FIJI Workshop resources

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

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