The mycorrhizae inside plant roots are difficult to see and to quantify, but arbuscules, conveniently, autofluoresce under ultraviolet light. As Gianinazzi and Gianinazzi-Pearson (in Norris et al. 1994) point out, this is one of the few non-destructive ways to observe mycorrhizae. Live arbuscules glow yellow under violet-blue light, allowing observation of mycorrhizal development over time. When paired with direct observation of external hyphae under a dissecting microscope, this technique can be particularly effective and allow mapping of the spread of mycorrhizal fungi.
I would second the suggestion given by Dr. Karen. Excise small portions of the root from various regions, and observe them under UV for autofluoresence. It can later be related to the mycorrhizal growth.