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RT @WimJHH: EMBL Heidelberg workshop "Cryo-EM in Industry & Academia", 6-8 February 2019. Success stories, new technologies, industry chall…
About 5 hours, 41 mins ago by: Kota Miura (@cmci_)

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@f_levet @BertrandVernay I made it.
About 6 hours, 31 mins ago by: Kota Miura (@cmci_)

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RT @haesleinhuepf: One more session on #ImageJ short cuts: SHIFT+U opens the command tree. I didn't know this one. Thanks @BertrandVernay a…
About 6 hours, 43 mins ago by: Kota Miura (@cmci_)

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@ManuelTHERY @martinjones78 @NEUBIAS_COST Slowly Manu
About 16 hours, 25 mins ago by: Kota Miura (@cmci_)

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@laure_plantard I can’t track JY himself with Trackmate. Metaphysical contradiction.
About 18 hours, 17 mins ago by: Kota Miura (@cmci_)

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“2 chapters of my dissertation was only possible with Trackmate”
About 19 hours, 45 mins 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)