README.md

Random Walker (RaW) segmentation

The code implements random walker (RaW) segmentations of myelinated axons in 3d electron microscopy (EM) data, developed in Lee, et al., Brain Struct Funct, 2019. All functions are implemented in MATLAB and defined in 3 classes:

• rawseg: Random walker segmentation for myelinated axons in 3d EM data.
• analyzeseg: Analyze segmented axons and calculate fiber orientation distribution (FOD), dispersion angle, axonal diameter, and g-ratio.
• plotseg: Visualize segmented axons into a 3d box or 3d polyhedrons.

The usage of the classes can be found in demo_*.m files.

The EM data and axon segmentation can be downloaded here.

References

• Random walker (RaW) segmentation, quantification of orientation and diameter of axons

  • Lee, et al., Brain Struct Funct, 2019

• Distortion correction

  • Sun, et al., IEEE CVPR, 2010
  • Sun, et al., IJCV, 2014

• Triangulated spherical surface

  • Efficient spherical design
  • Womersley, Contemporary Computational Mathematics, 2018

• Spherical harmonics

  • Spherical harmonic transform library
  • Politis, et al., 2016

• Bingham statistics library

• Magicwand2

Authors

• Hong-Hsi Lee
• Dmitry S Novikov
• Els Fieremans

License

This project is licensed under the LICENSE.