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 (FIJI is just ImageJ) is a “batteries-included” distribution of ImageJ, bundling many plugins which facilitate scientific image analysis, especially when it comes to the life sciences. Any AIR facility resources assume that you are using FIJI rather than ImageJ. Download it here.

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.

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