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Batch analysis and macro development in ImageJ/Fiji: going beyond the basics | 3rd Edition
24-26 November 2021 | i3S

This course is designed for ImageJ/Fiji users who want to go beyond the basics and progress to more intermediate/advanced analysis with this software. The course focuses on how to automate routine tasks (for conditions in which many images need to be processed), as well as how to deal with more complex image analysis situations and maximize information extraction. Although ImageJ can be used with its graphical user interface, the implementation of a workflow to multiple images requires the development of macros and/or scripts for batch processing. In this course, the process is tackled by building up from the development of very simple macros to more complex workflows, where images are processed and information acquired in an automated or semi-automated way.

Course organizer: Eduardo Conde-Sousa - i3S, INEB

Target audience: All scientific community

- Laptop with an updated version of Fiji (
- Previous knowledge on the basics of bioimage analysis is recommended, but no prior experience in ImageJ macro development is required or assumed, nor any prior programming skills



Program (provisory)

24 Nov
- Introduction to batch analysis: from macro recorder to simple scripts.
- ImageJ macro language syntax and elements.
- From GUI (graphical user interface) workflows to scripts: exploring ImageJ’s built-in functions.
- Workflow development

25 Nov
- Automatic data loading: access-list of files in a given directory and filter it by text patterns in file name or by extension.
- Batch processing from scripts.
- Organize and reuse code: user-defined functions.
- Combine multi-dimensional information: programmatically identifying image pairs (e.g. multichannel, time-lapse) and combine information.
- From Image data to tables: extract information to customized tables and personalize output variables on output tables (data logging).
- Save sample images and customized tables programmatically.
- Workflow development

26 Nov
- Accelerating image processing: run macros on GPU.
- Machine Learning for image analysis.
- Deep Learning for image analysis.
- Workflow development


Registration fees
Early bird registration until 30th September 2021
| Payment deadline: 7th October 2021
i3S members: 120€
External participants: 150€

Late registration from 1st October until 28th October 2021 | Payment deadline: 5th November 2021
i3S members: 150€
External participants: 200€

This workshop is now full. If you wish to stay in the waiting list, please fill in the following pre-registration form.

Registration Form


More Information:
Advanced Training Unit | E-mail: | Tel: +351 226 074 900