Intra-axonal Space Segmented from 3D Scanning Electron Microscopy of the Mouse Brain Genu of Corpus Callosum

Data and code for precise, sample-based modeling of axon microgeometry.

We are making available segmentation code and scanning electron microscopy (SEM) data used to characterize inner axon diameters and fiber orientation dispersion in a sample of murine corpus callosum.

We have used these tools and data to examine assumptions that underlie the practice of modeling axons as perfect cylinders in diffusion MRI (dMRI). Our findings indicate that such modeling may be too simplistic for dMRI in the brain. For more detail, see the related publication.

The SEM data include:

  1. datac.nii (a stack of SEM data, 200 slices; resolution: 24nm by 24nm by 100nm; volume: 36μm by 48μm by 20μm)
  2. maskc.nii (foreground mask)
  3. myelin_mask.nii (myelin mask generated by pixel-wise classifier in ilastik)
  4. fibers.nii (intra-axonal space segmented by using random-walker-based approach)

The code for Random Walker (RaW) segmentation and quantification of fiber orientation and axonal diameter is maintained on Github.

Related Publication

Lee HH, Yaros K, Veraart J, Pathan JL, Liang FX, Kim SG, Novikov DS, Fieremans E.
Along-axon diameter variation and axonal orientation dispersion revealed with 3D electron microscopy: implications for quantifying brain white matter microstructure with histology and diffusion MRI.
Brain Struct Funct. 2019 May;224(4):1469-1488. doi: 10.1007/s00429-019-01844-6

Please cite this work if you are using the intra-axonal space segmentation from 3D SEM of murine corpus callosum in your research.


Questions about this resource may be directed to Hong-Hsi Lee, PhD at