In this article, a strategy to track microparticles and link their trajectories adapted to the study of the melting of a quasi two-dimensional complex plasma crystal induced by the mode-coupling instability is presented. Because of the three-dimensional nature of the microparticle motions and the inhomogeneities of the illuminating laser light sheet, the scattered light intensity can change significantly between two frames, making the detection of the microparticles and the linking of their trajectories quite challenging. Thanks to a two-pass noise removal process based on Gaussian blurring of the original frames using two different kernel widths, the signal-to-noise ratio was increased to a level that allowed a better intensity thresholding of different regions of the images and, therefore, the tracking of the poorly illuminated microparticles. Then, by predicting the positions of the microparticles based on their previous positions, long particle trajectories could be reconstructed, allowing accurate measurement of the evolution of the microparticle energies and the evolution of the monolayer properties.