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In this work we consider the problem of tracking objects from a moving airborne platform in wide area surveillance through long occlusions and/or when their motion is unpredictable. The main idea is to take advantage of the known 3D scene structure to estimate a dynamic occlusion map, and to use the occlusion map to determine traffic entry and exit into these zones, which we call sources and sinks. Then the track linking problem is formulated as an alignment of sequences of tracks entering a sink and leaving a source. The sequence alignment problem is solved optimally and efficiently using dynamic programming. We have evaluated our algorithm on a vehicle tracking task in wide area motion imagery and have shown that track fragmentation is significantly decreased and outperforms the Hungarian algorithm.