This workshop has been written by Nicholas Condon and is available to all for use.

This workshop covers more advanced topics in FIIJ (FIJI is Just ImageJ) around automating tasks, and making use of plugins. The workshop contains information on scripting and macro generation in FIJI, however is not intended to be an introduction to programming workshop.


Topics Covered

  • Automating Image Analysis
  • Plugins in FIJI (how to find, install, update)
  • Example Plugin - TrackMate
  • Using commands in FIJI
  • Macro Recorder & batch processing
  • Scripting in FIJI Introduction
  • Worked Examples of scripts

Workshop Files

To access the exercise files please click on the following link. Here you can download the complete folder of data and PDFs of the workshop guides (63megabytes).

Advanced FIJI data