We describe a combined experimental, theoretical, and simulation study of the structural correlations between cross-linked highly monodisperse and swollen Poly(N-isopropylacrylamide) microgel dispersions in the fluid phase in order to obtain the effective pair-interaction potential between the microgels. The density-dependent experimental pair distribution functions g(r)'s are deduced from real space studies using fluorescent confocal microscopy and compared with integral equation theory and molecular dynamics computer simulations. We use a model of Hertzian spheres that is capable to well reproduce the experimental pair distribution functions throughout the fluid phase, having fixed the particle size and the repulsive strength. Theoretically, a monodisperse system is considered whose properties are calculated within the Rogers-Young closure relation, while in the simulations the role of polydispersity is taken into account. We also discuss the various effects arising from the finite resolution of the microscope and from the noise coming from the fast Brownian motion of the particles at low densities, and compare the information content from data taken in 2D and 3D through a comparison with the corresponding simulations. Finally different potential shapes, recently adopted in studies of microgels, are also taken into account to assess which ones could also be used to describe the structure of the microgel fluid.