Annotating 3D images in napari

Posted by Mara Lampert, on 30 March 2023

This blog post revolves around generating ground truth in 3D images for segmentation. Therefore, we will define what ground truth is and how we can generate it using napari in a time-efficient way. We will also learn about difficulties of annotating alone or in groups and address possible solutions for both. Challenges of image segmentation

Explorative image data science with napari

Posted by Robert Haase, on 23 May 2022

When analysing microscopy image data of biological systems, a major bottleneck is to identify image-based features that describe the phenotype we observe. For example when characterising phenotypes of nuclei in 2D images, often questions come up such as “Shall we use circularity, solidity, extend, elongation, aspect radio, roundness or Feret’s diameter to describe the shape