Fiji

Description

Fiji is an image processing package—a “batteries-included” distribution of ImageJ2, bundling a lot of plugins which facilitate scientific image analysis. For users - Fiji is easy to install and has an automatic update function, bundles a lot of plugins and offers comprehensive documentation. For developers - Fiji is an open source project hosted in a Git version control repository, with access to the source code of all internals, libraries and plugins, and eases the development and scripting of plugins.

Keywords

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

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.

Documentation

• User Guide
• Git Repo
• Website