## 4 Discussion  
An overarching goal of this study was to confirm that CF at canopy level could be detected and monitored with a relatively straightforward measurement technique. The general expectation that the increase in CF emission that would coincide with photosystem inhibition would manifest in an increase in the far-red peak of the spectra was confirmed. While individual measurements were too noisy to discriminate half-hourly or hourly decreases in plant function, likely due to the combination of an uncalibrated illumination source (LED) and dynamic and complex response of fluorescence, it was found that smoothed signals on a daily basis yielded CF information that could be used for daily plant function information, especially for indication of stress. Based on the results, CF measurements with this technique promise to evaluate more precisely the function and the stress than NDVI and PRI, which are both reflectance-based indices (RI). CF spectra and CF metrics, especially F\({}_{\text{red}}\) and F\({}_{\text{far}}\), capture the initial photosynthesis stress response and the decline of plant function to a greater degree than PRI and NDVI highlighting the capability of CF to better monitor dynamics of plant status. Because CF originates from photosynthetic machinery of plants, it was anticipated that if distinct CF signals were captured and distinguishable, the CF spectra and CF metrics would detect stress earlier and be more sensitive in monitoring it than RIs. NDVI is the most used vegetation index and is often referred to as a \"greenness index\" due to its widespread use to track large scale seasonality. NDVI is calculated from reflectance in the red and near-infrared portion of the spectrum, is sensitive to changes in biomass and leaf area index (LAI), is a good indicator of absorbed photosynthetically active radiation (APAR) of a canopy and mainly captures structural changes (biomass and LAI) seasonally [13; 1; 55]. However, the structural changes in the target plant lagged behind the functional response, i.e., conversion of short wavelength energy from the PAR range to longer wavelength emission byproduct of the photosystem in the CF range. PRI is significantly positively correlated with both F\({}_{\text{red}}\) and F\({}_{\text{far}}\), while NDVI is only significantly correlated with F\({}_{\text{far}}\). While NDVI and PRI can explain a good deal of variation in CF, RI sensitivity to plant function is lower than measurements of CF. PRI is also an RI, but unlike NDVI, has been shown to detect changes in photosynthetic activity on two timescales: (1) diurnally capturing responses of the xanthophyll cycle to changing illumination and (2) pH of thylakoid lumen and seasonally capturing changes in the chlorophyll-carotenoid ratios, i.e., pigment content of leaves. PRI has also been shown to correlate with light-use efficiency (LUE) of some vegetation [1; 56; 57; 58; 59]. In this experiment, CF response was more sensitive to the plant stress than either NDVI or PRI, but the decline in PRI over the last days of the experiment showed the changes in leaf pigment present were detectible with the PRI and was more sensitive to changes in the canopy than NDVI. This is consistent with several studies showing PRI as a good indicator of plant function, albeit the precise responses are still being studied for temporal and spatial interpretation in some ecosystems, e.g., [13; 59]. The comparison of the portions of the CF spectrum, \(\rm F_{red}\) and \(\rm F_{far}\), and their ratio, \(\rm F_{red}/F_{far}\), revealed dynamic responses to plant stress and show promise to make distinctions regarding physiology of the target plant. The shape of CF peaks for a plant at room temperature depend on leaf chlorophyll-a concentration, structure, and constituents, and the optical properties of the leaf determine the penetration depth of incident light and remission of CF from these depths [7; 21; 60; 61; 62; 63; 64].