Is your data already rendered into an image (say a topological surface) or do you only have raw data that first needs converted into an image format? ImageJ may have some plugins specific to AFM that could be useful.
As far as I know nanoscope (in the basic operation) is not enough powerful for nanoparticle size distribution i.e cannot discrimite among two NPs if the NPs are in contact
Start with this sentence and the reference : "The elaboration of the AFM data concerning the nucleation and the growth of tetracene films (described in Section 3.1), was conducted by means of the software WSxM v.5.0, whose functions are reviewed in reference [49]. "
page 75 starting from first paragraph describes how he made the theoretical calculations.
I am using Image J to prepare particle size histograms from TEM images. There are some helpful functions included under Process and binary. For me this program includes everything i need. When you need more options you can also try FIJI it's an upgrade of Image J.
I also use Image J to obtain information from FE-SEM images. If Your nanostructures distriubtion on the support is regular (e.g. hexagonal) You can obtain also a lot of information from Fast Fourier Transforms from the WSxM programme.
Jordi, take a look at the software listed in the thread "https://www.researchgate.net/post/What_GNU_GPL_microscopy_image_analysis_software_is_available". Any of these software you can use for nanoparticle size estimation from AFM image.