After root staining, you can follow (McGonigle et al., 1990), there are details in this paper.
McGonigle, T. P., Miller, M. H., Evans, D. G., Fairchild, G. L., and Swan, J. A. 1990. A new method which gives an objective measure of colonization of roots by vesicular-arbuscular mycorrhizal fungi. New Phytol. 115, 495–501.
first is necessary to obtain good samples of stained roots, then you can estimate a number of visual fields, for example (50 0100), you must help, with a cell counter and make a percentage ratio of each structure.
To avoid this tedious methodology, we are developing software that will allow you to export the images and do automatic counting of each fungal structure, this will not be possible until the end of this month. Stay in touch