Canopy Photochemical Reflectance Index Research Articles

Downscaling canopy photochemical reflectance index to leaf level by correcting for the soil effects

The photochemical reflectance index (PRI) is a promising remote sensing signal for monitoring vegetation physiology. Variations in leaf PRI are usually attributed to either the energy-dependent xanthophyll cycle or the carotenoid-chlorophyll ratio, both indicative of leaf physiology. However, canopy PRI is subject to soil, canopy structure, and incident and viewing angles, and thus has a weaker and more complicated relationship with vegetation photosynthetic activity or leaf pigment composition. Therefore, downscaling canopy PRI to the leaf level is essential for accurate remote sensing of vegetation physiology using PRI. An earlier investigation (P.Yang, RSE, 279, 113,133, 2022) illustrates that structural and angular variations in canopy PRI primarily result from varying degrees of soil interference. In this study, a soil correction method is proposed to mitigate the soil effects on top-of-canopy (TOC) reflectance at the PRI bands. The soil effects on TOC reflectance at 531 nm and 570 nm are respectively estimated as R531soil×R675/R675soil and R570soil×R675/R675soil, where R675 is TOC red reflectance, Rλsoil soil reflectance at wavelengthλ. R675/R675soil approximates the fraction of the observed sunlit soil, as leaves are nearly black at 675 nm due to strong absorption of chlorophyll, and R675 is mainly contributed from soil. To assess the effectiveness of the soil correction method, a wheat field dataset, a corn field dataset, and a simulated dataset, were utilized. The soil-adjusted and the original canopy PRI were compared with the leaf PRI for the real and synthetic scenarios that had various soil brightness, leaf chlorophyll content and canopy structure. Both the field and numerical experiments demonstrate that, for the canopies with low vegetation coverage and substantial soil contamination, the original canopy PRI was largely different from the leaf PRI, displaying substantial structural and angular dependence. In comparison, the soil-adjusted canopy PRI was more closely aligned with the PRI observed in the sunlit leaves in all three datasets. This study shows that accounting for the soil effects with TOC red reflectance allows downscaling canopy PRI to the leaf level. The soil-adjusted canopy PRI contributes to remote sensing of the xanthophyll cycle or the carotenoid-chlorophyll ratio from canopy PRI.

Exploring the interrelated effects of soil background, canopy structure and sun-observer geometry on canopy photochemical reflectance index

Photochemical reflectance index (PRI) is an intriguing avenue for monitoring photosynthetic light use efficiency (LUE), which is a crucial physiological variable and the primary source of uncertainty in gross primary production (GPP) prediction. The correlations between PRI and LUE induced by the energy-dependent xanthophyll cycle are overall convincing at the leaf scale. However, their relationship becomes complicated and less reliable at the canopy scale due to several confounding factors, such as soil background, canopy structure and sun-observer geometry. A fundamental understanding of the interrelated effects of these factors is still missing. In this study, the roles of soil reflectance, canopy structure and sun-observer geometry were examined by investigating radiative transfer processes that determine canopy PRI. Theoretical analysis shows that the deviation between canopy- and leaf-level PRI is mainly attributed to soil background, namely the fraction of sunlit soil in the scene and the discrepancy between leaf and soil reflectance. Canopy structure and sun-observer geometry are not the direct drivers of variations in canopy PRI. They affect canopy PRI by altering the contribution of soil to canopy reflectance. Furthermore, several numerical experiments based on 1D and 3D radiative transfer models, which compare PRI of canopies with black soil (i.e., soil reflectance is zero) and non-black background, were conducted to confirm and validate the decisive role of soil background in explaining the deviation between canopy and leaf PRI. Multi-angular canopy PRI from PROBA-CHRIS data was employed to examine the angular dependency of canopy PRI changing with vegetation coverage. The numerical experiments demonstrate that canpy PRI differs from leaf PRI as large as 150% when canopy leaf area index (LAI) or the fraction of vegetation coverage is small. Canopy PRI is almost identical to soil PRI (i.e., PRI computed from soil reflectance) when the contribution of soil background to canopy reflectance is large. In contrast, when the soil reflectance is zero or LAI is greater than four, canopy PRI is almost identical to leaf PRI and independent of canopy structure and sun-observer geometry. Nonetheless, when leaf and soil reflectance are similar, canopy PRI is always close to leaf PRI regardless canopy structure and sun-observer geometry. The analysis of multi-angular PRI reveals that the angular dependency decreases with vegetation coverage due to weaker soil background effect. This study narrows down the causes of variation in canopy PRI to the fraction of observed soil background and soil reflectance. It suggests that estimating and accounting for the soil contribution to canopy PRI are necessary to mitigate angular and canopy structural effects on canopy PRI and eventually extract leaf physiological information from canopy PRI.

