Multiple instances of ImageJ cannot be run, by default.
Try to double click on the ImageJ icon multiple times, after an instance of it is already opened, and the control will return to the already open instance.
To start multiple instances of ImageJ you need to
- change a default option that allows to run a single instance listener only; you can do that under Edit -> Options -> Misc ..., where you can uncheck the box close to Run single instance listener;
- start ImageJ by the command line with the option --allow-multiple, e.g., $ ImageJ-linux64 --allow-multiple
