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Massive MIMO has been recognized as a promising technology to meet the demand for higher data capacity for mobile networks in 2020 and beyond. Although promising, each base station needs accurate estimation of the channel state information (CSI), either through feedback or channel reciprocity schemes in order to achieve the benefits of massive MIMO in practice. Time division duplex (TDD) has been suggested as a better mode to acquire timely CSI in massive MIMO systems. The use of non-orthogonal pilot schemes, proposed for channel estimation in multi-cell TDD networks, is considered as a major source of pilot contamination in the literature due to the limitations of coherence time. Given the importance of pilot contamination in massive MIMO systems, we provide an extensive survey on pilot contamination, and identify other possible sources of pilot contamination, which include hardware impairment …