I think no. You could just estimate their number taking into account the observed size of NP.

Technically, 3D atom probe microscopy should be able to do that. In fact, it gives a 3D image of individual atoms in the small vol. of sample. However, you need to contact the research centers how can this instrument since it is expensive and needs a lot of time to do that work.

See here for an example of InGaN material system:

http://www.msm.cam.ac.uk/department/profiles/researchimg/Humphreys.jpg

The company who makes such instruments is located in Madison-WI, USA.

More on atom probe:

https://en.wikipedia.org/wiki/Atom_probe

Thank you

Atomic force microscopy (AFM) has the sensitivity to resolve individual atoms. Hope the article helps

http://www.nature.com/nature/journal/v446/n7131/full/nature05530.html

Atom probe with nanoparticles requires embedding them into a matrix and quite some sample prep but would work in principle (at least for nanoparticles that are conductive.). AFM theoretically has atomic resolution but only if you have a very sharp tip and on an atomically flat surface not on a particle. I would also estimate by the looking at the size. (there will be some variation in the number of atoms per particle so it is probably the best you can get anyways)