# Bioimage Analysis Wiki

### Sidebar

EMBL BioImage Data Analysis

EuBIAS

NEUBIAS

Popularity Ranking

 RT @_pm_lab: Unbiased quantitative phenotypic #BioImageAnalysis of #3D #microscopy images in #HighContentScreening is a fundamental challen… About 7 hours, 44 mins ago by: Kota Miura (@cmci_) RT @joachimgoedhart: Our recent preprint has several step-by-step guides that explain how timelapse imaging data can be processed and visua… About 5 days, 7 hours ago by: Kota Miura (@cmci_) RT @PLOSCompBiol: 3D #BioImageAnalysis for #HighContentScreening should be easy. Using data driven voxel-based features & #MachineLearning… About 6 days, 23 hours ago by: Kota Miura (@cmci_) RT @ArizonaImaging: ImageJ/FIJI ASU TEC Talk, Thursday March 18. Learn about techniques at the beginner and advanced in a two-part workshop… About 6 days, 23 hours ago by: Kota Miura (@cmci_) RT @jan_eglinger: Batch processing, image and data analysis with visual workflows using #KNIME - join @stelfrich and myself this Thursday f… About 1 week ago by: Kota Miura (@cmci_) RT @DrAnneCarpenter: Postdoc opening in Boston! Your expertise in machine learning, statistics and/or data science can be splendidly appli… About 1 week, 2 days 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.