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Digital in-line holography is a microscopy technique which has gotten an increasing amount of attention over the last few years in the fields of microbiology, medicine and physics, as it provides an efficient way of measuring 3D microscopic data over time. In this paper we approach the challenges of a high throughput analysis of holographic microscopy data and present a system for detecting particles in 3D reconstructed holograms and their 3D trajectory estimation over time. Our main contribution is a robust method which evolves from the Hungarian bipartite weighted graph matching algorithm and allows us to deal with newly entering and leaving particles and compensate for missing data and outliers. In the experiments we compare our fully automatic system with manually labeled ground truth data and we can report an accuracy between 76% and 91%.