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

• Published in: eLife Vol. 5; no. 5
• Main Authors: Etournay, Raphaël, Merkel, Matthias, Popović, Marko, Brandl, Holger, Dye, Natalie A, Aigouy, Benoît, Salbreux, Guillaume, Eaton, Suzanne, Jülicher, Frank
• Format: Journal Article
• Language: English
• Published: England eLife Sciences Publications Ltd 26.05.2016; eLife Sciences Publication; eLife Sciences Publications, Ltd
• Subjects: Animals; Bioinformatics; Cell Biology; Cellular Biology; Computational and Systems Biology; Computational Biology - methods; Computer applications; Computer Science; Databases, Factual; Datasets; Development Biology; Drosophila; Drosophila - physiology; epithelial cells; epithelial dynamics; Epithelium - physiology; Image Processing, Computer-Assisted - methods; Life Sciences; Morphogenesis; Motion pictures; Quantitative Methods; Segmentation; Software; systems biology; Time-Lapse Imaging; Tools and Resources; Visualization; computational biology; systems biology; epithelial cells; cell biology; D. melanogaster; epithelial dynamics; Epithelial Cells; Cell Biology
• ISSN: 2050-084X; 2050-084X
• DOI: 10.7554/elife.14334

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.