Publishing a Plugin (in a scientific journal)


Hi all,

I am preparing a manuscript for publication that compares several methods for quantifying the same parameters on the same set of images. One of these methods involves a plugin that I wrote. We want the plugin to be easily accessible to anyone who might want to use it, but also need to respect whatever the journal’s guidelines are. None of us biologist authors know anything about procedure and etiquette for this type of thing, so here I am.

We’re planning on submitting to Scientific Reports first, but I’m having trouble deciphering their guidelines on submitting code. I’ve also heard that I should go through GitHub and the Fiji developer page but I’m unsure about how those integrate with a journal.

Any advice would be much appreciated!



Micheal Double answered a similar question a few years back on the ImageJ mailing list, see the archive at Nabble:

For publication in JORS for example, you store your code in some permanent archive, e.g. at zenodo or figshare, and then reference that archived version (plus optionnally your live repository such as git, if you are using a public version control system) in your software description paper.

This is what I did for the Pendent drop plugin, if you care to see an example.



This is great information – thank you very much! It really makes sense to have some kind of permanent version of the plugin that actually accompanied the publication, even if I continue to update it later.


You’re welcome.
My apologies to Micheal Doube for misspelling his name above, too much coding memory in my fingers ;-).