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Leaf and Canopy Biochemical and Biophysical Variables Retrieval

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A special issue of Remote Sensing (ISSN 2072-4292). This special issue belongs to the section "Environmental Remote Sensing".

Deadline for manuscript submissions: closed (31 March 2022) | Viewed by 31866

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Prof. Dr. Yelu Zeng

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College of Land Science and Technology, China Agricultural University, Beijing 100081, China
Interests: remote sensing; vegetation; canopy; phenology; fluorescence

Dr. Aleixandre Verger

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CREAF, Cerdanyola Del Valles, 08193 Catalonia, Spain
Interests: remote sensing; vegetation-climate dynamics; global change; phenology

Prof. Dr. Gaofei Yin

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1. Faculty of Geosciences and Environmental Engineering, Southwest Jiaotong University, Chengdu 610031, China
2. CREAF, 08193 Bellaterra (Cerdanyola del Vallès), Catalonia, Spain
3. CSIC, Global Ecology Unit, CREAF-CSIC-UAB, 08193 Bellaterra (Cerdanyola del Vallès), Catalonia, Spain
Interests: vegetation remote sensing; radiative transfer; biophysical parameter retrieval; land surface phenology; photochemical reflectance index
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Dr. Jochem Verrelst

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Laboratory for Earth Observation, Image Processing Laboratory - Scientific Park, University of Valencia, C/ Catedrático José Beltrán, 2, 46980 Paterna, Valencia, Spain
Interests: imaging spectroscopy; vegetation properties retrieval; FLEX; vegetation fluorescence; optical remote sensing; radiative transfer models; retrieval methods
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Estimates of leaf and canopy biochemical and biophysical properties, e.g., leaf area index, leaf inclination angle, chlorophyll content, leaf mass per area, and nitrogen content, are required for a wide range of applications and scales: from the local scale of precision agriculture, through resources and environmental management at the landscape scale, forest inventory or biodiversity at the national scale, up to biogeochemical cycling at the global scale. Remote sensing observations from kilometric to centimetric spatial resolutions cover this wide range of scales and requirements. To improve the accuracy and generalization of remote sensing-based retrievals, scientists are developing more accurate radiative transfer models and retrieval algorithms, and are exploring the integration of datasets from various remote sensing platforms and spectral domains.

This Special Issue welcomes manuscripts that relate to any aspect of remote sensing-based vegetation property retrievals, including but not limited to (1) the development or application of more realistic and efficient 1D to 3D radiative transfer models for vegetation property retrievals, e.g., considering the discontinuous canopy structure, spatial heterogeneity, and rugged terrain; (2) the estimation of vegetation properties from a single or multiple platforms including satellite, airborne, unmanned aerial vehicle (UAV), smart phone, field camera, or radiation-based wireless sensor network (WSN); (3) combination of sensors and spectral domains from visible/near-infrared to thermal, solar-induced fluorescence, radar, LiDAR, and hyperspectral sensor; (4) model inversion, retrieval algorithms, and strategies to mitigate the underestimated and ill-posed nature of the inverse problem, e.g., selecting the best cost function, using machine learning-based algorithms to improve the efficiency and robustness, using a-priori information and spatiotemporal constraints; (5) systematic data pre-processing or quality control strategies to reduce the noise in the retrieval due to atmosphere, clouds, soil background, or sun-sensor geometry; (6) hybrid methods and ensemble products to improve the retrievals, e.g. combining products from different sensors to build continuous and consistent long-term time series.

Dr. Yelu Zeng
Dr. Aleixandre Verger
Dr. Gaofei Yin
Dr. Jochem Verrelst
Guest Editors

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Keywords

Vegetation properties
Leaf area index
Chlorophyll content
Physical model
Parameter retrieval
Cost-function
Machine learning

Published Papers (10 papers)

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24 pages, 10599 KiB

Open AccessArticle

Impact of Structural, Photochemical and Instrumental Effects on Leaf and Canopy Reflectance Variability in the 500–600 nm Range

by Adrián Moncholi-Estornell, Shari Van Wittenberghe, Maria Pilar Cendrero-Mateo, Luis Alonso, Zbyněk Malenovský and José Moreno

