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EMBL BioImage Data Analysis



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RT @haesleinhuepf: Thanks @gomez_mariscal for contributing to our #NEUBIAS satellite meeting! Looking forward to seed #DeepImageJ in action…
About 2 days ago by: Kota Miura (@cmci_)

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RT @EMBLEvents: #BioimageAnalysis is a keystone of biological research. Due to the complexity of data, it's likely that #ImageAnalysis algo…
About 2 days, 3 hours ago by: Kota Miura (@cmci_)

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RT @gomez_mariscal: Excited about introducing #deepImageJ during the #NEUBIASSatelliteMeeting @NEUBIAS_COST @COM
About 2 days, 15 hours ago by: Kota Miura (@cmci_)

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@fab_cordelieres @NEUBIAS_COST @BIC_Bordeaux :)
About 2 days, 22 hours ago by: Kota Miura (@cmci_)

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@haesleinhuepf @TalleyJLambert @Ulrike_Boehm "The intensity of this image sequence..."
About 3 days, 1 hour ago by: Kota Miura (@cmci_)

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RT @focalplane_jcs: Hi all, my name is Christos @KyprianouChr and I am the Community Manager of the FocalPlane site, launching this summer.…
About 6 days, 22 hours ago by: Kota Miura (@cmci_)

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();

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/'
… 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