OBIA4RTM – towards an operational open-source solution for coupling object-based image analysis with radiative transfer modelling

Physically-based approaches for estimating Leaf Area Index (LAI) using remote sensing data rely on radiative transfer (RT) models. Currently, many RT models are freely available, but determining the appropriate RT model for LAI retrieval is still problematic. This study aims to evaluate the necessity of RT model selection for LAI retrieval and to propose a retrieval methodology using different RT models for different vegetation types. Both actual experimental observations and RT model simulations were used to conduct the evaluation. Each of them includes needleleaf forests and croplands, which have contrasting structural attributes. The scattering from arbitrarily inclined leaves (SAIL) model and the four-scale model, which are 1D and 3D RT models, respectively, were used to simulate the synthetic test datasets. The experimental test dataset was established through two field campaigns conducted in the Heihe River Basin. The results show that the realistic representation of canopy structure in RT models is very important for LAI retrieval. If an unsuitable RT model is used, then the root mean squared error (RMSE) will increase from 0.43 to 0.60 in croplands and from 0.52 to 0.63 in forests. In addition, an RT model’s potential to retrieve LAI is limited by the availability of a priori information on RT model parameters. 3D RT models require more a priori information, which makes them have poorer generalization capability than 1D models. Therefore, physically-based retrieval algorithms should embed more than one RT model to account for the availability of a priori information and variations in structural attributes among different vegetation types.

Deriving high-spatiotemporal-resolution leaf area index for agroecosystems in the U.S. Corn Belt using Planet Labs CubeSat and STAIR fusion data

Radiative transfer models (RTMs) are often used to retrieve biophysical parameters from earth observation data. RTMs with multi-temporal and realistic forest representations enable radiative transfer (RT) modeling for real-world dynamic processes. To achieve more realistic RT modeling for dynamic forest processes, this study presents the 3D-explicit reconstruction of a typical temperate deciduous forest in 2015 and 2022. We demonstrate for the first time the potential use of bitemporal 3D-explicit RT modeling from terrestrial laser scanning on the forward modeling and quantitative interpretation of: (1) remote sensing (RS) observations of leaf area index (LAI), fraction of absorbed photosynthetically active radiation (FAPAR), and canopy light extinction, and (2) the impact of canopy gap dynamics on light availability of explicit locations. Results showed that, compared to the 2015 scene, the hemispherical-directional reflectance factor (HDRF) of the 2022 forest scene relatively decreased by 3.8% and the leaf FAPAR relatively increased by 5.4%. At explicit locations where canopy gaps significantly changed between the 2015 scene and the 2022 scene, only under diffuse light did the branch damage and closing gap significantly impact ground light availability. This study provides the first bitemporal RT comparison based on the 3D RT modeling, which uses one of the most realistic bitemporal forest scenes as the structural input. This bitemporal 3D-explicit forest RT modeling allows spatially explicit modeling over time under fully controlled experimental conditions in one of the most realistic virtual environments, thus delivering a powerful tool for studying canopy light regimes as impacted by dynamics in forest structure and developing RS inversion schemes on forest structural changes.

Leaf pigment contents, such as chlorophylls a and b content (C a b ) or carotenoid content (Car), and the leaf area index (LAI) are recognized indicators of plants’ and forests’ health status that can be estimated through hyperspectral imagery. Their measurement on a seasonal and yearly basis is critical to monitor plant response and adaptation to stress, such as droughts. While extensively done over dense canopies, estimation of these variables over tree-grass ecosystems with very low overstory LAI (mean site LAI < 1 m 2 /m 2 ), such as woodland savannas, is lacking. We investigated the use of look-up table (LUT)-based inversion of a radiative transfer model to retrieve LAI and leaf C a b and Car from AVIRIS images at an 18 m spatial resolution at multiple dates over a broadleaved woodland savanna during the California drought. We compared the performances of different cost functions in the inversion step. We demonstrated the spatial consistency of our LAI, C a b , and Car estimations using validation data from low and high canopy cover parts of the site, and their temporal consistency by qualitatively confronting their variations over two years with those that would be expected. We concluded that LUT-based inversions of medium-resolution hyperspectral images, achieved with a simple geometric representation of the canopy within a 3D radiative transfer model (RTM), are a valid means of monitoring woodland savannas and more generally sparse forests, although for maximum applicability, the inversion cost functions should be selected using validation data from multiple dates. Validation revealed that for monitoring use: The normalized difference vegetation index (NDVI) outperformed other indices for LAI estimations (root mean square error (RMSE) = 0.22 m 2 /m 2 , R 2 = 0.81); the band ratio ρ 0.750 μ m ρ 0.550 μ m retrieved C a b more accurately than other chlorophylls indices (RMSE = 5.21 μ g/cm 2 , R 2 = 0.73); RMSE over the 0.5–0.55 μ m interval showed encouraging results for Car estimations.

