# Ground Based Hyperspectral Imaging to Characterize Canopy-Level Photosynthetic Activities
## 4 Discussion  
The developed approach used a passive hyperspectral imaging system to retrieve diurnal SIF values that were used for estimating maximal fluorescence, effective quantum yields of PSII, and ETR values at the canopy level. Irrespective of the approach utilized to model SIF to diurnal light intensity, the following conclusions can be made. Maximal fluorescence estimates for the canopy, derived from the best fit function of SIF versus the reciprocal of PAR in both the Diuron-treated plots and the control plots were used to calculate actual quantum yield of the canopy. \(\phi_{HSI}\) estimates were strongly correlated with \(\phi_{PAM}\) estimates when considered across multiple diurnal sampling times of all treatments or for the two different species of cotton evaluated (Figure 6). Furthermore, \(\phi_{HSI}\) values were used to calculate ETR at a given diurnal PAR level, and diurnal light response curves were generated for both PAM and HSI-based methods. From these data, a standardized measure of ETR at a common light intensity (1500 \(\upmu\) mol/m\({}^{2}\)/s) was calculated for both PAM and HSI-based methods. There was a strong correlation between HSI- and PAM-derived sETR values (r = 0.95; Figure 8), and canopy estimates of ETR were also predictive of whole-crop growth responses in the weeks following treatment. Thus, we suggest that is possible to estimate canopy-level photosynthetic efficiency from passive, diurnal measurements of SIF and PAR at the canopy at the time of measurement. This is a particularly notable achievement, since a number previous studies have collected diurnal SIF measurements at the agro-ecosystem scale in attempts to model gross primary productivity [12; 60; 61]. The methodology reported herein would allow researchers to obtain a direct measure of ecosystem-scale photosynthetic efficiencies from existing data sets. Furthermore, the use of hyperspectral imaging to delineate plot-scale photosynthetic efficiencies would allow for direct selection of genotypes with higher diurnal photosynthetic activities. Last, the developed method measures chlorophyll fluorescence in field conditions, which could expand fluorescence-based early detection of plant stresses (described by [62; 63; 64]) from the laboratory to the field. This could be particularly useful for agricultural production systems. The developed approach has two major limiting factors, however. First, ETR values measured by HSI data showed a larger absolute differences than those measured by PAM data. This can be solved by improving the spectral sampling resolution [65]. The hyperspectral camera and spectrometer used the spectral sampling resolution of 2 nm in the present study, utilizing only around 50% depth of the Fraunhofer \(O_{2}\)-\(A\) line [65]. This limits the SIF retrieval accuracy, and thus, the derivation of effective quantum yield of PSII and ETR values. On the contrary, the spectral sampling resolution of the hyperspectral camera and downwelling spectrometer can be configured to approximately 0.2 nm, which could provide greater potential for further improvement of measurement accuracy. The finest spectral resolution will result in a large increase of data volume, presenting potential challenges in data collection, management, and processing. In addition to the hardware improvement, other SIF retrieval methods (e.g., 3 FLD and improved FLD) can be used to increase the retrieval accuracy [24]. Second, estimation of maximal fluorescence dramatically affected the calculations of effective quantum yield, ETR, and RLC models. In the present study, a linear model provided the poorest results in which control and Diuron-treated groups showed a large overlap. Although fitted RLC models still showed a significant difference between treatments, it could be problematic to identify subtle differences of photosynthetic efficiency among genotypes. This could limit the potential of using the developed method for genetics/genomics studies and breeding programs.