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<p>Organoids replicate tissue architecture and function and offer a unique opportunity to explore the impact of external perturbations in vitro. However, conducting large-scale screening procedures to investigate the effects of various stresses on cellular morphology and topology in these systems poses important challenges, including limitations in high-resolution three-dimensional (3D) imaging and accessible 3D analysis platforms. In this study, we introduce an AI-based multilevel segmentation and cellular topology pipeline for screening morphology and topology modifications in 3D cell culture at both the nuclear and cytoplasmic levels, as well as at the whole-organoid scale. We demonstrate the versatility of our approach through proof-of-concept experiments, encompassing well-characterized conditions and poorly explored mechanical stressors such as microgravity. By offering a user-friendly interface named 3DCellScope and a comprehensive set of tools for discovery-like assays in screening 3D organoid models, our pipeline demonstrates wide-ranging potential for applications in biomedical research.</p>

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Digitalized organoids: integrated pipeline for high-speed 3D analysis of organoid structures using multilevel segmentation and cellular topology

  • 期刊论文

  • 出版模式：

    开放获取

  • 发表日期：

    2025年5月14日

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  • Hui Ting Ong,
  • Esra Karatas,
  • Titouan Poquillon,
  • Gianluca Grenci,
  • Alessandro Furlan,
  • Florian Dilasser,
  • Saburnisha Binte Mohamad Raffi,
  • Damien Blanc,
  • Elise Drimaracci,
  • Dimitri Mikec,
  • Gaetan Galisot,
  • Blake A. Johnson,
  • Albert Zou Liu,
  • Cora Thiel,
  • Oliver Ullrich,
  • Audrey Vincent,
  • Victor Racine,
  • Anne Beghin

摘要

Organoids replicate tissue architecture and function and offer a unique opportunity to explore the impact of external perturbations in vitro. However, conducting large-scale screening procedures to investigate the effects of various stresses on cellular morphology and topology in these systems poses important challenges, including limitations in high-resolution three-dimensional (3D) imaging and accessible 3D analysis platforms. In this study, we introduce an AI-based multilevel segmentation and cellular topology pipeline for screening morphology and topology modifications in 3D cell culture at both the nuclear and cytoplasmic levels, as well as at the whole-organoid scale. We demonstrate the versatility of our approach through proof-of-concept experiments, encompassing well-characterized conditions and poorly explored mechanical stressors such as microgravity. By offering a user-friendly interface named 3DCellScope and a comprehensive set of tools for discovery-like assays in screening 3D organoid models, our pipeline demonstrates wide-ranging potential for applications in biomedical research.