# Ground Based Hyperspectral Imaging to Characterize Canopy-Level Photosynthetic Activities
## Results
### Calculated Effective Quantum Yield and RLCs  
Overall, the Pima and Upland cultivars showed the similar trends and patterns for \(\phi_{PSII}\) and ETR values calculated using PAM and hyperspectral data (Figure 5). For all four methods, \(\phi_{PSII}\) values decreased with increasing PAR values in the range from 0 to 2000 \(\mu\) mol/m\({}^{2}\)/s for control groups, whereas \(\phi_{PSII}\) values were relatively lower and showed no correlation with PAR values for Diuron-treated groups. Control and Diuron-treated groups were distinctively different from each other in \(\phi_{PSII}\) over PAR calculated using PAM data. While control and Diuron-treated groups were still separable, overlaps between the two groups were identified with different magnitudes in \(\phi_{PSII}\) over PAR calculated using HSI data. The overlaps between control and Diuron-treated groups for quantum yield were the largest when \(\phi_{PSII}\) values were calculated using maximal fluorescence estimated by the linear model, and the overlaps became smaller, being minimal when \(\phi_{PSII}\) values were calculated using maximal fluorescence estimated by the average and quadratic models, respectively. This occurred primarily because of the differences between estimated maximal fluorescence values for the Diuron-treated groups. The HSI quadratic model provided the lowest value of the estimated maximal fluorescence, resulting in the lowest \(\phi_{PSII}\) values. In particular, a lower maximal fluorescence value led to more negative \(\phi_{PSII}\) values that were treated as zero, which increased the magnitude of the differences between the control and the Diuron-treated groups. ETR values rapidly increased with increasing PAR values in the range from 0 to 600 \(\upmu\) mol/m\({}^{2}\)/s, and gradually reached a plateau afterwards for control groups. This trend held true for ETR values calculated using PAM- and HSI-derived \(\phi_{PSII}\). ETR values calculated using PAM-derived \(\phi_{PSII}\) remained low (near zero) in the PAR range from 0 to 2000 \(\upmu\) mol/m\({}^{2}\)/s for Diuron-treated groups, showing a clear separation from control groups. In contrast, ETR values calculated using HSI-derived \(\phi_{PSII}\) showed different magnitudes of overlap between control and Diuron-treated groups. In the PAR range from 0 to 1500 \(\upmu\) mol/m\({}^{2}\)/s, all three HSI-based methods showed a distinction between control and Diuron-treated groups, with the largest overlap by the HSI linear method followed by average and quadratic methods. In the PAR range from 1500 to 2000 \(\upmu\) mol/m\({}^{2}\)/s, the HSI linear method showed no distinction between two treatment groups, whereas the HSI quadratic and average methods still showed a distinct difference. This matched with the observations of \(\phi_{PSII}\). Figure 4: Estimation of maximal fluorescence values for control and Diuron treatments. An exponential model was used to fit the SIF and PAR reciprocal values for plots in the control group, whereas three models (linear, quadratic, and average) were used to fit the SIF and PAR reciprocal values for plots in the Diuron-treated group. The maximal fluorescence value was defined as the value when the PAR reciprocal equaled zero. Quantitative RLC models further validated the aforementioned observations (Table 1). For all four methods, control groups had a substantially higher value of \(mETR\) and a lower value of initial slope (\(\alpha\)) than Diuron-treated groups for both cultivars. Although the HSI linear method provided ETR values that had a large overlap between control and Diuron-treated groups, the quantitative characteristics of the fitted RLC models were dramatically different from each other, showing that even in the worst case (HSI linear method), the developed method could be used to identify the photosynthetic efficiency difference between the two groups. Although different methods showed a similar trend in the RLC characteristics between different treatments, the absolute values of those characteristics were different.