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EMBL BioImage Data Analysis



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RT @_pm_lab: Unbiased quantitative phenotypic #BioImageAnalysis of #3D #microscopy images in #HighContentScreening is a fundamental challen…
About 7 hours, 13 mins ago by: Kota Miura (@cmci_)

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RT @joachimgoedhart: Our recent preprint has several step-by-step guides that explain how timelapse imaging data can be processed and visua…
About 5 days, 6 hours ago by: Kota Miura (@cmci_)

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RT @PLOSCompBiol: 3D #BioImageAnalysis for #HighContentScreening should be easy. Using data driven voxel-based features & #MachineLearning…
About 6 days, 22 hours ago by: Kota Miura (@cmci_)

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RT @ArizonaImaging: ImageJ/FIJI ASU TEC Talk, Thursday March 18. Learn about techniques at the beginner and advanced in a two-part workshop…
About 6 days, 22 hours ago by: Kota Miura (@cmci_)

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RT @jan_eglinger: Batch processing, image and data analysis with visual workflows using #KNIME - join @stelfrich and myself this Thursday f…
About 1 week ago by: Kota Miura (@cmci_)

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RT @DrAnneCarpenter: Postdoc opening in Boston! Your expertise in machine learning, statistics and/or data science can be splendidly appli…
About 1 week, 2 days 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 12:46 by kota