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RT @_pm_lab: Unbiased quantitative phenotypic #BioImageAnalysis of #3D #microscopy images in #HighContentScreening is a fundamental challen…
About 7 hours, 11 mins ago by: Kota Miura (@cmci_)

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RT @joachimgoedhart: Our recent preprint has several step-by-step guides that explain how timelapse imaging data can be processed and visua…
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RT @PLOSCompBiol: 3D #BioImageAnalysis for #HighContentScreening should be easy. Using data driven voxel-based features & #MachineLearning…
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RT @ArizonaImaging: ImageJ/FIJI ASU TEC Talk, Thursday March 18. Learn about techniques at the beginner and advanced in a two-part workshop…
About 6 days, 22 hours ago by: Kota Miura (@cmci_)

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RT @jan_eglinger: Batch processing, image and data analysis with visual workflows using #KNIME - join @stelfrich and myself this Thursday f…
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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)