Retrieval Of Chlorophyll Fluorescence Research Articles

Retrieval of chlorophyll fluorescence from a large distance using oxygen absorption bands

The detection of solar induced chlorophyll fluorescence (SIF) in the field with spectrometers is based on the depth of the solar Fraunhofer or oxygen absorption lines in the upwelling radiance compared to that in the downwelling irradiance. This relative depth enables the differentiation of SIF from the reflected radiation. Recent studies have shown that if oxygen bands are used to retrieve SIF from tower-based measurements, then atmospheric correction is required. This study presents a band shape fitting (BSF) approach to retrieve both the relative optical path length (deepening) and SIF (infilling) from field measurements at the same time, using information in the measured spectral shape of the O2 feature. This approach is an alternative to using radiative transfer process models for estimating atmospheric transmittance. The method was applied to measurements taken from 100 m elevation above a forest, yielding plausible results for SIF in the O2A and O2B bands. The sensitivity to combined atmospheric and instrument characteristics prohibits application at much greater distances from the surface.

Investigating the Potential Accuracy of Spaceborne Solar-Induced Chlorophyll Fluorescence Retrieval for 12 Capable Satellites Based on Simulation Data

Remote sensing of solar-induced chlorophyll fluorescence (SIF) has been widely investigated with satellites/sensors covering the spectral range of SIF emission with fine spectral resolutions. The potential precision of SIF retrievals is limited by instruments’ spectral specifications. Here, the influence of spectral characteristics (spectral resolution (SR), signal-to-noise ratio (SNR), and spectral coverage) on data-driven SIF retrieval was assessed using simulations, and the SIF retrieval capability of the obsolete, in-orbit, and planned satellites was evaluated from the spectral perspective. As a result, the 757–759nm and 735–758nm fitting windows were found to be optimal for far-red SIF retrieval on satellites with fine (<0.1 nm) and moderate (0.1–0.5nm) SR. The 682–697 nm fitting window was found to perform better for red SIF retrievals. For far-red SIF retrievals, OCO-2 and TanSat were found to have the best SIF retrieval performance, with a root-mean-squared-error (RMSE*) of lower than 0. 25 mW m <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">-2</sup> sr <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">-1</sup> nm <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">-1</sup> , followed by satellites with moderate SRs (0.1–0.5 nm) such as CO <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sub> M, TROPOMI and GOME-2 (RMSE* < 0.5 mW m <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">-2</sup> sr <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">-1</sup> nm <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">-1</sup> ). The high SNR of SCIAMACHY did not improve the far-red SIF retrieval greatly (RMSE* = 0.47 mW m <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">-2</sup> sr <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">-1</sup> nm <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">-1</sup> ) but obtained a low RMSE* at the red band (0.43 mW m <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">-2</sup> sr <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">-1</sup> nm <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">-1</sup> ). The highest red SIF retrieval potential was found on TROPOMI, with an RMSE* of 0.41 mW m <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">-2</sup> sr <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">-1</sup> nm <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">-1</sup> . TEMPO and FLEX gave poor performance (RMSE* > 0.9 mW m <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">-2</sup> sr <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">-1</sup> nm <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">-1</sup> ) with their current spectral specifications. Improvement of the spectral characteristics is still needed to obtain precise SIF retrievals.

Uncertainty analysis of SVD-based spaceborne far–red sun-induced chlorophyll fluorescence retrieval using TanSat satellite data

