Fiji

Fiji is an image processing package—a “batteries-included” distribution of ImageJ2, bundling a lot of plugins which facilitate scientific image analysis.

Keywords

Fiji, ImageJ, threshold, ROI, Ome-Zarr, Bio-Formats, trackmate

Documentation

• User Guide
• Git Repo

Supported Versions

• 1.54p (vanila)

  • This version of Fiji runs on Java 21.0.7 with no additional plugin installed.

• 1.54p (with plugins)

  • This version of Fiji runs on Java 1.8.0 with the following additional plugins preinstalled
    • ImageScience
    • IJPB-plugins
    • MoBIE
    • clijx-assistant
    • CLIJ,CLIJ2
    • BigDataProcessor
    • BIG-EPFL
    • 3DImageJSuite
    • ilastik
    • CSBDeep (Deprecated)
    • StarDist
    • TrackMate-StarDist
    • FeatureJ
    • Fluidity Calculator

Add additional plugins

Since applications on BARD are all containerised, users do not have write permission to the container. Therefore, installing your own plugins via Update sites is only possible by BARD admins. You have three options to install additional plugins.

Option 1:

1. Create a folder called .plugins under your home directory, e.g. /home/YOURUSERNAME/.plugins
2. Find all the jar files of your plugins, and store them in the .plugins folder.
3. Restart Fiji.

Option 2:

• Since you have write permission to your home directory. Download your own copy of Fiji to your home directory and then use it as usual.

Option 3

• Talk to us by requesting a consultation. We will help you find a solution.