# Ground Based Hyperspectral Imaging to Characterize Canopy-Level Photosynthetic Activities
## Results
### Calculated Effective Quantum Yield and RLCs
\(mETR\) values calculated using HSI methods were 60% to 70% lower than those calculated using the PAM method, and \(\alpha\) values were 15% to 20% higher. The reduction of absolute values for mETR was partially because the PAM and HSI methods provided measurements at different levels. The PAM method measured a single leaf near the top of a plant with little or no shading, whereas the HSI methods measured a whole canopy that had leaves at different levels of shading. So, it would be expected that the HSI methods provided a lower ETR than the PAM method. In addition to herbicide treatment differences, the two cultivars showed certain differences. The Pima cultivar had a lower  
Figure 5: Calculated effective quantum yield of PSII (\(\phi_{PSII}\)) and electron transport rate (ETR) for the two genotypes under control and Diuron treatments. PAR is short for photosynthetically active radiation. minimum saturating irradiance (estimated by \(\frac{mETR}{\alpha}\)[55]) than the Upland cultivar. This suggests that the Pima cultivar would enter into the stage dominated by non-photochemical quenching at lower light intensities than the Upland cultivar [58]. This finding is in agreement with a previous study showing that individual leaves of Pima cotton reached light saturation for net photosynthesis at a lower light intensity than Upland cotton [46]. \(\phi_{PSII}\) measured using different HSI methods also showed different correlations with those measured using the PAM method (Figure 6). In fact, a high correlation (\(R^{2}\) = 0.73) was achieved between PAM and HSI methods for control groups. Differences in correlations mainly came from the measurements for Diuron-treated groups. The quadratic model provided the best estimate of maximal fluorescence, exhibiting the strongest correlation between PAM and HSI-based estimates of quantum efficiency at the canopy level. This suggests that the quadratic model could be an optimal method for estimating maximal fluorescence for Diuron-treated groups. The average model showed a reduced but comparable performance with the quadratic model. Considering its engineering rationale, the average model could also be an option for estimating maximal fluorescence for Diuron-treated groups. Additional experiments are needed to determine which method (the quadratic or average model) would be the most optimal in terms of model generalization capability to different datasets. However, the linear model provided the lowest correlation, suggesting that the linear model would not be suitable for maximal fluorescence estimation for Diuron-treated groups. \begin{table}
\begin{tabular}{l l l l l l l} \hline \hline
**Method** & **Cultivar** & **Treatment** & **mETR** & \(\alpha\) & \(E_{k}\) & **R2** \\ \hline PAM & Pima & Control & 296.70 & 0.3989 & 743.73 & 0.94 \\ PAM & Pima & Diuron & 0.00 & 0.5000 & 0.00 & \\ PAM & Upland & Control & 303.90 & 0.3771 & 805.98 & 0.99 \\ PAM & Upland & Diuron & 2.12 & 0.5000 & 4.24 & \\ HSI\_Linear & Pima & Control & 177.51 & 0.4780 & 371.33 & 0.92 \\ HSI\_Linear & Pima & Diuron & 50.13 & 77.0580 & 0.65 & \\ HSI\_Linear & Upland & Control & 210.07 & 0.4348 & 483.13 & 0.99 \\ HSI\_Linear & Upland & Diuron & 46.19 & 93.9418 & 0.49 & \\ HSI\_Quadratic & Pima & Control & 177.51 & 0.4780 & 371.33 & 0.92 \\ HSI\_Quadratic & Pima & Diuron & 0.00 & 0.5000 & 0.00 & \\ HSI\_Quadratic & Upland & Control & 210.07 & 0.4348 & 483.13 & 0.99 \\ HSI\_Quadratic & Upland & Diuron & 0.00 & 0.5000 & 0.00 & \\ HSI\_Avg & Pima & Control & 177.51 & 0.4780 & 371.33 & 0.92 \\ HSI\_Avg & Pima & Diuron & 0.00 & 95.0250 & 0.00 & \\ HSI\_Avg & Upland & Control & 210.07 & 0.4348 & 483.13 & 0.99 \\ HSI\_Avg & Upland & Diuron & 0.00 & 0.5000 & 0.00 & \\ \hline \hline \end{tabular}
\end{table} 
Table 1: Rapid light curves (RLCs) calculated using ETR and PAR values for each genotype-treatment combination. The RLC model was \(ETR=mETR\times(1-e^{\alpha\times PAR/mETR})\).