In my opinion, you cannot calculate permeability through microscopic means. There are a lot of permeability-dependent parameters that SEM microscopy cannot determine, such as hidrophilicity, roughness, to name a few.
However, the details that top-view and cross-section SEM images offer are of help in understanding why permeability is high, low, equal or zero.
You need a cross-flow or dead-end filtration cell in order to measure permeability.