ImageJ is an open source image processing software. Is is highly extensible through the user of plugins and scripts that can perform all manner of tasks.
Fiji / Image J is the workhorse of the bioimage analysis community. It is freely available, open source and there is a huge community of users and developers who contribute to it.
Facility Resources
- A general guide to using FIJI as well as more specific protocols that we thought would be helpful for users can be found here.
- We have also developed some videos for some common processes.
- Analysis workflows can be automated in FIJI using scripts. Facility scripts can be found on our Github along with a short guide of how to utilise them.
- More general information on image analysis concepts and terms can be found here.
- If you would like to know if there is a relevant workshop coming up soon or see slides from past workshops please check here.
External resources
- Pete Bankhead produced a great, open source, online textbook called “Introduction to Bioimage Analysis“. It includes questions and practicals that you can follow along with in ImageJ or using Python in Jupyter.
- Kevin Eliceiri, the head of the lab that maintained FIJI has done an iBiology Seminar talking about the history of the software.
IGC Advanced Imaging Resource 