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A characteristic feature of the photon counting imaging technique is the possibility of calculating the true position of a photon event that covers several pixels with subpixel accuracy.\cite{Suhling2002,Suhling1999,Boksenberg1985} Originally developed for implementation in hardware and based on a simple center-of-mass calculation,\cite{Boksenberg1985} the centroiding is nowadays done in software but the algorithms employed in photon counting imaging are still usually simple, one-iteration algorithms.\cite{Postma2011}  The discovery development  of photoswitchable and photoactivatable fluorophores in the past decade fluorescent probes  \cite{Fernandez_2008} has allowed the same centroiding principle to be employed in circumventing the diffraction limit in fluorescence microscopy. microscopy in the past decade.  Single-molecule localisation fluorescence microscopy techniques are based on the activation of a small subpopulation of the fluorescent proteins or fluorophores used to stain the sample. They are imaged and subsequently deactivated before the process is repeated with a different subset of fluorophores.\cite{Betzig2006,Rust2006,Hess2006} The centroid positions of the fluorescent probes are calculated in each frame, and the final image is formed by summing many frames. Single-molecule localisation fluorescence microscopy is now a well-established technique, and much effort has been put into the development and optimisation of many different types of centroiding algorithms, including iterative fitting algorithms.\cite{Small2014} We recently reported that single-molecule localisation algorithms produce good results when applied to centroiding single photon events imaged with an MCP-intensified CMOS camera.\cite{Hirvonen2015_OL} Here, we extend this work and apply super-resolution software for centroiding photon events detected with an EBCCD camera. Moreover, multi-emitter fitting analysis was used for separating overlapping photon events, an important aspect not reported before, which allows an increased count rate and shorter acquisition times.