Installing Scripts to ImageJ
Various methods to run script in ImageJ / Fiji
Open script Editor ([File > New > Script]) and load the file into the script editor by [File > Open] menu of the editor. Then click “Run” button. This method is suitable for scripts that you use only once, or to test the code.
Copy the file to the directory <Fiji root>/plugins/scripts/ and restart Fiji. The script then appears in the menu. Then select that menu item will run the script. This method is sutied for script that you use routinely.
Specifically for macro, installation by [Plugins > Macros > Install…] allows you to have the macro appearing under [Plugins > Macros > ] menu-tree.