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<p>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 show that 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.</p>

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SAMJ: fast image annotation on ImageJ/Fiji via segment anything model

  • 期刊论文

  • 出版模式：

    开放获取

  • 发表日期：

    2026年6月18日

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  • Carlos García-López-de-Haro,
  • Caterina Fuster-Barceló,
  • Curtis T. Rueden,
  • Jónathan Heras,
  • Vladimír Ulman,
  • Daniel Franco-Barranco,
  • Adrián Inés,
  • Kevin W. Eliceiri,
  • Jean-Christophe Olivo-Marin,
  • Jean-Yves Tinevez,
  • Daniel Sage,
  • Arrate Muñoz-Barrutia

摘要

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 show that 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.