## 3 Results  
Days 0 and 1 show the near and far-red peaks expected for the fluorescence range, which become less distinguishable on Days 2-4 as the variability for each increase (Figures 2a and A1a-e). While the plant canopy is visibly unchanged from Day 0 to Day 3 (Figures 2a and A1a-d), the red peak increases by Day 3 compared to Day 0 by approximately 4 times, while the far-red peak increases by 3.5 times, likely due to the increase in CF corresponding to photosynthetic inhibition. After the Day 3 peak in the fluorescence values, both peaks are decreased by Day 4, when the first signs of leaf discoloration and some wilting appear in the canopy, yet CF is still elevated compared to before DCMU application (Figures 2c and A1e). By Day 5 of the experiment, the two peaks of fluorescence are indistinguishable, eventually reducing to noise around zero by Day 7 (Figure A1f-h) and most leaves on Day 5 show some withering, discoloration, spots, or slightly less green at a minimum and some portions of soil began to show through the canopy when viewed from above continuing to degrade through Day 8, the final day of measurements, the recorded CF spectra and photos show little to no green vegetation being measured by the HH2 (Figures 2d and A1a-i). From Day 0-3, Fred and Ffar increase dramatically (333% and 166%, respectively, Figure 3a) going from approximately 0.2 and 0.3 of maximum to 1.0 (maximum values) in this time period, while PRI increased from 0.8 of maximum to 1.0, an increase of 35%, only subtly capturing photosynthetic response (Figure 3d,e). On Days 3-5, Fred and Ffar decline close to Day 2 levels (183% and 32% of Day 0 values, respectively) reaching approximately 0.2 and 0.3 of maximum (Figure 3a,e) and PRI performs more similarly going from maximum (reached on Day 2) to 0.4 of maximum, indicating the pigment changes occurring in the plant leaves. Day 5 and beyond Fred and Ffar are below the Day 0 values for Fred and Ffar, reaching values on Day 8 of 84% and 80% decrease from Day 0, while PRIreaches a value of \(-0.05\) by Day 8 capturing pigment changes and structural changes ion with structural changes in the plant, e.g., [1, 13] (Figure 3d,e). Fred/Ffar increases to a maximum value of 1.2 on Day 4, when Fred surpasses the value of Ffar, then declines (Figure 3b inset shows Day 0-Day 5 detail) which highlights the capability of the instrument to record CF signals that increase when PSII is initially blocked and excess energy dissipation as CF increases, capturing initial stress reactions. The Fred/Ffar (Figure 3b) shows variability so large after Day 5 (due to increasingly low values of Fred and Ffar compared to instrument noise) that the trend over the first five days is obscured by the scale of the graph. The decrease in signal for the Ffar region of the spectrum results in dramatic increase in noise and extreme variability in Fred/Ffar on Days 6-8. Figure 2: CF spectra, images and descriptions of selected days of experiment: (**a**) Day 0, (**b**) Day 3, (**c**) Day 4, (**d**) Day 8. Left column: Daily average smoothed fluorescence (Fsm), blue lines indicate Fsm spectra, shaded pink region indicates standard deviation for the day. Middle column: photographs of tomato plant each day. Right column: description of visual inspection of plant for each day. Daily fluorescence spectra, pictures and visual descriptions are included in Appendix A. In contrast, NDVI decreases throughout the experiment from approximately 0.87 to 0.69 at an average of 0.03 per day (a total decrease of only 21%, and approximately 0.8 of maximum value) and does not capture dynamic changes during photosystem inhibition and does not show a response to the DCMU poisoning of the plant prior to visible signs of stress on the plant on Day 4 (Figure 3c,e). Additionally, the value of 0.67 for NDVI at the end of the experiment indicates NDVI does not fully capture the reduced functioning of the plant (Figure 3c).