Fraunhofer Line Depth Research Articles

Area-ratio Fraunhofer line depth (aFLD) method approach to estimate solar-induced chlorophyll fluorescence in low spectral resolution spectra in a cool-temperate deciduous broadleaf forest.

Solar-induced chlorophyll fluorescence (SIF) emissions were estimated by the "area-ratio Fraunhofer line depth (aFLD) method", a new retrieval methodology in spectra from a low spectral resolution (SR) spectroradiometer (MS-700: full width half maximum (FWHM) of 10nm and spectral sampling interval of 3.3nm), assisted with a scaling to reference SIF detected from high SR spectrum. The sparse pixels of a spectrum of low SR misses detecting the minimum of the O2A absorption band around at 760nm, which makes the SIF detection by conventional FLD methods lose accuracy considerably. To overcome this, the aFLD method uses the definite integral of spectra over a wide interval between 750 and 780nm. The integration of the spectrum is insusceptible to the change in shape of the depression curve, leading to higher accuracy of the aFLD method. Daily SIF, calculated by the aFLD method using the spectra obtained with MS-700, was scaled to reference daily SIF calculated by the spectral fitting method using the spectra obtained from August to December 2019 with an ultrafine SR spectroradiometer (QE Pro, FWHM = 0.24nm). As a result, SIF calculated from MS-700 spectra by aFLD method was strongly correlated with the reference SIF from QE Pro spectra (r2 = 0.81) and was successfully scaled. Then, the scaled 11-year SIF from MS-700 at a deciduous broadleaf forest showed the correlation with GPP at multiple time steps: daily, monthly, and yearly, consistently during 2008-2018. The comparison of aFLD-derived SIF with the global Orbiting Carbon Observatory-2 (OCO-2) SIF data set (GOSIF) showed high correlation on monthly values during 2008-2017 (r2 = 0.85). The combining approach of the aFLD method with a scaling to reference SIF successfully detected long-term canopy SIF emissions, which has great potential to provide essential information on ecosystem-level photosynthesis.

Sun-Induced Chlorophyll Fluorescence III: Benchmarking Retrieval Methods and Sensor Characteristics for Proximal Sensing

The interest of the scientific community on the remote observation of sun-induced chlorophyll fluorescence (SIF) has increased in the recent years. In this context, hyperspectral ground measurements play a crucial role in the calibration and validation of future satellite missions. For this reason, the European cooperation in science and technology (COST) Action ES1309 OPTIMISE has compiled three papers on instrument characterization, measurement setups and protocols, and retrieval methods (current paper). This study is divided in two sections; first, we evaluated the uncertainties in SIF retrieval methods (e.g., Fraunhofer line depth (FLD) approaches and spectral fitting method (SFM)) for a combination of off-the-shelf commercial spectrometers. Secondly, we evaluated how an erroneous implementation of the retrieval methods increases the uncertainty in the estimated SIF values. Results show that the SFM approach applied to high-resolution spectra provided the most reliable SIF retrieval with a relative error (RE) ≤6% and <5% for F687 and F760, respectively. Furthermore, although the SFM was the least affected by an inaccurate definition of the absorption spectral window (RE = 5%) and/or interpolation strategy (RE = 15–30%), we observed a sensitivity of the SIF retrieval for the simulated training data underlying the SFM model implementation.

Effects of Heterogeneity within Tree Crowns on Airborne-Quantified SIF and the CWSI as Indicators of Water Stress in the Context of Precision Agriculture

This research focused on understanding the effects of structural heterogeneity within tree crowns on the airborne retrieval of solar-induced chlorophyll fluorescence (SIF) and the Crop Water Stress Index (CWSI). We explored the SIF and CWSI variability observed within crowns of trees subjected to different water stress regimes and its effect on the relationships with leaf physiological measurements. High-resolution (20 cm) hyperspectral imagery was acquired to assess fluorescence retrieval from sunlit portions of the tree crowns using the Fraunhofer line depth method, and from entire crowns using automatic object-based tree crown detection methods. We also measured the canopy temperature distribution within tree crowns using segmentation algorithms based on temperature percentiles applied to high-resolution (25 cm) thermal imagery. The study was conducted in an almond orchard cultivated under three watering regimes in Cordoba, in southern Spain. Three airborne campaigns took place during the summer of 2015 using high-resolution hyperspectral and thermal cameras on board a manned aircraft. Relationships between SIF and the assimilation rate improved significantly when the sunlit tree crown pixels extracted through segmentation were used for all flight dates. By contrast, the SIF signal extracted from the entire tree crowns was highly degraded due to the canopy heterogeneity observed within tree crowns. The quartile crown segmentations applied to the thermal images showed that the CWSI values obtained were within the theoretically expected CWSI range only when the pixels were extracted from the 50th percentile class. However, the CWSI values were biased in the upper quartile (Q75) for all watering regimes due to the soil background effects on the calculated mean crown temperature. The relationship between the CWSI and Gs was heavily affected by the crown segmentation levels applied and improved remarkably when the CWSI values were calculated from the middle quartile crown segmentation (Q50), corresponding to the coldest and purest vegetation pixels (r2 = 0.78 in pure vegetation pixels vs. r2 = 0.52 with the warmer pixels included in the upper quartile). This study highlights the importance of using high-resolution hyperspectral and thermal imagery for pure-object segmentation extractions from tree crowns in the context of precision agriculture and water stress detection.

