dc.contributor.author | Wershof, E | |
dc.contributor.author | Park, D | |
dc.contributor.author | Barry, DJ | |
dc.contributor.author | Jenkins, RP | |
dc.contributor.author | Rullan, A | |
dc.contributor.author | Wilkins, A | |
dc.contributor.author | Schlegelmilch, K | |
dc.contributor.author | Roxanis, I | |
dc.contributor.author | Anderson, KI | |
dc.contributor.author | Bates, PA | |
dc.contributor.author | Sahai, E | |
dc.coverage.spatial | United States | |
dc.date.accessioned | 2022-09-13T09:10:42Z | |
dc.date.available | 2022-09-13T09:10:42Z | |
dc.date.issued | 2021-03-01 | |
dc.identifier | ARTN e202000880 | |
dc.identifier | 4/3/e202000880 | |
dc.identifier.citation | Life Science Alliance, 2021, 4 (3), pp. e202000880 - | |
dc.identifier.issn | 2575-1077 | |
dc.identifier.uri | https://repository.icr.ac.uk/handle/internal/5446 | |
dc.identifier.eissn | 2575-1077 | |
dc.identifier.eissn | 2575-1077 | |
dc.identifier.doi | 10.26508/lsa.202000880 | |
dc.description.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. | |
dc.format | Electronic-Print | |
dc.format.extent | e202000880 - | |
dc.language | eng | |
dc.language.iso | eng | |
dc.publisher | LIFE SCIENCE ALLIANCE LLC | |
dc.relation.ispartof | Life Science Alliance | |
dc.rights.uri | http://creativecommons.org/licenses/by/4.0/ | |
dc.subject | Algorithms | |
dc.subject | Animals | |
dc.subject | Extracellular Matrix | |
dc.subject | Humans | |
dc.subject | Image Processing, Computer-Assisted | |
dc.subject | Software | |
dc.subject | Workflow | |
dc.title | A FIJI macro for quantifying pattern in extracellular matrix. | |
dc.type | Journal Article | |
dcterms.dateAccepted | 2021-01-08 | |
dc.date.updated | 2022-09-13T09:00:38Z | |
rioxxterms.version | VoR | |
rioxxterms.versionofrecord | 10.26508/lsa.202000880 | |
rioxxterms.licenseref.startdate | 2021-03-01 | |
rioxxterms.type | Journal Article/Review | |
pubs.author-url | https://www.ncbi.nlm.nih.gov/pubmed/33504622 | |
pubs.issue | 3 | |
pubs.organisational-group | /ICR | |
pubs.organisational-group | /ICR/Primary Group | |
pubs.organisational-group | /ICR/Primary Group/ICR Divisions | |
pubs.organisational-group | /ICR/Primary Group/ICR Divisions/Cancer Biology | |
pubs.organisational-group | /ICR/Primary Group/ICR Divisions/Cancer Biology/Targeted Therapy | |
pubs.organisational-group | /ICR/Primary Group/ICR Divisions/Radiotherapy and Imaging | |
pubs.organisational-group | /ICR/Primary Group/ICR Divisions/Radiotherapy and Imaging/Targeted Therapy | |
pubs.organisational-group | /ICR/Students | |
pubs.organisational-group | /ICR/Students/PhD and MPhil | |
pubs.organisational-group | /ICR/Students/PhD and MPhil/17/18 Starting Cohort | |
pubs.organisational-group | /ICR/ImmNet | |
pubs.organisational-group | /ICR/Students/PhD and MPhil/13/14 Starting Cohort | |
pubs.publication-status | Published online | |
pubs.publisher-url | http://dx.doi.org/10.26508/lsa.202000880 | |
pubs.volume | 4 | |
icr.researchteam | Targeted Therapy | |
dc.contributor.icrauthor | Corbett, Anna | |
icr.provenance | Deposited by Mr Arek Surman on 2022-09-13. Deposit type is initial. No. of files: 1. Files: A FIJI macro for quantifying pattern in extracellular matrix. .pdf | |