Batch analysis and macro development in ImageJ/Fiji: going beyond the basics

November 18-20, 2020 | i3S, Porto

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 will focus on how to automate routine tasks (for conditions where many images need to be processed), as well as how to deal with more complex image analysis situations, to 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. At the course, this 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. 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.