The singular value decomposition (SVD) method, a sun-induced chlorophyll fluorescence (SIF) retrieval approach, has been used widely in far-red SIF spaceborne retrievals on a global scale. However, due to its semi-empirical nature, setting different parameter values may affect its retrieval accuracy, and ultimately have a large impact on its application. Hence, in this study, we evaluated the impact of parameter selection on the far-red SIF retrieval of this approach using TanSat satellite data. We first retrieved the far-red SIF within a narrow spectral window of 757.4–759.2 nm using the first four singular vectors (SVs) that were derived from the snow and soil spectra in a globally distributed training set. The retrievals are highly consistent with TanSat mission SIF (R2 = 0.72), indicating the reliability of our retrieval results. Then, the uncertainty was executed based on the above SIF retrievals and evaluated from five metrics: the number of SVs, length of the fitting window, type of training set elements, proportion of training set elements, and spatial distribution of the training set. Results showed that an unwise selection of the number of SVs would result in large retrieval errors (R2 = 0.03). Meanwhile, a fitting window that is too short or does not include a strong Fraunhofer line would cause severe errors and a large number of negative values (R2 = 0.06). Further, failure to include training samples below the equatorial zone in the Southern Hemisphere, and high latitude samples in the Northern Hemisphere, leads to poorer outcomes (R2 = 0.57). In contrast, the other global sampling metrics had little effect on the retrieval results (generally, R2 > 0.97). Accordingly, the relevant suggestions for using this method in the future are listed in this study for reference, with the potential to improve the accuracy of SIF retrievals from ultra-high spectral resolution instruments in the far-red spectrum.

Estimation of Chlorophyll Fluorescence at Different Scales: A Review.

Measuring chlorophyll fluorescence is a direct and non-destructive way to monitor vegetation. In this paper, the fluorescence retrieval methods from multiple scales, ranging from near the ground to the use of space-borne sensors, are analyzed and summarized in detail. At the leaf-scale, the chlorophyll fluorescence is measured using active and passive technology. Active remote sensing technology uses a fluorimeter to measure the chlorophyll fluorescence, and passive remote sensing technology mainly depends on the sun-induced chlorophyll fluorescence filling in the Fraunhofer lines or oxygen absorptions bands. Based on these retrieval principles, many retrieval methods have been developed, including the radiance-based methods and the reflectance-based methods near the ground, as well as physically and statistically-based methods that make use of satellite data. The advantages and disadvantages of different approaches for sun-induced chlorophyll fluorescence retrieval are compared and the key issues of the current sun-induced chlorophyll fluorescence retrieval algorithms are discussed. Finally, conclusions and key problems are proposed for the future research.

MEASUREMENT OF SUN INDUCED CHLOROPHYLL FLUORESCENCE USING HYPERSPECTRAL SATELLITE IMAGERY

Abstract. Solar Induced Chlorophyll Fluorescence (SIF), can be used as an indicator of stress in vegetation. Several scientific approaches have been made and there is considerable evidence that steady state Chlorophyll fluorescence is an accurate indicator of plant stress hence a reliable tool to monitor vegetation health status. Retrieval of Chlorophyll fluorescence provides an insight into photochemical and carbon sequestration processes within vegetation. Detection of Chlorophyll fluorescence has been well understood in the laboratory and field measurement. Fluorescence retrieval methods were applied in and around the atmospheric absorption bands 02B (Red wavelength) approximately 690 nm and 02A (Far red wavelengths) 740 nm. Hyperion satellite images were acquired for the years 2012 to 2015 in different seasons. Atmospheric corrections were applied using the 6S Model. The Fraunhofer Line Discrimanator (FLD) method was applied for retrieval of SIF from the Hyperion images by measuring the signal around the absorption bands in both vegetated and non vegetated land cover types. Absorption values were extracted in all the selected bands and the fluorescence signal was detected. The relationships between NDVI and Fluorescence derived from the satellite images are investigated to understand vegetation response within the absorption bands.

MEASUREMENT OF SUN INDUCED CHLOROPHYLL FLUORESCENCE USING HYPERSPECTRAL SATELLITE IMAGERY

Solar Induced Chlorophyll Fluorescence (SIF), can be used as an indicator of stress in vegetation. Several scientific approaches have been made and there is considerable evidence that steady state Chlorophyll fluorescence is an accurate indicator of plant stress hence a reliable tool to monitor vegetation health status. Retrieval of Chlorophyll fluorescence provides an insight into photochemical and carbon sequestration processes within vegetation. Detection of Chlorophyll fluorescence has been well understood in the laboratory and field measurement. Fluorescence retrieval methods were applied in and around the atmospheric absorption bands 02B (Red wavelength) approximately 690 nm and 02A (Far red wavelengths) 740 nm. Hyperion satellite images were acquired for the years 2012 to 2015 in different seasons. Atmospheric corrections were applied using the 6S Model. The Fraunhofer Line Discrimanator (FLD) method was applied for retrieval of SIF from the Hyperion images by measuring the signal around the absorption bands in both vegetated and non vegetated land cover types. Absorption values were extracted in all the selected bands and the fluorescence signal was detected. The relationships between NDVI and Fluorescence derived from the satellite images are investigated to understand vegetation response within the absorption bands.

