FIJI Workshop resources

FIJI/Image J is a freeware that can be used for the Visualisation & Quantification of digital images. This workshop series is split into two sections around those two functions.

FIJI for Beginners: Aims to provide new users with an introduction into FIJI. This workshop includes details on how to import data, change colours, split/merge images, add scale bars and present 2D & 3D datasets for presentations/publications.

FIJI for Quantification: Aims to provide an overview of the quantitative functions available within FIJI. Using real-life examples to show researchers the step-by-step functions required to extract the quantitative information from their images.

FIJI Macro writing for Biologists: Aims to provide advanced FIJI users with the understanding and tools to perform more complicated batch analyses and custom data logging.

The below workshop content includes presentations pdfs, demo data, workshop recordings and short instructional videos of all hands-on examples.

If you have any queries regarding FIJI analyses or the workshops then please contact BOMP.

  • FIJI for Beginners Workshop

    This workshop covers how to use FIJI to open, visualise and modify your fluorescence images. The workshop is split into two sections:

    1) Intro to Digital Imaging: Provides an overview of the how the digital image is generated and how to image correctly using a microscope

    2) Hands on Session: Provides a demonstration of how to open, visualise and modify your fluorescence images. You can download the demo data and work through the presentation pdf or watch the instructional videos

    FIJI for Beginners Resources (Feb 2021)Links
    Intro to Digital Imaging Lecture File DownloadVideo Playlist
    Hands on session: Activity Instruction
    Hands on session: Demo data
  • FIJI for Quantification Workshop

    This workshop covers how to use FIJI to extract numerical data from your images. The workshop is split into two sections:

    1) Fundamentals of Image Quantification: Provides an overview of the quantitative functions possible within FIJI

    2) Hands on Session: Provides a demonstration of some quantitative readouts. You can download the demo data and work through the presentation pdf or watch the instructional videos

    FIJI for Quantification Resources (Feb 2021)Links
    Fundamentals of Image Quantification LectureFile DownloadVideo Playlist
    Hands on session: Activity Instruction 
    Hands on session: Demo data
  • FIJI Macro writing for Biologists

    This workshop covers the tools to perform more complicated batch analyses and custom data logging.

    Please follow the below links to the presentation pdfs, demo images, macro files and workshop recordings.

    FIJI Macro Writing for Biologists ResourcesLinks
    Presentation filesFile Download
    Demo data
    Macro files
    Workshop presentation recordingsVideo Playlist

Download: http://fiji.sc/#download

Citing: http://imagej.net/Citing

We would like to thank Cameron Nowell (Monash Institute of Pharmaceutical Sciences) for allowing us to use content from his FIJI manual. Further instruction manuals, including the one developed by Cameron Nowell, are available via the FIJI website