Analyzing the behavior of axons in the developing nervous systems is essential for biologists to understand the biological mechanisms underlying how growing axons reach their target cells. The analysis of the motion patterns of growing axons requires detecting axonal tips and tracking their trajectories within complex and large data sets. When performed manually, the tracking task is arduous and time-consuming. To this end, we propose a tracking method, based on the particle filtering technique, to follow the traces of axonal tips that appear as small bright spots in the 3D+t fluorescent two-photon microscopy images exhibiting low signal-to-noise ratios (SNR) and complex background. The proposed tracking method uses multiple dynamic models in the proposal distribution to predict the positions of the growing axons. Furthermore, it incorporates object appearance, motion characteristics of the growing axons, and filament information in the computation of the observation model. The integration of these three sources prevents the tracker from being distracted by other objects that have appearances similar to the tracked objects, resulting in improved accuracy of recovered trajectories. The experimental results obtained from the microscopy images show that the proposed method can successfully estimate trajectories of growing axons, demonstrating its effectiveness even under the presence of noise and complex background.