ArticleNature methods2025
Digitalized organoids: integrated pipeline for high-speed 3D analysis of organoid structures using multilevel segmentation and cellular topology.
Article in Nature methods, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 38 papers, 2 of them syntheses that pooled it.
What it found
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The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
38 citing papers in PubMed, 2 syntheses or guidelines pooled it.
- [Organoid-based strategies and challenges in tissue regeneration].Zhonghua shao shang yu chuang mian xiu fu za zhi · 2026Pooled it
- Pooled it
- Organoid Intelligent Morphomics: Decoding the organoid morphome through artificial intelligence from phenotypic quantification to mechanistic insight.Bioactive materials · 2027Review
- Construction and application of mammary and breast cancer organoids.Cell insight · 2026Review
- Converging engineered models of cancer and artificial intelligence.Nature reviews. Cancer · 2026Article
- Quantitative imaging of dynamic processes in intestinal organoids.Nature protocols · 2026Review
- Trastuzumab treatment is associated with ferroptosis-related alterations in HER2-positive breast cancer organoids.Cancer chemotherapy and pharmacology · 2026Article
- Tuning epigenetics to enhance cancer virotherapy.Acta pharmaceutica Sinica. B · 2026Review
- Using human 3D organoid models to gain mechanistic insight in motor neuron diseases.Nature reviews. Neuroscience · 2026Review
- Artificial intelligence virtual bone organoids (AIVBOs).Journal of orthopaedic translation · 2026Review
- From pixels to patterns: the AI revolution in stem cell-derived models.Nature methods · 2026Review
- Review
- Bioengineering advances in pancreatic cancer organoids for reproducible tumor microenvironment modeling.iScience · 2026Review
- CenSegNet: a generalist high-throughput deep learning framework for centrosome phenotyping at spatial and single-cell resolution in heterogeneous tissues.Nature communications · 2026Article
- Human organoids: Fit for drug discovery?Stem cell reports · 2026Review
- Construction of liver organoid models by hepatobiliary differentiation from human induced pluripotent stem cells: state of the art, challenges and improving strategies.Stem cell research & therapy · 2026Review
- Cells Dynamically Adapt Their Nuclear Volumes and Proliferation Rates During Single to Multicellular Transitions.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Article
- Recent advances and expanding applications of organoid models in unveiling drug ADME profiles.Journal of pharmaceutical analysis · 2026Review
- Organoids, organ-on-a-chip, and microtumors: Biomimetic 3D tumor models advancing drug development and precision medicine.Acta pharmaceutica Sinica. B · 2026Review
- A quantitative pipeline for whole-mount deep imaging and analysis of multi-layered organoids across scales.eLife · 2026Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
18 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
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.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.