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RT @laure_plantard: Taggers at work #Neubias https://t.co/vnxjfiaVse
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RT @Boutroslab: CytoData 2019 Symposium and Hackathon @DKFZ on image profiling, single cell analysis and deep learning. Oct 27-30, 2019 i…
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documents:20190416ijmacro_passingarguments

Passing stdout to ImageJ / Fiji

In case you want to pass stdout to ImageJ macro headlessly, use getArgument.

For example, create a test macro like this and save it as test.ijm:

tt = getArgument();
print(tt);

Then the bash command for passing stdout to this macro headlessly is:

echo "hello" | (read arg; fiji --headless -macro test.ijm "$arg")

There could be more sophisticated ways, but the command above does work. For the command “fiji” to work, it should be set in your .profile or .bash_profile

alias fiji='/Applications/Fiji.app/Contents/MacOS/ImageJ-macosx'
… you need to change the path above according to the place where your Fiji resides.

The command could also be

echo "hello" | (read arg; fiji -batch test.ijm "$arg")

but it's slower somehow.

documents/20190416ijmacro_passingarguments.txt · Last modified: 2019/04/16 05:46 by kota