New Spectral Fitting Method for Full-Spectrum Solar-Induced Chlorophyll Fluorescence Retrieval Based on Principal Components Analysis

The full-spectrum Solar-Induced chlorophyll Fluorescence (SIF) within the 650-800 nm spectral region can provide important information regarding physiological and biochemical activities in vegetation. This paper proposes a new Full-spectrum Spectral Fitting Method (F-SFM) for the retrieval of SIF spectra based on Principal Components Analysis (PCA). Using F-SFM, both the full-spectrum reflectance and SIF within the 650-800 nm region were modeled by PCA based on a training dataset simulated by the Soil Canopy Observation, Photochemistry and Energy fluxes (SCOPE) model, and the weighting coefficients of the principal components were estimated by the least-squares fitting method. An iterative process was employed to improve the accuracy of the estimation of the reflectance. In each iteration, the SIF spectra retrieved from the last run were removed from the total upwelling radiance to minimize the small contribution of the SIF to the apparent reflectance outside the absorption bands. Then, the F-SFM algorithm was tested using both simulated and field-measured data with different Spectral Resolutions (SRs) and Signal-to-Noise Ratios (SNRs). For data with an SR of 0.3 nm and without noise, the Relative Root Mean Square Error (RRMSE) was less than 14% within the spectral region that was studied, and the peak-value ratio (SIF735/SIF685) was accurately estimated with an RRMSE of 3.56%. In addition, the F-SFM algorithm proved less sensitive to the SR than the three-band Fraunhofer Line Discrimination (3 FLD) and improved FLD (iFLD) methods. In the case of the field spectral data with SRs of 3 nm and 0.3 nm, the double-peak shape and the diurnal variation trend of the SIF spectra could be reasonably reconstructed by F-SFM, and the retrieved SIF values at the O2-A and O2-B bands were consistent with those retrieved by 3FLD from data with a high SR (0.3 nm) and SNR (1000). Therefore, the F-SFM method can provide full-spectrum SIF information with high accuracy even at relatively low SRs and SNRs, and shows promise for use in applications involving the SIF shape information.

A Method for Uncertainty Assessment of Passive Sun-Induced Chlorophyll Fluorescence Retrieval Using an Infrared Reference Light

Measurements of sun-induced chlorophyll fluorescence (SIF) over plant canopies provide a proxy for plant photosynthetic capacity and are of high interest for plant research. Together with spectral reflectance, SIF has the potential to act as a noninvasive approach to quantify photosynthetic plant traits from field to air and spaceborne scales. However, SIF is a small signal contribution to the reflected sunlight and often not distinguishable from sensor noise. SIF estimation is, therefore, affected by an unquantified uncertainty, making it difficult to estimate accurately how much SIF is truly emitted from the plant. To investigate and overcome this, we designed a device based on a spectrometer covering the visible range and equipped it with an LED emitting at the wavelength of SIF. Using this as a reference and applying thorough calibrations, we present consistent evidence of the instrument's capability of SIF retrieval and accuracy estimations. The LED's intensity was measured under sunlight with 1.27 ± 0.27 mW × sr -1 m -2 nm -1 stable over the day. The large increase of SIF due to the Kautsky effect was measured spectrally and temporally proving the biophysical origin of the signal. We propose rigorous tests for instruments intended to measure SIF and show ways to further improve the presented methods.

