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RT @empleo_mid: Puesto: 1 PhD student position available for "Image analysis of cardiac development in the mouse" - CNIC https://t.co/0AfJ8
About 14 hours, 6 mins ago by: Kota Miura (@cmci_)

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RT @CanonMedicalEDI: Five #vacancies currently open: Image Analysis Scientist, Software Engineer (various) & IT Administrator. Rewarding #H…
About 1 day, 15 hours ago by: Kota Miura (@cmci_)

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@haesleinhuepf @ReynaudEmmanuel @BioImagingUK @BBSRC @NEUBIAS_COST ... and fun!
About 1 day, 15 hours ago by: Kota Miura (@cmci_)

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RT @thewtex: @cmci_ @ProjectJupyter @UCBIDS @stefanvdwalt @cziscience @thefreemanlab @ctrueden @FijiSc @cmci_ sorry about the quality. Here…
About 1 day, 15 hours ago by: Kota Miura (@cmci_)

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@thewtex @ProjectJupyter @UCBIDS @stefanvdwalt @cziscience @thefreemanlab @ctrueden @FijiSc thanks!
About 1 day, 15 hours ago by: Kota Miura (@cmci_)

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@thewtex @ProjectJupyter @UCBIDS @stefanvdwalt @cziscience @thefreemanlab @ctrueden @FijiSc great! do you have an y… https://t.co/Xnyd9VhAip
About 1 day, 16 hours ago by: Kota Miura (@cmci_)
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 05:46 (external edit)