Installation
Fiji is just ImageJ ("Fiji"). This is a "batteries included" version of ImageJ which includes a collection of key plugins installed from the start.
Fiji can be downloaded here.
Please download, extract the files and install Fiji to your User space (the Desktop is a suggested) rather than the "Program Files" or other system-wide directories.
Workshop materials
This workshop requires a few additional images, and is also accompanied by a presentation. Some key points are also sumarised in the Fiji cheatsheets included.
All these files can be dowloaded from the following GitHub repository
Select the green "Code" button, Download ZIP and extract files.
Workshop contents
- What is an image?
- Making figures
- Recorder and Programming Basics
- Quantitative measurements
- Loops and conditions
Resources
- Join the Exeter University Imaging Forum group on Teams for discussion, advice, imaging-related seminars, and other events
- Pete Bankhead's excellent Introduction to Bioimage Analysis
- A very accessible introduction to bioimage analysis
- Can be used as a starting point for learning ImageJ macro and Python for image analysis
- Koto Miura's book, Bioimage Data Analysis.
- A thorough manual touching on numerous types of analyses and multiple programming languages (ImageJ, R, MatLab)
- When writing ImageJ macro code, the library of built in functions is a helpful reference
- This includes many examples of functions being used, which you can hack up an cannibalise!
- The Image.sc forum
- If you have a problem, someone else has probably had it too, and posted it here
- Can't find your problem? Post it! The community is very responsive and supportive
- YouTube is a great source of training material, with Robert Haase being particularly prolific and engaging