Improving Chlorophyll Fluorescence Retrieval Using Reflectance Reconstruction Based on Principal Components Analysis

Methods based on Fraunhofer line discrimination (FLD) for solar-induced chlorophyll fluorescence retrieval require making assumptions or estimations about true reflectance, which is a large source of error, particularly at the O <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sub> -B band. This letter presents an alternative solution, which is named the pFLD method, based on principal components analysis to reconstruct the reflectance spectra. The principal components were generated with simulated reflectance spectra covering the most common conditions of vegetation. The pFLD method has been tested with both simulated and field experiment data sets. Compared with the widely used three-band FLD and improved FLD methods, pFLD showed better performance at the O <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sub> -B band, particularly when the spectral resolution (SR) or the signal-to-noise ratio was relatively low. The pFLD method can be also successfully applied to field measurements with credible accuracy even at low SR.

Global retrieval of marine and terrestrial chlorophyll fluorescence at its red peak using hyperspectral top of atmosphere radiance measurements: Feasibility study and first results

Chlorophyll fluorescence is directly linked to the physiology of phytoplankton or plants. Here, we present a new satellite remote sensing approach to retrieve chlorophyll fluorescence at its red peak (~685nm) by using measurements from the hyperspectral instruments SCanning Imaging Absorption SpectroMeter for Atmospheric CHartographY (SCIAMACHY) and Global Ozone Monitoring Experiment-2 (GOME-2). This method, which is based on the Differential Optical Absorption Spectroscopy (DOAS) technique, was used to exploit narrow spectral structures resulting from the filling-in of the Fraunhofer Fe I line, which originates from fluorescence. The reference spectra for chlorophyll fluorescence were calculated by the coupled ocean–atmosphere radiative transfer model SCIATRAN. We compared our results on marine chlorophyll fluorescence observations with the MODIS Terra normalized Fluorescence Line Height (nFLH) product for the average of years 2003–2011 and year 2009. Our method also enables the retrieval of chlorophyll fluorescence above land vegetation scenes. The results for the fluorescence observed above terrestrial vegetation for July and December 2009 were compared to MODIS Enhanced Vegetation Index (EVI). The comparisons show good spatial agreement between different retrievals providing evidence for the good performance of our algorithm. The method presented is generic and can be applied to other hyperspectral instruments in the future. Having established the retrieval technique, extensive studies of chlorophyll fluorescence will improve global knowledge on physiology and photosynthetic efficiency, in both the marine and terrestrial realms, and its dependence on environmental factors.

Simplified physically based retrieval of sun-induced chlorophyll fluorescence from GOSAT data

First global retrievals of sun-induced chlorophyll fluorescence (F <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">8</sub> ) have been achieved in the last years by using data from the Fourier transform spectrometer (FTS) onboard the Japanese Greenhouse Gases Observing Satellite (GOSAT). The high spectral resolution (approximately 0.025 nm) of the FTS enables measurements of F <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">8</sub> by the evaluation of the in-filling of solar Fraunhofer lines around 755 nm. This study presents a new F <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">8</sub> retrieval algorithm (GARLiC, for GOSAT retrieval of chlorophyll fluorescence) and compares its results to F <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">8</sub> from two previously implemented approaches. GARLiC is intended to simplify some of the assumptions of existing retrieval approaches without a loss in retrieval accuracy. We show that GARLiC F <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">8</sub> retrievals are comparable to the previously used methods. We also assess the effect of clouds on F <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">8</sub> retrieval from GOSAT data through the analysis of the effect of different cloud filter thresholds on F <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">8</sub> time series. Our results show a low sensitivity of Fraunhofer-line-based F <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">8</sub> retrievals to cloud contamination.

Prospects for chlorophyll fluorescence remote sensing from the Orbiting Carbon Observatory-2