Remote Sens. 2022, 14(1), 56; https://doi.org/10.3390/rs14010056 - 23 Dec 2021

Cited by 6 | Viewed by 2736

Abstract

Current rapid technological improvement in optical radiometric instrumentation provides an opportunity to develop innovative measurements protocols where the remote quantification of the plant physiological status can be determined with higher accuracy. In this study, the leaf and canopy reflectance variability in the PRI spectral region (i.e., 500–600 nm) is quantified using different laboratory protocols that consider both instrumental and experimental set-up aspects, as well as canopy structural effects and vegetation photoprotection dynamics. First, we studied how an incorrect characterization of the at-target incoming radiance translated into an erroneous vegetation reflectance spectrum and consequently in an incorrect quantification of reflectance indices such as PRI. The erroneous characterization of the at-target incoming radiance translated into a 2% overestimation and a 31% underestimation of estimated chlorophyll content and PRI-related vegetation indexes, respectively. Second, we investigated the dynamic xanthophyll pool and intrinsic Chl vs. Car long-term pool changes affecting the entire 500–600 nm spectral region. Consistent spectral behaviors were observed for leaf and canopy experiments. Sun-adapted plants showed a larger optical change in the PRI range and a higher capacity for photoprotection during the light transient time when compared to shade-adapted plants. Outcomes of this work highlight the importance of well-established spectroscopy sampling protocols to detect the subtle photochemical features which need to be disentangled from the structural and biological effects. Full article

(This article belongs to the Special Issue Leaf and Canopy Biochemical and Biophysical Variables Retrieval)

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18 pages, 2269 KiB

Open AccessArticle

Validation of Sentinel-2, MODIS, CGLS, SAF, GLASS and C3S Leaf Area Index Products in Maize Crops

by Huinan Yu, Gaofei Yin, Guoxiang Liu, Yuanxin Ye, Yonghua Qu, Baodong Xu and Aleixandre Verger

Remote Sens. 2021, 13(22), 4529; https://doi.org/10.3390/rs13224529 - 11 Nov 2021

Cited by 5 | Viewed by 2442

Abstract

We proposed a direct approach to validate hectometric and kilometric resolution leaf area index (LAI) products that involved the scaling up of field-measured LAI via the validation and recalibration of the decametric Sentinel-2 LAI product. We applied it over a test study area of maize crops in northern China using continuous field measurements of LAINet along the year 2019. Sentinel-2 LAI showed an overall accuracy of 0.67 in terms of Root Mean Square Error (RMSE) and it was used, after recalibration, as a benchmark to validate six coarse resolution LAI products: MODIS, Copernicus Global Land Service 1 km Version 2 (called GEOV2) and 300 m (GEOV3), Satellite Application Facility EUMETSAT Polar System (SAF EPS) 1.1 km, Global LAnd Surface Satellite (GLASS) 500 m and Copernicus Climate Change Service (C3S) 1 km V2. GEOV2, GEOV3 and MODIS showed a good agreement with reference LAI in terms of magnitude (RMSE ≤ 0.29) and phenology. SAF EPS (RMSE = 0.68) and C3S V2 (RMSE = 0.41), on the opposite, systematically underestimated high LAI values and showed systematic differences for phenological metrics: a delay of 6 days (d), 20 d and 24 d for the start, peak and the end of growing season, respectively, for SAF EPS and an advance of −4 d, −6 d and −6 d for C3S. Full article

(This article belongs to the Special Issue Leaf and Canopy Biochemical and Biophysical Variables Retrieval)

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15 pages, 2804 KiB

Open AccessArticle

Optimized Estimation of Leaf Mass per Area with a 3D Matrix of Vegetation Indices

by Yuwen Chen, Jia Sun, Lunche Wang, Shuo Shi, Wei Gong, Shaoqiang Wang and Torbern Tagesson

Remote Sens. 2021, 13(18), 3761; https://doi.org/10.3390/rs13183761 - 19 Sep 2021

