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 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.

The below workshop content includes presentations pdfs, demo data 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) Fundamentals of 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 short instructional videos

    FIJI for Beginners ResourcesLinks
    Fundamentals of Digital Imaging (Presentation pdf)File
    Hands on session (Presentation pdf)File
    Hands on session (Demo data)Download
    FIJI for Beginners: You Tube Playlist (Feel Free to bookmark it)Playlist
    FIJI for Beginners: Opening dataVideo
    FIJI for Beginners: Channel Tool for creating RGB imagesVideo
    FIJI for Beginners: Splitting RGB imagesVideo
    FIJI for Beginners: Merge channelsVideo
    FIJI for Beginners: Calibrating an image & adding a scale barVideo
    FIJI for Beginners: Z projection of 3D dataVideo
    FIJI for Beginners: Montage of 3D dataVideo
    FIJI for Beginners: Orthogonal views for 3D dataVideo
    FIJI for Beginners: Movie translation of 3D data (Z translation)Video
    FIJI for Beginners: Movie rotation of 3D data (3D projection)Video
    FIJI for Beginners: Movies of 3D dataVideo
    FIJI for Beginners: Visualising timelapse dataVideo
    FIJI for Beginners: Annotating timelapse dataVideo
  • 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 short instructional videos

    FIJI for Quantification ResourcesLinks
    Fundamentals of Image Quantification (Presentation pdf)File
    Hands on Session (Presentation pdf)File
    Hands on Session (Demo data)Download
    FIJI for Quantification: You Tube Playlist (Feel Free to bookmark it) Playlist
    FIJI for Quantification: Line AnalysisVideo
    FIJI for Quantification: Auto-ThresholdVideo
    FIJI for Quantification: Area of StainVideo
    FIJI for Quantification: Cell ConfluencyVideo
    FIJI for Quantification: Nuclei countingVideo
    FIJI for Quantification: Cell SegmentationVideo
    FIJI for Quantification: Advanced SegmentationVideo
    FIJI for Quantification: Intensity over timeVideo
    FIJI for Quantification: Euclidean Distance MeasurementVideo
    FIJI for Quantification: KymogramVideo
    FIJI for Quantification: Recording and running a MacroVideo
    FIJI for Quantification: Batch Macro AnalysesVideo

Download: http://fiji.sc/#download

Citing: http://imagej.net/Citing

Further instruction manuals, including the one developed by Cameron Nowell (Monash Institute of Pharmaceutical Sciences), are available via the FIJI website