## 4 Discussion
### Diurnal Cycles and Short Term Changes in Fluorescence
Additional experiments, using for example active measurements of fluorescence and/or simulations with a canopy fluorescence model like SCOPE are necessary to evaluate this hypothesis. Other phenomena (like leaf movements) could also play a role in the diurnal cycle of SIF by modifying radiative transfer inside the canopy along the day. On the other hand, physiological effects should also be taken into account to interpret diurnal cycles of SIF. Red SIF originates solely from PSII, whose emission varies with photochemical and non-photochemical quenching (PQ and NPQ, respectively), while far red SIF additionally includes a constant PSI component. In this view, parallel changes of SIF687 and SIF760 with physiology (i.e., fluorescence quenching) are expected, with a larger amplitude for SIF687. Physiological effects can be accounted for by active fluorescence measurements at leaf level. In this study, \(F_{s}\), \(F_{m}^{\prime}\), and \(\Phi_{P}\) were assessed on leaves randomly distributed in the canopy. These measurements showed a parallel decrease of \(F_{m}^{\prime}\) and \(\Phi_{P}\) at noon, which indicates an accumulation of non-photochemical quenching. A slight but statistically significant decrease of \(F_{s}\) was also observed. This decrease of \(F_{s}\) is in good agreement with the observed change in ASFY760, but not with the increase of ASFY687. This means that physiological effects are masked or tightly coupled to other types of effects, such as radiative transfer effects induced by changes in the illumination geometry. We should point out that the approach used here to compare active and passive measurements is oversimplified, as it does not take into account the possible interaction between the distribution of physiological effects on fluorescence (e.g., different fluorescence yields between shaded and sunlit leaves, or between upper and lower leaves) and the radiative transfer of incident and emitted light in the canopy. A more sophisticated approach based on a radiative transfer modelling would be necessary to take these effects into account. A good agreement between PAM fluorescence and far red SIF has already been observed on a maize canopy after treatment with the herbicide DCMU [6]. Additionally, significant positive correlations between \(F_{s}\) measured at leaf level and SIF760 extracted from pure crown pixels obtained by airborne imaging spectrometer have been observed on olive and peach orchards [55] and vineyard [56]. Short term changes include changes in the distribution function of incoming light incident angles due to aerosol content or cloud cover. It can be assessed by the relationship between apparent fluorescence yield and the diffuse PAR fraction (\(F_{diffPAR}\)). Here, we observe an increase of the median value of ASFY687 by about 50% when comparing overcast sky conditions (\(f_{diffPAR}\geq 0.9\)) to clear sky conditions (\(f_{diffPAR}\leq 0.3\)), while the corresponding change in ASFY760 does not exceed 13%. Overcast is associated with a large decrease of PAR (from about 1600 to 500 \(\mathrm{\SIUnitSymbolMicro mol\cdot m^{-2}\cdot s^{-1}}\) in this case), which induces changes in the rate of PQ and NPQ, but we did not observe such high changes at leaf level in \(F_{s}\). Therefore, we infer that non-physiological effects are playing a role in ASFY687. They might be linked to bidirectional reflectance (BR) effects associated with a spectral anisotropy of irradiance that are not taken into account in the SIF retrieval algorithm and/or to changes in radiative transfer through the canopy in link with the illumination geometry.