User Tools

Site Tools


Sidebar

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


EMBL BioImage Data Analysis

EuBIAS

NEUBIAS

—- Contact
CMCI Alumni
ALMF
EMBL Heidelberg
EMBL Intranet


Popularity Ranking


Timeline of @cmci_

cmci_ avatar

RT @J_Cell_Sci: Registration is now open for our 2023 Journal Meeting 'Imaging Cell Dynamics', organised by Erika Holzbaur @ErikaHolzbaur,…
About 6 hours, 43 mins ago by: Kota Miura (@cmci_)

cmci_ avatar

RT @joachimgoedhart: This online resource that introduces data visualization using #rstats & ggplot2 has 12 complete protocols available fo…
About 11 hours, 33 mins ago by: Kota Miura (@cmci_)

cmci_ avatar

The code for image analysis is the "provided upon request" style ... it would be much better to have it openly acce… https://t.co/mdEZhFkrF3
About 12 hours, 58 mins ago by: Kota Miura (@cmci_)

cmci_ avatar

RT @SXS_biophysics: Why do cells move faster in higher viscosity environments? Debonil's paper on this question is out: https://t.co/dlpIX7
About 6 days, 2 hours ago by: Kota Miura (@cmci_)

cmci_ avatar

The first day of online “defragmentation” NEUBIAS academy / EOSC-Life ended, lead by @RogerDAntuono . Great job Roc… https://t.co/98YNB7QpOa
About 6 days, 5 hours ago by: Kota Miura (@cmci_)

cmci_ avatar

RT @hpke1980: Our annotator software is coming soon on BiorXiv. Check it out! #napari @napari_imaging #singlecell https://t.co/Irb9i5Qjw8 h…
About 6 days, 7 hours ago by: Kota Miura (@cmci_)
documents:101126x11setup

Using X Windows to use ImageJ and Fiji in server

We could save a lot of time by minimizing data transfer between physical disks. Many of groups in EMBL has its own data server, and people transfer huge files between remote and local machines to do analysis. But if you want to just do some simple jobs, you do not need to transfer files to your local machine: use X-forwarding. With this, processing is done in remote server and receive only the graphical output via network to see results.

Both ImageJ and Fiji could be used in this way, as they both are in EMBL network already.

This short instruction is for setting up such environment.

Windows

You need following two tools:

Xming is an X-server to run in your local machine to show content of window sent from remote server. This will run silently in your local machine to connect remote machine output to your desktop window (called 'X window').

Putty is a SSH client, which securely connect your desktop to the remote machine. Follow the installation procedure explained here or in youtube.

Mac OSX

You need to setup following tool:

  • X11

This application is not installed to OSX machine by default, so you should install it from DVD that came with your machine or install from Apple developer website. Download and nstall Xcode, then you will have X11 in your machine automatically.

To setup, you only need to change two configurations:

  • SSH configuration
  • X11 configuration (might be ok with default)

Detailed instruction could be found here.

Starting Up ImageJ

Log in to the server 'submaster' you could then start up ImageJ by the following command:

/usr/struct/bin/java -cp /g/almf/software/ImageJ/ij.jar -server ij.ImageJ -ijpath /g/almf/software/ImageJ
  • instead of java normally added to the path, java in SCB unit is used because /usr/bin/java is gcc compiled and does not work well with ImageJ.
  • you could add memory argument if your image is too big to load.
  • In my case, I place the above command in .tcshrc as an alias, so that I could invoke just by a command 'ij'. Command 'ImageJ' will start up ImageJ in SCB server, and its version is not the latest.
documents/101126x11setup.txt · Last modified: 2016/05/24 12:46 (external edit)