Hyperspectral radiative transfer modeling to explore the combined retrieval of biophysical parameters and canopy fluorescence from FLEX – Sentinel-3 tandem mission multi-sensor data

The FLuorescence EXplorer (FLEX) satellite mission, selected as ESA's 8th Earth Explorer, has been designed for the measurement of sun-induced fluorescence (F) spectra emitted by plants. This will be accomplished through a multi-sensor approach by placing it in a common orbit in tandem with the Sentinel-3 (S3) mission, which will have two optical sensors on board, OLCI (Ocean and Land Colour Instrument) and SLSTR (Sea and Land Surface Temperature Radiometer) to complement FLEX. These S3 instruments will be used in combination with the imaging spectrometers on board FLEX to provide data useful for atmospheric correction of FLEX data. However, a fully synergetic approach, i.e. by exploiting the spectral and directional information from all tandem mission instruments together, is an attractive alternative which is explored in this paper. By employing all combined top-of-atmosphere (TOA) spectral radiance data, one can (i) characterize the relevant optical properties of the atmosphere, (ii) retrieve biophysical canopy properties including the associated reflectance anisotropy, and (iii) retrieve a more accurate and consistent canopy F.Regarding retrieval methods, Fraunhofer Line Depth (FLD) and Spectral Fitting (SF) are well-known techniques applied to hyperspectral data. Both methods depend on a high spectral resolution and assume a Lambertian (isotropic) canopy reflectance. However, most vegetation canopies are non-Lambertian. This implies that, in particular when ignoring the anisotropic surface reflection, substantial retrieval errors can occur due to the interaction between atmospheric absorption bands and surface reflectance anisotropy. In this paper, a novel method based on spectral radiative transfer (RT) modeling is proposed, in which coupled RT models are used to simulate TOA radiance spectra. These are then matched with ‘measured’ spectra in order to retrieve surface fluorescence, along with a suite of biophysical parameters, by model inversion through optimization. By applying coupled RT models of the soil-leaf-canopy and the surface-atmosphere systems, TOA radiance spectra can be simulated for all optical sensors of this tandem mission. In this way, complex effects due to surface reflectance anisotropy and the spectral sampling by the various instruments, which are difficult to compensate for in the end products, are properly taken into account by their incorporation in the forward modeling. Next, by model inversion of TOA radiance data via optimization, the most accurate F retrievals can be achieved in a consistent manner, along with important canopy level biophysical parameters that may help interpret the F spectrum, such as chlorophyll content and leaf area index (LAI). The potential of this approach has been explored in a numerical experiment, and the results are presented in this paper. We find that, with the assumed well-characterized and plausible FLEX/S3 instrument performances, the simultaneous retrieval of biophysical canopy parameters and F spectra would be possible with a remarkable accuracy, provided the correct atmospheric characterization is available.

Estimating Chlorophyll Fluorescence Parameters Using the Joint Fraunhofer Line Depth and Laser-Induced Saturation Pulse (FLD-LISP) Method in Different Plant Species

A comprehensive evaluation of the recently developed Fraunhofer line depth (FLD) and laser-induced saturation pulse (FLD-LISP) method was conducted to measure chlorophyll fluorescence (ChlF) parameters of the quantum yield of photosystem II (ΦPSII), non-photochemical quenching (NPQ), and the photosystem II-based electron transport rate (ETR) in three plant species including paprika (C3 plant), maize (C4 plant), and pachira (C3 plant). First, the relationships between photosynthetic photon flux density (PPFD) and ChlF parameters retrieved using FLD-LISP and the pulse amplitude-modulated (PAM) methods were analyzed for all three species. Then the relationships between ChlF parameters measured using FLD-LISP and PAM were evaluated for the plants in different growth stages of leaves from mature to aging conditions. The relationships of ChlF parameters/PPFD were similar in both FLD-LISP and PAM methods in all plant species. ΦPSII showed a linear relationship with PPFD in all three species whereas NPQ was found to be linearly related to PPFD in paprika and maize, but not for pachira. The ETR/PPFD relationship was nonlinear with increasing values observed for PPFDs lower than about 800 μmol m−2 s−1 for paprika, lower than about 1200 μmol m−2 s−1 for maize, and lower than about 800 μmol m−2 s−1 for pachira. The ΦPSII, NPQ, and ETR of both the FLD-LISP and PAM methods were very well correlated (R2 = 0.89, RMSE = 0.05), (R2 = 0.86, RMSE = 0.44), and (R2 = 0.88, RMSE = 24.69), respectively, for all plants. Therefore, the FLD-LISP method can be recommended as a robust technique for the estimation of ChlF parameters.

