ArticleCommunications biology2024
OrgaSegment: deep-learning based organoid segmentation to quantify CFTR dependent fluid secretion.
Article in Communications biology, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 21 papers.
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Who cites it
21 citing papers in PubMed, 28 citations in OpenAlex.
- Organoid Intelligent Morphomics: Decoding the organoid morphome through artificial intelligence from phenotypic quantification to mechanistic insight.Bioactive materials · 2027Review
- An AI-integrated organoid platform enables high-throughput functional evaluation of bioactive metal ions.Bioactive materials · 2026Article
- A Single-organoid Workflow for quantitative Imaging classiFication and Tracking (SWIFT).Communications biology · 2026Article
- OrgLine: A versatile pipeline for organoid morphometry using detector-guided prompts.Cell reports methods · 2026Article
- Deep Learning-Based Prediction of Epithelial Cytokine Responses for the Selection of Functionally Consistent Airway Organoids.Biomimetics (Basel, Switzerland) · 2026Article
- Cellular Models and Functional Assays for Assessing CFTR Function: A Comprehensive Review.International journal of molecular sciences · 2026Review
- BrAIn: A comprehensive artificial intelligence-based morphology analysis system for brain organoids and neuroscience.Bioengineering & translational medicine · 2026Article
- DeShiftNet: a deformable-shifted cross-attention network for lightweight and robust organoid image segmentation.BMC bioinformatics · 2026Article
- Review
- An automated image analysis pipeline for wide-field optical redox imaging of patient-derived cancer organoids.Scientific reports · 2026Article
- Fast learning-free organoid quantification and tracking with OrganoSeg2.Scientific reports · 2026Article
- Research progress of artificial intelligence in high-throughput drug screening.Frontiers in pharmacology · 2026Review
- Lightweight Deep Learning Model for Classification of Normal and Abnormal Vasculature in Organoid Images.Sensors (Basel, Switzerland) · 2025Article
- Organoids in Genetic Disorders: from Disease Modeling to Translational Applications.Stem cell reviews and reports · 2025Review
- A semi-automated algorithm for image analysis of respiratory organoids.PLoS computational biology · 2025Article
- Biomedical applications of organoids in genetic diseases.Medical review (2021) · 2025Review
- Review
- Development and validation of the Normalized Organoid Growth Rate (NOGR) metric in brightfield imaging-based assays.Communications biology · 2024Article
- Organoids: development and applications in disease models, drug discovery, precision medicine, and regenerative medicine.MedComm · 2024Review
- A Convexity-Preserving Level-Set Method for the Segmentation of Tumor Organoids.Bioengineering (Basel, Switzerland) · 2024Article
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Authors and funding
9 authors at 2 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Epithelial ion and fluid transport studies in patient-derived organoids (PDOs) are increasingly being used for preclinical studies, drug development and precision medicine applications. Epithelial fluid transport properties in PDOs can be measured through visual changes in organoid (lumen) size. Such organoid phenotypes have been highly instrumental for the studying of diseases, including cystic fibrosis (CF), which is characterized by genetic mutations of the CF transmembrane conductance regulator (CFTR) ion channel. Here we present OrgaSegment, a MASK-RCNN based deep-learning segmentation model allowing for the segmentation of individual intestinal PDO structures from bright-field images. OrgaSegment recognizes spherical structures in addition to the oddly-shaped organoids that are a hallmark of CF organoids and can be used in organoid swelling assays, including the new drug-induced swelling assay that we show here. OrgaSegment enabled easy quantification of organoid swelling and could discriminate between organoids with different CFTR mutations, as well as measure responses to CFTR modulating drugs. The easy-to-apply label-free segmentation tool can help to study CFTR-based fluid secretion and possibly other epithelial ion transport mechanisms in organoids.
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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.