Chlorophyll a fluorescence measured in vivo is frequently used to study the role of different processes influencing the distribution of excitation energy in PSII complexes. Such studies are important for understanding the regulation of photosynthetic electron transport. However, at the present time, there is no unified methodology to analyse the energy partitioning in PSII. In this article, we critically assess several approaches recently developed in this area of research and propose new simple equations, which can be used for de-convolution of non-photochemical energy quenching in PSII complexes.