Assessing the effects of forest health on sun-induced chlorophyll fluorescence using the FluorFLIGHT 3-D radiative transfer model to account for forest structure

Sun-induced fluorescence (SIF) has been proven to serve as a proxy of photosynthesis activity and therefore, as an early indicator of physiological alterations for global monitoring of vegetation. However, the interpretation of SIF over different spatial resolutions is critical to bridge the existing gap between local and global scales. This study provides insight into the influence of scene components, and forest structure and composition on the quantification of the red and far-red fluorescence signal as an early indicator of forest decline. The experiments were conducted over an oak forest (Quercus ilex) affected by water stress and Phytophthora infection in the southwest of Spain. SIF retrievals through the Fraunhofer Line Depth (FLD) principle with three spectral bands F (FLD3) was assessed using high resolution (60cm) hyperspectral imagery extracting sunlit crown, full crown and aggregated pixels. Results showed the link between F (FLD3) extracted from sunlit crown pixels and the tree physiological condition in this context of disease infection, yielding significant relationships (r2=0.57, p<0.01) for midday xylem water potential (ψ), (r2=0.63, p<0.001) for the de-epoxidation state of the xanthophyll cycle (DEPS), and (r2=0.74, p<0.001) for leaf-level measurements of steady-state fluorescence yield (Fs). In contrast, a poor relationship was obtained when using aggregated pixels at 30m spatial resolution, where the relationship between the image-based F (FLD3) and Fs yielded a non-significant relationship (r2=0.25, p>0.05). These results demonstrate the need for methods to accurately retrieve crown SIF from aggregated pixels in heterogeneous forest canopies with large physiological variability among individual trees. This aspect is critical where structural canopy variations and the direct influence of background and shadows affect the SIF amplitude masking the natural variations caused by physiological condition. FluorFLIGHT, a modified version of the three dimensional (3-D) radiative transfer model FLIGHT was developed for this work, enabling the simulation of canopy radiance and reflectance including fluorescence at different spatial resolutions, such as may be derived from proposed satellite missions such as FLEX, and accounting for canopy structure and varying percentage cover. The 3-D modelling approach proposed here significantly improved the relationship between Fs and F (FLD3) extracted from aggregated pixels (r2=0.70, p<0.001), performing better than when aggregation effects were not considered (r2=0.42, p<0.01). The FluorFLIGHT model used in this study improved the retrieval of SIF from aggregated pixels as a function of fractional cover, Leaf Area Index and chlorophyll content yielding significant relationships between Fs ground-data measurements and fluorescence quantum yield estimated with FluorFLIGHT at p<0.01 (r2=0.79). The methodology presented here using FluorFLIGHT also demonstrated its capabilities for mapping SIF at the tree level for single tree assessment of forest physiological condition in the context of early disease detection.

An Automated Comparative Observation System for Sun-Induced Chlorophyll Fluorescence of Vegetation Canopies.

Detecting sun-induced chlorophyll fluorescence (SIF) offers a new approach for remote sensing photosynthesis. However, to analyse the response characteristics of SIF under different stress states, a long-term time-series comparative observation of vegetation under different stress states must be carried out at the canopy scale, such that the similarities and differences in SIF change law can be summarized under different time scales. A continuous comparative observation system for vegetation canopy SIF is designed in this study. The system, which is based on a high-resolution spectrometer and an optical multiplexer, can achieve comparative observation of multiple targets. To simultaneously measure the commonly used vegetation index and SIF in the O2-A and O2-B atmospheric absorption bands, the following parameters are used: a spectral range of 475.9 to 862.2 nm, a spectral resolution of approximately 0.9 nm, a spectral sampling interval of approximately 0.4 nm, and the signal-to-noise ratio (SNR) can be as high as 1000:1. To obtain data for both the upward radiance of the vegetation canopy and downward irradiance data with a high SNR in relatively short time intervals, the single-step integration time optimization algorithm is proposed. To optimize the extraction accuracy of SIF, the FluorMOD model is used to simulate sets of data according to the spectral resolution, spectral sampling interval and SNR of the spectrometer in this continuous observation system. These data sets are used to determine the best parameters of Fraunhofer Line Depth (FLD), Three FLD (3FLD) and the spectral fitting method (SFM), and 3FLD and SFM are confirmed to be suitable for extracting SIF from the spectral measurements. This system has been used to observe the SIF values in O2-A and O2-B absorption bands and some commonly used vegetation index from sweet potato and bare land, the result of which shows: (1) the daily variation trend of SIF value of sweet potato leaves is basically same as that of photosynthetically active radiation (PAR); and (2) the bare land is a non-fluorescent emitter, the SIF of which is significantly smaller than that of sweet potato; and (3) analysis result based on the measured data is basically same as that based on simulated data. The above results verified the reliability of the SIF extracted from the measured data and the feasibility of comparatively observing the SIF value and the commonly used vegetation index of multiple vegetation canopy with this continuous observation system. This approach is beneficial for comprehensively analysing the stress response characteristics of vegetation canopies.