The growth of rice is a sequence of three different phenological phases. This sequence of change in rice phenology implies that the condition of the plant during the vegetative phase relates directly to the health of leaves functioning during the reproductive and ripening phases. As such, accurate monitoring is important towards understanding rice growth dynamics. Leaf Area Index (LAI) is an important indicator of rice yields and the availability of this information during key phenological phases can support more informed farming decisions. Satellite remote sensing has been adopted as a proxy to field measurements of LAI and with the launch of freely available high resolution Satellite images such as Sentinel-2, it is imperative that accurate retrieval methods are adopted towards monitoring LAI at irrigated rice fields. Here, we evaluate the potential of a hybrid radiative transfer model (i.e., PROSAIL - Gaussian Process Regression (GPR), for estimating the phenological dynamics of irrigated rice LAI using imager derived from the Sentinel-2 multispectral instrument. LAI field measurements were obtained from an experimental rice field in Nasarawa state, Nigeria during the dry season. We used the PROSAIL radiative transfer model to create a look up table (LUT) that was subsequently used to train a GPR model. Afterwards, we evaluated the potential of the hybrid modelling approach by assessing the overall model accuracy and the extent to which LAI was able to accurately predict LAI during key rice phenological phases. We compared the predicted hybrid GPR LAI values with LAI values generated from the SNAP toolbox, based on a hybrid Artificial Neural Network (ANN) modelling approach. Our results show that the overall predictive accuracy of the hybrid GPR model (R2 = 0.82, RMSE = 1.65) was more accurate than that of the hybrid ANN model (R2 = 0.66, RMSE = 3.89) for retrieving LAI values from Sentinel-2 imagery. Both models underestimated LAI values during the reproductive and ripening phases . However, the accuracy during the phenological phases were more significant when using the hybrid GPR model (P < 0.05). During the different phenological phases, the hybrid GPR model predicted LAI more accurately during the reproductive (R2 = 0.7) and ripening (R2 = 0.59) phases compared to the hybrid ANN reproductive and ripening phases. When monitoring LAI phenological profiles of both hybrid models, the hybrid GPR and ANN models underestimated LAI during the reproductive and ripening phases. However, the ANN model underestimations were statistically significantly greater than those for the hybrid GPR model (P < 0.05). Our results highlight the potential of hybrid GPR models for estimating the phenological dynamics of irrigated rice LAI from Sentinel-2 data. They provided more accurate estimation of LAI patterns from varying nitrogen and water applications than hybrid ANN models.

Leaf area index (LAI) and LCC, as the two most important crop growth variables, are major considerations in management decisions, agricultural planning and policy making. Estimation of canopy biophysical variables from remote sensing data was investigated using a radiative transfer model. However, the ill-posed problem is unavoidable for the unique solution of the inverse problem and the uncertainty of measurements and model assumptions. This study focused on the use of agronomy mechanism knowledge to restrict and remove the ill-posed inversion results. For this purpose, the inversion results obtained using the PROSAIL model alone (NAMK) and linked with agronomic mechanism knowledge (AMK) were compared. The results showed that AMK did not significantly improve the accuracy of LAI inversion. LAI was estimated with high accuracy, and there was no significant improvement after considering AMK. The validation results of the determination coefficient (R2) and the corresponding root mean square error (RMSE) between measured LAI and estimated LAI were 0.635 and 1.022 for NAMK, and 0.637 and 0.999 for AMK, respectively. LCC estimation was significantly improved with agronomy mechanism knowledge; the R2 and RMSE values were 0.377 and 14.495 μg cm -2 for NAMK, and 0.503 and 10.661 μg cm -2 for AMK, respectively. Results of the comparison demonstrated the need for agronomy mechanism knowledge in radiative transfer model inversion.

