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

  1. Raphaël Etournay
  2. Matthias Merkel
  3. Marko Popovi
  4. Holger Brandl
  5. Natalie A Dye
  6. Benoît Aigouy
  7. Guillaume Salbreux
  8. Suzanne Eaton
  9. Frank Jülicher  Is a corresponding author
  1. Max Planck Institute of Molecular Cell Biology and Genetics, Germany
  2. Max Planck Institute for the Physics of Complex Systems, Germany
  3. Institut de Biologie du Développement de Marseille, France

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.

Article and author information

Author details

  1. Raphaël Etournay

    Division of cell polarity, Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
    Competing interests
    No competing interests declared.
  2. Matthias Merkel

    Max Planck Institute for the Physics of Complex Systems, Dresden, Germany
    Competing interests
    No competing interests declared.
  3. Marko Popovi

    Max Planck Institute for the Physics of Complex Systems, Dresden, Germany
    Competing interests
    No competing interests declared.
  4. Holger Brandl

    Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
    Competing interests
    No competing interests declared.
  5. Natalie A Dye

    Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
    Competing interests
    No competing interests declared.
  6. Benoît Aigouy

    Institut de Biologie du Développement de Marseille, Marseille, France
    Competing interests
    No competing interests declared.
  7. Guillaume Salbreux

    Max Planck Institute for the Physics of Complex Systems, Dresden, Germany
    Competing interests
    No competing interests declared.
  8. Suzanne Eaton

    Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
    Competing interests
    Suzanne Eaton, Reviewing editor, eLife.
  9. Frank Jülicher

    Max Planck Institute for the Physics of Complex Systems, Dresden, Germany
    For correspondence
    julicher@pks.mpg.de
    Competing interests
    Frank Jülicher, Reviewing editor, eLife.

Reviewing Editor

  1. W James Nelson, Stanford University, United States

Publication history

  1. Received: February 5, 2016
  2. Accepted: May 25, 2016
  3. Accepted Manuscript published: May 26, 2016 (version 1)
  4. Accepted Manuscript updated: May 27, 2016 (version 2)
  5. Version of Record published: July 15, 2016 (version 3)

Copyright

© 2016, Etournay et al.

This article is distributed under the terms of the Creative Commons Attribution License permitting unrestricted use and redistribution provided that the original author and source are credited.

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  1. Raphaël Etournay
  2. Matthias Merkel
  3. Marko Popovi
  4. Holger Brandl
  5. Natalie A Dye
  6. Benoît Aigouy
  7. Guillaume Salbreux
  8. Suzanne Eaton
  9. Frank Jülicher
(2016)
TissueMiner: a multiscale analysis toolkit to quantify how cellular processes create tissue dynamics
eLife 5:e14334.
https://doi.org/10.7554/eLife.14334
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