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Most living organisms show highly conserved physiological changes following a 24-hour cycle which goes by the name of circadian rhythm. Among experimental models, the effects of light-dark cycle have been recently investigated in the larval zebrafish. Owing to its small size and transparency, this vertebrate enables optical access to the entire brain. Indeed, the combination of this organism with light-sheet imaging grants high spatio-temporal resolution volumetric recording of neuronal activity. This imaging technique, in its multiphoton variant, allows functional investigations without unwanted visual stimulation. Here, we employed a custom two-photon light-sheet microscope to study brain-wide differences in neuronal activity between diurnal and nocturnal periods in larval zebrafish assessed at the transition between day and night. We describe for the first time an activity increase in the low frequency domain of the pretectum and a frequency-localized activity decrease of the anterior rhombencephalic turning region during the nocturnal period. Moreover, our data confirm a nocturnal reduction in habenular activity. Furthermore, brain-wide detrended fluctuation analysis revealed a nocturnal decrease in the self-affinity of the neuronal signals in parts of the dorsal thalamus and the medulla oblongata and an increase in the pretectum. Our data show that brain-wide nonlinear light-sheet imaging represents a useful tool to investigate circadian rhythm effects on neuronal activity., Comment: 22 pages, 8 figures