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 the most widely used software in our imaging facility. It is freely available, open source and there is a huge community of users and developers who contribute to it.
- 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 a range of videos for common applications in FIJI.
- 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. Scripts can be published and distributed.
- 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 please check here.
- If you are having trouble opening files from the Dragonfly in FIJI then follow these instructions.
- Pete Bankhead produced a great, open source, online textbook called “Analyzing fluorescence microscopy images with ImageJ“. It includes questions and practicals that you can follow along with. There is also a printed version in the image analysis room for reference.
- Kevin Eliceiri, the head of the lab that maintained FIJI has done an iBiology Seminar talking about the history of the software.