Detailed workinar content overview:

  • Basic ImageJ macro recording of a general image analysis pipeline
  • Basics about variables and macro command and how to use them
  • Looping over image files, table data, ROIs
  • Interaction between user and macro
  • Automatic customized measurements
  • Creating and interacting with customized tables
  • Automatically creating folders and flexibly saving all data as needed
  • Testing conditions and creating automatic macro decisions
  • Creating reusable functions
  • Creating different customized dialogs for user input
  • Making your own ImageJ menu with your own macros
  • Optional: tips for individual solutions

All methods are learned hands-on with plenty of practical exercises to get confidence in applying them in your daily work.


Hard Skill


The workshop will be held as a virtual live event via Zoom. Login information and preparation instructions will be send in advance.


2 days, each day 9:00 ~ 15:30 (max, mostly 15:00 but plan some buffer time)


Prior participation in the BioVoxxel Workshop – “Basic Microscopic Image Processing and Analysis” is mandatory to be able to follow the complete content of this workshop. Participation without prior basic course attendance can only be permitted in exceptional cases in agreement with the trainer and a sound prior knowledge of image processing techniques and ImageJ.

Main Target Group:

Life or Natural Scientists (optimally around PhD student level and above, imaging experience is helpful, knowledge from the Basic Microscopic Image Processing and Analysis workshop is assumed!).

Difficulty Level:

The difficulty level is medium to advanced but easy to follow in step by step procedures and in-depth explanation of the necessary background to the individual methods. No prior programming knowledge is necessary.


During the course we will use exclusively Fiji (ImageJ bundle) in a customized setup. Prior experience with Fiji as shown in the basic course is assumed.

Registered participants will receive all information regarding software preparation on time before the workshop via email.