User Tools

Site Tools


Sidebar

Top
Seminar
Courses -2016
Courses 2018-
Textbooks
Documents
Downloads (-2016)
Downloads (2016-)
Weblog
RSS aggregates
Discussions
Archives


EMBL BioImage Data Analysis

EuBIAS

NEUBIAS

โ€”- Contact
CMCI Alumni
ALMF
EMBL Heidelberg
EMBL Intranet


Popularity Ranking


Timeline of @cmci_

cmci_ avatar

RT @EuroBioImaging: Last chance to present your bioimaging analysis work at 4th NEUBIAS conference ๐Ÿ‘‡ https://t.co/D4jfEVfWGo
About 1 day, 9 hours ago by: Kota Miura (@cmci_)

cmci_ avatar

RT @f_levet: You have until next monday to submit an abstract to the @NEUBIAS_COST Symposium. It's your last chance ! Go go go !
About 1 day, 10 hours ago by: Kota Miura (@cmci_)

cmci_ avatar

Bioimage Analysis Lunch Heidelberg, Jan 2020 https://t.co/6FcCNzu1QJ
About 1 day, 10 hours ago by: Kota Miura (@cmci_)

cmci_ avatar

RT @Datascience__: DL@MBL: Deep Learning for Microscopy Image Analysis https://t.co/DT25zxxaRn #DeepLearning
About 2 days, 9 hours ago by: Kota Miura (@cmci_)

cmci_ avatar

@LauLauThom well done Laurent!
About 2 days, 13 hours ago by: Kota Miura (@cmci_)

cmci_ avatar

RT @LauLauThom: Another documentation gem for #ImageJ / #Fiji geeks https://t.co/GgC2rRSEYo https://t.co/Gce9E0o8Xt
About 4 days, 7 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 ยท Last modified: 2016/05/24 05:46 (external edit)