Biowulf High Performance Computing at the NIH
Fiji: an open-source platform for biological-image analysis on Biowulf

Fiji is a distribution of the popular open-source software ImageJ focused on biological-image analysis. Fiji uses modern software engineering practices to combine powerful software libraries with a broad range of scripting languages to enable rapid prototyping of image-processing algorithms. Fiji facilitates the transformation of new algorithms into ImageJ plugins that can be shared with end users through an integrated update system.


Important Notes

Interactive job
Interactive jobs should be used for debugging, graphics, or applications that cannot be run as batch jobs.

Allocate an interactive session and run the program. You should see the Fiji logo appear, and then the Fiji console window.
In order to use Fiji, you have to create graphical X11 connection to Biowulf.
Both MobaXterm (recommended) and NX will work for Windows users, while XQuartz works well for Mac users.

Sample session:

[user@biowulf]$ sinteractive
[user@@cn3316 ~]$ module load Fiji 
[user@@cn3316 ~]$ fiji &

Fiji display