":0,"oa_status":null,"license":null,"views":0,"total_file_size_bytes":0,"version_count":0,"fair_f":null,"fair_a":null,"fair_i":null,"fair_r":null,"fair_zscore":null,"fair_rationale":null,"fair_model":null,"fair_agent_version":null,"fair_fulltext_source":null,"fair_has_llm":null,"fair_computed_at":null,"clinical_trials":[],"software_tools":[],"db_accessions":[],"linked_datasets":[],"topics":[]}