I open a similar question some days ago (https://www.researchgate.net/post/Which_is_the_best_program_free_to_calculate_the_nanoparticle_size_from_an_AFM_image), you can find interesting answers that maybe can help you!
A member of my group recently looked at this challenge systematically. He developed a method utilizing ImageJ, which is a free software. The details are described in the following publication:
Article Quantitatively Probing the Means of Controlling Nanoparticle...