# Bioimage Analysis Wiki

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EMBL BioImage Data Analysis

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 RT @jytinevez: LimeSeg on bioRXiv: LimeSeg: A coarsed-grained lipid membrane simulation for 3D image segmentation https://t.co/jECl7deOVG About 9 hours, 23 mins ago by: Kota Miura (@cmci_) Impressive and swift moderation @helenajambor ! About 2 days, 14 hours ago by: Kota Miura (@cmci_) RT @LuisDVerde: Now available as a #ggplot2 geom thanks to @naupakaz https://t.co/zOaMWvzd8k https://t.co/AXYBCeGyw6 About 2 days, 14 hours ago by: Kota Miura (@cmci_) RT @helenajambor: awesome, within 2 days .@naupakaz made a code publicly available for anyone wanting to make the half-and-half-plot FYI @… About 2 days, 14 hours ago by: Kota Miura (@cmci_) RT @dgaboriau: Thread on data visualisation: ggplots, boxplots and violin plots https://t.co/QZE7xQtaa3 About 2 days, 20 hours ago by: Kota Miura (@cmci_) RT @christlet: SUSHI from Valentin Nāgerl lab allows super-resolution microscopy of neuronal morphology by STED imaging of extracellular sp… About 2 days, 23 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.