TWOMBLI, which stands for The Workflow Of Matrix BioLogy Informatics, is a tool designed to quantify diverse extracellular matrix (ECM) patterns observed in both normal and pathological tissues. The name TWOMBLI also pays homage to the American artist Cy Twombly, whose works are renowned for their varied marks and patterning.
TWOMBLI enables the quantification of the following key metrics, illustrated above:
- Number of fibre endpoints
- Number of fibre branchpoints
- Percentage of image occupied by high-density matrix (HDM)
- Fibre curvature
- Fractal dimension of the fibre network
TWOMBLI was initially released as an ImageJ/FIJI macro:
Wershof E, Park D, Barry DJ, Jenkins RP, Rullan A, Wilkins A, Schlegelmilch K, Roxanis I, Anderson KI, Bates PA, Sahai E (2021) A FIJI macro for quantifying fibrillar patterns. Life Science Alliance, 4 (3) e202000880; DOI: 10.26508/lsa.202000880
However, maintaining and developing this macro became challenging as the user base grew and requests for new features and improved functionality increased.
To address these challenges, TWOMBLI was reimplemented as a FIJI plugin, adhering to best practices in software engineering. This transition to Java not only simplifies future maintenance but also allows for a more user-friendly interface and easier integration of new functionalities.
For users, the main distinction between TWOMBLI Version 1 (macro) and Version 2 (Java plugin) is the significantly improved graphical user interface (GUI). While the look and feel are much more user-friendly in Version 2, rest assured that the underlying analysis remains identical. You'll set the exact same parameters and get virtually the same results and data as you did with Version 1.
In Fiji, you just need to add the TWOMBLI site to your list of update sites:
- From the FIJI menu, navigate to
Help›Update…to launch the updater. - Click on
Manage update sites. This will open a dialog where you can activate additional update sites. - Activate the TWOMBLI update site and close the dialog.
- Click
Apply changesand restart FIJI.
Read the documentation here (insert link to readthedocs) to get started.
Clone this repository locally, open the project in your IDE of choice, build using maven. Artifact deployments may be automated in future using github workflows + PRs.
This repository uses GitHub's built-in issues, pull requests, and workflow tools. Please conform to the existing repository styles and standards.
- To contribute to the documentation, please submit an issue with your desired changes.
- To report a bug or feature request please submit an issue here: https://github.com/FrancisCrickInstitute/TWOMBLI/issues
- To contribute please submit a pull request here: https://github.com/FrancisCrickInstitute/TWOMBLI/pulls
The best place to ask for help is the Image.sc forum:
- Create an account if you don't have one already
- Search to see if someone has already asked a similar question - there may already be a relevant answer
- If not, create a new topic using the #twombli hashtag