Cited by 4 | Viewed by 2079

Abstract

Leaf mass per area (LMA) is a key plant functional trait closely related to leaf biomass. Estimating LMA in fresh leaves remains challenging due to its masked absorption by leaf water in the short-wave infrared region of reflectance. Vegetation indices (VIs) are popular variables used to estimate LMA. However, their physical foundations are not clear and the generalization ability is limited by the training data. In this study, we proposed a hybrid approach by establishing a three-dimensional (3D) VI matrix for LMA estimation. The relationship between LMA and VIs was constructed using PROSPECT-D model simulations. The three-VI space constituting a 3D matrix was divided into cubical cells and LMA values were assigned to each cell. Then, the 3D matrix retrieves LMA through the three VIs calculated from observations. Two 3D matrices with different VIs were established and validated using a second synthetic dataset, and two comprehensive experimental datasets containing more than 1400 samples of 49 plant species. We found that both 3D matrices allowed good assessments of LMA (R² = 0.76 and 0.78, RMSE = 0.0016 g/cm² and 0.0017 g/cm², respectively for the pooled datasets), and their results were superior to the corresponding single Vis, 2D matrices, and two machine learning methods established with the same VI combinations. Full article

(This article belongs to the Special Issue Leaf and Canopy Biochemical and Biophysical Variables Retrieval)

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20 pages, 9157 KiB

Open AccessArticle

Sensitivity Analysis of Canopy Structural and Radiative Transfer Parameters to Reconstructed Maize Structures Based on Terrestrial LiDAR Data

by Bitam Ali, Feng Zhao, Zhenjiang Li, Qichao Zhao, Jiabei Gong, Lin Wang, Peng Tong, Yanhong Jiang, Wei Su, Yunfei Bao and Juan Li

Remote Sens. 2021, 13(18), 3751; https://doi.org/10.3390/rs13183751 - 18 Sep 2021

Cited by 2 | Viewed by 2315

Abstract

The maturity and affordability of light detection and ranging (LiDAR) sensors have made possible the quick acquisition of 3D point cloud data to monitor phenotypic traits of vegetation canopies. However, while the majority of studies focused on the retrieval of macro scale parameters of vegetation, there are few studies addressing the reconstruction of explicit 3D structures from terrestrial LiDAR data and the retrieval of fine scale parameters from such structures. A challenging problem that arises from the latter studies is the need for a large amount of data to represent the various components in the actual canopy, which can be time consuming and resource intensive for processing and for further applications. In this study, we present a pipeline to reconstruct the 3D maize structures composed of triangle primitives based on multi-view terrestrial LiDAR measurements. We then study the sensitivity of the details with which the canopy architecture was represented for the computation of leaf angle distribution (LAD), leaf area index (LAI), gap fraction, and directional reflectance factors (DRF). Based on point clouds of a maize field in three stages of growth, we reconstructed the reference structures, which have the maximum number of triangles. To get a compromise between the details of the structure and accuracy reserved for later applications, we carried out a simplified process to have multiple configurations of details based on the decimation rate and the Hausdorff distance. Results show that LAD is not highly sensitive to the details of the structure (or the number of triangles). However, LAI, gap fraction, and DRF are more sensitive, and require a relatively high number of triangles. A choice of 100−500 triangles per leaf while maintaining the overall shapes of the leaves and a low Hausdorff distance is suggested as a good compromise to represent the canopy and give an overall accuracy of 98% for the computation of the various parameters. Full article

(This article belongs to the Special Issue Leaf and Canopy Biochemical and Biophysical Variables Retrieval)

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18 pages, 14385 KiB

Open AccessArticle

Tree Extraction from Airborne Laser Scanning Data in Urban Areas

by Hangkai You, Shihua Li, Yifan Xu, Ze He and Di Wang

Remote Sens. 2021, 13(17), 3428; https://doi.org/10.3390/rs13173428 - 29 Aug 2021