Use of Reflectance Indices to Assess Vine Water Status under Mild to Moderate Water Deficits

The monitoring of vine water status is of interest for irrigation management in order to improve water use while optimizing both berry yield and quality. Remote-sensing techniques might provide accurate, rapid, and non-destructive estimates of vine water status. The objective of this study was to test the capability of the reflectance-based water index (WI) and the photochemical reflectance index (PRI) to characterize Vitis vinifera L. cv. Xarel·lo water status under mild to moderate water deficits. The study was conducted at the leaf level in irrigated potted plants and at the plant level on five commercial rain-fed vineyards in 2009 and 2010. In potted plants, the reflectance indices PRI and WI closely tracked variation in the leaf-to-air temperature difference (ΔT) with r2 = 0.81 and r2 = 0.83, for WI and PRI, respectively (p < 0.01). In addition, in potted plants, both PRI and WI showed significant relationships with light-use efficiency (LUE)—calculated as the ratio between net CO2 assimilation rate (An) and incident photosynthetic active radiation (PAR) at the leaf surface—with r2 = 0.92 and r2 = 0.74 for PRI and WI, respectively. At the canopy level, vine predawn water potential (Ψpd) was related to the canopy-to-air temperature difference (ΔTm) across years (r2 = 0.37, p < 0.05). In the years of study, the relationships between PRI and WI showed variable degrees of correlation against Ψpd and ΔTm. Across years, PRI and WI showed significant relationships with Ψpd, with r2 = 0.41 and r2 = 0.37 (p < 0.01), for WI and PRI, respectively. Indices formulated to account for variation in canopy structure (i.e., PRInorm and WInorm) showed similar degrees of correlation against Ψpd to their original formulations. In addition, PRI and WI were capable of differentiating (p < 0.01) between mild (Ψpd > −0.4 MPa) and moderate (Ψpd < −0.4 MPa) water deficits, and a similar response was observed when PRInorm and WInorm—formulated to account for variation in canopy structure—were considered. Thus, at the leaf level, our result suggest that WI and PRI can be used to adequately predict the diurnal dynamics of stomatal aperture and transpiration. In addition, at the canopy level, PRI and WI effectively differentiated vines under mild water deficits from those experiencing moderate water deficits. Thus, our results show the capability of WI and PRI in characterizing vine water status under mild to moderate water deficits.

Measurement of Diurnal Variation in Needle PRI and Shoot Photosynthesis in a Boreal Forest

The photochemical reflectance index (PRI) is calculated from vegetation narrowband reflectance in two bands in the visible part of the spectrum. Variations in PRI are associated with changes in the xanthophyll cycle pigments which regulate the light use efficiency of vegetation. Correlations have been found between remotely-sensed PRI and various photosynthetic productivity parameters at the scales from leaves to landscapes. Environmental satellites can provide only an instantaneous value of this index at the time of overpass. The diurnal course of needle (leaf) PRI needs to be known in order to link the instantaneous values robustly with photosynthetic parameters at time scales exceeding one day. This information is not currently available in the scientific literature. Here we present the daily cycle of Scots pine needle and canopy PRI in a southern boreal forest zone in the presence of direct solar radiation during the peak growing season of two consecutive years. We found the PRI of the needles which are exposed to direct radiation to have a distinct diurnal cycle with constant or slightly increasing values before noon and a daily minimum in the afternoon. The cycle in needle PRI was not correlated with that in the incident photosynthetic photon flux density (PPFD). However, when PPFD was above 1000 μmol m−2 s−1, approximately between 8 a.m. and 5 p.m., needle PRI was correlated with the light use efficiency (LUE), measured with shoot chambers. The timing of the minimum needle PRI coincided with the minimum canopy value, as measured by an independent sensor above the canopy, but the correlation between the two variables was not significant. Our field results corroborate the applicability of needle PRI in monitoring the daily variation in LUE. However, to apply this to remote sensing of seasonal photosynthetic productivity, the daily cycle of leaf PRI needs to be known for the specific vegetation type.

