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

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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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Raphaël Etournay

Division of cell polarity, Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany

Competing interests
No competing interests declared.
Matthias Merkel

Max Planck Institute for the Physics of Complex Systems, Dresden, Germany

Competing interests
No competing interests declared.
Marko Popovi

Max Planck Institute for the Physics of Complex Systems, Dresden, Germany

Competing interests
No competing interests declared.
Holger Brandl

Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany

Competing interests
No competing interests declared.
Natalie A Dye

Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany

Competing interests
No competing interests declared.
Benoît Aigouy

Institut de Biologie du Développement de Marseille, Marseille, France

Competing interests
No competing interests declared.
Guillaume Salbreux

Max Planck Institute for the Physics of Complex Systems, Dresden, Germany

Competing interests
No competing interests declared.
Suzanne Eaton

Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany

Competing interests
Suzanne Eaton, Reviewing editor, eLife.
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.

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