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With the recent developments in single-molecule localisation microscopy, there is a large choice of well-characterized and user-friendly software packages and algorithms freely available. We have shown previously that when applied to centroiding photon counting imaging data from an MCP-intensified camera system, these programs can produce results with better resolution, lower FPN, and in some cases even better event recognition than the traditional single-iteration photon centroiding algorithms. In this work we have shown that these programs produce excellent results when applied to centroiding smaller and dimmer single photon events from an EBCCD camera with significant background noise. Moreover, we have also demonstrated that multi-emitter fitting analysis can separate overlapping photon events -- an important consideration for photon counting imaging fluorescence microscopy where the count rate is usually limited by the need to avoid overlapping photon events.    %\section{Acknowledgements}  We thank UK's Medical Research Council (MRC) for funding this work.