Canopy Level Chlorophyll Fluorescence and the PRI in a Cornfield

Two bio-indicators, the Photochemical Reflectance Index (PRI) and solar-induced red and far-red Chlorophyll Fluorescence (SIF), were derived from directional hyperspectral observations and studied in a cornfield on two contrasting days in the growing season. Both red and far-red SIF exhibited higher values on the day when the canopy in the early senescent stage, but only the far-red SIF showed sensitivity to viewing geometry. Consequently, the red/far-red SIF ratio varied greatly among azimuth positions while the largest values were obtained for the "hotspot" at both growth stages. This ratio was lower (approx.0.88 +/- 0.4) in early July than in August when the ratio approached equivalence (near approx.1). In concert, the PRI exhibited stronger responses to both zenith and azimuth angles and different values on the two growth stages. The potential of using these indices to monitor photosynthetic activities needs further investigatio

Ground-Based Measurements and Validation Protocols for Flex

The upcoming ESA Fluorescence Explorer (FLEX) mission will incorporate ground-based validations for fluorescence parameters and reflectance indices, drawing on an international network of sensors located at eddy covariance tower sites. A program has been initiated by the OPTIMISE program to develop methods and protocols for this network. A sensor system suite under evaluation by OPTIMISE includes the FLoX hyperspectral spectroradiometers. The NASA team at GSFC is participating in this experiment and we report first results from the 2017 summer measurements made above the canopy at the USDA/ARS Beltsville cornfield using the DFLoX and two other leaf-level measurement systems, the MONI-PAM and the FluoWat

두 개의 기하학적 관찰 구성을 통합하는 자동화된 지상 기반 초 분광 시스템 개발

학위논문(석사) -- 서울대학교대학원 : 농업생명과학대학 협동과정 농림기상학, 2022. 8. 류영렬.Hyperspectral remote sensing is becoming a powerful tool for monitoring vegetation structure and functions. Especially, Sun-Induced chlorophyll fluorescence (SIF) and canopy reflectance monitoring have been widely used to understand physiological and structural changes in plants, and field spectroscopy has become established as an important technique for providing high spectral-, temporal resolution in-situ data as well as providing a means of scaling-up measurements from small areas to large areas. Recently, several tower-based remote sensing systems have been developed. However, in-situ studies have only monitored either BRF or BHR and there is still a lack of understanding of the geometric and optical differences in remote sensing observations, particularly between hemispheric-conical and bi-hemispheric configurations. Here, we developed an automated ground-based field spectroscopy system measuring far-red SIF and canopy hyperspectral reflectance (400–900 nm) with hemispherical-conical as well as bi-hemispherical configuration. To measure both bi-hemispherical and hemispherical-conical reflectance, we adopted a rotating prism by using a servo motor to face three types of ports that measure incoming-, outgoing irradiance and outgoing radiance. A white diffuse glass and collimating lens were used to measure the irradiance, and a collimating lens was used to measure the radiance with a field of view of 20 degrees. Additionally, we developed data management protocol that includes radiometric-, and wavelength calibrations. Finally, we report how BRF and BHR data differ in this system and investigated SIF and vegetation index from both hemispherical-conical and bi-hemispherical observation configurations for their ability to track GPP in the growing seasons of a deciduous broad-leaved forests.초 분광 원격 감지는 식생 구조와 기능을 모니터링하는 강력한 도구가 되고 있다. 특히, 식물의 생리적, 구조적 변화를 이해하기 위해 태양광 유도 엽록소 형광 (SIF)과 캐노피 반사율 모니터링이 널리 이용되고 있다. 현장 분광법은 높은 스펙트럼, 시간 분해능 현장 데이터를 제공하고 작은 영역에서 큰 영역으로 측정을 확장하는 수단을 제공하기 위한 중요한 기술로 확립되었다. 그러나, 수많은 연구가 현장 분광 시스템을 개발했지만, 반구-원추형 및 양 반구 구성 간의 원격 감지 관찰의 기하학적 및 광학적 차이에 대한 이해가 부족할 뿐만 아니라 초 분광 데이터를 지속적으로 수집하는 것은 여전히 어렵다. 우리는 반구형-원추형 및 이중 반구형 구성으로 원적외선 태양광 유도 엽록소 형광 및 캐노피 초 분광 반사율(400–900nm)을 측정하는 자동화된 지상 기반 필드 분광 시스템을 개발했다. 양방향 반사율과 반구형 원추형 반사율을 모두 측정하기 위해 서보 모터를 사용하여 프리즘을 회전하여 세가지 타입의 포트를 측정한다. 각 포트는 들어오는 복사 조도, 나가는 복사 조도 및 나가는 복사를 측정하는 세 가지 유형의 포트다. 조사조도는 백색확산유리와 굴절 렌즈를 사용하였고, 굴절 렌즈를 이용하여 조도를 측정하였다. 또한, 우리는 방사 측정 및 파장 교정을 포함하는 데이터 관리 프로토콜을 개발했다. 마지막으로, 우리는 낙엽 활엽수림의 성장기에 이 시스템에서 측정된 BRF와 BHR 데이터가 어떻게 다른지 보고하였다.Chapter 1. Introduction １ 1.1. Study Background １ 1.2. Purpose of Research ４ Chapter 2. Developing and Testing of Hyperspectral System ５ 2.1 Development of Hyperspectral System and Data Collecting ５ 2.1.1 The Central Control Unit and Spectrometer ５ 2.1.2 RotaPrism ７ 2.1.3 Data Collection ９ 2.3 Data Managing and Processing １１ 2.3.1 Preprocessing of Spectra １１ 2.3.2 Radiometric Calibration １３ 2.3.3 Retrieval of SIF and Vegetation Indices １５ 2.4 Ancillary Measurements to Monitoring Ecosystem. １７ Chapter 3. Application of Hyperspectral System １９ 3.1 Study Site １９ 3.2 Diurnal and Variation of Spectral Reflectance and SIF ２０ 3.3 Seasonal Variation of Vegetation Index and SIF ２２ 3.4 Broader Implications ２４ Chapter 4. Summary and Conclusions ２６ Bibliography ２８석

