Tools
Many of our tools and plugins are now available on Github.
Please follow the links below for most up to date versions of each of the tools.
Where relevant please cite originating papers
For bugs/issues and queries please contact the lab here
Picrosirius Red Fluorescence Analyser
Platform: FIJI / ImageJ
Github
Citation:
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HIT-MAP
Automated annotation and visualisation of high-resolution spatial proteomic mass spectrometry imaging data
Platform: R (Windows, MacOS and Linux)
Github
Docker
Citation:
Guo G*, Papanicolaou M* et al. Nature Communications (2021)
PubMed
Platform: Standalone Windows and MacOS application
Github
Citation:
Warren SC et al. eLife (2018)
PubMed
Automated ECM fibre orientation and alignment script
Platform: FIJI / ImageJ
Github
Citation:
Mayorca-Guiliani AE*, Madsen CD*, Cox TR* et al. Nature Medicine (2017)
PubMed
Automated Picrosirius Red (PR) birefringence (BRF) analysis of collagen I using polarised light
Platform: FIJI / ImageJ
Github
Citation:
Vennin C et al. Nature Communications (2019)
PubMed
Automated Picrosirius Red (PR) analysis of collagen I using transmitted light
Platform: FIJI / ImageJ
Download v1.11
Citation:
Vennin C et al. Nature Communications (2019)
PubMed
Automated Masson’s Trichrome Analysis of collagen I/bone (blue)
Platform: FIJI / ImageJ
Download v1.03
Citation:
…
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