ArticleNature communications2022
Multiscale light-sheet organoid imaging framework.
Article in Nature communications, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 66 papers.
What it found
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Who cites it
66 citing papers in PubMed.
- Organoid Intelligent Morphomics: Decoding the organoid morphome through artificial intelligence from phenotypic quantification to mechanistic insight.Bioactive materials · 2027Review
- Power-law scaling of mitotic spindles with genome sizes across eukaryotes is driven by chromosome crowding.Nature cell biology · 2026Article
- The Interplay of Curvature, Geometry, and Topology Shapes Tissue Organisation in Epithelial Shells.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Article
- Quantitative imaging of dynamic processes in intestinal organoids.Nature protocols · 2026Review
- Inverse scattering in biological samples via beam propagation.Science advances · 2026Article
- Article
- Identifying phenotype-genotype-function coupling in 3D organoid imaging using Shape, Appearance and Motion Phenotype Observation Tool (SPOT).Nature communications · 2026Article
- Image-based, pooled phenotyping reveals multidimensional, disease-specific variant effects.Cell · 2026Article
- Advancing mechanobiology from single molecules to complex cellular systems.Nature nanotechnology · 2026Review
- A quantitative pipeline for whole-mount deep imaging and analysis of multi-layered organoids across scales.eLife · 2026Article
- Image Tracing of Inflammatory Intestinal Organoids via Computational Clearing.Nanomaterials (Basel, Switzerland) · 2026Article
- Organoids to Model Tumor Microenvironment in Progression of Pathogenesis and Treatment Resistance in Glioblastoma Multiforme.Brain sciences · 2026Review
- UNIQUE: ultrasound non-destructive in-situ quantitative evaluation of stem cell spheroid deformability during differentiation into specific lineages.Microsystems & nanoengineering · 2026Article
- Proceedings of the ... AAAI Conference on Artificial Intelligence. AAAI Conference on Artificial Intelligence · 2026Article
- Multiscale imaging of polarity in bovine oviductal organoids.Frontiers in cell and developmental biology · 2026Article
- Non-Destructively Quantifying the Whole-Course Growth and Drug-Response of PDOs by an Automatic Microfluidic System Utilizing Chemiluminescence Detection.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Article
- Integrative functional optical imaging approaches: Optics, microfluidics, and machine learning for neuroscience in organoids and small-animal models.Biophysical journal · 2025Review
- CELLECT: contrastive embedding learning for large-scale efficient cell tracking.Nature methods · 2025Article
- Cell tracking with accurate error prediction.Nature methods · 2025Article
- A knowledge-driven deep learning framework for organoid morphological segmentation and characterization.BMC biology · 2025Article
6 more citing papers are in PubMed but not listed here.
Corrections and comments
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Authors and funding
9 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Organoids provide an accessible in vitro system to mimic the dynamics of tissue regeneration and development. However, long-term live-imaging of organoids remains challenging. Here we present an experimental and image-processing framework capable of turning long-term light-sheet imaging of intestinal organoids into digital organoids. The framework combines specific imaging optimization combined with data processing via deep learning techniques to segment single organoids, their lumen, cells and nuclei in 3D over long periods of time. By linking lineage trees with corresponding 3D segmentation meshes for each organoid, the extracted information is visualized using a web-based "Digital Organoid Viewer" tool allowing combined understanding of the multivariate and multiscale data. We also show backtracking of cells of interest, providing detailed information about their history within entire organoid contexts. Furthermore, we show cytokinesis failure of regenerative cells and that these cells never reside in the intestinal crypt, hinting at a tissue scale control on cellular fidelity.
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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.