Seasonal stability of chlorophyll fluorescence quantified from airborne hyperspectral imagery as an indicator of net photosynthesis in the context of precision agriculture

Abstract The seasonal stability of solar-induced chlorophyll fluorescence (SIF) vs field-measured leaf CO2 assimilation (A) was assessed over a period of 2 years by means of airborne flights performed at midday and diurnally over a citrus (evergreen) crop canopy. The orchard was cultivated under a control treatment (ET) that received 100% of its water requirements and two regulated deficit irrigation (RDI) treatments with water supply reduced to 37% and 50% of the control level during the summer. Field measurements consisted of assimilation rate, stomatal conductance, stem water potential, leaf fluorescence and leaf reflectance. The airborne campaigns took place in 2012 and 2013, and were flown on the solar plane in order to acquire hyperspectral imagery at 40 cm resolution, 260 spectral bands and 1.85 nm/pixels in the 400–885 nm spectral region. A thermal camera was installed in tandem in all flights, acquiring imagery in the 7.5–13 μm spectral region at 640 × 480 pixel resolution, yielding a 50 cm pixel size. The robustness of the SIF quantification through the Fraunhofer Line Depth (FLD) principle based on three spectral bands (FLD3), as well as the performance of physiological and structural hyperspectral indices, was evaluated in order to understand their ability to track photosynthesis at different phenological and stress stages throughout the season. Solar induced fluorescence quantified as FLD3 was the most robust indicator of photosynthesis in all the airborne campaigns performed in the course of the two-year experiment, which comprised seven midday flights and two diurnals. The relationships between fluorescence (FLD3) and assimilation rates yielded correlation coefficients (R) between 0.64 and 0.82 across all dates, these being statistically significant with p-values between p

Sun-induced fluorescence - a new probe of photosynthesis: First maps from the imaging spectrometerHyPlant.

Variations in photosynthesis still cause substantial uncertainties in predicting photosynthetic CO2 uptake rates and monitoring plant stress. Changes in actual photosynthesis that are not related to greenness of vegetation are difficult to measure by reflectance based optical remote sensing techniques. Several activities are underway to evaluate the sun-induced fluorescence signal on the ground and on a coarse spatial scale using space-borne imaging spectrometers. Intermediate-scale observations using airborne-based imaging spectroscopy, which are critical to bridge the existing gap between small-scale field studies and global observations, are still insufficient. Here we present the first validated maps of sun-induced fluorescence in that critical, intermediate spatial resolution, employing the novel airborne imaging spectrometer HyPlant. HyPlant has an unprecedented spectral resolution, which allows for the first time quantifying sun-induced fluorescence fluxes in physical units according to the Fraunhofer Line Depth Principle that exploits solar and atmospheric absorption bands. Maps of sun-induced fluorescence show a large spatial variability between different vegetation types, which complement classical remote sensing approaches. Different crop types largely differ in emitting fluorescence that additionally changes within the seasonal cycle and thus may be related to the seasonal activation and deactivation of the photosynthetic machinery. We argue that sun-induced fluorescence emission is related to two processes: (i) the total absorbed radiation by photosynthetically active chlorophyll; and (ii) the functional status of actual photosynthesis and vegetation stress.

FLD-based retrieval of sun-induced chlorophyll fluorescence from medium spectral resolution airborne spectroscopy data

Sun-induced chlorophyll fluorescence (Fs) is the radiation flux emitted from chlorophyll molecules and can be used as a remote sensing (RS) observable to be linked to plant photosynthesis. Recently, significant progress has been made to quantify Fs from RS data, but both retrieval and interpretation of Fs remain challenging. In the case of airborne sensors with a medium spectral resolution (<2–4nm), Fs is typically estimated using the Fraunhofer Line Depth (FLD) approach focusing on atmospheric O2 absorption bands. Most critical for accurate Fs retrievals based on such methods is the characterization of atmospheric scattering and absorption processes during data acquisition. So far, detailed experimental evidence on the retrieval accuracy of airborne measured Fs is lacking. We performed an experiment using a low-flying aircraft equipped with a non-imaging spectrometer acquiring medium spectral resolution data during the course of one day, using a repeat-track approach with changing flight altitudes. Fs in the near infrared was retrieved using a semi-empirical approach constraining the FLD based Fs retrieval from the O2-A absorption band at 760nm by using non-fluorescent surfaces. We used a local sensitivity analysis to assess Fs retrieval biases related to observational and atmospheric parameters. Our results demonstrate a reliable Fs retrieval from airborne data using reference surfaces and indicate the need for accurate knowledge of atmospheric scattering and absorption processes. This study contributes to an estimation of the total error budget of Fs retrievals and will serve as a practical guideline for Fs retrieval schemes to be applied to medium resolution airborne spectroscopy data.

