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EMBL BioImage Data Analysis

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RT @dgaboriau: #BioImageAnalysis Training Schools by @NEUBIAS_COST in Bordeaux Highly recommended if you want world-class teaching ! #NEU…
About 3 days, 6 hours ago by: Kota Miura (@cmci_)

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RT @NEUBIAS_COST: BIAFLOWS: A collaborative framework to benchmark bioimage analysis workflows https://t.co/I23P1BaNUd
About 3 days, 6 hours ago by: Kota Miura (@cmci_)

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RT @SimonFlyvbjerg: Nice collection of papers from 2019 -- Focus on Deep Learning in Microscopy: https://t.co/CfUyLdEiDw #BioImageAnalysi…
About 3 days, 9 hours ago by: Kota Miura (@cmci_)

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RT @mariana_deniz: Here is our @preLights highlight on BIAFLOWS, an exciting tool for sharing, deploying, and comparing bioimage analysis w…
About 6 days, 1 hour ago by: Kota Miura (@cmci_)

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RT @NEUBIAS_COST: NEUBIAS Training Schools TS14 & TS15 – Bordeaux, France, Feb 29 - March 3, 2020 | Applications Now Open - https://t.co/hX
About 1 week ago by: Kota Miura (@cmci_)

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RT @jan_eglinger: Should #TrackMate change its default #colormap ? @FijiSc/#ImageJ users, please contribute your opinions: https://t.co/r5q
About 1 week 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)