06. 01. 2026
Basic information
This course is aimed at participants who are familiar with the basics of image processing and want to automate their analysis using scripting. We will work with the ImageJ macro language to create a workflow for the segmentation and analysis of fluorescence microscopy images. We will also introduce Cellpose, a machine-learning algorithm for cell segmentation, demonstrate how to use it through an ImageJ plugin, and integrate its output into the ImageJ workflow. In the second part of the course, we will focus on batch processing multiple images in a folder. We will also demonstrate how AI prompting can assist with the process of writing and developing macros.
No previous programming knowledge is expected, and the course will therefore also briefly introduce basic programming concepts, such as variables, for loops and conditionals (if-else statements).
Date: December 8-9, 2026
Duration: 2 days
Language: English
Requirements: bring your own laptop
The course is organized in person and online. Please note that, due to organizational constraints, we may not be able to provide full support to online participants during the sessions.
