I want to run a macro automatically each time that ImageJ starts. How do I do it?
Include your macro code in the AutoRun macro, which is in the StartupMacros.txt file (this file is located in the /ImageJ/macros/ folder).
Note: if you distribute your macros and used the method above to set default options, then other users have to know your Autorun settings, otherwise, their defaults will be different and the macro may not run as intended.
One possible solution is to paste the AutoRun set of commands at the start of your macro. The disadvantage is that this may override the current settings of the other users without them knowing.
Two macro commands
may be useful to save the current state of IJ: