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RT @xuepan3: @palankarr @manorlaboratory Hi Raghva, We compared the results generated by IMARIS and Trackmate in ImageJ. There are some min…
About 2 days, 13 hours ago by: Kota Miura (@cmci_)

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RT @albertcardona: Plotting from your @FijiSc #python scripts, using ImageJ's internal plotting library, and with @jfreechart for prettier…
About 2 days, 14 hours ago by: Kota Miura (@cmci_)

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RT @CefapConfocal: If you struggle with image analysis, check our webpage with few ImageJ and Zen tutorials: https://t.co/9ExHi8MkL1 ps .:…
About 3 days, 11 hours ago by: Kota Miura (@cmci_)

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RT @iefforts: The cells were visualized on a Nikon AR1 or Leica SP8 confocal microscope. At least 30 cells were analysed for each condition…
About 3 days, 11 hours ago by: Kota Miura (@cmci_)

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RT @MarJungle: BigStitcher on ImageJ for 3D model reconstructions. A beta-version is available via the Fiji Updater. I am going to try this…
About 3 days, 11 hours ago by: Kota Miura (@cmci_)

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RT @ARVOtvst: New in the August issue: 25-MHz ultrasound biomicroscopy combined with #ImageJ software can be used to evaluate the opacity d…
About 3 days, 11 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)