The Orbiting Carbon Observatory-2 (OCO-2), scheduled to launch in July 2014, is a NASA mission designed to measure atmospheric CO2. Its main purpose is to allow inversions of net flux estimates of CO2 on regional to continental scales using the total column CO2 retrieved using high-resolution spectra in the 0.76, 1.6, and 2.0μm ranges. Recently, it was shown that solar-induced chlorophyll fluorescence (SIF), a proxy for gross primary production (GPP, carbon uptake through photosynthesis), can be accurately retrieved from space using high spectral resolution radiances in the 750nm range from the Japanese GOSAT and European GOME-2 instruments. Here, we use real OCO-2 thermal vacuum test data as well as a full repeat cycle (16days) of simulated OCO-2 spectra under realistic conditions to evaluate the potential of OCO-2 for retrievals of chlorophyll fluorescence and also its dependence on clouds and aerosols. We find that the single-measurement precision is 0.3–0.5Wm−2sr−1μm−1 (15–25% of typical peak values), better than current measurements from space but still difficult to interpret on a single-sounding basis. The most significant advancement will come from smaller ground-pixel sizes and increased measurement frequency, with a 100-fold increase compared to GOSAT (and about 8 times higher than GOME-2). This will largely decrease the need for coarse spatial and temporal averaging in data analysis and pave the way to accurate local studies. We also find that the lack of full global mapping from the OCO-2 only incurs small representativeness errors on regional averages. Eventually, the combination of net ecosystem exchange (NEE) derived from CO2 source/sink inversions and SIF as proxy for GPP from the same satellite will provide a more process-based understanding of the global carbon cycle.

An inherent limitation of solar-induced chlorophyll fluorescence retrieval at the O2-A absorption feature in high-altitude areas

The Fraunhofer line discriminator (FLD) principle applied on the atmospheric oxygen absorption feature around 761 nm ( O2-A band) has been widely used to retrieve solar-induced chlorophyll fluorescence (Fs) from remotely sensed data. In this letter, however, we address a violation of the basic assumption caused by O2 absorption feature changes, and we evaluate the impact of diminishing O2 absorption with the increase in ground altitude on Fs retrieval accuracy. The Fs retrieval accuracy substantially decreases in higher ground altitude areas for the standard FLD and three-band FLD methods, in which relative estimation errors increase approximately 70%-80% and 10%-16%, respectively, with an increase in ground altitude from 0.01 to 4.5 km. However, this increasing trend in Fs retrieval error does not occur with the use of the improved FLD (iFLD) method, which exhibits smaller than 5% of changes in relative estimation errors. Analytical analyses reveal the causes of the changes in Fs retrieval accuracy by the three methods. Based on these findings, the iFLD method is recommended to be used in cross-altitude studies or for Fs estimation in higher ground altitude areas under conditions of low radiometric noise, although its high sensitivity to noise should be taken into account. The investigations in this letter further indicate that the impact of ground altitude should be included in the uncertainty budgets of Fs retrievals and should be considered in the interpretation of Fs signals at the O2-A absorption feature.

Remote sensing of terrestrial chlorophyll fluorescence from space

High-resolution spectrometers enable new avenues in global carbon cycle research, including the first accurate retrievals of chlorophyll fluorescence from space as an indicator of photosynthetic activity.

Retrieval of chlorophyll fluorescence from GOSAT TANSO-FTS data based on weighted least square fitting

Retrieval of chlorophyll fluorescence from GOSAT TANSO-FTS data based on weighted least square fitting

Remote sensing of near-infrared chlorophyll fluorescence from space in scattering atmospheres: implications for its retrieval and interferences with atmospheric CO&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt; retrievals

Abstract. With the advent of dedicated greenhouse gas space-borne spectrometers sporting high resolution spectra in the O2 A-band spectral region (755–774 nm), the retrieval of chlorophyll fluorescence has become feasible on a global scale. If unaccounted for, however, fluorescence can indirectly perturb the greenhouse gas retrievals as it perturbs the oxygen absorption features. As atmospheric CO2 measurements are used to invert net fluxes at the land–atmosphere interface, a bias caused by fluorescence can be crucial as it will spatially correlate with the fluxes to be inverted. Avoiding a bias and retrieving fluorescence accurately will provide additional constraints on both the net and gross fluxes in the global carbon cycle. We show that chlorophyll fluorescence, if neglected, systematically interferes with full-physics multi-band XCO2 retrievals using the O2 A-band. Systematic biases in XCO2 can amount to +1 ppm if fluorescence constitutes 1% to the continuum level radiance. We show that this bias can be largely eliminated by simultaneously fitting fluorescence in a full-physics based retrieval. If fluorescence is the primary target, a dedicated but very simple retrieval based purely on Fraunhofer lines is shown to be more accurate and very robust even in the presence of large scattering optical depths. We find that about 80% of the surface fluorescence is retained at the top-of-atmosphere, even for cloud optical thicknesses around 2–5. We further show that small instrument modifications to future O2 A-band spectrometer spectral ranges can result in largely reduced random errors in chlorophyll fluorescence, paving the way towards a more dedicated instrument exploiting solar absorption features only.

