Bioimage Analysis Wiki

Sidebar

EMBL BioImage Data Analysis

EuBIAS

NEUBIAS

Popularity Ranking

 RT @mycroscopy: 📢📢📢It's time for our next Neubias Academy @ home webinar: CellPose Date: 25.1.2022 15:30-17:00 CET Registration and more in… About 1 day, 7 hours ago by: Kota Miura (@cmci_) RT @RogerDAntuono: The video of "Introduction to ImJoy: AI-powered image analysis on the web" - [NEUBIAS Academy@Home] Webinar held by @wei… About 1 day, 13 hours ago by: Kota Miura (@cmci_) RT @haesleinhuepf: Jeey! 🥳 Big thanks to Anna @APoetsch for this joint #BioImageAnalysis / #BioStatistics / #Python / #MachineLearning teac… About 1 day, 13 hours ago by: Kota Miura (@cmci_) RT @i3S_UPorto: General introduction to ImageJ/Fiji & methods to extract quantitative data. Design of typical workflows to automate image a… About 3 days, 1 hour ago by: Kota Miura (@cmci_) @vdneuro download the unix version, unpack .tar file and then copy the jar file to the plugin folder. I believe it… https://t.co/bdHcQRRv3M About 3 days, 1 hour ago by: Kota Miura (@cmci_) Beautiful work https://t.co/GQ2bbBSXkM About 4 days, 6 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 (with fonts)
• Putty

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.