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RT @CornellBiotech: Join us for the Fiji (ImageJ) Summer Workshop Aug 10-12 https://t.co/hRVTW6JJyL
About 3 days, 11 hours ago by: Kota Miura (@cmci_)

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RT @christlet: Extending the classic full-width at half-maximum (FWHM) method for estimating image resolution on sub-resolutive structures…
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RT @CiminiLab: I've made a Twitter Community for Bioimage Analysis- feel free to join and share widely! I'll fully admit this is an experim…
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RT @kjaMartens: We created a very simple method to get high precision and density in spectrally-resolved single-molecule localization micro…
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RT @random_walker: There’s a reproducibility crisis brewing in almost every scientific field that has adopted machine learning. On July 28,…
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documents:101213imagej_silent

ImageJ with fake X server

Ruben found a way to setup fake X-server in server side, that one could use ImageJ silently from client. In a sense, ImageJ head is existing so it's not really headless but it might be even less problem than using headless.jar since the silent mode described below could handle awt instances within fake-X so that ImageJ works as same as what you see on your local machine (but silently).

Startup your ssh client (putty or so) and connect to a server. Foe example

ssh YOURNAME@clnode336

You need to enter password, then

setenv DISPLAY :1
Xvfb :1 &

(error, but return) then invoke ij such as

imagej

with this, nothing happens but imagej is running remotely. You could then pass macro or scripts by adding argument.

after finishing the process, terminate the Xvfb by

fg

to bring the X forward, then kill the session if you are done.

An example command could be

fiji -macro whatevermacro.ijm
documents/101213imagej_silent.txt · Last modified: 2016/05/24 12:46 (external edit)