Flexible and robust cell-type annotation for highly multiplexed tissue imagesShow others and affiliations
2025 (English)In: Cell Systems, ISSN 2405-4712, Vol. 16, no 9, article id 101374Article in journal (Refereed) Published
Abstract [en]
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.
Place, publisher, year, edition, pages
Elsevier BV , 2025. Vol. 16, no 9, article id 101374
Keywords [en]
bioimage analysis, cell-type annotation, highly multiplexed imaging, machine learning, marker imputation, spatial proteomics, vision transformer
National Category
Medical Imaging
Identifiers
URN: urn:nbn:se:kth:diva-370605DOI: 10.1016/j.cels.2025.101374ISI: 001577687700003PubMedID: 40925369Scopus ID: 2-s2.0-105015853735OAI: oai:DiVA.org:kth-370605DiVA, id: diva2:2001986
Note
QC 20250929
2025-09-292025-09-292025-12-08Bibliographically approved