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The field for bioimage analyst expanding. British museum! https://t.co/KClNvxP948
About 2 days, 6 hours ago by: Kota Miura (@cmci_)

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RT @dgaboriau: Panel session: should I aim to become a bioimage analyst? With Robert Hasse @haesleinhuepf , Kota Miura @cmci_ and Arianne B…
About 3 days, 20 hours ago by: Kota Miura (@cmci_)

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RT @martinjones78: Shoutout by @cmci_ for @clathrin's book https://t.co/x6d2OmfdxR as a great resource, here at #CBIAS2022 in the panel ses…
About 3 days, 20 hours ago by: Kota Miura (@cmci_)

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RT @alex_paynedwyer: The one and only Kota Miura @cmci_ calling out all those dodgy contrast-mismatched figures #ethics in classic humorou…
About 4 days, 5 hours ago by: Kota Miura (@cmci_)

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RT @RekadZeinab: Kicking the last session of #CBIAS2022 with the great master @cmci_ on the challenges of doing image analysis at the inter…
About 4 days, 5 hours ago by: Kota Miura (@cmci_)

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RT @MaKaefer: Fear not: there is something that can be done! Abide by the guidelines or report everything that has been done - whether it i…
About 4 days, 5 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 12:46 (external edit)