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.

New global observations of the terrestrial carbon cycle from GOSAT: Patterns of plant fluorescence with gross primary productivity

Our ability to close the Earth's carbon budget and predict feedbacks in a warming climate depends critically on knowing where, when and how carbon dioxide is exchanged between the land and atmosphere. Terrestrial gross primary production (GPP) constitutes the largest flux component in the global carbon budget, however significant uncertainties remain in GPP estimates and its seasonality. Empirically, we show that global spaceborne observations of solar induced chlorophyll fluorescence – occurring during photosynthesis – exhibit a strong linear correlation with GPP. We found that the fluorescence emission even without any additional climatic or model information has the same or better predictive skill in estimating GPP as those derived from traditional remotely-sensed vegetation indices using ancillary data and model assumptions. In boreal summer the generally strong linear correlation between fluorescence and GPP models weakens, attributable to discrepancies in savannas/croplands (18–48% higher fluorescence-based GPP derived by simple linear scaling), and high-latitude needleleaf forests (28–32% lower fluorescence). Our results demonstrate that retrievals of chlorophyll fluorescence provide direct global observational constraints for GPP and open an entirely new viewpoint on the global carbon cycle. We anticipate that global fluorescence data in combination with consolidated plant physiological fluorescence models will be a step-change in carbon cycle research and enable an unprecedented robustness in the understanding of the current and future carbon cycle.

Developments for vegetation fluorescence retrieval from spaceborne high‐resolution spectrometry in the O2‐A and O2‐B absorption bands

Solar‐induced chlorophyll fluorescence is a weak electromagnetic signal emitted in the red and far‐red spectral regions by vegetation chlorophyll under excitation by solar radiation. Chlorophyll fluorescence has been demonstrated to be a close proxy to vegetation physiological functioning. The basis for fluorescence retrieval from passive space measurements is the exploitation of the O2‐A and O2‐B atmospheric absorption features to isolate the fluorescence signal from the solar radiation reflected by the surface and the atmosphere. High spectral resolution measurements and a precise modeling of the atmospheric radiative transfer in the visible and near‐infrared regions are mandatory. Recent developments for fluorescence retrieval from passive high spectral resolution spaceborne measurements are presented in this work, which has been performed in preparation of the FLuorescence EXplorer (FLEX) mission, which is currently under development by the European Space Agency. A large data set of FLEX‐like measurements has been simulated for the purpose of methodology development and testing. Issues related to vegetation chlorophyll fluorescence retrieval from space, a description of the proposed methodology, initial results from simulated test cases, and general guidelines for the specification of fluorescence retrieval instruments are presented and discussed in this work.

Retrieval of chlorophyll fluorescence from reflectance spectra through polarization discrimination: modeling and experiments

The polarization discrimination technique we recently developed, shows that it is possible to separate the elastic scattering and the chlorophyll fluorescence signal from the water-leaving radiance by making use of the fact that the elastically scattered components are partially polarized, while the fluorescence signal is unpolarized. The technique has been shown to be applicable to a wide range of water conditions. We present an extension of experimental and analytical results, which serve to define the scope of this technique and its range of applicability. A new analysis, based on vector radiative transfer computations, and on laboratory and field measurements on eastern Long Island and in the Chesapeake Bay, shows that the technique is generally effective for both open ocean and coastal waters, but that it is limited if the ocean bottom albedo and/or multiple scattering due to very high mineral particle concentrations result in depolarizing the water-leaving radiance. In addition, we show that in contrast with the polarization-based retrieval, the traditional method of extracting fluorescence height using the baseline method can give significant errors, particularly for coastal waters where it strongly overestimates the fluorescence values.