From the Fiji website: Fiji is an image processing package. It can be described as a distribution of ImageJ (and ImageJ2) together with Java, Java3D and a lot of plugins organized into a coherent menu structure. The main focus of Fiji is to assist research in life sciences.


  • 1.49c

Authorized Users

  • CIRCE account holders
  • SC account holders


  • CIRCE cluster
  • SC cluster


Fiji requires the following module file to run:

  • apps/fiji/1.49c

Running Fiji on CIRCE/SC

The Fiji user guide is essential to understanding the application and making the most of it. The guide and this page should help you to get started with your simulations. Please refer to the Documentation section for a link to the guide.

  • Note on CIRCE: Make sure to run your jobs from your $WORK directory!
  • Note: Scripts are provided as examples only. Your SLURM executables, tools, and options may vary from the example below. For help on submitting jobs to the queue, see our SLURM User’s Guide.

Launching Fiji

Establishing a GUI connection to CIRCE/SC

To use Fiji, you will need to connect to CIRCE/SC with GUI redirection, either using:

  • CIRCE/SC Desktop Environment
  • SSH with X11 redirection
    • If connecting from OSX or Linux via SSH, please ensure that you use one of the following commands to properly redirect X11:
      • [user@localhost ~]$ ssh -X
      • [user@localhost ~]$ ssh -X

Once connected to CIRCE/SC, you can open Fiji using the steps below:

[user@login0 ~]$ module add apps/fiji/1.49c
[user@login0 ~]$ fiji

You should then see the Fiji splash screen, followed by the main window several seconds later.

You can find example images in the File->Open Samples menu of the main command window. For a verbose list of keyboard shortcuts, select Plugins->Shortcuts->List shortcuts from the menu. Use Control+L to open the Command Launcher, to call menu entries by name. To open a list of some recent commands, and a list of the most frequently called commands, hit Control+9. To open new images, type Control+O.


Home Page, User Guides, and Manuals

Benchmarks, Known Tests, Examples, Tutorials, and Other Resources

Reporting Bugs

Report bugs with Fiji to the IT Help Desk: