This depends on 3 things 1) Resolution of your microscope 2) Magnitude of your pores 3) Clear images where you can see all the porous structures one by one
If you can see the clear images and pores together on the nanofibers obtained from microscope you can simply use the scale bar for all settings. But 50 micron scale bar is not promising. http://pubs.rsc.org/en/content/articlelanding/2016/ta/c5ta09166g#!divAbstract In this link you can find an article where you can see the real pores in Fgure 1c obtained by TEM. Therefore your light microscope images possibly dont have enough resolution to see such a detailed information.
Total porosity is the overall pore space present in a 3D scaffold. Image J can be used for measuremnt of pore size . Liquid displacement method is one of the simplest methods which is generally used to understand the porosity of a scaffold. There are other standard methods to analyse porosity of scaffolds such as mercury porsoimetry or BET depending on the nature of your scaffolds. You can refer to ISO/ ASTM standards methods for the same.