Spectral Similarity and PRI Variations for a Boreal Forest Stand Using Multi-angular Airborne Imagery

The photochemical reflectance index (PRI) is a proxy for light use efficiency (LUE), and is used in remote sensing to measure plant stress and photosynthetic downregulation in plant canopies. It is known to depend on local light conditions within a canopy indicating non-photosynthetic quenching of incident radiation. Additionally, when measured from a distance, canopy PRI depends on shadow fraction—the fraction of shaded foliage in the instantaneous field of view of the sensor—due to observation geometry. Our aim is to quantify the extent to which sunlit fraction alone can describe variations in PRI so that it would be possible to correct for its variation and identify other possible factors affecting the PRI–sunlit fraction relationship. We used a high spatial and spectral resolution Aisa Eagle airborne imaging spectrometer above a boreal Scots pine site in Finland (Hyytiälä forest research station, 61°50′N, 24°17′E), with the sensor looking in nadir and tilted (off-nadir) directions. The spectral resolution of the data was 4.6 nm, and the spatial resolution was 0.6 m. We compared the PRI for three different scatter angles ( β = 19 ° , 55 ° and 76 °, defined as the angle between sensor and solar directions) at the forest stand level, and observed a small (0.006) but statistically significant (p < 0.01) difference in stand PRI. We found that stand mean PRI was not a direct function of sunlit fraction. However, for each scatter angle separately, we found a clear non-linear relationship between PRI and sunlit fraction. The relationship was systematic and had a similar shape for all of the scatter angles. As the PRI–sunlit fraction curves for the different scatter angles were shifted with respect to each other, no universal curve could be found causing the observed independence of canopy PRI from the average sunlit fraction of each view direction. We found the shifts of the curves to be related to a leaf structural effect on canopy scattering: the ratio of needle spectral reflectance to transmittance. We demonstrate that modeling PRI–sunlit fraction relationships using high spatial resolution imaging spectroscopy data is suitable and needed in order to quantify PRI variations over forest canopies.

Improving the ability of the photochemical reflectance index to track canopy light use efficiency through differentiating sunlit and shaded leaves

Accurate estimation of light use efficiency (LUE) of plant canopies is essential for calculating gross primary productivity (GPP) using LUE models and is also useful for calibrating process-based models for regional and global applications. A promising method for estimating LUE is through remote sensing of the photochemical reflectance index (PRI). However, there are internal (e.g. pigment concentrations) and external factors (e.g. environmental conditions and sun-target-view geometry) that affect PRI signals. Considering the reflectance difference between sunlit and shaded leaves, the ratio of observed canopy reflectance to leaf reflectance is used to represent the observed fraction of sunlit leaves, and the observed fraction of shaded leaves is calculated with a geometrical optical model. Thus, a canopy-level PRI observation is separated into sunlit and shaded PRI values, and a two-leaf canopy PRI (PRIt) is calculated as sum of these two values weighted by their respective sunlit and shaded leaf area indices. The usefulness of PRIt in assessing the canopy-level LUE is evaluated with automated multi-angle PRI observations acquired on a flux tower from April to September 2013 over a sub-tropical coniferous forest in southern China. In each 15-minute observation cycle, PRI is observed at four view zenith angles fixed at (37°, 47°, 57°) or (42°, 52°, 62°) and the instantaneous solar zenith angle in the azimuth angle range from 45° to 325° (from the geodetic north). In both the half-hourly and daily time steps, PRIt can effectively improve (>50% and >35% increases in R2, respectively) the ability as a proxy of LUE derived from the tower flux measurements over the big-leaf PRI taken as the arithmetic average of the multi-angle measurements in a given time interval. In the dry season from July to September, correlations of PRI with LUE at daily time steps are much stronger in the two-leaf case than in the big-leaf case. The correlation between PRIt and LUE is the strongest (R2=0.785, p<0.001) in July. PRIt is very effective in detecting the light and low-moderate drought stress on LUE at half-hourly time steps, while ineffective in detecting severe atmospheric water and heat stress, which is probably due to alternative radiative energy sink, i.e. photorespiration. Overall, the two-leaf approach well overcomes some external effects (e.g. sun-target-view geometry) that interfere with PRI signals.

