What is the best way to take the derivative of a surface plot (2D) data?

I have a data set that is a measurement of a defect. I'd like to programatically characterize the defect for depth and area of each defect, is it possible to count the number of pixels/cells below or above a threshold value? If i know that it's simple math to calculate defect area. Defect counting i'm totally baffled as to how to do it or if it's even possible.

Any help would be appreciated. I've attached a sample of the data.