At Light Microscopy Australia 2019, I am co-organising a one day satellite symposium on bioimage analysis. After a keynote by @royerloic (), we will have a “tools” session where we present various open source tools for image analysis. I’m aiming for this session to highlight the advantage of open source when developing your own workflows, and serve as a gentle on-ramp for people to move from analysis to development.
As regards Fiji, various bits of documentation have warnings that they might be outdated, see e.g. Plugin Design Guidelines. My impression from lurking on the gitter imglib2 channel is that all these things are evolving rapidly so I wanted to query the community on the latest information on the best way to do this. Specific questions:
- If I only point people to one document on Fiji plugin/command development, what should it be?
- Is there a documented gentle path to go from macro recording -> script (preferably in the user’s preferred language, Jython would of course be my top choice -> command in the GUI -> more full-featured plugin?
- If not, would anyone care to volunteer to write it? I think it would be enormously valuable.
- for the last step above, what kind of things could you do with “real”, Java plugin development compared to a script with parameters? (ie should most users worry about this?)
I’d like the talk to be appealing to boldly-enterprising-curious-biologists, rather than programmers, so I think that this “Writing plugins” page would be too intimidating to start with. “Script parameters” is more in line with what I would like to point people to, but then I would need instructions for turning scripts into plugins and distributing said plugins.