Cited by 12 | Viewed by 3657

Abstract

Tree information in urban areas plays a significant role in many fields of study, such as ecology and environmental management. Airborne LiDAR scanning (ALS) excels at the fast and efficient acquisition of spatial information in urban-scale areas. Tree extraction from ALS data is an essential part of tree structural studies. Current raster-based methods that use canopy height models (CHMs) suffer from the loss of 3D structure information, whereas the existing point-based methods are non-robust in complex environments. Aiming at making full use of the canopy’s 3D structure information that is provided by point cloud data, and ensuring the method’s suitability in complex scenes, this paper proposes a new point-based method for tree extraction that is based on 3D morphological features. Considering the elevation deviations of the ALS data, we propose a neighborhood search method to filter out the ground and flat-roof points. A coarse extraction method, combining planar projection with a point density-filtering algorithm is applied to filter out distracting objects, such as utility poles and cars. After that, a Euclidean cluster extraction (ECE) algorithm is used as an optimization strategy for coarse extraction. In order to verify the robustness and accuracy of the method, airborne LiDAR data from Zhangye, Gansu, China and unmanned aircraft vehicle (UAV) LiDAR data from Xinyang, Henan, China were tested in this study. The experimental results demonstrated that our method was suitable for extracting trees in complex urban scenes with either high or low point densities. The extraction accuracy obtained for the airborne LiDAR data and UAV LiDAR data were 99.4% and 99.2%, respectively. In addition, a further study found that the aberrant vertical structure of the artificially pruned canopy was the main cause of the error. Our method achieved desirable results in different scenes, with only one adjustable parameter, making it an easy-to-use method for urban area studies. Full article

(This article belongs to the Special Issue Leaf and Canopy Biochemical and Biophysical Variables Retrieval)

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17 pages, 2573 KiB

Open AccessArticle

A Method for Quantifying Understory Leaf Area Index in a Temperate Forest through Combining Small Footprint Full-Waveform and Point Cloud LiDAR Data

by Jinling Song, Xiao Zhu, Jianbo Qi, Yong Pang, Lei Yang and Lihong Yu

Remote Sens. 2021, 13(15), 3036; https://doi.org/10.3390/rs13153036 - 02 Aug 2021

Cited by 9 | Viewed by 4928

Abstract

Understory vegetation plays an important role in the structure and function of forest ecosystems. Light detection and ranging (LiDAR) can provide understory information in the form of either point cloud or full-waveform data. Point cloud data have a remarkable ability to represent the three-dimensional structures of vegetation, while full-waveform data contain more detailed information on the interactions between laser pulses and vegetation; both types have been widely used to estimate various forest canopy structural parameters, including leaf area index (LAI). Here, we present a new method for quantifying understory LAI in a temperate forest by combining the advantages of both types of LiDAR data. To achieve this, we first estimated the vertical distribution of the gap probability using point cloud data to automatically determine the height boundary between overstory and understory vegetation at the plot level. We then deconvolved the full-waveform data to remove the blurring effect caused by the system pulse to restore the vertical resolution of the LiDAR system. Subsequently, we decomposed the deconvolved data and integrated the plot-level boundary height to differentiate the waveform components returned from the overstory, understory, and soil layers. Finally, we modified the basic LiDAR equations introducing understory leaf spectral information to quantify the understory LAI. Our results, which were validated against ground-based measurements, show that the new method produced a good estimation of the understory LAI with an R² of 0.54 and a root-mean-square error (RMSE) of 0.21. Our study demonstrates that the understory LAI can be successfully quantified through the combined use of point cloud and full-waveform LiDAR data. Full article

(This article belongs to the Special Issue Leaf and Canopy Biochemical and Biophysical Variables Retrieval)

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18 pages, 6383 KiB

Open AccessArticle

Retrieving and Validating Leaf and Canopy Chlorophyll Content at Moderate Resolution: A Multiscale Analysis with the Sentinel-3 OLCI Sensor

by Charlotte De Grave, Luca Pipia, Bastian Siegmann, Pablo Morcillo-Pallarés, Juan Pablo Rivera-Caicedo, José Moreno and Jochem Verrelst

