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Flexible and robust cell-type annotation for highly multiplexed tissue images
Ray and Stephanie Lane Computational Biology Department, Carnegie Mellon University, Pittsburgh, PA, USA; Department of Bioengineering, Stanford University, Stanford, CA, USA.
Ray and Stephanie Lane Computational Biology Department, Carnegie Mellon University, Pittsburgh, PA, USA.
Department of Bioengineering, Stanford University, Stanford, CA, USA.
KTH, Centres, Science for Life Laboratory, SciLifeLab. KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Protein Science, Cellular and Clinical Proteomics. Department of Bioengineering, Stanford University, Stanford, CA, USA.
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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

Available from: 2025-09-29 Created: 2025-09-29 Last updated: 2025-12-08Bibliographically approved

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Bäckström, AnnaKäller Lundberg, Emma

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