Digitalized organoids: integrated pipeline for high-speed 3D analysis of organoid structures using multilevel segmentation and cellular topology
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.
Authors
- Titouan Poquillon
- Florian Dilasser
- Hui Ting Ong (ORCID: https://orcid.org/0000-0002-3434-4683)
- Victor Racine (ORCID: https://orcid.org/0000-0002-1486-8973)
- Gaëtan Galisot (ORCID: https://orcid.org/0000-0002-1456-7134)
- Saburnisha Binte Mohamad Raffi
- Anne Béghin (ORCID: https://orcid.org/0000-0002-7231-6245)
- Albert Z. Liu (ORCID: https://orcid.org/0000-0002-9387-0878)
- Blake A. Johnson (ORCID: https://orcid.org/0000-0001-7830-2453)
- Dimitri Mikec (ORCID: https://orcid.org/0009-0000-7880-5640)
- Alessandro Furlan (ORCID: https://orcid.org/0000-0001-6502-8416)
- D Blanc (ORCID: https://orcid.org/0000-0002-3254-7751)
- Gianluca Grenci (ORCID: https://orcid.org/0000-0001-9313-6748)
- Cora S. Thiel (ORCID: https://orcid.org/0000-0002-4120-9420)
- Elise Drimaracci
- Oliver Ullrich (ORCID: https://orcid.org/0000-0002-4721-1038)
- Esra Karatas
Institutions
- Centre National de la Recherche Scientifique (FR)
- Johns Hopkins University (US)
- Inserm (FR)
- National University of Singapore (SG)
- Université de Lille (FR)
- Johns Hopkins Medicine (US)
- Centre Hospitalier Universitaire de Lille (FR)
- Micos Engineering (Switzerland) (CH)
- Centre Oscar Lambret (FR)
- Hôpital Saint Eloi (FR)
- Swiss Federal Institute of Aquatic Science and Technology (CH)
Publication Details
- Journal
- Nature Methods
- Published
- 2025-05-14
- DOI
- https://doi.org/10.1038/s41592-025-02685-4
- Citations
- 34
- Primary Topic
- Cell Image Analysis Techniques
- Type
- article
- Field-Weighted Citation Impact
- 55.56
Funders
- Economic Development Board - Singapore
- Technische Universiteit Delft
- Universität Zürich