== Running Scripts in Headless Mode ==
If you want to run scripts in headless mode (i.e. without the GUI, by invoking fiji with the --headless option) then you have to make sure you run the appropriate "Refresh ... Scripts" plugin first. Also, you need to append -batch to the command. For example, if you have a script called test_ruby.rb, which appears in the Plugins menu somewhere as "test ruby", then you can run that with: fiji --headless -eval 'run("Refresh JRuby Scripts",""); run("test ruby","");'