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.
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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 Links Intro to Digital Imaging Lecture File Download Video Playlist Hands on session: Activity Instruction (Full workshop) Hands on session: Demo data Hands on activity: Opening files Short video Hands on activity: Splitting RGB Short Video Hands on activity: Merge Channels Short Video Hands on activity: Channel Tool Short Video Hands on activity: Calibrating and adding a scale bar Short Video Hands on activity: Z-projection of 3D data Short Video Hands on activity: Orthogonal views of 3D data Short Video Hands on activity: Montage of 3D data Short Video Hands on activity: Z translation of 3D data Short Video Hands on activity: 3D rotation movie Short Video Hands on activity: Movies of 3D data Short Video Hands on activity: Kymograms Short Video Hands on activity: Visualising timelapse data Short Video Hands on activity: Annotating timelapse data Short Video -
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 Links Fundamentals of Image Quantification Lecture File Download Video Playlist Hands on session: Activity Instruction (Full workshop) Hands on session: Demo data Hands on activity: Line Analysis Short Video Hands on activity: Auto Threshold Short Video Hands on activity: Area of Stain Short Video Hands on activity: Cell Confluency Short Video Hands on activity: Nuclei Counting Short Video Hands on activity: Cell Segmentation Short Video Hands on activity: Advanced Segmentation Short Video Hands on activity: Intensity over time Short Video Hands on activity: Euclidean Distance Measurements Short Video Hands on activity: Kymograms Short Video Hands on activity: Recording and Running a Macro Short Video Hands on activity: Batch Macro Analyses Short Video -
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 Resources Links Presentation files File Download Demo data Macro files Workshop presentation recordings Video 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