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EMBL BioImage Data Analysis

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RT @IgnacioArganda: #DeepImageJ turn now! 😍 Now even more compatible with more platforms besides @FijiSc Fantastic job by @gomez_mariscal a…
About 1 day, 11 hours ago by: Kota Miura (@cmci_)

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beautiful lab website! https://t.co/X3YaujiVFE
About 1 day, 19 hours ago by: Kota Miura (@cmci_)

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moderately reproducible image analysis (some parts are without scripts.) protocols combining Imaris, Fiji, Matlab,… https://t.co/YDihoLmCZG
About 1 day, 19 hours ago by: Kota Miura (@cmci_)

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wow... https://t.co/sAjaZ0irwN
About 1 week, 1 day ago by: Kota Miura (@cmci_)

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@notjustmoore @haesleinhuepf @LaineBioImaging @alicepyne @RSE_Sheffield @sebastianmunck How about reverse coding -… https://t.co/8MhZOclxyn
About 1 week, 1 day ago by: Kota Miura (@cmci_)

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does this have to be deep-learning? https://t.co/hMrdeCfFO5
About 1 week, 4 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 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)