Spatial variation of canopy PRI with shadow fraction caused by leaf-level irradiation conditions

Abstract Photochemical reflectance index (PRI) is one of the best proxies to estimate the light use efficiency and photosynthetic activity of vegetation from remote sensing observations, especially if diurnal variations can be monitored. The calculation of PRI from leaf-level spectral reflectance measurements is unambiguous. Interpretation of the value of this index is more complicated, as it is affected by leaf structure and its carotenoid and chlorophyll content. Generally, a change in leaf-level PRI indicates a change in its photosynthetic capacity. At the scales of the canopy and beyond, various non-physiological factors modulate the leaf-level PRI signal inducing large angular and spatial variations in PRI. Specifically, previous studies have shown that within-canopy illumination variations and shadowing effects directly affect the PRI of a canopy. When observing a forest with a resolution finer than the size of a tree crown, large areas of shaded and sunlit foliage become visible. The spectral distribution of irradiance in these canopy regions is different from the average top-of-canopy irradiance used in the calculation of the canopy PRI. Thus, the leaf and canopy PRI can become decoupled. To date, no thorough analytical and empirical analysis of how the spectrally variable within-canopy light conditions cause apparent, non-physiological variation in canopy PRI has been published. In this study, we propose a new method to assess these PRI variations in structured vegetation from high spatial resolution (pixel size smaller than 1 m) imaging spectroscopy data. We used airborne imaging spectroscopy of boreal forest stands to evaluate the spectral irradiance in different locations inside the canopy and calculated a correction term for the canopy PRI estimates defined using top-of-canopy irradiance. We determined the maximum value of the correction term by sampling the most sunlit and shaded road surface locations adjacent to tree crowns. Results indicated that under the particular illumination-view geometry, irradiance variations decreased the canopy PRI by as much as 0.06 (relative change > 100%). The correction depended only slightly on atmospheric correction parameters. Finally, we reduced the illumination-related apparent variation in canopy PRI using the two-leaf canopy photosynthesis modeling scheme, canopy shadow fraction and the maximum correction term. In a test scene, the average illumination-corrected PRI was 0.027 smaller than non-corrected canopy PRI and showed no correlation with the shadow fraction, indicating a lack of down-regulation at the time of measurement. In theory, approach can be applied to all canopy level PRI measurements from towers, aircrafts and satellites under any observation geometry. However, further validation, preferably using in situ leaf reflectance data from different biomes, would be required before the algorithm can be routinely applied.

Chlorophyll fluorescence, photochemical reflective index and normalized difference vegetative index during plant senescence

The relationship between the Photochemical Reflectance Index (PRI), Normalized Difference Vegetation Index (NDVI) and chlorophyll fluorescence along senescence was investigated in this work. Reflectance and radiance measurements were performed at canopy level in grass species presenting different photosynthetic metabolism: Avena sativa (C3) and Setaria italica (C4), at different stages of the natural senescence process. Sun induced-chlorophyll fluorescence at 760nm (SIF760) and the apparent fluorescence yield (SIF760/a, with a=irradiance at time of measurement) were extracted from the radiance spectra of canopies using the Fraunhofer Line Discrimination-method. The photosynthetic parameters derived from Kautsky kinetics and pigment content were also calculated at leaf level.Whilst stand level NDVI patterns were related to changes in the structure of canopies and not in pigment content, stand level PRI patterns suggested changes both in terms of canopy and of pigment content in leaves. Both SIF760/a and ΦPSII decreased progressively along senescence in both species. A strong increment in NPQ was evident in A. sativa while in S. italica NPQ values were lower. Our most important finding was that two chlorophyll fluorescence signals, ΦPSII and SIF760/a, correlated with the canopy PRI values in the two grasses assessed, even when tissues at different ontogenic stages were present. Even though significant changes occurred in the Total Chlr/Car ratio along senescence in both studied species, significant correlations between PRI and chlorophyll fluorescence signals might indicate the usefulness of this reflectance index as a proxy of photosynthetic RUE, at least under the conditions of this study. The relationships between stand level PRI and the fluorescence estimators (ΦPSII and SIF760/a) were positive in both cases. Therefore, an increase in PRI values as in the fluorescence parameters would indicate higher RUE.