Indirect, non-destructive methods to derive biophysical parameters, such as leaf area index (LAI), are of major importance for optimal grassland growth modelling and management. In this study, we compared different methods for the estimation of LAI in permanent grassland including (i) two direct methods, (ii) two indirect optical methods (AccuPAR and LAI-2200C), (iii) a proximal (field spectrometer) and a satellite remote sensing approach using Sentinel-2 (S-2) data, both based on radiative transfer modelling (RTM) of vegetation. To consider the seasonal variability of LAI sufficiently, we performed in situ measurements weekly during the entire growing season of 2018 and 2019. The RTM-based methods showed the lowest root-mean-square error (RMSE) when compared with direct green LAI measurements, which ranged from 1.68 to 7.85. The indirect optical methods resulted in higher RMSE values but in similar high correlation coefficients (r). The comparison between the indirect optical methods showed that the AccuPAR and the LAI-2200C highly correlate with a systematic underestimation of the AccuPAR in the upper range of LAI values. As expected, S-2 and the field spectrometer showed the highest correlation (RMSE: 0.40 and r: 0.95). Generally, we observed a significant influence of the seasonal changes of the canopy structure and morphology on the estimation accuracy.

Retrieving leaf area index using a genetic algorithm with a canopy radiative transfer model

The leaf area index (LAI) is a key crop biophysical variable influencing many vegetation processes. Spatial LAI estimates are essential to develop and improve spatial modeling tools to monitor vegetation conditions at large regional scales. Numerous optical remote sensing methods have been explored to retrieve crop-specific LAI at a regional scale using satellite observations. However, a major challenge is selecting a method that performance well under various conditions without local scale calibration. As such, we assessed the performance of existing statistical and physical approaches, developed based on parametric, non-parametric and radiative transfer model (RTM)-look-up-table based inversion, using field observations from two geographically distant locations and Landsat 5, 7, and 8 satellite observations. These methods were implemented for corn and soybeans cultivated at two locations in the U.S (i.e., Mead, Nebraska, and Bushland, Texas). The evaluation metrics (i.e., Root Mean Square Error (RMSE), Mean Absolute Error (MAE), and Coefficient of Determination (R2)) were used to study the performance of each method, and then the methods were ranked based on these metrics. Our study showed that overall parametric methods outperformed other methods. The RMSE (MAE) for the top five methods was less than 1.3 (0.95) for corn and 1.0 (0.8) for soybeans, irrespective of location. Even though they outperformed, parametric methods exhibited inconsistency in their performance. For instance, the SR_CA_cross method ranked 1 for corn, however, it performed poorly for soybean (ranked 15). The non-parametric methods showed moderate accuracy partly due to the availability of a smaller number of observations for training. The RTM-LUT inversion physical-based approach was found to perform reasonably well RMSE (MAE) less than 1.5 (1.0) consistently irrespective of location and crop, implying that this approach is more suitable for regional-scale LAI estimation. The results of this study highlighted the drawbacks and advantages of available optical remote sensing approaches to estimate LAI for corn and soybean crops using Landsat imagery. These results are of interest for remote sensing and modeling communities developing spatial-scale approaches to model and monitor agricultural vegetation.

