A FIJI Macro for quantifying pattern in extracellular matrix

Wershof, E.; Barry, D. J.; Jenkins, R. P.; Rullan, A.; Wilkins, A.; Roxanis, I.; Anderson, K. I.; Park, D.; Bates, P. A.; Sahai, E.

doi:10.1101/867507

bioRxiv · 10.1101/867507

A FIJI Macro for quantifying pattern in extracellular matrix

Wershof, E.·Barry, D. J.·Jenkins, R. P.·Rullan, A.·Wilkins, A.·Roxanis, I.·Anderson, K. I.·Park, D.·Bates, P. A.·Sahai, E.

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Abstract

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. 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. Here we present an overview of the pipeline together with examples from a wide range of contexts where matrix patterns are generated.

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Wershof, E., Barry, D. J., Jenkins, R. P., Rullan, A., Wilkins, A., Roxanis, I., Anderson, K. I., Park, D., Bates, P. A., Sahai, E.. 2019-12-06. A FIJI Macro for quantifying pattern in extracellular matrix. https://doi.org/10.1101/867507

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