Fiji ( Fiji Is Just ImageJ )

Fiji is an open source image processing package based on ImageJ. Fiji's main purpose is to provide a distribution of ImageJ with many bundled plugins. This is a brief guide on how to use it.


Go to the official site and download the version that works on your current operational system (Windows, Mac or Linux). It requires Java. Please upgrade to the latest version.

Open Fiji

On your personal computer.

The location of the executable may vary depending on the fiji version you are going to use. For version 2020, double click on:

On Oscar

Applications that require a graphics UI ( window ) needs a visual/interactive interface to work with. If you want to use the installed version of Fiji in Oscar you have to open a VNC session.
  1. 2.
    Doble click on the CCV_VNC_2.0.1.jar
  1. 1.
    Use your ccv user and password (usually are the same brown credentials)
  2. 2.
    In the following pop up window select the last option ( 3 Cores - 15 GB Memory 2 GPU) and click on ‘Create VNC Session’’
Wait a few seconds (at least 60 seconds) to get the virtual desktop
Opening Fiji UI
  1. 1.
    Open terminal: Applications - > Utilities -> Terminal (this might differ depending on the Operating System UI)
  2. 2.
    Run the command
$ module load fiji/2020
3. Run the command
$ ImageJ-linux64
You will see the Fiji Window


For instructions on how to use the basic functionalities please follow the guide at:
Also, You can follow this video playlist from the Melbourne Advanced Microscopy Facility.

Data Examples

Fiji has a list of data samples you can play with. They are located at.