Three-dimensional (3D) phase maps are used in a digital inline holography system to measure the coordinates of tiny particles. The phase signature, previously applied to spherical particles by Yang et al. [Opt. Lett.31, 1399 (2006)OPLEDP0146-959210.1364/OL.31.001399], is extended here to the case of an infinite cylindrical filament to determine the optimal focus plane. The practical implementation of this method is described. Simulations show that this technique provides a very efficient tool to examine the 3D coordinates of micrometric objects. A practical application is given with the investigation of the dynamics of beads-on-a-string structures under an air flow current. These structures, obtained by stretching a viscoelastic fluid element, are of particular interest in this study, since they are characterized by several quasi-spherical beads (i.e., drops) linked by a quasi-cylindrical filament (i.e., thread).