Description

Fiji is an image processing distribution of ImageJ, bundling a lot of plugins which facilitate scientific image analysis.
Software Category: tools

For detailed information, visit the Fiji website.

Available Versions

The current installation of Fiji incorporates the most popular packages. To find the available versions and learn how to load them, run:

module spider fiji

The output of the command shows the available Fiji module versions.

For detailed information about a particular Fiji module, including how to load the module, run the module spider command with the module’s full version label. For example:

module spider fiji/1.52
ModuleVersion Module Load Command
fiji1.52 module load fiji/1.52

Interactive Use of Fiji via FastX

We recommend to launch the Graphical User Interface (GUI) of Fiji as an interactive job via FastX. These are the steps:

  1. Create or connect to a FastX session via https://rivanna-desktop.hpc.virginia.edu. If you started a MATE desktop session, open a terminal window.

  2. In the terminal window, start an ijob via this command:

ijob -p standard -A <YOUR_ALLOCTION> -c 8 --mem=32G -t 4:00:00

In this example we are requesting 8 cpu cores and 32GB of memory for 4 hours. Replace <YOUR_ALLOCATION> with your allocation account.

  1. Load the fiji module and start the application:
module load fiji
ImageJ-linux --mem=32G &

Run a Fiji script as SLURM Job

To execute a Fiji script non-interactively on a compute node, you can use the following SLURM job script template.

#!/bin/bash
#SBATCH --job-name=fiji_example
#SBATCH --cpus-per-task=8
#SBATCH --mem=32G
#SBATCH --time=04:00:00
#SBATCH --partition=standard
#SBATCH --account=<YOUR_ALLOCATION>

#Load the Fiji Module
module load fiji

# Change to temp working directory with example files
ImageJ-linux --mem=32G --headless <FIJI_SCRIPT> <SCRIPT_ARGS>
  • Adjust the --cpus-per-task, --mem and --time options as needed. Note that not all built-in Fiji functions or Fiji scripts are designed to utilize multiple cpu cores.

  • Replace <YOUR_ALLOCATION> with your allocation account.

  • Replace <FIJI_SCRIPT> and <SCRIPT_ARGS> with your custom Fiji script and add script arguments as required by the particular Fiji script.