Skeleton analysis with Skan 🦴📏

Skan is a pure Python library to analyse skeleton images.

• Getting started
  • Installing Skan
    • Getting the Python package and dependencies
  • Getting started: Skeleton analysis with Skan
    • 0. Extracting a skeleton from an image
    • 1. Measuring the length of skeleton branches
    • 2. Comparing different skeletons
• Examples
  • Complete analysis with Skan
    • 0. Getting the data
    • 1. Using skan.pipe to get a branch dataset for analysis
    • 2. Cleaning up the data
    • 3. Making the figure
  • Sholl analysis in Skan
  • Display 3D skeletons in napari
    • Using the Shapes layer
    • Using the Labels layer
• Skan API Reference
  • skan.csr: CSR Graph representation of skeletons
  • skan.draw: Skeleton visualisation
  • skan.pipe:: Pipeline functions for skeleton analysis
  • skan.pre: Image preprocessing
• Using Skan’s GUI
  • Launching the GUI
  • Interpreting the GUI
  • Configuration files
• Miscellaneous
  • FAQ
    • I just upgraded from skan v0.8 or 0.9 and my measurements are slightly different. What gives?
    • What’s unique_junctions or junction_mode?
    • Why are coordinates floats and not integers?
    • Why is coordinate (0, 0, 0) always in my coordinate list? / Why is the coordinate array larger than the number of nodes in the pixel graph?
  • Skan release notes
    • skan v0.10.0rc0
    • skan v0.9
  • Citing Skan

Indices and tables

• Index

• Module Index

• Search Page

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Getting started