Remote Sens. 2021, 13(8), 1419; https://doi.org/10.3390/rs13081419 - 07 Apr 2021

Cited by 14 | Viewed by 3277

Abstract

ESA’s Eighth Earth Explorer mission “FLuorescence EXplorer” (FLEX) will be dedicated to the global monitoring of the chlorophyll fluorescence emitted by vegetation. In order to properly interpret the measured fluorescence signal, essential vegetation variables need to be retrieved concomitantly. FLEX will fly in tandem formation with Sentinel-3 (S3), which conveys the Ocean and Land Color Instrument (OLCI) that is designed to characterize the atmosphere and the terrestrial vegetation at a spatial resolution of 300 m. In support of FLEX’s preparatory activities, this paper presents a first validation exercise of OLCI vegetation products against in situ data coming from the 2018 FLEXSense campaign. During this campaign, leaf chlorophyll content (LCC) and leaf area index (LAI) measurements were collected over croplands, while HyPlant DUAL images of the area were acquired at a 3 m spatial resolution. A multiscale validation strategy was pursued. First, estimates of these two variables, together with the combined canopy chlorophyll content (CCC = LCC × LAI), were obtained at the HyPlant spatial resolution and were compared against the in situ measurements. Second, the fine-scale retrieval maps from HyPlant were coarsened to the S3 spatial scale as a reference to assess the quality of the OLCI vegetation products. As an intermediary step, vegetation products extracted from Sentinel-2 data were used to compare retrievals at the in-between spatial resolution of 20 m. For all spatial scales, CCC delivered the most accurate estimates with the smallest prediction error obtained at the 300 m resolution (R

^{2}

of 0.74 and RMSE = 26.8 μg cm

^{- 2}

). Results of a scaling analysis suggest that CCC performs well at the different tested spatial resolutions since it presents a linear behavior across scales. LCC, on the other hand, was poorly retrieved at the 300 m scale, showing overestimated values over heterogeneous pixels. The introduction of a new LCC model integrating mixed reflectance spectra in its training enabled to improve by 16% the retrieval accuracy for this variable (RMSE = 10 μg cm

^{- 2}

for the new model versus RMSE = 11.9 μg cm

^{- 2}

for the former model). Full article

(This article belongs to the Special Issue Leaf and Canopy Biochemical and Biophysical Variables Retrieval)

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19 pages, 22455 KiB

Open AccessArticle

Error Analysis of LAI Measurements with LAI-2000 Due to Discrete View Angular Range Angles for Continuous Canopies

by Jun Geng, Gang Yuan, J. M. Chen, Chunguang Lyu, Lili Tu, Weiliang Fan, Qingjiu Tian, Zhaofu Wu, Tingye Tao, Min Yu, Yongchao Zhu, Jianwei Huang, Kaijian Xu, Jinchao Li and Shaoteng Wang

Remote Sens. 2021, 13(7), 1405; https://doi.org/10.3390/rs13071405 - 06 Apr 2021

Cited by 5 | Viewed by 2703

Abstract

As a widely used ground-based optical instrument, the LAI-2000 or LAI-2200 plant canopy analyzer (PCA) (Li-Cor, Inc., Lincoln, NE) is designed to measure the plant effective leaf area index (L_e) by measuring the canopy gap fraction at several limited or discrete view zenith angles (VZAs) (usually five VZAs: 7, 23, 38, 53, and 68°) based on Miller’s equation. Miller’s equation requires the probability of radiative transmission through the canopy to be measured over the hemisphere, i.e., VZAs in the range from 0 to 90°. However, the PCA view angle ranges are confined to several limited ranges or discrete sectors. The magnitude of the error produced by the discretization of VZAs in the leaf area index measurements remains difficult to determine. In this study, a theoretical deduction was first presented to definitely prove why the limited or discrete VZAs or ranges can affect the L_e measured with the PCA, and the specific error caused by the limited or discrete VZAs was described quantitatively. The results show that: (1) the weight coefficient of the last PCA ring is the main cause of the error; (2) the error is closely related to the leaf inclination angles (IAs)—the L_e measured with the PCA can be significantly overestimated for canopies with planophile IAs, whereas it can be underestimated for erectophile IAs; and (3) the error can be enhanced with the increment of the discrete degree of PCA rings or VZAs, such as using four or three PCA rings. Two corrections for the error are presented and validated in three crop canopies. Interestingly, although the leaf IA type cannot influence the L_e calculated by Miller’s equation in the hemispheric space, it affects the L_e measured with the PCA using the discrete form of Miller’s equation for several discrete VZAs. Full article

(This article belongs to the Special Issue Leaf and Canopy Biochemical and Biophysical Variables Retrieval)

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19 pages, 7428 KiB

Open AccessArticle

Influencing Factors in Estimation of Leaf Angle Distribution of an Individual Tree from Terrestrial Laser Scanning Data

by Hailan Jiang, Ronghai Hu, Guangjian Yan, Shiyu Cheng, Fan Li, Jianbo Qi, Linyuan Li, Donghui Xie and Xihan Mu

