e202000880.full (1).pdf (2.97 MB)

A FIJI macro for quantifying pattern in extracellular matrix.

Download (2.97 MB)
journal contribution
posted on 04.02.2021, 14:24 by Esther Wershof, Danielle Park, David J Barry, Robert P Jenkins, Antonio Rullan, Anna Wilkins, Karin Schlegelmilch, Ioannis Roxanis, Kurt I Anderson, Paul A Bates, Erik Sahai
Diverse extracellular matrix patterns are observed in both normal and pathological tissue. However, most current tools for quantitative analysis focus on a single aspect of matrix patterning. Thus, an automated pipeline that simultaneously quantifies a broad range of metrics and enables a comprehensive description of varied matrix patterns is needed. To this end, we have developed an ImageJ plugin called TWOMBLI, which stands for The Workflow Of Matrix BioLogy Informatics. This pipeline includes metrics of matrix alignment, length, branching, end points, gaps, fractal dimension, curvature, and the distribution of fibre thickness. TWOMBLI is designed to be quick, versatile and easy-to-use particularly for non-computational scientists. TWOMBLI can be downloaded from https://github.com/wershofe/TWOMBLI together with detailed documentation and tutorial video. Although developed with the extracellular matrix in mind, TWOMBLI is versatile and can be applied to vascular and cytoskeletal networks. Here we present an overview of the pipeline together with examples from a wide range of contexts where matrix patterns are generated.

Funding

Crick (Grant ID: 10010, Grant title: STP Light Microscopy) Crick (Grant ID: 10144, Grant title: Sahai FC001144) Crick (Grant ID: 10316, Grant title: Bates FC001003)

History

Licence

Exports