EPFL | Biomedical Imaging Group

SAMJ: Fast Image Annotation on ImageJ/Fiji via Segment Anything Model

C. García-López-de-Haro, C. Fuster-Barceló, C.T. Rueden, J. Heras, V. Ulman, D. Franco-Barranco, A. Inés, K.W. Eliceiri, J.-C. Olivo-Marin, J.-Y. Tinevez, D. Sage, A. Muñoz-Barrutia

Nature Communications, vol. 17, paper no. 5402, 9 p., June 18, 2026.

Accurate image annotation is essential for training artificial intelligence (AI) systems in biomedical image analysis, enabling tasks such as cell detection, tissue quantification, and disease characterization. However, creating pixel-level annotations is a time-consuming and labor-intensive process that requires expert input, limiting the development and adoption of AI methods. Recent advances in foundation models, such as the Segment Anything Model (SAM), enable interactive object segmentation from simple user prompts, but their integration into widely used bioimage analysis platforms remains limited and often requires technical expertise. Here we showthat SAMJ, a user-friendly plugin for ImageJ/Fiji, enables fast, interactive, and accurate image annotation on standard computers without requiring programming skills or specialized hardware. SAMJ integrates efficient SAM variants into a familiar graphical interface, allowing users to delineate objects in large scientific images in real time using simple clicks or bounding boxes. This approach significantly reduces annotation effort, accelerates dataset creation, and broadens access to advanced AI-assisted annotation tools for the biomedical research community.

@ARTICLE(http://bigwww.epfl.ch/publications/garcialopezdeharo2601.html,
AUTHOR="{Garc{\'{i}}a-L{\'{o}}pez-de-Haro}, C. and Fuster-Barcel{\'{o}},
	C. and Rueden, C.T. and Heras, J. and Ulman, V. and Franco-Barranco,
	D. and In{\'{e}}s, A. and Eliceiri, K.W. and Olivo-Marin, J.-C. and
	Tinevez, J.-Y. and Sage, D. and Mu{\~{n}}oz-Barrutia, A.",
TITLE="{SAMJ}: Fast Image Annotation on {ImageJ}/{Fiji} via Segment
	Anything Model",
JOURNAL="Nature Communications",
YEAR="2026",
volume="17",
number="5402",
pages="",
month="June 18,",
note="paper no.\ 5402")

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