napari-toska

Welcome to the documentation of napari-toska.

Overview

This page provides an overview over the following.

• Example notebooks on how to use the plugins from code:

  • Skeleton analysis in 2D

  • Skeleton analysis in 3D

• Definitions & glossary:

  • What is a topological skeleton?

  • What are branches, endpoints, branching points and spines?

  • What are neighborhoods?

  • What do the measurements mean?

References & Acknowledgements

Used algorithms to cite if this plugin is used are listed in more detail in the documentation section on skeletonization. If you use this plugin in your analysis, please make sure to cite our preprint

[Blu67]

Harry Blum. A transformation for extracting new descriptions of shape. Models for the perception of speech and visual form, pages 362–380, 1967.

[Blu73]

Harry Blum. Biological shape and visual science (part i). Journal of theoretical Biology, 38(2):205–287, 1973.

[BN78]

Harry Blum and Roger N Nagel. Shape description using weighted symmetric axis features. Pattern recognition, 10(3):167–180, 1978.

[LKC94]

Ta-Chih Lee, Rangasami L Kashyap, and Chong-Nam Chu. Building skeleton models via 3-d medial surface axis thinning algorithms. CVGIP: Graphical Models and Image Processing, 56(6):462–478, 1994.