By assuming spherical particles with uniform density, the sizes and 3D positions can be derived via Wiener deconvolution (WD) using a series of kernels prepared by the convolution of the 3D point spread function of the electron beam and 3D density distribution of spheres with different radii. 
Wiener deconvolution
Model-based deconvolution for particle analysis applied to a through-focus series of HAADF-STEM images.This paper presents an approach for determining the sizes and three-dimensional (3D) positions of nanoparticles from a through-focus series of high-angle annular dark-field scanning transmission electron microscopy (HAADF-STEM) images.  This process is referred to as a model-based deconvolution (MBD). 
model-based deconvolution