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Measurements of the photon second-order correlation function, g(2)( τ), is a common tool for the characterization of single photon emitters, like nitrogen-vacancy color centers in diamond. Such measurement requires background photoluminescence correction, which is easy when this background is homogeneous on a few wavelengths scale. However, if the sample contains emitting centers separated by a distance smaller than the optical diffraction limit, and having different and overlapping emission, these background correction techniques cannot be applied. We have recently shown that cathodoluminescence (CL) can be used to measure g(2)( τ) at the subwavelength scale. Here we propose a method, based on spatially and spectrally resolved CL, to subtract the background taking into account the nanometer spatial distribution of the emitted light. To this end, a nanometer-resolved spectrum image is acquired on the same region where the g(2)( τ) is measured. As an example, we show the use of this method to the subtraction of the H3 background signal from a g(2)( τ) measurement done on NV0 color centers. [ABSTRACT FROM AUTHOR]