Diffuse sky radiation influences the relationship between canopy PRI and shadow fraction

The Photochemical Reflectance Index (PRI) of green leaves is an indicator of photosynthetic downregulation: when the photosynthetic apparatus is close to the saturation limit, PRI becomes dependent on light conditions. Therefore, by measuring the PRI of leaves under different local irradiance conditions, it should be possible to determine the saturation level of the leaves and obtain information on the light use efficiency (LUE) of a vegetation canopy. The dependence of PRI on the ratio of sunlit to shaded foliage (quantified by the canopy shadow fraction) in the field of view of an instrument has been used to remotely measure canopy LUE on clear days. However, besides photosynthetic downregulation, the dependence of canopy PRI on shadow fraction is affected by the blue sky radiation caused by scattering in the atmosphere. To quantify this effect on remotely sensed PRI, we present the underlying definitions relating leaf and canopy PRI and perform the required calculations for typical midsummer conditions in Central Finland. We demonstrate that the effect of blue sky radiation on the variation of PRI with canopy shadow fraction is similar in shape and magnitude to that of LUE variations reported in literature.

Retrieval of the photochemical reflectance index for assessing xanthophyll cycle activity: a comparison of near-surface optical sensors

Abstract. Unattended optical sensors are increasingly being deployed on eddy covariance flux towers and are often used to complement existing vegetation and micrometeorological measurements to enable assessment of biophysical states and biogeochemical processes over a range of spatial scales. Of particular interest are sensors that can measure the photochemical reflectance index (PRI), which can provide information pertaining to leaf pigments and photosynthetic activity. This interest has facilitated the production of a new range of lower-cost multispectral sensors specifically designed to measure temporal changes in the PRI signal. However, little is known about the characteristics (spectral, radiometric and temporal) of many of these PRI sensors, making it difficult to compare data obtained from these sensors across time, geographical locations and instruments. Furthermore, direct testing of the capability of these sensors to actually detect the conversion of the xanthophyll cycle, which is the original biological basis of the PRI diurnal signal, is largely absent, often resulting in an unclear interpretation of the signal, particularly given the wide range of factors now known to influence PRI. Through a series of experiments, we assess the sensitivity of one of the leading brands of PRI sensor (Skye SKR 1800) to changes in vegetation photosynthetic activity in response to changing irradiance. We compare the results with those obtained using a more expensive industry-standard visible to near-infrared hyperspectral spectrometer (PP Systems UniSpec) and determine the radiometric compatibility of measurements made by the different instruments. Results suggest that the SKR 1800 instrument is able to track rapid (seconds to minutes) and more gradual diurnal changes in photosynthetic activity associated with xanthophyll cycle pigment conversion. Measurements obtained from both the high and lower cost instrument were significantly linearly correlated but were subject to a large systematic bias, illustrating that differences in instrument configuration (e.g. spectral response functions and band positions) can have a large impact on the PRI measurement values obtained. Despite differences in absolute PRI values, significant correlations were observed between the canopy PRI derived from both the SKR 1800 and the UniSpec instruments, and the epoxidation state of the xanthophyll cycle (r2 = 0.46 p &lt; 0.05 and r2 = 0.76 p &lt; 0.01, respectively). However, the dynamic range of the SKR 1800 PRI signal was often lower than more expensive instruments and thus the lower cost multispectral instrument may be less sensitive to pigment dynamics related to photosynthetic activity. Based on our findings, we make a series of recommendations for the effective use of such sensors under field conditions and advocate that sensors should be fully characterized prior to their field deployment.

The photochemical reflectance index from directional cornfield reflectances: Observations and simulations