Ability of remotely sensed solar-induced chlorophyll fluorescence (SIF) to serve as a vegetation productivity and stress indicator is impaired by confounding factors, such as varying crop-specific canopy structure, changing solar illumination angles, and SIF-soil optical interactions. This study investigates two normalisation approaches correcting diurnal top-of-canopy SIF observations retrieved from the O2-A absorption feature at 760 nm (F760 hereafter) of summer barley crops for these confounding effects. Nadir SIF data was acquired over nine breeding experimental plots simultaneously by an airborne imaging spectrometer (HyPlant) and a drone-based high-performance point spectrometer (AirSIF). Ancillary measurements, including leaf pigment contents retrieved from drone hyperspectral imagery, destructively sampled leaf area index (LAI), and leaf water and dry matter contents, were used to test the two normalisation methods that are based on: i) the fluorescence correction vegetation index (FCVI), and ii) three versions of the near-infrared reflectance of vegetation (NIRV). Modelling in the discrete anisotropic radiative transfer (DART) model revealed close matches for NIRv-based approaches when corrected canopy SIF was compared to simulated total chlorophyll fluorescence emitted by leaves (R2 = 0.99). Normalisation with the FCVI also performed acceptably (R2 = 0.93), however, it was sensitive to variations in LAI when compared to leaf emitted chlorophyll fluorescence efficiency. Based on the results modelled in DART, the NIRvH1 normalisation was found to have a superior performance over the other NIRv variations and the FCVI normalisation. Comparison of the SIF escape fractions suggests that the escape fraction estimated with NIRvH1 matched escape fraction extracted from DART more closely. When applied to the experimental drone and airborne nadir canopy SIF data, the agreement between NIRvH1 and FCVI produced chlorophyll fluorescence efficiency was very high (R2 = 0.93). Nevertheless, NIRvH1 showed higher uncertainties for areas with low vegetation cover indicating an unaccounted contribution of SIF-soil interactions. The diurnal courses of chlorophyll fluorescence efficiency for both approaches differed not significantly from simple normalisation by incoming and apparent photosynthetically active radiation. In conclusion, SIF normalisation with NIRvH1 more accurately compensates the effects of canopy structure on top of canopy far red SIF, but when applied to top of canopy in-situ data of spring barley, the effects of NIRvH1 and FCVI on the diurnal course of SIF had a similar influence.

Leaf chlorophyll content (LCC) and leaf area index (LAI) are crucial for rice growth and development, serving as key parameters for assessing nutritional status, growth, water management, and yield prediction. This study introduces a novel canopy radiative transfer model (RTM) by coupling the radiation transfer model for rice leaves (RPIOSL) and unified BRDF model (UBM) models, comparing its simulated canopy hyperspectra with those from the PROSAIL model. Characteristic wavelengths were extracted using Sobol sensitivity analysis and competitive adaptive reweighted sampling methods. Using these wavelengths, rice phenotype estimation models were constructed with back propagation neural network (BPNN), extreme learning machine (ELM), and broad learning system (BLS) methods. The results indicate that the RPIOSL-UBM model’s hyperspectra closely match measured data in the 500–650 nm and 750–1000 nm ranges, reducing the root mean square error (RMSE) by 0.0359 compared to the PROSAIL model. The ELM-based models using the RPIOSL-UBM dataset proved most effective for estimating the LAI and LCC, with RMSE values of 0.6357 and 6.0101 μg · cm−2, respectively. These values show significant improvements over the PROSAIL dataset models, with RMSE reductions of 0.1076 and 6.3297 μg · cm−2, respectively. The findings demonstrate that the proposed model can effectively estimate rice phenotypic parameters from UAV-measured hyperspectral data, offering a new approach to assess rice nutritional status and enhance cultivation efficiency and yield. This study underscores the potential of advanced modeling techniques in precision agriculture.

Estimation of shrub willow biophysical parameters across time and space from Sentinel-2 and unmanned aerial system (UAS) data

