Fiji

Fiji is an image processing package. It can be described as a “batteries-included” distribution of ImageJ (and ImageJ2), bundling Java, Java3D and a lot of plugins organized into a coherent menu structure. Fiji compares to ImageJ as Ubuntu compares to Linux. (from Fiji website)

Fiji has a graphical interface, and thus requires X11.

Mac OS X Setup

OS X no longer comes with X11 by default, but it is easily obtained. Install the XQuartz package from here

After you install XQuartz, connect to a standalone server with ssh, including the -Y command line argument.

benji-macbookpro: ~ $ ssh -Y benji@ford.ibest.uidaho.edu

Then load the module and start fiji

benji@ford ~ $ module load fiji
benji@ford ~ $ fiji
[INFO] Found 672 plugins.
log4j:WARN No appenders could be found for logger (org.bushe.swing.event.EventService).
log4j:WARN Please initialize the log4j system properly.
log4j:WARN See http://logging.apache.org/log4j/1.2/faq.html#noconfig for more info.
[INFO] Found 11 DataType plugins.
[INFO] Found 1 Platform plugins.
...

You may encounter several warnings, but these seem not to impact the operation of Fiji. You should see the graphical interface show up shortly.

Windows Setup

Setting up X11 for Windows is somewhat more complex. Download Cygwin from the official website. Then, follow the instructions from this page when running the installer. If you choose the defaults through the installation prompts, X11 will not be installed. At the package selection screen you have to select the following packages: (click the until it shows a version number)

Under the X11 submenu:

  • xauth
  • xorg-server
  • xorg-server-common
  • xinit
  • xorg-docs
  • xterm

Under the Net submenu:

  • openssh

The installation can take a while depending on the mirror you choose to download from.

Start an XWin Server Terminal and log into a standalone server with ssh, including the -Y command line argument.

ssh -Y benji@ford.ibest.uidaho.edu

Start fiji

module load fiji
fiji