Hi David,

Image J (or Fiji) is a very easy and free software to use which I personally, and colleagues within my lab have used to measure myelin thickness.

See some papers below which simply used Image J:

http://www.iovs.org/content/53/10/6093.full

http://www.sciencedirect.com/science/article/pii/S0028390813003511

Feel free to email me personally if you have any questions regarding this analysis.

Cheers,

Ryan

Would quantification of the myelin be helpful for your studies?

Then see: Myelin Isolation Beads (Miltenyi)