Installing Scripts to ImageJ

Various methods to run script in ImageJ / Fiji

To use a script such as ImageJ macro file (.ijm), javascript file (.js) or Jython file (.py), There are two ways, and for macro is a third way:

  1. 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.

  2. 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.

  3. Specifically for macro, installation by [Plugins > Macros > Install…] allows you to have the macro appearing under [Plugins > Macros > ] menu-tree.