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EMBL BioImage Data Analysis

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wow... https://t.co/sAjaZ0irwN
About 5 days, 12 hours ago by: Kota Miura (@cmci_)

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@notjustmoore @haesleinhuepf @LaineBioImaging @alicepyne @RSE_Sheffield @sebastianmunck How about reverse coding -… https://t.co/8MhZOclxyn
About 5 days, 12 hours ago by: Kota Miura (@cmci_)

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does this have to be deep-learning? https://t.co/hMrdeCfFO5
About 1 week, 1 day ago by: Kota Miura (@cmci_)

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RT @BioImagingUK: Lots of people were asking if this was recorded, so thank you @EuroBioImaging for uploading Anna Kreshuk's great talk to…
About 1 week, 1 day ago by: Kota Miura (@cmci_)

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RT @NEUBIAS_COST: Job offer for #BIOIMAGE_ANALYST at Core Facility for Integrated Microscopy (CFIM), the Faculty of Health Sciences, Univer…
About 1 week, 2 days ago by: Kota Miura (@cmci_)

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RT @NEUBIAS_COST: Job offer for #BIOIMAGEANALYST at @GuckLab Apply until 30.11.2020 https://t.co/Rk6F5cN4Hp https://t.co/4z5Y52Caig
About 1 week, 2 days 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)