A FIJI macro for quantifying pattern in extracellular matrix.
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Embargo End Date
ICR Authors
Authors
Wershof, E
Park, D
Barry, DJ
Jenkins, RP
Rullan, A
Wilkins, A
Schlegelmilch, K
Roxanis, I
Anderson, KI
Bates, PA
Sahai, E
Park, D
Barry, DJ
Jenkins, RP
Rullan, A
Wilkins, A
Schlegelmilch, K
Roxanis, I
Anderson, KI
Bates, PA
Sahai, E
Document Type
Journal Article
Date
2021-03-01
Date Accepted
2021-01-08
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. 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.
Citation
Life Science Alliance, 2021, 4 (3), pp. e202000880 -
Source Title
Life Science Alliance
Publisher
LIFE SCIENCE ALLIANCE LLC
ISSN
2575-1077
eISSN
2575-1077
2575-1077
2575-1077
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Research Team
Targeted Therapy