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

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

Hong-Hsi Lee

Clockwise from top left: SEM data; myelin mask generated by pixel-wise classifier; intra-axonal space segmented by using random-walker-based approach; myelin sheath of segmented axons.


We are making available our 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 in diffusion MRI (dMRI) as perfect cylinders. 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 codes for Random Walker (RaW) segmentation and quantification of fiber orientation and axonal diameter can be downloaded from our github webpage at

Related Publication

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 Structure and Function, 2019 (
Hong-Hsi Lee, Katarina Yaros, Jelle Veraart, Jasmine L. Pathan, Feng-Xia Liang, Sungheon G. Kim, Dmitry S. Novikov, Els Fieremans.

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We gratefully acknowledge generous support for radiology research at NYU Langone Health from:
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