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Promising as a gene carrier, the Foamy virus (FV) is an atypical retrovirus that shares similarities with HIV and the hepatitis B virus. Despite numerous biochemical studies, its entry pathway remains unclear, namely whether entry occurs through fusion at the plasma membrane or after endocytosis. To investigate this issue, dual-color fluorescent viruses were engineered with a GFP-labeled capsid and a mCherry-labeled envelope. Thus, the release of the capsid from the envelope would result in a loss of colocalization of the two colors at the single virus level. Using 3D single virus tracing, we followed the entry of the fluorescent viruses in living cells. In such experiments, a compromise is made between low phototoxicity for the cells and sufficient signal-to-noise ratio for tracking. Therefore, it is often difficult to rely on the fluorescence intensity to estimate colocalization. Cross-correlation approaches are highly sensitive to colocalization and coordinated motion but none of the existing methods are applicable to single particle tracking. We developed a novel approach, Tracking Image Cross-correlation (TrIC), which combines image cross-correlation and single particle tracking. The image cross-correlation analysis yields the colocalization status of the particle as well as the average distance between the two labels. The combination of this dynamical colocalization information with the instantaneous velocity of the particle and its position within the cell allows us to clarify the Foamy virus entry pathway. We compared two types of FVs and demonstrated that the prototype FV can enter the cell by either endocytosis or membrane fusion whereas the simian FV was only observed to fuse after endocytosis. Interestingly, our analysis revealed an intermediate stage during the fusion process where the capsid and envelope separate by ∼400nm but are still attached for ∼5 minutes before fusion is completed.