when i do imaging of tissue to look at collagen structure using a 2 photon microscopy, but im not familiarized with the methods to measure the diameter of the collagen and the area occupied by it. Does anyone know how do researchers measure them

I am not familiar with the technique and had to look it up here:

http://en.wikipedia.org/wiki/Two-photon_excitation_microscopy

The device has a scanning mirror. It should be precalibrated for spatial scale. Check the instruction manual for the spatial field of view at various magnification settings