Particle estimation is a classical problem arising in many science fields, such as biophysics, fluid mechanics, bio-medical imaging. Many interesting applications in these areas involve 3D imaging data: this work presents a technique to estimate the 3D coordinates of the center of spherical particles. This procedure has its core in the processing of the images of the scanned volume: it firstly applies denoising techniques to each frame of the scanned volume, then provides an estimation of both the center and the profile of the 2D intersections of the particles with the frames, by coupling the usage of Total Variation functional and of a regularized weighted Least Square fit. Then, the 2D information is used to retrieve the 3D coordinates using geometrical properties. The experiments provide evidence that image denoising has a large impact on the performance of the particle tracking procedures, since they strongly depend on the quality of the initial acquisition. This work shows that the choice of tailored image denoising technique for Poisson noise leads to a better estimation of the particle positions.