Make Z-stack from 2D images


I need to make a z-stack from 2D images. I know how to make the z-stack but then there are a whole lot of settings that you need to get right if later you want to make a 3d model.

I have miscroscope images (they are all aligned) that are taken at 7 different focal points. I am guessing that I need to input pixel widht height and dept in order to make a 3d model? If so, how do I determine that? What about the distance between stacks?

I am really confused here and Im not sure where to start.

Does the microscope tell you what the focal distances are?
If not, did you do it manually and wrote those down?

I can’t imagine how you can determine that afterwards for an arbitrary stack without any other information.