Lea Kabjesz

Hi! My name is Lea. I’m a bioinformatician by training and currently working as a research assistant with Robert Haase at ScaDS.AI, Leipzig. As part of the NFDI4BioImage project, I’m passionate about addressing the day-to-day challenges life scientists face when working with imaging data. My goal is to support the community in this field - whether through developing practical tools or creating training materials. Feel free to reach out or connect!

Annotating Images in Cellpose

Posted by Lea Kabjesz, on 5 June 2025

In this blog post, I’ll show you how to manually annotate cells in 2D and 3D images using the Cellpose Graphical User Interface (GUI). Manual annotation is a key step in many bioimage analysis workflows. It allows you to create labeled data that can serve as a reference for evaluating segmentation quality – or even