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 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.

External resources

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