The two-layer Markov chain Analytical Canopy Reflectance Model (ACRM) was linked with in situ hyperspectral leaf optical properties to simulate the Photochemical Reflectance Index (PRI) for a corn crop canopy at three different growth stages. This is an extended study after a successful demonstration of PRI simulations for a cornfield previously conducted at an early vegetative growth stage. Consistent with previous in situ studies, sunlit leaves exhibited lower PRI values than shaded leaves. Since sunlit (shaded) foliage dominates the canopy in the reflectance hotspot (coldspot), the canopy PRI derived from field hyperspectral observations displayed sensitivity to both view zenith angle and relative azimuth angle at all growth stages. Consequently, sunlit and shaded canopy sectors were most differentiated when viewed along the azimuth matching the solar principal plane. These directional PRI responses associated with sunlit/shaded foliage were successfully reproduced by the ACRM. As before, the simulated PRI values from the current study were closer to in situ values when both sunlit and shaded leaves were utilized as model input data in a two-layer mode, instead of a one-layer mode with sunlit leaves only. Model performance as judged by correlation between in situ and simulated values was strongest for the mature corn crop (r=0.87, RMSE=0.0048), followed by the early vegetative stage (r=0.78; RMSE=0.0051) and the early senescent stage (r=0.65; RMSE=0.0104). Since the benefit of including shaded leaves in the scheme varied across different growth stages, a further analysis was conducted to investigate how variable fractions of sunlit/shaded leaves affect the canopy PRI values expected for a cornfield, with implications for remote sensing monitoring options. Simulations of the sunlit to shaded canopy ratio near 50/50±10 (e.g., 60/40) matching field observations at all growth stages were examined. Our results suggest the importance of the sunlit/shaded fraction and canopy structure in understanding and interpreting PRI.

Modelling PRI for water stress detection using radiative transfer models

This paper presents a methodology for water stress detection in crop canopies using a radiative transfer modelling approach and the Photochemical Reflectance Index (PRI). Airborne imagery was acquired with a 6-band multispectral camera yielding 15 cm spatial resolution and 10 nm FWHM over 3 crops comprising two tree-structured orchards and a corn field. The methodology is based on the PRI as a water stress indicator, and a radiative transfer modelling approach to simulate PRI baselines for non-stress conditions as a function of leaf structure, chlorophyll concentration (Cab), and canopy leaf area index (LAI). The simulation work demonstrates that canopy PRI is affected by structural parameters such as LAI, Cab, leaf structure, background effects, viewing angle and sun position. The modelling work accounts for such leaf biochemical and canopy structural inputs to simulate the PRI-based water stress thresholds for non-stress conditions. Water stress levels are quantified by comparing the image-derived PRI and the simulated non-stress PRI (sPRI) obtained through radiative transfer. PRI simulation was conducted using the coupled PROSPECT-SAILH models for the corn field, and the PROSPECT leaf model coupled with FLIGHT 3D radiative transfer model for the olive and peach orchards. Results obtained confirm that PRI is a pre-visual indicator of water stress, yielding good relationships for the three crops studied with canopy temperature, an indicator of stomatal conductance ( r 2 = 0.65 for olive, r 2 = 0.8 for peach, and r 2 = 0.72 for maize). PRI values of deficit irrigation treatments in olive and peach were consistently higher than the modelled PRI for the study sites, yielding relationships with water potential ( r 2 = 0.84) that enabled the identification of stressed crowns accounting for within-field LAI and Cab variability. The methodology presented here for water stress detection is based on the visible part of the spectrum, and therefore it has important implications for remote sensing applications in agriculture. This method may be a better alternative to using the thermal region, which has limitations to acquire operationally high spatial resolution thermal imagery.

Assessing canopy PRI for water stress detection with diurnal airborne imagery

A series of diurnal airborne campaigns were conducted over an orchard field to assess the canopy Photochemical Reflectance Index (PRI) as an indicator of water stress. Airborne campaigns over two years were conducted with the Airborne Hyperspectral Scanner (AHS) over an orchard field to investigate changes in PRI, in the Transformed Chlorophyll Absorption in Reflectance Index (TCARI) normalized by the Optimized Soil-Adjusted Vegetation Index (OSAVI) (TCARI/OSAVI), and in the Normalized Difference Vegetation Index (NDVI) as function of field-measured physiological indicators of water stress, such as stomatal conductance, stem water potential, steady-state fluorescence, and crown temperature. The AHS sensor was flown at three times on each 2004 and 2005 years, collecting 2 m spatial resolution imagery in 80 spectral bands in the 0.43–12.5 μm spectral range. Indices PRI, TCARI/OSAVI, and NDVI were calculated from reflectance bands, and thermal bands were assessed for the retrieval of land surface temperature, separating pure crowns from shadows and sunlit soil pixels. The Photochemical Reflectance Index, originally developed for xanthophyll cycle pigment change detection was calculated to assess its relationship with water stress at a canopy level, and more important, to assess canopy structural and viewing geometry effects for water stress detection in diurnal airborne experiments. The FLIGHT 3D canopy reflectance model was used to simulate the bi-directional reflectance changes as function of the viewing geometry, background and canopy structure. This manuscript demonstrates that the airborne-level PRI index is sensitive to the de-epoxidation of the xanthophyll pigment cycle caused by water stress levels, but affected diurnally by the confounding effects of BRDF. Among the three vegetation indices calculated, only airborne PRI demonstrated sensitivity to diurnal changes in physiological indicators of water stress, such as canopy temperature minus air temperature (Tc–Ta), stomatal conductance (G), and stem water potential (ψ) measured in the field at the time of each image acquisition. No relationships were found from the diurnal experiments between NDVI and TCARI/OSAVI with the tree-measured physiological measures. FLIGHT model simulations of PRI demonstrated that PRI is highly affected by the canopy structure and background.

