Wershof, Esther;
Park, Danielle;
Barry, David J;
Jenkins, Robert P;
Rullan, Antonio;
Wilkins, Anna;
Schlegelmilch, Karin;
... Sahai, Erik; + view all
(2021)
A FIJI macro for quantifying pattern in extracellular matrix.
Life Science Alliance
, 4
(3)
, Article e202000880. 10.26508/lsa.202000880.
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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. 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.
| Type: | Article |
|---|---|
| Title: | A FIJI macro for quantifying pattern in extracellular matrix |
| Location: | United States |
| Open access status: | An open access version is available from UCL Discovery |
| DOI: | 10.26508/lsa.202000880 |
| Publisher version: | https://doi.org/10.26508/lsa.202000880 |
| Language: | English |
| Additional information: | Copyright © 2021 Wershof et al. This article is available under a Creative Commons License (Attribution 4.0 International, as described at https://creativecommons.org/licenses/by/4.0/). |
| Keywords: | Algorithms, Animals, Extracellular Matrix, Humans, Image Processing, Computer-Assisted, Software, Workflow |
| UCL classification: | UCL UCL > Provost and Vice Provost Offices > School of Life and Medical Sciences UCL > Provost and Vice Provost Offices > School of Life and Medical Sciences > Faculty of Medical Sciences UCL > Provost and Vice Provost Offices > School of Life and Medical Sciences > Faculty of Medical Sciences > Div of Infection and Immunity |
| URI: | https://discovery.ucl.ac.uk/id/eprint/10195471 |
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