Remote Sens. 2021, 13(6), 1159; https://doi.org/10.3390/rs13061159 - 18 Mar 2021

Cited by 6 | Viewed by 2782

Abstract

Leaf angle distribution (LAD) is an important attribute of forest canopy architecture and affects the solar radiation regime within the canopy. Terrestrial laser scanning (TLS) has been increasingly used in LAD estimation. The point clouds data suffer from the occlusion effect, which leads to incomplete scanning and depends on measurement strategies such as the number of scans and scanner location. Evaluating these factors is important to understand how to improve LAD, which is still lacking. Here, we introduce an easy way of estimating the LAD using open source software. Importantly, the influence of the occlusion effect on the LAD was evaluated by combining the proposed complete point clouds (CPCs) with the simulated data of 3D tree models of Aspen, Pin Oak and White Oak. We analyzed the effects of the point density, the number of scans and the scanner height on the LAD and G-function. Results show that: (1) the CPC can be used to evaluate the TLS-based normal vector reconstruction accuracy without an occlusion effect; (2) the accuracy is slightly affected by the normal vector reconstruction method and is greatly affected by the point density and the occlusion effect. The higher the point density (with a number of points per unit leaf area of 0.2 cm⁻² to 27 cm⁻² tested), the better the result is; (3) the performance is more sensitive to the scanner location than the number of scans. Increasing the scanner height improves LAD estimation, which has not been seriously considered in previous studies. It is worth noting that relatively tall trees suffer from a more severe occlusion effect, which deserves further attention in further study. Full article

(This article belongs to the Special Issue Leaf and Canopy Biochemical and Biophysical Variables Retrieval)

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17 pages, 3955 KiB

Open AccessTechnical Note

Comparison of Absorbed and Intercepted Fractions of PAR for Individual Trees Based on Radiative Transfer Model Simulations

by Wojciech Wojnowski, Shanshan Wei, Wenjuan Li, Tiangang Yin, Xian-Xiang Li, Genevieve Lai Fern Ow, Mohamed Lokman Mohd Yusof and Andrew J. Whittle

Remote Sens. 2021, 13(6), 1069; https://doi.org/10.3390/rs13061069 - 11 Mar 2021

Cited by 8 | Viewed by 2207

Abstract

The fraction of absorbed photosynthetically active radiation (fAPAR) is a key parameter for estimating the gross primary production (GPP) of trees. For continuous, dense forest canopies, fAPAR, is often equated with the intercepted fraction, fIPAR. This assumption is not valid for individual trees in urban environments or parkland settings where the canopy is sparse and there are well-defined tree crown boundaries. Here, the distinction between fAPAR and fIPAR can be strongly influenced by the background and large illumination variations due to multi-scattering and shadows of buildings. This study investigates the radiative budget of PAR bands using a coupled leaf-canopy radiative transfer model (PROSPECT-DART), considering a suite of tropical tree species over a wide range of assumed leaf chlorophyll contents. The analyses simulate hyperspectral images (5 nm bandwidth) of individual tree crowns for the selected background (concrete vs. grass) and illumination conditions. We then use an artificial neural network-based method to partition sunlit vs. shaded leaves within each crown, as the latter have lower fAPAR and fIPAR values. Our results show fAPAR of sunlit leaves decreases with the ratio of diffuse to direct scene irradiance (SKYL), while SKYL has minimal influence for shaded leaves. Both fAPAR and fIPAR decrease at more oblique solar zenith angles (SZA). Higher values of fAPAR and fIPAR occur with concrete backgrounds and the influence of the background is larger at higher diffuse ratio and solar zenith angles. The results show that fIPAR is typically 6–9% higher than fAPAR, and up to 14% higher for sunlit leaves with a concrete background at SKYL = 0. The differences between the fIPAR and fAPAR also depend on the health condition of the leaves, such as chlorophyll content. This study can improve the understanding of urban individual trees fAPAR/fIPAR and facilitate the development of protocols for fAPAR field measurements. Full article

(This article belongs to the Special Issue Leaf and Canopy Biochemical and Biophysical Variables Retrieval)

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