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

—- Contact
CMCI Alumni
ALMF
EMBL Heidelberg
EMBL Intranet


Popularity Ranking


Timeline of @cmci_

cmci_ avatar

RT @SimonFlyvbjerg: PhD position in Plant Cell Mechanobiology - Montreal University. Experiments and image analysis. Anne-Lise is a lovely…
About 1 day, 4 hours ago by: Kota Miura (@cmci_)

cmci_ avatar

RT @RetoPaul: We have submitted a manuscript yesterday... Sneak peak of ‘natural born killer’ cell at work, courtesy of @alexcarisey. http…
About 1 day, 20 hours ago by: Kota Miura (@cmci_)

cmci_ avatar

RT @SimonFlyvbjerg: Fast grants for: - PIs at an academic institution - Already working on a project that could help with the COVID-19 pan…
About 1 day, 20 hours ago by: Kota Miura (@cmci_)

cmci_ avatar

RT @dwaithe: Want to learn #Python #Bioimage analysis? We just made some video updates to the course and pledge to answer your #Python ques…
About 1 day, 20 hours ago by: Kota Miura (@cmci_)

cmci_ avatar

Vaccine Formula-1.
About 3 days, 1 hour ago by: Kota Miura (@cmci_)

cmci_ avatar

RT @BristolUncover: Pre-clinical trails for a #COVID19 vaccine candidate to begin WITHIN WEEKS, thanks to novel technology used by Universi…
About 3 days, 1 hour 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)