Fluorescence, PRI and canopy temperature for water stress detection in cereal crops

Narrow-band multispectral remote sensing techniques and thermal imagery were investigated for water stress detection in cereal crops. Visible and near infrared AISA Eagle (Specim, Finland) and thermal AHS-160 (Sensytech Inc., USA) imageries were acquired with an airborne survey on a farm-level experimental site where maize (Zea mays L.) and sorghum (Sorghum bicolor L.) were grown with three different irrigation treatments. Vegetation biophysical and eco-physiological measurements were collected concurrently with the airborne campaign. Leaf fluorescence yield (ΔF/Fm′) resulted to be a good indirect measure of water stress. Therefore, ΔF/Fm′ measurements were compared against remotely sensed indicators: (i) the Photochemical Reflectance Index (PRI), (ii) the sun-induced chlorophyll fluorescence at 760nm (F760), retrieved by the Fraunhofer line depth method and (iii) the canopy temperature (TC) calculated decoupling soil and vegetation contributions. TC was related to ΔF/Fm′ with the highest determination coefficient (R2=0.65), followed by PRI586 (reference band at 586nm) (R2=0.51). The relationship with F760 was significant but weaker (R2=0.36). The coefficient of determination increased up to 0.54 when pigment concentration was considered by multiplying ΔF/Fm′ and chlorophyll content, confirming the close relationship between passive fluorescence signal, pigment content and light photosystem efficiency. PRI586, F760 and TC maps were produced in maize and sorghum plots. The differences in the average values of PRI586, F760 and TC extracted from the plots with different water treatments showed that water treatments were well discriminated in maize plots by the three remotely sensed indicators. This was confirmed by the visual observation of the PRI586, F760 and TC maps, while in sorghum plots, F760 and TC appeared more sensitive to water stress compared to PRI586.

Spatial Resolution Effects on Chlorophyll Fluorescence Retrieval in a Heterogeneous Canopy Using Hyperspectral Imagery and Radiative Transfer Simulation

Increasing attention is being given to chlorophyll fluorescence (F) for global monitoring of vegetation due to its relationship with physiology. New progress has been made in the methodological and technical aspects of signal retrieval with the recently published low-resolution global maps of fluorescence. Nevertheless, little progress has been made in the interpretation of the F signal when quantified in large pixels, an important issue due to the effects of structure, percentage cover, shadows, and background. High-resolution (40 cm) airborne hyperspectral imagery is used in this letter to assess the retrieval of fluorescence by the Fraunhofer line depth method from pure tree crowns and aggregated pixels. Due to canopy heterogeneity, the F signal extracted from aggregated pixels is highly degraded. A poor relationship is obtained between fluorescence extracted from pure tree crowns (Fcrown) and that quantified from pixels aggregating pure tree crowns, shadows, and background (Faggregated) (R <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> = 0.25; p <; 0.01). The relationship between F and stomatal conductance (used as a physiological indicator) decreases as a function of aggregation, yielding R <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> = 0.69 (p <; 0.01) when calculated from pure tree crowns and R <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> = 0.38 (p <; 0.05) from pixels containing crown, shadows, and soil. This letter demonstrates the need for methods to accurately retrieve a pure-vegetation fluorescence signal from aggregated pixels. The FluorMODleaf and FluorSAIL models were combined with the geometric forest light interaction model (FLIM) model and led to the “FluorFLIM” model developed for this letter. Simulations conducted with FluorFLIM obtain predictive relationships between Fcrown and Faggregated pixels as a function of percentage cover, enabling the estimation of pure-crown F from aggregated pixels (R <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> = 0.72, p <; 0.01).

