ArticleDevelopment (Cambridge, England)2020
EPySeg: a coding-free solution for automated segmentation of epithelia using deep learning.
Article in Development (Cambridge, England), 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 29 papers.
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Who cites it
29 citing papers in PubMed, 53 citations in OpenAlex.
- Short-term memory of past caspase activity biases cell elimination in vivo.Nature communications · 2026Article
- Protocol for inferring mechanical stresses in tissues using ForSys, an open-source Python tool.STAR protocols · 2026Article
- EpiCure (Epithelial Curation): a versatile and handy tool for curation of epithelial segmentation.bioRxiv : the preprint server for biology · 2026Article
- FishFeats: streamlined quantification of multimodal labeling at the single-cell level in 3D tissues.Bioinformatics (Oxford, England) · 2026Article
- FISH-Dist: An Automated Pipeline for 3D Genomic Spatial Distance Quantification in FISH Imaging.Bioengineering (Basel, Switzerland) · 2026Article
- A key role of Canoe's intrinsically disordered region in linking cell junctions to the cytoskeleton.The Journal of cell biology · 2025Article
- Article
- Resolving the design principles that control post-natal vascular growth and scaling.Cell systems · 2025Article
- Mechanical strain focusing at topological defect sites in regenerating Hydra.Development (Cambridge, England) · 2025Article
- EGFR-dependent actomyosin patterning coordinates morphogenetic movements between tissues in Drosophila melanogaster.Developmental cell · 2025Article
- Peeking into the future: inferring mechanics in dynamical tissues.Biochemical Society transactions · 2024Review
- Deep learning for rapid analysis of cell divisions in vivo during epithelial morphogenesis and repair.eLife · 2024Article
- E-cadherin tunes tissue mechanical behavior before and during morphogenetic tissue flows.Current biology : CB · 2024Article
- Piezo regulates epithelial topology and promotes precision in organ size control.Cell reports · 2024Article
- Proliferation-driven mechanical compression induces signalling centre formation during mammalian organ development.Nature cell biology · 2024Article
- Automated counting of Drosophila imaginal disc cell nuclei.Biology open · 2024Article
- EGFR-dependent actomyosin patterning coordinates morphogenetic movements between tissues.bioRxiv : the preprint server for biology · 2023Article
- Spatiotemporal remodeling of extracellular matrix orients epithelial sheet folding.Science advances · 2023Article
- DeXtrusion: automatic recognition of epithelial cell extrusion through machine learning in vivo.Development (Cambridge, England) · 2023Article
- The RhoGEF protein Plekhg5 regulates medioapical and junctional actomyosin dynamics of apical constriction duringMolecular biology of the cell · 2023Article
Corrections and comments
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Authors and funding
4 authors at 2 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Epithelia are dynamic tissues that self-remodel during their development. During morphogenesis, the tissue-scale organization of epithelia is obtained through a sum of individual contributions of the cells constituting the tissue. Therefore, understanding any morphogenetic event first requires a thorough segmentation of its constituent cells. This task, however, usually involves extensive manual correction, even with semi-automated tools. Here, we present EPySeg, an open-source, coding-free software that uses deep learning to segment membrane-stained epithelial tissues automatically and very efficiently. EPySeg, which comes with a straightforward graphical user interface, can be used as a Python package on a local computer, or on the cloud via Google Colab for users not equipped with deep-learning compatible hardware. By substantially reducing human input in image segmentation, EPySeg accelerates and improves the characterization of epithelial tissues for all developmental biologists.
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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.