fiji

  • About: Fiji is just ImageJ with plugins
  • Category: Graphics
  • URL: http://fiji.sc
  • Interactive executable: ImageJ_mem
module (bold = default) build dependencies
fiji/1.49q self-contained jre/1.7.0
fiji/1.50a self-contained jre/1.7.0 j3d/1.5.2
fiji/continuous/64bit self-contained jre/1.7.0

Running Fiji/ImageJ Interactively

Use the interactive command to get connected to a compute node with X11 forwarding enabled.

interactive -t 2:00:00 -n 1 --mem=16gb

Once your job starts, you should find yourself on a compute node. Then you can load fiji and launch ImageJ using

module load fiji
ImageJ_mem

Note the use of ImageJ_mem. This is a script that extracts the amount of memory for your job from the slurm environment and launches ImageJ with that amount of memory.

also see Using Software.