ArticleeLife2016
TissueMiner: A multiscale analysis toolkit to quantify how cellular processes create tissue dynamics.
Article in eLife, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 62 papers.
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Who cites it
62 citing papers in PubMed.
- EpiCure (Epithelial Curation): a versatile and handy tool for curation of epithelial segmentation.bioRxiv : the preprint server for biology · 2026Article
- StrainMapperJ: An Easy-to-Use Digital Image Correlation Toolkit for Exploring and Quantifying the Mechanics of Deforming Tissues.Results and problems in cell differentiation · 2026Article
- Article
- Searching for physical principles of morphogenesis.Development (Cambridge, England) · 2025Review
- Single-cell analysis of the early Drosophila salivary gland reveals that morphogenetic control involves both the induction and exclusion of gene expression programs.PLoS biology · 2025Article
- Mechanical strain focusing at topological defect sites in regenerating Hydra.Development (Cambridge, England) · 2025Article
- Peeking into the future: inferring mechanics in dynamical tissues.Biochemical Society transactions · 2024Review
- Article
- Deep learning for rapid analysis of cell divisions in vivo during epithelial morphogenesis and repair.eLife · 2024Article
- Deep learning reveals a damage signalling hierarchy that coordinates different cell behaviours driving wound re-epithelialisation.Development (Cambridge, England) · 2024Article
- Active shape programming drivesScience advances · 2024Article
- Automated Layer Analysis (ALAn): An Image Analysis Tool for the Unbiased Characterization of Mammalian Epithelial Architecture in Culture.Bio-protocol · 2024Article
- Programmed disassembly of a microtubule-based membrane protrusion network coordinates 3D epithelial morphogenesis in Drosophila.The EMBO journal · 2024Article
- Patterned apoptosis has an instructive role for local growth and tissue shape regulation in a fast-growing epithelium.Current biology : CB · 2024Article
- α-Spectrin regulates cell shape changes during disassembly of microtubule-driven protrusions inmicroPublication biology · 2024Article
- Core PCP mutations affect short-time mechanical properties but not tissue morphogenesis in theeLife · 2023Article
- Protein phosphatase 1 regulates core PCP signaling.EMBO reports · 2023Article
- SCRIB controls apical contractility during epithelial differentiation.The Journal of cell biology · 2023Article
- Movies tell us how tissues develop a 3D shape.Nature methods · 2023Article
- DeXtrusion: automatic recognition of epithelial cell extrusion through machine learning in vivo.Development (Cambridge, England) · 2023Article
2 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
9 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Segmentation and tracking of cells in long-term time-lapse experiments has emerged as a powerful method to understand how tissue shape changes emerge from the complex choreography of constituent cells. However, methods to store and interrogate the large datasets produced by these experiments are not widely available. Furthermore, recently developed methods for relating tissue shape changes to cell dynamics have not yet been widely applied by biologists because of their technical complexity. We therefore developed a database format that stores cellular connectivity and geometry information of deforming epithelial tissues, and computational tools to interrogate it and perform multi-scale analysis of morphogenesis. We provide tutorials for this computational framework, called TissueMiner, and demonstrate its capabilities by comparing cell and tissue dynamics in vein and inter-vein subregions of the Drosophila pupal wing. These analyses reveal an unexpected role for convergent extension in shaping wing veins.
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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.