Leaf area index (LAI) is an important biophysical parameter of vegetation and serves as a significant indicator for assessing forest ecosystems. Multi-source remote sensing data enables large-scale and dynamic surface observations, providing effective data for quantifying various indices in forest and evaluating ecosystem changes. However, employing single-source remote sensing spectral or LiDAR waveform data poses limitations for LAI inversion, making the integration of multi-source remote sensing data a trend. Currently, the fusion of active and passive remote sensing data for LAI inversion primarily relies on empirical models, which are mainly constructed based on field measurements and do not provide a good explanation of the fusion mechanism. In this study, we aimed to estimate LAI based on physical model using both spectral imagery and LiDAR waveform, exploring whether data fusion improved the accuracy of LAI inversion. Specifically, based on the physical model geometric-optical and radiative transfer (GORT), a fusion strategy was designed for LAI inversion. To ensure inversion accuracy, we enhanced the data processing by introducing a constraint-based EM waveform decomposition method. Considering the spatial heterogeneity of canopy/ground reflectivity ratio in regional forests, calculation strategy was proposed to improve this parameter in inversion model. The results showed that the constraint-based EM waveform decomposition method improved the decomposition accuracy with an average 12% reduction in RMSE, yielding more accurate waveform energy parameters. The proposed calculation strategy for the canopy/ground reflectivity ratio, considering dynamic variation of parameter, effectively enhanced previous research that relied on a fixed value, thereby improving the inversion accuracy that increasing on the correlation by 5% to 10% and on R2 by 62.5% to 132.1%. Based on the inversion strategy we proposed, data fusion could effectively be used for LAI inversion. The inversion accuracy achieved using both spectral and LiDAR data (correlation=0.81, R2 = 0.65, RMSE=1.01) surpassed that of using spectral data or LiDAR alone. This study provides a new inversion strategy for large-scale and high-precision LAI inversion, supporting the field of LAI research.

The capability of spaceborne stereogrammetry using very high-resolution (VHR, <2 m) imagery with various environmental, experimental, and sensor configurations for characterizing forest canopy surfaces has not been completely explored. Existing archives of VHR imagery include a limited subset of potential stereo image acquisition configurations and may therefore exclude optimal configurations for capturing critical structural features of forest canopy surface. By contrast, simulated VHR imagery from 3-D radiative transfer models (RTM) can explore the full range of spatial, spectral, and sun-sensor configurations to identify factors that contribute to uncertainties in stereo-derived estimates of forest canopy structure. We developed a novel method to simulate VHR stereopairs using the discrete anisotropic radiative transfer (DART) model and then derive surface elevations from the simulated images. We reconstructed one open-canopy and one closed-canopy forest scene and created a reference digital surface model/digital terrain model (DSM/DTM) using airborne small-footprint lidar points over the study sites. The VHR simulations were configured to match three independent WorldView stereopairs. The results showed that, compared to the reference DSM, the surface elevations derived using simulated and WorldView image data were consistent, with differences of <1.6 m in vertical bias, < 1 m in root mean square error (RMSE), and < 0.07 in correlation coefficient (R). We demonstrated that realistic 3-D RTM simulations could be georeferenced with a camera model for DSM generation from simulated stereopairs. This work will support a follow-up investigation that examines stereo-derived DSM quality over a broad range of surface types and acquisition parameters to suggest optimal configurations for actual VHR stereo data acquisition of vegetation canopy surfaces.

Monitoring crop growth and estimating crop yield are essential for managing agricultural production, ensuring food security, and maintaining sustainable agricultural development. Combining the mechanistic framework of a crop growth model with remote sensing observations can provide a means of generating realistic and spatially detailed crop growth information that can facilitate accurate crop yield estimates at different scales. The main objective of this study was to develop a robust estimation methodology of within-field winter wheat yield at a high spatial resolution (20 m × 20 m) by combining a light use efficiency-based model and Sentinel-2 data. For this purpose, Sentinel-2 derived leaf area index (LAI) time series were assimilated into the Simple Algorithm for Yield Estimation (SAFY) model using an ensemble Kalman filter (EnKF). The study was conducted on rainfed winter wheat fields in southern Sweden. LAI was estimated using vegetation indices (VIs) derived from Sentinel-2 data with semi-empirical models. The enhanced two-band vegetation index (EVI2) was found to be a useful VI for LAI estimation, with a coefficient of determination (R2) and a root mean square error (RMSE) of 0.80 and 0.65 m2/m2, respectively. Our findings demonstrate that the assimilation of LAI derived from Sentinel-2 into the SAFY model using EnKF enhances the estimation of within-field spatial variability of winter wheat yield by 70% compared to the baseline simulation without the assimilation of remotely sensed data. Additionally, the assimilation of LAI improves the accuracy of winter wheat yield estimation by decreasing the RMSE by 53%. This study demonstrates an approach towards practical applications of freely accessible Sentinel-2 data and a crop growth model through data assimilation for fine-scale mapping of crop yield. Such information is critical for quantifying the yield gap at the field scale, and to aid the optimization of management practices to increase crop production.