Skip to Main content Skip to Navigation
New interface
Journal articles

TissueMiner: A multiscale analysis toolkit to quantify how cellular processes create tissue dynamics

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.
Complete list of metadata

Cited literature [26 references]  Display  Hide  Download
Contributor : Raphael Etournay Connect in order to contact the contributor
Submitted on : Friday, June 23, 2017 - 12:56:47 PM
Last modification on : Thursday, April 7, 2022 - 10:10:33 AM
Long-term archiving on: : Wednesday, January 10, 2018 - 10:16:45 PM


Publication funded by an institution

  •  Etournay et al. - 2016 - TissueMiner a multiscale analysis toolkit to quan.pdf    Embargoed until : jamais  Files produced by the author(s)


Distributed under a Creative Commons Attribution 4.0 International License




Raphael Etournay, Matthias Merkel, Marko Popović, Holger Brandl, Natalie A. Dye, et al.. TissueMiner: A multiscale analysis toolkit to quantify how cellular processes create tissue dynamics. eLife, 2016, eLife 2016 (5), pp.14334. ⟨10.7554/eLife.14334⟩. ⟨pasteur-01545827⟩



Record views


Files downloads