Relationships between net photosynthesis and steady-state chlorophyll fluorescence retrieved from airborne hyperspectral imagery

Previous studies have demonstrated the link between leaf chlorophyll fluorescence and photosynthesis, mainly at the leaf level and under controlled laboratory conditions. The present study makes progress in demonstrating the relationship between steady-state fluorescence and net photosynthesis measured under natural light field conditions both at the leaf and image levels. Ground measurements and airborne campaigns were conducted over two summers to acquire hyperspectral imagery at 40cm resolution and 260 spectral bands in the 400–885nm spectral region. This enabled the identification of pure vegetation pixels to extract their radiance spectra. The datasets were collected in August 2010 and 2011 in the western part of the area included in the Ribera del Duero Designation of Origin (Denominación de Origen), in northern Spain. The experiments were conducted in twelve full production vineyards where two study plots per field were selected to ensure adequate variability in leaf biochemistry and physiological condition. The vineyard fields were selected on the basis of their gradient in leaf nutrition and plant water status and showed variability in leaf pigment values and stomatal conductance. Leaves were collected for destructive sampling and biochemical determination of chlorophyll a+b, carotenoids and anthocyanins in the laboratory. Leaf steady-state and dark-adapted fluorescence parameters, net photosynthesis (Pn) and stomatal conductance (Gs) were measured in the field under natural light conditions. Such data were used as a validation dataset to assess fluorescence–photosynthesis relationships both at the leaf and the image level. The Fraunhofer Line Depth (FLD) principle based on three spectral bands (FLD3) was the method used to quantify fluorescence emission from radiance spectra extracted from pure vegetation pixels identified in the hyperspectral imagery. Fluorescence retrievals conducted using the FLD3 method yielded significant results when compared to ground-measured steady-state Fs (r2=0.48; p<0.01) and Fv′/Fm′ (r2=0.53; p<0.01). The two-year assessment yielded consistent results on the relationship between Pn and Fs both at the leaf level and based on the airborne hyperspectral imagery. At the leaf level, significant relationships were found between leaf Fs and Pn (r2=0.55; p<0.001 for 2010; r2=0.59; p<0.001 for 2011). At the hyperspectral image level, the agreement between leaf Pn and airborne F was consistent for both years separately, yielding significant relationships at p<0.01 for 2010 (r2=0.54) and 2011 (r2=0.41) and a significant relationship at p<0.001 for the aggregated years (r2=0.52). Results show the link between net photosynthesis and steady-state fluorescence obtained under natural sunlight conditions at both leaf and airborne hyperspectral imagery levels.

Spatio-temporal patterns of chlorophyll fluorescence and physiological and structural indices acquired from hyperspectral imagery as compared with carbon fluxes measured with eddy covariance

This study provides insight into the assessment of the spatio-temporal trends of chlorophyll fluorescence, narrow-band physiological indices, and structural indices acquired with a hyperspectral imager flown over a flux tower in a canopy characterized by small seasonal structural changes and a heterogeneous architecture. A total of seven flights between summer and autumn were conducted with a hyperspectral camera that captured 30cm resolution imagery and 260 spectral bands in the 400-900nm region. This enabled the identification of pure-vegetation tree crown pixels around an eddy covariance flux tower without shadow components or background effects. The hyperspectral imagery was used to study the temporal patterns of canopy fluorescence and reflectance indices related to physiology and canopy structure. The seasonal trends observed in the airborne indices and fluorescence and their relationship with gross primary production (GPP) demonstrated that vegetation indices mostly related to structure such as the normalized difference vegetation index (NDVI) and the enhanced vegetation index (EVI) yielded non-significant relationships (r2=0.17; p>0.05) due to the small structural changes in the canopy through the season. By contrast, physiological indices related to chlorophyll content (TCARI/OSAVI), light use efficiency (PRI570), and canopy chlorophyll fluorescence calculated through the Fraunhofer Line Depth principle (FLD3) showed a similar seasonal trend to that of GPP measured at the same time of the flights (r2 in the range 0.75–0.84; p<0.01). These results are consistent with the physiological trend observed during summer and autumn, which showed that chlorophyll content increased by 17.9% while the NDVI and the estimated tree crown projected LAI (LAIp) remained almost constant during the experiment (3% variation). The time-series hyperspectral dataset demonstrated that the seasonal trajectories of the NDVI and EVI were weakly related (p>0.05) to the physiological indicators such as TCARI/OSAVI, PRI570 and fluorescence. The spatial variability of the hyperspectral indices investigated through the coefficient of variation (CV) showed that fluorescence around the tower varied up to 17% at the time of the maximum stress (summer), while LAIp showed little variation during that time (CV=1.8%). After the summer stress period, the CV for fluorescence and chlorophyll content decreased in autumn down to 9%. This study demonstrates that small physiological changes occurring in an evergreen canopy were still captured by remote sensing physiological indices and high-resolution airborne fluorescence. These indicators are required for GPP monitoring when the vegetation dynamics are not captured by remote sensing structural indices.

