Fiji

Fiji is an image processing package—a "batteries-included" distribution of ImageJ, bundling a lot of plugins which facilitate scientific image analysis.

In order to use this application you will first need to start an interactive Qlogin session to one of the GPU nodes

[gqd693@login-0-0 ~]$ qlogin -q gpu.q
local configuration login-0-0.cm.cluster not defined - using global configuration
Your job 377 ("QLOGIN") has been submitted
waiting for interactive job to be scheduled ...
Your interactive job 377 has been successfully scheduled.
Establishing /cm/shared/apps/sge/var/cm/qlogin_wrapper session to host compute021.cm.cluster ...
Last login: Wed Aug 24 09:44:29 2016 from login-0-0.cm.cluster
[gqd693@compute021 ~]$

Now load the module

[gqd693@compute021 ~]$ module load fiji

Start the application (it may take awhile the first time)

[gqd693@compute021 ~]$ ImageJ-linux64

Fiji may prompt you to update, click Ok to update the application and restart the application when prompted

Now you'll need to install the Mosaic Suite plugin

Open Fiji again with the command above

Within the Fiji application window click Help -> Update

Now click Manage update sites then in the next window click Ok then Add update site. Add this address

http://mosaic.mpi-cbg.de/Downloads/update/Fiji/MosaicToolsuite

Click Apply changes and it will beging to install the Mosaic Suite plugin

-- AdminUser - 25 Aug 2016