{"entity": "publication", "iuid": "1ec94466ddc34664ada4dac55c1ca098", "timestamp": "2026-10-01T11:58:02.546Z", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/1ec94466ddc34664ada4dac55c1ca098.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/1ec94466ddc34664ada4dac55c1ca098"}}, "title": "Flexible and robust cell-type annotation for highly multiplexed tissue images.", "authors": [{"family": "Sun", "given": "Huangqingbo", "initials": "H"}, {"family": "Yu", "given": "Shiqiu", "initials": "S"}, {"family": "Casals", "given": "Anna Martinez", "initials": "AM"}, {"family": "B\u00e4ckstr\u00f6m", "given": "Anna", "initials": "A"}, {"family": "Lu", "given": "Yuxin", "initials": "Y"}, {"family": "Lindskog", "given": "Cecilia", "initials": "C"}, {"family": "Ruffalo", "given": "Matthew", "initials": "M"}, {"family": "Lundberg", "given": "Emma", "initials": "E"}, {"family": "Murphy", "given": "Robert F", "initials": "RF"}], "type": "journal article", "published": "2025-09-17", "journal": {"title": "Cell Syst", "issn": "2405-4720", "volume": "16", "issue": "9", "pages": "101374", "issn-l": null}, "abstract": "Identifying cell types in highly multiplexed images is essential for understanding tissue spatial organization. Current cell-type annotation methods often rely on extensive reference images and manual adjustments. In this work, we present a tool, the Robust Image-Based Cell Annotator (RIBCA), that enables accurate, automated, unbiased, and fine-grained cell-type annotation for images with a wide range of antibody panels without requiring additional model training or human intervention. Our tool has successfully annotated over 3 million cells, revealing the spatial organization of various cell types across more than 40 different human tissues. It is open source and features a modular design, allowing for easy extension to additional cell types.", "doi": "10.1016/j.cels.2025.101374", "pmid": "40925369", "labels": [], "xrefs": [{"db": "mid", "key": "NIHMS2120417"}, {"db": "pmc", "key": "PMC12728825"}, {"db": "pii", "key": "S2405-4712(25)00207-8"}], "notes": [], "created": "2026-10-01T08:28:36.965Z", "modified": "2026-10-01T08:28:36.992Z"}