Segmentation with StarDist and SplineDist

Trainer: Martin Weigert, Soham Mandal, Virginie Uhlmann

Overview: Segmentation is the process of partitioning a digital image into multiple image objects. This session will go over what segmentation is and introduce two methods: SplineDist, a machine learning framework for automated cell segmentation with spline curves, and StarDist, cell nuclei localisation via star-convex polygons.

Learning outcomes

By the end of this session you will be able to:

• Describe what segmentation is, it’s main challenges and outputs
• Name main algorithms for segmentation
• Give examples of ML applied to cell segmentation through spline curves and star-convex polygons

Materials

• Link to presentation slides

Suggested reading articles

• SplineDist: Automated Cell Segmentation with Spline Curves
• Cell Detection with Star-convex Polygons

Data repositories for SplineDist and StarDist

• SplineDist repository
• StarDist repository