I realize that you would prefer to do this digitally but one of the simple ways is to make a copy and cut it out and compare the weight of it with the weight of one square dm of the same paper..
with only one photo, you can only guess , the darkness of a spot gives you some idea of how deep that spot is, May be that is what some of the software does (I am not familiar with these softwares)
if you have several photos taken through different angles , the guess can improve.
Do some calibration first, to find out the relation between depth and darkness under the same environment.