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EMBL BioImage Data Analysis

EuBIAS

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cmci_ avatar

RT @martinjones78: Very interesting #BioImageAnalysis PhD position! https://t.co/85QLBKiANx
About 3 mins, 51 secs ago by: Kota Miura (@cmci_)

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RT @jobRxiv: #ScienceJobs: Image Analyst / Python programmer Francis Crick Institute (@TheCrick), London, UK https://t.co/T7cDhv9PX0 #P…
About 3 mins, 56 secs ago by: Kota Miura (@cmci_)

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... so don't think that you need to submit a full text.
About 4 days, 21 hours ago by: Kota Miura (@cmci_)

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The deadline next week for NEUBAIS Gateway article is just for the **PROPOSAL.** you just need to fill and submit… https://t.co/2aTmNDxtvz
About 4 days, 21 hours ago by: Kota Miura (@cmci_)

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I really like the article refers to the MoU of NEUBIAS. We made pretty much of efforts in polishing our initial "Ma… https://t.co/E1417kBAAF
About 5 days ago by: Kota Miura (@cmci_)

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recommendation to read https://t.co/3BAl3lzcMc
About 5 days, 5 hours ago by: Kota Miura (@cmci_)
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.1555417896.txt.gz · Last modified: 2019/04/16 05:31 by kota