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 20 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 in the importance of the sunlit/shaded fraction and canopy structure in understanding and interpreting PRI

CEFLES2: the remote sensing component to quantify photosynthetic efficiency from the leaf to the region by measuring sun-induced fluorescence in the oxygen absorption bands

The CEFLES2 campaign during the Carbo Europe Regional Experiment Strategy was designed to provide simultaneous airborne measurements of solar induced fluorescence and CO2 fluxes. It was combined with extensive ground-based quantification of leaf- and canopy-level processes in support of ESA's Candidate Earth Explorer Mission of the "Fluorescence Explorer" (FLEX). The aim of this campaign was to test if fluorescence signal detected from an airborne platform can be used to improve estimates of plant mediated exchange on the mesoscale. Canopy fluorescence was quantified from four airborne platforms using a combination of novel sensors: (i) the prototype airborne sensor AirFLEX quantified fluorescence in the oxygen A and B bands, (ii) a hyperspectral spectrometer (ASD) measured reflectance along transects during 12 day courses, (iii) spatially high resolution georeferenced hyperspectral data cubes containing the whole optical spectrum and the thermal region were gathered with an AHS sensor, and (iv) the first employment of the high performance imaging spectrometer HYPER delivered spatially explicit and multi-temporal transects across the whole region. During three measurement periods in April, June and September 2007 structural, functional and radiometric characteristics of more than 20 different vegetation types in the Les Landes region, Southwest France, were extensively characterized on the ground. The campaign concept focussed especially on quantifying plant mediated exchange processes (photosynthetic electron transport, CO2 uptake, evapotranspiration) and fluorescence emission. The comparison between passive sun-induced fluorescence and active laser-induced fluorescence was performed on a corn canopy in the daily cycle and under desiccation stress. Both techniques show good agreement in detecting stress induced fluorescence change at the 760 nm band. On the large scale, airborne and ground-level measurements of fluorescence were compared on several vegetation types supporting the scaling of this novel remote sensing signal. The multi-scale design of the four airborne radiometric measurements along with extensive ground activities fosters a nested approach to quantify photosynthetic efficiency and gross primary productivity (GPP) from passive fluorescence

Response of green reflectance continuum removal index to the xanthophyll de-epoxidation cycle in Norway spruce needles

A dedicated field experiment was conducted to investigate the response of a green reflectance continuum removal-based optical index, called area under the curve normalized to maximal band depth between 511nm and 557nm (ANMB511-557), to light-induced transformations in xanthophyll cycle pigments of Norway spruce [Picea abies (L.) Karst] needles. The performance of ANMB511-557 was compared with the photochemical reflectance index (PRI) computed from the same leaf reflectance measurements. Needles of four crown whorls (fifth, eighth, 10th, and 15th counted from the top) were sampled from a 27-year-old spruce tree throughout a cloudy and a sunny day. Needle optical properties were measured together with the composition of the photosynthetic pigments to investigate their influence on both optical indices. Analyses of pigments showed that the needles of the examined whorls varied significantly in chlorophyll content and also in related pigment characteristics, such as the chlorophyll/carotenoid ratio. The investigation of the ANMB511-557 diurnal behaviour revealed that the index is able to follow the dynamic changes in the xanthophyll cycle independently of the actual content of foliar pigments. Nevertheless, ANMB511-557 lost the ability to predict the xanthophyll cycle behaviour during noon on the sunny day, when the needles were exposed to irradiance exceeding 1000 µmol m-2 s-1. Despite this, ANMB511-557 rendered a better performance for tracking xanthophyll cycle reactions than PRI. Although declining PRI values generally responded to excessive solar irradiance, they were not able to predict the actual de-epoxidation state in the needles examine

