Fiji – ImageJ
Overview
Fiji is an image processing package — a “batteries-included” distribution of ImageJ, bundling many plugins which facilitate scientific image analysis.
Fiji is mainly used through a java based interactive graphical user interface (GUI). On the CSF3 the GUI can be started remotely on a compute node as an interactive job.
Fiji also provides a headless mode, which is suitable for running batch jobs in the CSF3. For more info on headless mode please read the official project documentation.
Restrictions on use
Fiji is free software, licensed under the GNU General Public License. It builds on top of the ImageJ2 core, which is licensed under the permissive BSD 2-clause license. Plugins and other components have their own licenses.
All CSF users may use this software, as long as they follow the license terms.
Set up procedure
Before running fiji, load the module below:
module load apps/binapps/fiji/2.16.0
Running the application
Running the GUI interactively from a compute node
To be able to run workflows that can utilise multiple CPU cores, in this case 8 cores:
srun-x11 -p interactive -n 1 -c 8 -t 0-1 module load apps/binapps/fiji/2.16.0 fiji &
Running a batch job in headless mode
Create a jobscript similar to the one below:
#!/bin/bash --login #SBATCH -p multicore # Partition is required. Runs on an AMD Genoa hardware. #SBATCH -n 8 # (or --ntasks=) where numcores is between 2 and 168. #SBATCH -t 1-0 # Wallclock limit (days-hours). Required! # Max permitted is 7 days (7-0). # Load any required modulefiles. A purge is used to start with a clean environment. module purge module load apps/binapps/fiji/2.16.0 fiji --headless -macro path-to-Macro.ijm
Then submit your jobscript from within the scratch directory:
sbatch jobscript