PT  - JOURNAL ARTICLE
AU  - Esther Wershof
AU  - Danielle Park
AU  - David J Barry
AU  - Robert P Jenkins
AU  - Antonio Rullan
AU  - Anna Wilkins
AU  - Karin Schlegelmilch
AU  - Ioannis Roxanis
AU  - Kurt I Anderson
AU  - Paul A Bates
AU  - Erik Sahai
TI  - A FIJI macro for quantifying pattern in extracellular matrix
AID  - 10.26508/lsa.202000880
DP  - 2021 Mar 01
TA  - Life Science Alliance
PG  - e202000880
VI  - 4
IP  - 3
4099  - https://www.life-science-alliance.org/content/4/3/e202000880.short
4100  - https://www.life-science-alliance.org/content/4/3/e202000880.full
SO  - Life Sci. Alliance2021 Mar 01; 4
AB  - 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.