User Tools

Site Tools


Sidebar

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


EMBL BioImage Data Analysis

EuBIAS

NEUBIAS

—- Contact
CMCI Alumni
ALMF
EMBL Heidelberg
EMBL Intranet


Popularity Ranking


Timeline of @cmci_

cmci_ avatar

RT @BoSoxBioBeth: 2 days left to submit an abstract proposal! We want all your best ideas on image analysis!
About 7 hours, 42 mins ago by: Kota Miura (@cmci_)

cmci_ avatar

RT @ManuelTHERY: Here we are. The combination of biochemically controled differentiation of iPS cells with microprinting to direct cell sel…
About 7 hours, 43 mins ago by: Kota Miura (@cmci_)

cmci_ avatar

RT @haesleinhuepf: "Do you also spend a substantial amount of your time waiting for automated image analysis to finish? [...] And, then, th…
About 19 hours, 9 mins ago by: Kota Miura (@cmci_)

cmci_ avatar

RT @ALM_i3S: Do you want to extract quantitative data from images and automate this process by learning ImageJ Macro Language? Apply to t…
About 1 day, 14 hours ago by: Kota Miura (@cmci_)

cmci_ avatar

RT @martinjones78: Very interesting #BioImageAnalysis PhD position! https://t.co/85QLBKiANx
About 1 day, 14 hours ago by: Kota Miura (@cmci_)

cmci_ avatar

RT @jobRxiv: #ScienceJobs: Image Analyst / Python programmer Francis Crick Institute (@TheCrick), London, UK https://t.co/T7cDhv9PX0 #P…
About 1 day, 14 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 05:46 by kota