Liisa Hirvonen edited Introduction.tex  about 8 years ago

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The detection of single photons is a technique used in many fields of science and technology, including fluorescence microscopy and spectroscopy, bioluminescence studies, optical tomography, DNA sequencing, lidar, quantum information science and encryption, and optical communications both on earth and in space.\cite{Hadfield2009,Buller2010,Eisaman2011,Seitz2011} Photon counting imaging is a well-established low light level imaging technique where an image is assembled from individually detected photons. In conventional photon counting imaging, photon events on the phosphor screen of a microchannel plate (MCP)-based image intensifier are imaged with a charge-coupled device (CCD) or a complementary metal-oxide-semiconductor (CMOS) camera at high frame rates, and many frames are accumulated to build up an image.\cite{Hirvonen2014_ol} Photon counting imaging is also possible with electron-bombarded (EB) sensors, where single photoelectrons liberated from the photocathode are accelerated by a high voltage directly into the CCD or CMOS sensor \cite{Barbier_2011} to produce a photon event.\cite{Spring1998} These are smaller and less bright than MCP-intensified photon events, due to a generally lower gain of electron-bombarded sensors, with a narrow, voltage-dependent pulse height distribution.\cite{Hirvonen2014_rsi} EBCCD or EBCMOS-based photon counting imaging avoids distortion of the image due to the coupling of the intensifier to the camera, and image lag due to the phosphor decay time, and there is no need for spectral matching of the camera sensitivity and the phosphor.  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 - a processes termed centoiding.\cite{Suhling2002, centroiding.\cite{Suhling2002,  Suhling1999, Boksenberg1985} The original centroiding algorithms, based on a simple center-of-mass calculation,\cite{Boksenberg1985} were developed for implementation in hardware. In the advent of more powerful computers, it became possible to implement increasingly complex centroiding algorithms in software. However, the algorithms employed in photon counting imaging are still usually simple, one-iteration algorithms.\cite{Postma2011} In the past decade, photoswitchable and photoactivatable fluorescent probes \cite{Fernandez_2008} have allowed the same centroiding principle to be employed in circumventing the diffraction limit in fluorescence microscopy. 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}