A FIJI Macro for quantifying pattern in extracellular matrix

Diverse extracellular matrix patterns are observed in both normal and pathological tissue; however only piecemeal tools currently exist for quantitative analysis of matrix pattern features. Thus, there is a need for an automated pipeline for quantifying these matrix patterns. To this end we have developed an ImageJ plugin called TWOMBLI, which stands for The Workflow Of Matrix BioLogy Informatics. The aim of TWOMBLI is to quantify matrix patterns, including branch points, endpoints, curvature, gaps, and fractal dimension. It is designed to be easy-to-use, quick and versatile. TWOMBLI can be downloaded from https://github.com/wershofe/TWOMBLI together with detailed documentation. Here we present an overview of the pipeline and demonstrate its utility for quantifying extracellular matrix patterns in both experimental and clinical samples.