Diurnal and Seasonal Solar Induced Chlorophyll Fluorescence and Photosynthesis in a Boreal Scots Pine Canopy

Solar induced chlorophyll fluorescence has been shown to be increasingly an useful proxy for the estimation of gross primary productivity (GPP), at a range of spatial scales. Here, we explore the seasonality in a continuous time series of canopy solar induced fluorescence (hereafter SiF) and its relation to canopy gross primary production (GPP), canopy light use efficiency (LUE), and direct estimates of leaf level photochemical efficiency in an evergreen canopy. SiF was calculated using infilling in two bands from the incoming and reflected radiance using a pair of Ocean Optics USB2000+ spectrometers operated in a dual field of view mode, sampling at a 30 min time step using custom written automated software, from early spring through until autumn in 2011. The optical system was mounted on a tower of 18 m height adjacent to an eddy covariance system, to observe a boreal forest ecosystem dominated by Scots pine. (Pinus sylvestris) A Walz MONITORING-PAM, multi fluorimeter system, was simultaneously mounted within the canopy adjacent to the footprint sampled by the optical system. Following correction of the SiF data for O2 and structural effects, SiF, SiF yield, LUE, the photochemicsl reflectance index (PRI), and the normalized difference vegetation index (NDVI) exhibited a seasonal pattern that followed GPP sampled by the eddy covariance system. Due to the complexities of solar azimuth and zenith angle (SZA) over the season on the SiF signal, correlations between SiF, SiF yield, GPP, and LUE were assessed on SZ

Diurnal and Seasonal Variations in Chlorophyll Fluorescence Associated with Photosynthesis at Leaf and Canopy Scales

There is a critical need for sensitive remote sensing approaches to monitor the parameters governing photosynthesis, at the temporal scales relevant to their natural dynamics. The photochemical reflectance index (PRI) and chlorophyll fluorescence (F) offer a strong potential for monitoring photosynthesis at local, regional, and global scales, however the relationships between photosynthesis and solar induced F (SIF) on diurnal and seasonal scales are not fully understood. This study examines how the fine spatial and temporal scale SIF observations relate to leaf level chlorophyll fluorescence metrics (i.e., PSII yield, YII and electron transport rate, ETR), canopy gross primary productivity (GPP), and PRI. The results contribute to enhancing the understanding of how SIF can be used to monitor canopy photosynthesis. This effort captured the seasonal and diurnal variation in GPP, reflectance, F, and SIF in the O2A (SIFA) and O2B (SIFB) atmospheric bands for corn (Zea mays L.) at a study site in Greenbelt, MD. Positive linear relationships of SIF to canopy GPP and to leaf ETR were documented, corroborating published reports. Our findings demonstrate that canopy SIF metrics are able to capture the dynamics in photosynthesis at both leaf and canopy levels, and show that the relationship between GPP and SIF metrics differs depending on the light conditions (i.e., above or below saturation level for photosynthesis). The sum of SIFA and SIFB (SIFA+B), as well as the SIFA+B yield, captured the dynamics in GPP and light use efficiency, suggesting the importance of including SIFB in monitoring photosynthetic function. Further efforts are required to determine if these findings will scale successfully to airborne and satellite levels, and to document the effects of data uncertainties on the scaling

Investigation of atmospheric effects on retrieval of sun-induced fluorescence using hyperspectral imagery

Significant research progress has recently been made in estimating fluorescence in the oxygen absorption bands, however, quantitative retrieval of fluorescence data is still affected by factors such as atmospheric effects. In this paper, top-of-atmosphere (TOA) radiance is generated by the MODTRAN 4 and SCOPE models. Based on simulated data, sensitivity analysis is conducted to assess the sensitivities of four indicators—depth_absorption_band, depth_nofs-depth_withfs, radiance and Fs/radiance—to atmospheric parameters (sun zenith angle (SZA), sensor height, elevation, visibility (VIS) and water content) in the oxygen absorption bands. The results indicate that the SZA and sensor height are the most sensitive parameters and that variations in these two parameters result in large variations calculated as the variation value/the base value in the oxygen absorption depth in the O2-A and O2-B bands (111.4% and 77.1% in the O2-A band; and 27.5% and 32.6% in the O2-B band, respectively). A comparison of fluorescence retrieval using three methods (Damm method, Braun method and DOAS) and SCOPE Fs indicates that the Damm method yields good results and that atmospheric correction can improve the accuracy of fluorescence retrieval. Damm method is the improved 3FLD method but considering atmospheric effects. Finally, hyperspectral airborne images combined with other parameters (SZA, VIS and water content) are exploited to estimate fluorescence using the Damm method and 3FLD method. The retrieval fluorescence is compared with the field measured fluorescence, yielding good results (R2 = 0.91 for Damm vs. SCOPE SIF; R2 = 0.65 for 3FLD vs. SCOPE SIF). Five types of vegetation, including ailanthus, elm, mountain peach, willow and Chinese ash, exhibit consistent associations between the retrieved fluorescence and field measured fluorescence