RT Journal Article SR Electronic T1 A FIJI macro for quantifying pattern in extracellular matrix JF Life Science Alliance JO Life Sci. Alliance FD Life Science Alliance LLC SP e202000880 DO 10.26508/lsa.202000880 VO 4 IS 3 A1 Esther Wershof A1 Danielle Park A1 David J Barry A1 Robert P Jenkins A1 Antonio Rullan A1 Anna Wilkins A1 Karin Schlegelmilch A1 Ioannis Roxanis A1 Kurt I Anderson A1 Paul A Bates A1 Erik Sahai YR 2021 UL https://www.life-science-alliance.org/content/4/3/e202000880.abstract 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.