A FIJI macro for quantifying pattern in extracellular matrix.
Date
2021-03-01ICR Author
Author
Wershof, E
Park, D
Barry, DJ
Jenkins, RP
Rullan, A
Wilkins, A
Schlegelmilch, K
Roxanis, I
Anderson, KI
Bates, PA
Sahai, E
Type
Journal Article
Metadata
Show full item recordAbstract
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.
Collections
Subject
Algorithms
Animals
Extracellular Matrix
Humans
Image Processing, Computer-Assisted
Software
Workflow
Research team
Targeted Therapy
Language
eng
Date accepted
2021-01-08
License start date
2021-03-01
Citation
Life Science Alliance, 2021, 4 (3), pp. e202000880 -
Publisher
LIFE SCIENCE ALLIANCE LLC