User Tools

Site Tools


Courses -2016
Courses 2018-
Downloads (-2016)
Downloads (2016-)
RSS aggregates

EMBL BioImage Data Analysis



—- Contact
CMCI Alumni
EMBL Heidelberg
EMBL Intranet

Popularity Ranking

Timeline of @cmci_

cmci_ avatar

... so don't think that you need to submit a full text.
About 4 days, 20 hours ago by: Kota Miura (@cmci_)

cmci_ avatar

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

cmci_ avatar

I really like the article refers to the MoU of NEUBIAS. We made pretty much of efforts in polishing our initial "Ma…
About 4 days, 23 hours ago by: Kota Miura (@cmci_)

cmci_ avatar

recommendation to read
About 5 days, 4 hours ago by: Kota Miura (@cmci_)

cmci_ avatar

RT @florianjug: If you missed the webinar but are interested to have a look, a recording is now available: Thanks a…
About 1 week, 5 days ago by: Kota Miura (@cmci_)

cmci_ avatar

RT @SuperResoluSian: We've collated all the links from our @NEUBIAS_COST webinar on SMLM analysis into a post!⬇️ From here you can navigate…
About 2 weeks, 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 05:46 by kota