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.
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
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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) Activity 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 Workshop Overview Workshop Instruction & Demo data File Download Workshop playlist Video Playlist Introductory lecture Fundamentals of Digital Imaging Video FIJI Set up & Basic Functions Activity 1: Installing FIJI Short video Activity 2: Installing a FIJI plugin Short video Activity 3: Opening files Short video Activity 4: Stacks vs Hyperstacks Short video Activity 5: Basic FIJI functions Short video Manipulating Images Activity 6: ROI tools and image cropping Short video Activity 7: Splitting RGB Short video Activity 8: Merge Channels Short video Activity 9: Channel Tool Short video Activity 10: LUT & Calibration bar Short video Activity 11: Adjusting Brightness and Contrast Short video Presenting 2D data Activity 12: Calibrating and adding a scale bar Short video Activity 13: Preparing a 2D panel Short video Activity 14: Figure J Short video Presenting 3D data Activity 15: Z-projection of 3D data Short video Activity 16: Orthogonal views of 3D data Short video Activity 17: Montage of 3D data Short video Activity 18: Z translation of 3D data Short video Activity 19: 3D rotation movie Short video Presenting Timelapse data Activity 20: Visualising timelapse data Short video Activity 21: Annotating timelapse data Short video Activity 22: Kymograms Short video -
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) Activity 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 Workshop Overview Workshop downloads (Instructions, demo data, software) File Download Workshop Video playlist Video Playlist Introductory lecture Fundamentals of Image Quantification Lecture Hands on Activities Activity 1: Line Analysis Short Video Activity 2: Auto Threshold Short Video Activity 3: Area of Stain Short Video Activity 4: Cell Confluency Short Video Activity 5: Auto Local threshold Short Video Activity 6: Machine learning Short Video Activity 7: Nuclei Counting Short Video Activity 8: Stardist Deep Learning Short Video Activity 9: Cell Segmentation Short Video Activity 10: Advanced Segmentation Short Video Activity 11: Intensity over time Short Video Activity 12: Euclidean Distance Measurements Short Video Activity 13: Recording and Running a Macro Short Video Activity 14: Batch Macro Analyses Short Video -
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