Fluorescence, temperature and narrow-band indices acquired from a UAV platform for water stress detection using a micro-hyperspectral imager and a thermal camera

The remote detection of water stress in a citrus orchard was investigated using leaf-level measurements of chlorophyll fluorescence and Photochemical Reflectance Index (PRI) data, seasonal time-series of crown temperature and PRI, and high-resolution airborne imagery. The work was conducted in an orchard where a regulated deficit irrigation (RDI) experiment generated a gradient in water stress levels. Stomatal conductance (Gs) and water potential (Ψ) were measured over the season on each treatment block. The airborne data consisted on thermal and hyperspectral imagery acquired at the time of maximum stress differences among treatments, prior to the re-watering phase, using a miniaturized thermal camera and a micro-hyperspectral imager on board an unmanned aerial vehicle (UAV). The hyperspectral imagery was acquired at 40 cm resolution and 260 spectral bands in the 400-885 nm spectral range at 6.4 nm full width at half maximum (FWHM) spectral resolution and 1.85 nm sampling interval, enabling the identification of pure crowns for extracting radiance and reflectance hyperspectral spectra from each tree. The FluorMOD model was used to investigate the retrieval of chlorophyll fluorescence by applying the Fraunhofer Line Depth (FLD) principle using three spectral bands (FLD3), which demonstrated that fluorescence retrieval was feasible with the configuration of the UAV micro-hyperspectral instrument flown over the orchard. Results demonstrated the link between seasonal PRI and crown temperature acquired from instrumented trees and field measurements of stomatal conductance and water potential. The sensitivity of PRI and Tc–Ta time-series to water stress levels demonstrated a time delay of PRI vs Tc–Ta during the recovery phase after re-watering started. At the time of the maximum stress difference among treatment blocks, the airborne imagery acquired from the UAV platform demonstrated that the crown temperature yielded the best coefficient of determination for Gs (r 2 = 0.78; p < 0.05) and Ψ (r 2 = 0.34; p < 0.001). Among the narrow-band indices calculated, the PRI 515 index (reference band = 515 nm) obtained better results than PRI 570, with r 2 = 0.59 (p < 0.01) for Gs, and r 2 = 0.38 (p < 0.001) for Ψ. The BGI1 index calculated from the blue (R 400) and green (R 550) bands resulted on the highest significance levels (p < 0.001) for both Gs (r 2 = 0.62) and Ψ (r 2 = 0.49). Out of the structural indices assessed, RDVI, MTVI1 and TVI showed greater sensitivity for Gs (r 2 = 0.6; p < 0.01) and Ψ (p < 0.001) than NDVI. Chlorophyll fluorescence calculated from the micro-hyperspectral imagery with the FLD3 method tracked stress levels, obtaining r 2 = 0.67 (p < 0.05) with stomatal conductance, and r 2 = 0.66 (p < 0.001) with water potential. The work presented in this manuscript demonstrates the feasibility of thermal, narrow-band indices and fluorescence retrievals obtained from a micro-hyperspectral imager and a light-weight thermal camera on board small UAV platforms for stress detection in a heterogeneous tree canopy where very high resolution is required.

Modeling the impact of spectral sensor configurations on the FLD retrieval accuracy of sun-induced chlorophyll fluorescence

Chlorophyll fluorescence is related to photosynthesis and can serve as a remote sensing proxy for estimating photosynthetic energy conversion and carbon uptake. Recent advances in sensor technology allow remote measurements of the sun-induced chlorophyll fluorescence signal (Fs) at leaf and canopy scale. The commonly used Fraunhofer Line Depth (FLD) principle exploits spectrally narrow atmospheric oxygen absorption bands and relates Fs to the difference of the absorption feature depth of a fluorescensing and a non-fluorescensing surface. However, due to the nature of these narrow bands, Fs retrieval results depend not only on vegetation species type or environmental conditions, but also on instrument technology and processing algorithms. Thus, an evaluation of all influencing factors and their separate quantification is required to further improve Fs retrieval and to allow a reproducible interpretation of Fs signals. Here we present a modeling study that isolates and quantifies the impacts of sensor characteristics, such as spectral sampling interval (SSI), spectral resolution (SR), signal to noise ratio (SNR), and spectral shift (SS) on the accuracy of Fs measurements in the oxygen A band centered at 760 nm (O 2-A). Modeled high resolution radiance spectra associated with known Fs were spectrally resampled, taking into consideration the various sensor properties. Fs was retrieved using the three most common FLD retrieval methods, namely the original FLD method (sFLD), the modified FLD (3FLD) and the improved FLD (iFLD). The analysis investigates parameter ranges, which are representative for field and airborne instruments currently used in Fs research (e.g., ASD FieldSpec, OceanOptics HR, AirFLEX, AISA, APEX, CASI, and MERIS). Our results show that the most important parameter affecting the retrieval accuracy is SNR, SR accounts for ≤ 40% of the error, the SSI for ≤ 12%, and SS for ≤ 7% of the error. A trade-off study revealed that high SR can partly compensate for low SNR. There is a strong interrelation between all parameters and the impact of specific parameters can compensate or amplify the influence of others. Hence, the combination of all parameters must be considered by the evaluation of sensors and their potential for Fs retrieval. In general, the standard FLD method strongly overestimates Fs, while 3FLD and iFLD provide a more accurate estimation of Fs. We conclude that technical sensor specifications and the retrieval methods cause a significant variability in retrieved Fs signals. Results are intended to be one relevant component of the total uncertainty budget of Fs retrieval and have to be considered in the interpretation of retrieved Fs signals.

