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Scripting Headless

    ImageJ scripts are designed to operate independently of user interface—including headless, with no user interface. This is made easy with the use of script parameters.

    To start ImageJ in the ImageJ2 headless mode, run (with the launcher appropriate for your system substituted):

    ./ImageJ-linux64 --ij2 --headless

    By default, when ImageJ runs headlessly it acts like a one-off program: it will only perform the requested operations, then quit. To run a script headlessly, use:

    ./ImageJ-linux64 --ij2 --headless --run path/to/script [key1=value1,key2=value2,...]

    In many cases, it is necessary to enclose the entire list of key/value pairs in single quotes, to avoid shell expansion. See the following examples.

    Basic run

    Let’s say we have the following Python script saved in a file, hello.py:

    #@String name
    print('Hello ' + name)

    we could run this script with the command:

    ./ImageJ-linux64 --ij2 --headless --console --run hello.py 'name="Mr Kraken"'

    Note that the name parameter must be enclosed in double quotes, since it is a string literal.

    The optional --console argument allows to have print, IJ.log and error statements returned to the console window.

    On Windows systems, single/double quotes might be inverted though, such that strings are enclosed in single quotes while the list of argument as well as the path to the py script are in double quotes.

    ImageJ-win64.exe --ij2 --headless --console --run "PathTo/hello.py" "name='Mr Kraken'"

    Multiple parameters

    If your script has more than one parameter:

    #@String name1
    #@String name2
    print('Hello ' + name1 + " and " + name2)

    then these are filled by using a comma-separated list of parameter pairs—e.g.:

    ./ImageJ-linux64 --ij2 --headless --console --run hello.py 'name1="Mr",name2="Mrs Kraken"'

    Similarly for Windows (again respect single/double quotes),

    ImageJ-win64.exe --ij2 --headless --console --run "PathTo/hello.py" "name1='Mr', name2='Kraken'"