Where Ideas grow

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 (https://fiji.sc/)
- 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
ImageJ Elements and Syntax
Workflow development I

25 Nov
User-defined functions
Export results
Workflow development II

26 Nov
ImageJ on GPU
Machine and Deep Learning on ImageJ
Workflow development III


Registration fees
Early bird registration until 15th September 2021
| Payment deadline: 24th September 2021
i3S members: 120€
External participants: 150€

Late registration from 16th September until 15th October 2021 | Payment deadline: 25th October 2021
i3S members: 150€
External participants: 200€

Registration Form