Using optical remote sensing techniques to track the development of ozone-induced stress

In this paper, a literature review about optical remote sensing (RS) of O 3 stress is presented. Studies on O 3-induced effects on vegetation reflectance have been conducted since late ‘70s based on the analysis of optical RS data. Literature review reveals that traditional RS techniques were able to detect changes in leaf and canopy reflectance related to O 3-induced stress when visible symptoms already occurred. Only recently, advanced RS techniques using hyperspectral sensors, demonstrated the feasibility of detecting the stress in its early phase by monitoring excess energy dissipation pathways such as chlorophyll fluorescence and non-photochemical quenching (NPQ). Steady-state fluorescence (Fs), measured by exploiting the Fraunhofer line depth principle and NPQ related xanthophyll-cycle, estimated through the photochemical reflectance index (PRI) responded to O 3 fumigation before visible symptoms occurred. This opens up new possibilities for the early detection of vegetation O 3 stress by means of hyperspectral RS.

Comparison of measurements and FluorMOD simulations for solar‐induced chlorophyll fluorescence and reflectance of a corn crop under nitrogen treatments

Laboratory and field measurements previously acquired from foliage and canopies of corn (Zea mays L.) under controlled nitrogen (N) fertilization were used to parameterize and evaluate a new spectral vegetation Fluorescence Model (FluorMOD) developed to include the effects of steady‐state solar‐induced chlorophyll fluorescence (SIF) on canopy reflectance. These data included biophysical properties, fluorescence (F) and reflectance spectra for leaves; reflectance spectra of canopies and soil; solar irradiance; plot‐level leaf area index (LAI); and canopy SIF emissions determined using the Fraunhofer line‐depth (FLD) principle for the atmospheric telluric oxygen absorption features at 688 nm (O2β) and 760 nm (O2α). FluorMOD simulations implemented in the default mode did not reproduce the observed magnitudes of leaf F, canopy SIF, or canopy reflectance. However, simulations for all of these parameters agreed with observations when the default FluorMOD information was replaced with measurements, although N treatment responses were underestimated. The observed shift in the red/far‐red SIF ratio (from <1 to ∼2) that occurred in scaling from leaves to canopies, partially attributed to the paucity of abaxial leaf information incorporated in the model, was not expressed in the simulations. Recommendations were provided to enhance the potential utility of FluorMOD in support of SIF field experiments and studies of agriculture and ecosystems.

Detection of selected solar-stimulated fluorophores with a Fraunhofer line radiometer

In this paper we report the use of Fraunhofer Line Radiometry and the Fraunhofer Line Depth (FLD) method to measure the passive fluorescence of select, high quantum yield (> 0.7) fluorophores. The measurements we describe involved direct solar illumination of both a non-fluorescent standard material (NIST, Spectralon), and the fluorescent target materials (in solution) within several relevant Fraunhofer lines: 486 nm (H-beta), 518 nm (Mg), 589 nm (Na), and 656 nm (H-alpha). Of the selected labels, Rhodamine B demonstrated the highest fluorescence coefficient of 2.2, at 589 nm, and possessed a fluorescence intensity of 1.1 x 106 cps at an optical density of 1.0. These results show fluorescent labels can be selectively measured and observed passively in relevant Fraunhofer lines. The implications for such findings indicate the potential daytime measurement of environmental labels and probes as a promising sensing technology.

Leaf level detection of solar induced chlorophyll fluorescence by means of a subnanometer resolution spectroradiometer

A leaf level investigation on the spectral signature of Phaseolus vulgaris was undertaken by using a very high spectral resolution spectroradiometer featuring full width at half maximum of 0.06 nm and spectral range of 635.5–802.5 nm. High spectral resolution allows detection of leaf reflected and emitted radiance fields in two narrow absorption bands at 687 and 760 nm, respectively, where solar irradiance is strongly reduced owing to molecular oxygen absorption of the terrestrial atmosphere. The flux emitted due to chlorophyll fluorescence was measured using the Fraunhofer line depth principle by spectrally modelling the signal, capitalizing on the high resolution of the spectroradiometer devices. An experiment was conducted on two potted bean plants. One was maintained in good health for use as a reference while the other was treated with a photosystem II inhibitor. Collected spectra show that the fluorescence emission produces a pair of characteristic peaks superimposed on the typical leaf-specific reflectance curve. The magnitude of the fluorescence signal of the herbicide-treated leaf was four times greater than that of the control plant, thus indicating damage to the photosynthetic apparatus of the plant.