User Tools

Site Tools


Sidebar

Top
Profile
Seminar
Courses -2016
Courses 2018-
Textbooks
Documents
Downloads (-2016)
Downloads (2016-)
Weblog
RSS aggregates
Discussions
Archives
日本語


EMBL BioImage Data Analysis

EuBIAS

NEUBIAS

—- Contact
CMCI Alumni
ALMF
EMBL Heidelberg
EMBL Intranet


Popularity Ranking


Timeline of @cmci_

cmci_ avatar

RT @martinjones78: After a covid-enforced 1 year hiatus, undergrad #SandwichStudent placements resume in 2022 @TheCrick, including this one…
About 1 day, 20 hours ago by: Kota Miura (@cmci_)

cmci_ avatar

Portugueses, aqui está! https://t.co/vXaxWRhC03
About 1 day, 20 hours ago by: Kota Miura (@cmci_)

cmci_ avatar

Fiji / ImageJ course @ Lisbon https://t.co/Vqi31iWvxu
About 2 days, 20 hours ago by: Kota Miura (@cmci_)

cmci_ avatar

RT @iii_imaging: interested in #SuperResolution #ElectronMicroscopy and Image Analysis in #Toxoplasma? we have all this in this great work…
About 2 days, 20 hours ago by: Kota Miura (@cmci_)

cmci_ avatar

RT @dukebiochem: Don't forget about tomorrow's research seminar with Dr. Alberto Bartesaghi, when he will speak about "High-resolution cryo…
About 2 days, 20 hours ago by: Kota Miura (@cmci_)

cmci_ avatar

RT @PhelpsLab_UF: @UFBME is hiring in the AI space. Image analysis folks working on AI or DL like #StarDist and #ZeroCostDL4mic, can you sh…
About 2 days, 20 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.txt · Last modified: 2019/04/16 12:46 by kota