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ImageJ / Fiji

Overview

ImageJ is a GUI-based program that is used to process and analyze scientific images and videos.

Fiji is a distribution of ImageJ2 (rewritten version of ImageJ) that contains several community plugins all packaged together into a single program for easy use.

While separate, both of these are similar enough to put them together into a single guide.

Availability

Cluster Module/Version
BOSE imagej/1.53
imagej-fiji/2.15.0
BGSC N/A

Note: You can simply use module load imagej or module load imagej-fiji to activate the most recently installed version of each of these software.

GUI-Mode

Due to its interactive and visual nature, running ImageJ and Fiji is best done by using Desktop Mode in our web-based Open OnDemand platform, which lets you access our computing infrastructure using your web brower.

Desktop Mode

  1. Log into Open OnDemand - https://ondemand.hpc.uwec.edu
  2. Click "Desktop" on the dashboard, or by first clicking "Interactive Apps" in the top bar.
  3. Fill out your required resources to the best of your abilities. Unsure what to use?
  4. Wait for the job to start, then click "Launch Desktop"
  5. Start the terminal by clicking on the black square icon in the top bar, or by going to Applications --> System Tools --> MATE Terminal"

ImageJ:

  1. Type: module load imagej
  2. Type: Imagej

Fiji:

  1. Type: module load imagej-fiji
  2. Type: Fiji

Your Desktop session for ImageJ/Fiji will remain operational based on the number of hours you entered in the form. Once the time limit is hit, it'll automatically quit without saving.

Done using ImageJ or Fiji?

To free up resources for other users, we ask that you stop your Desktop instance when you are done using the cluster.

  1. In Open OnDemand, click on "My Interactive Sessions"
  2. Find your running Desktop and click "Cancel"

Batch-Mode (Using Macros)

While primarily used as a GUI-based program in Desktop Mode, ImageJ/Fiji also includes the ability to automate image processing through the use of ImageJ's macros in 'headless mode'.

The following Slurm script uses Fiji, which will cover most (if not all) use cases, but you can refer to this table to change between the two:

Program Load Module Executable Name
Fiji imagej-fiji Fiji
ImageJ imagej ImageJ

Sample Slurm Script

submit.sh
#!/bin/bash
# -- SLURM SETTINGS -- #
# [..] other settings here [..]

# The following settings are for the overall request to Slurm
#SBATCH --ntasks-per-node=32     # How many CPU cores do you want to request
#SBATCH --nodes=1                # How many nodes do you want to request

# -- SCRIPT COMMANDS -- #

# Load the needed modules
module load imagej-fiji    # Load Fiji
Fiji --headless --console -macro my-macro.ijm

Real Example

Has your research group used ImageJ or Fiji in a project? Contact the HPC Team and we'd be glad to feature your work.

Citation

Please include the following citation in your papers to support continued development of ImageJ and Fiji. Please check out the full citation page for more details, including how to cite individual plugins.

ImageJ:

Schneider, C. A., Rasband, W. S., & Eliceiri, K. W. (2012). NIH Image to ImageJ: 25 years of image analysis. Nature Methods, 9(7), 671–675. doi:10.1038/nmeth.2089

Fiji:

Schindelin, J., Arganda-Carreras, I., Frise, E., Kaynig, V., Longair, M., Pietzsch, T., … Cardona, A. (2012). Fiji: an open-source platform for biological-image analysis. Nature Methods, 9(7), 676–682. doi:10.1038/nmeth.2019

Resources