bonej-scripts

Helper scripts and macros using BoneJ.

The intention of this repository is to archive and share code examples where BoneJ has been used from other code, in particular ImageJ macros or Jython / Python scripts. All examples of using BoneJ's API from client code are welcome.

There is no strict code style required and contributors are encouraged to share their work 'warts and all', early and often. It will help everyone (especially future you) if you include documentation in each script or as a README alongside each script.

Minimal documentation should include:

• The date
• Your name
• A description of what the code is meant to do and how to run it.
• Assumptions about the environment such as operating system, Fiji/ImageJ version, BoneJ version, and image characteristics.
• Any related documents, such as the DOI and citation details of a publication for which the code was used.
• A licence

It is helpful to include line-by-line documentation so that the intention of each piece of code is clear.

Files uploaded to this repository remain the intellectual property of their authors and are made available under licence terms set in each file by the authors. If authors have not set a licence, assume Creative Commons Attribution 4.0 International (CC-BY 4.0).

Code is automatically archived at Zenodo with DOI, and can be cited from there. Note that the Zenodo DOI changes as the code is updated. Best practice is to cite the DOI specific to the 'version of record' of your scripts. The DOI linked from this README is the universal one that always resolves to the latest code version.

How to contribute

1. Fork this repository, using the 'Fork' button at the top right of this page.
2. Commit your scripts and documentation to your fork, using the organisational convention code_language/project_name/MyScriptName.extension
3. Submit a pull request to merge your fork's master to bonej-org/bonej-scripts/master
4. Respond to conversations about your pull request
5. When code is merged, check the Zenodo archive and make sure it's there: we have to make a new release in order for Zenodo to issue a DOI that you can cite.