Point-intersect line sampling is a method of sampling of element in a region whereby an element is sampled if a chosen line segment, called a transect intersects the element. It is a reliable, versatile and easy to implement method. For more details, please consult the below references which may help you.

The problem with optical methods for the estimation of surface coverage is that, when the fungal colony is raised over the substrate, there is a shielding effect which affects the measurement.

For different mycelial patterns check the site below:

http://microbiologyonline.org/teachers/observing-microbes/observing-fungi-in-a-petri-dish

One method which is practised in my laboratory is to grow the colonies over dialysis membranes which can be easily lifted from the plate, and removed from the mycelium. The biomass can then be dried and weighed. The method allows for multiple measurements and statistically acceptable results. One does not obtain a measurement of the rate of branching anastomosis or other morphometric features, however.

If one requires data from colonies that produce submarine hyphae, some authors have treated the colonies with warm water to remove the agar, but I have no experience with this technique.

For a general reference of the techniques discuss, consult the link below:

http://onlinelibrary.wiley.com/doi/10.1111/j.1574-6968.2009.01780.x/full