Seasonal patterns of reflectance indices, carotenoid pigments and photosynthesis of evergreen chaparral species.

This study examined the ability of the Photochemical Reflectance Index (PRI) to track seasonal variations in carotenoid pigments and photosynthetic activity of mature evergreen chaparral shrubs. Our results confirm that PRI scales with photosystem two (PSII) photochemical efficiency across species and seasons, as demonstrated by PRI's strong correlation with de-epoxidized (photoprotective) xanthophyll cycle pigment levels (normalized to chlorophyll) and with the chlorophyll fluorescence index, ΔF/Fm'. PRI and carotenoid pigment levels (de-epoxidized xanthophyll cycle pigments normalized to chlorophyll or total carotenoid pigments normalized to chlorophyll) were correlated with seasonal fluctuations in midday net CO2 uptake of top-canopy leaves. By contrast, chlorophyll levels (as measured by the Chlorophyll Index) were not as strongly linked to photosynthetic activity, particularly when all species were considered together. Likewise, the Normalized Difference Vegetation Index (NDVI, an index of canopy greenness) did not correlate with net CO2 uptake. Canopy NDVI also did not correlate with canopy PRI, demonstrating that these indices were largely independent over the temporal and spatial scales of this study. Together, these patterns provide evidence for coordinated regulation of carotenoid pigments, PSII electron transport, and carboxylation across seasons and indicate that physiological adjustments are more important than structural ones in modifying CO2-fixation capacity during periods of photosynthetic down-regulation for these evergreen species. The strong correlation between PRI of whole canopies and PRI of top-canopy leaves suggests that the canopy can be treated as a "big leaf" in terms of this reflectance index and that PRI can be used in "scalable" models. This along with the links between carotenoid pigments, PSII photochemical efficiency and carboxylation across species and seasons supports the use of optical assays of pigment levels and PSII activity in CO2 flux models to derive photosynthetic rates.

Remote sensing of canopy light use efficiency using the photochemical reflectance index: Model and sensitivity analysis

A growing number of studies have shown that reflectance changes at 531 nm, associated with the xanthophyll cycle and the related thylakoid energisation are widespread among plant species. The photochemical reflectance index (PRI), derived from narrow band reflectance at 531 and 570 nm has been related with some success to photosynthetic light use efficiency (LUE). Such a relationship would enable the estimation of stand photosynthesis from remotely sensed data. However, canopy PRI is an integral of the component leaf response weighted by the strength of the signal from each leaf to the sensor. This analysis investigates the extent to which canopy structure, view, and illumination angles are likely to influence the measured canopy PRI. A one-dimensional ray tracing radiative transfer model was used to estimate light distribution within a canopy and the dynamic response of individual foliar elements, based on a published relationship between PRI and LUE and a simple photosynthetic light response function. The model estimated the LUE of the canopy, based on both incident and absorbed light, and reflectance of the canopy at the desired wavelengths and hence the canopy PRI. A range of solar zenith, leaf area index (LAI), leaf angle distributions (LAD), and soil types were used to determine the likely influence on measured canopy PRI. The results show a positive correlation between PRI and LUE variation at canopy scale. However, the index shows a greater variation of view angle than most vegetation indices. The index is strongly influenced by varying soil background for LAI<3. At large viewing angles (>30°) the index is also sensitive to LAD. Correction for Rayleigh scattering is necessary to relate the index to ground measured PRI. Results show that the PRI value is most sensitive to changes in LAI. Utilisation of the relationship to predict or improve estimates of canopy LUE based on either absorbed or incident light will require an independent estimate of LAI change between dates/locations of in situ measurements and of remote sensing observations.