Retrieving spectral and biophysical parameters of land vegetation by the Earth Observation Land Data Assimilation System

In this thesis, a new methodology for retrieval of land spectral and biophysical parameters from optical remote sensing data has been designed and used. The result of the work was a physically based methodology for Fraction of Photosynthetically Active Radiation (FAPAR) and Leaf Area Index (LAI) retrievals, simulation of hyper-spectral information and estimation of associated uncertainties. The presented methodology is based on the generic Earth Observation-Land Data Assimilation System (EO-LDAS). In the course of the work it was found that EO-LDAS can be used for daily estimation of FAPAR and associated uncertainties without any in-situ information and when the number of available observations is low. The results were in line with the field measurements with r2 varying from 0.84 to 0.92 and Root Mean Square Error (RMSE) from 0.11 to 0.16. This was the highest rate among compared products (Two Stream Inversion Package - JRC-TIP, Medium Resolution Imaging Spectrometer - MERIS FR and Moderate Resolution Imaging Spectro-radiometer - MODIS MCD15). It was shown, that using MISR information, EO-LDAS temporal regularization and generic dynamic prior, it was possible to stabilize results of the retrieval and to obtain better results than MERIS FAPAR or JRC-TIP MISR. In addition, inclusion of generic static and dynamic prior information, decreases posterior uncertainties and can increase accuracies compared to in-situ data. The results showed that proper estimation of LAI and soil parameters were sufficient to simulate a hyper-spectral signal between 400 and 1000 nm with acceptable precision: best RMSE is equal to 0.03 for real data and less than 0.008 for synthetic data. This implies that in case of the given experimental set-up, LAI and soil parameters are the major mechanisms controlling spectral variations in the visible and near infrared regions

Evaluation of Sentinel-3A and Sentinel-3B ocean land colour instrument green instantaneous fraction of absorbed photosynthetically active radiation

This article presents the evaluation of the Copernicus Sentinel-3 Ocean Land Colour Instrument (OLCI) operational terrestrial products corresponding to the green instantaneous Fraction of Absorbed Photosynthetically Active Radiation (FAPAR) and its associated rectified channels. These products are estimated using OLCI spectral measurements acquired at the top of the atmosphere by a physically-based approach and are available operationally at full (300 m) and reduced (1.2 km) spatial resolution daily. The evaluation of the quality of the FAPAR OLCI values was based on the availability of data acquired over several years by Sentinel-3A (S3A) and Sentinel-3B (S3B). The evaluation exercise consisted of several stages: first, an overall comparison of the two S3 platform products was carried out during the tandem phase; second, comparison with an FAPAR climatology derived from the Medium Resolution Imaging Spectrometer (MERIS) provided information on the seasonality of various types of land cover. Then, direct comparisons were made with the same type of FAPAR products retrieved from two sensors, the Moderate Resolution Imaging Spectroradiometer (MODIS) and the Sentinel-2 (S2) Multispectral Instrument (MSI), and with several ground-based estimates. In addition, an analysis of the efficiency of the retrieval algorithm with 3D radiative transfer simulations was performed. The results indicated that the consistency between daily and monthly S3A and S3B on a global scale was very good during the tandem phase (RMSD = 0.01 and a correlation R2 of 0.99 with a bias of 0.003); we found an agreement with a correlation of 0.95 and 0.93 (RMSD = 0.07 and 0.09) with JRC FAPAR S2 and JRC FAPAR MODIS, respectively. Compatibility with the ground-based data was between 0.056 and 0.24 in term of RMSD depending on the type of vegetation with an overall R2 of 0.89. Immler diagrams demonstrate that their variances were lower than the total uncertainties. The quality assurance using 3D radiative transfer model has shown that the apparent performance of the algorithm depends strongly on the type of in-situ measurement and canopy type

Assimilation of remote sensing into crop growth models: Current status and perspectives

Timely monitoring of crop lands is important in order to make agricultural activities more sustainable, as well as ensuring food security. The use of Earth Observation (EO) data allows crop monitoring at a range of spatial scales, but can be hampered by limitations in the data. Crop growth modelling, on the other hand, can be used to simulate the physiological processes that result in crop development. Data assimilation (DA) provides a way of blending the monitoring properties of EO data with the predictive and explanatory abilities of crop growth models. In this paper, we first provide a critique of both the advantages and disadvantages of both EO data and crop growth models. We use this to introduce a solid and robust framework for DA, where different DA methods are shown to be derived from taking different assumptions in solving for the a posteriori probability density function (pdf) using Bayes’ rule. This treatment allows us to provide some recommendation on the choice of DA method for particular applications. We comment on current computational challenges in scaling DA applications to large spatial scales. Future areas of research are sketched, with an emphasis on DA as an enabler for blending different observations, as well as facilitating different approaches to crop growth models. We have illustrated this review with a large number of examples from the literature

Measuring and modelling fAPAR for satellite product validation

This thesis presents a comprehensive approach to satellite Fraction of Absorbed Photosynthetically Active Radiation (fAPAR) product validation. This draws on 3D radiative transfer modelling and metrology to characterise the biases associated with a satellite fAPAR algorithm and the uncertainty associated with fAPAR estimates. This extends existing approaches which tend to assume that the in situ measurement technique produces the same fAPAR quantity as the satellite product. The validation procedure involves creating a closure experiment where every aspect of the satellite product definition and its associated assumptions can be tested from the perspective of the in situ and satellite sensors. The intrinsic differences created by the satellite product assumptions are also assessed, where a new reference is created. This is known as the “true” fAPAR since it is perfectly knowable within the context of the radiative transfer model used. Correction factors between the in situ and satellite-derived fAPAR are created to correct data collected over Wytham Woods. The results indicate that the corrections reduce differences of >10% to near zero. However, the uncertainty estimates for the satellite-derived fAPAR show that it does not meet the requirements given by Global Climate Observing System (GCOS) (≤(10% or 0.05)). The wider implications of the retrieved uncertainties are also presented showing that it is unlikely that the GCOS requirements associated with downstream applications that use satellite fAPAR can be met currently. This work represents an important step forward in the validation of satellitederived fAPAR because it is the first time that the absence of satellite and in situ data uncertainty and traceability, and satellite product definition differences have been addressed. This paves the way for the improvement of satellite fAPAR products because their uncertainties can now be quantified effectively and their validation conducted fairly, meaning there is now a benchmark to base improvements on

Coupled canopy-atmosphere modelling for radiance-based estimation of vegetation properties

Vegetation is an important component of the Earth’s biosphere and therefore plays a crucial role in the carbon exchange of terrestrial ecosystems. Vegetation variables, such as leaf area index (LAI) and leaf chlorophyll content (Cab), can be monitored at global scale using remote sensing (RS). There are two main categories of approaches for estimating the vegetation variables from RS data: empirical and physically-based approaches. Physically-based approaches are more widely applicable because they rely on radiative transfer (RT) models, which can be adapted to the observation conditions and to the observed vegetation. For estimating the vegetation variables, however, the RT model has to be inverted, and this inversion is usually an ill-posed and under-determined problem. Several regularization methods have been proposed to allow finding stable and unique solutions: model coupling, using multi-angular data, using a priori information, as well as applying spatial or temporal constraints. Traditionally, radiance data measured at top-of the atmosphere (TOA) are pre-processed to top-of-canopy (TOC) reflectances. Corrections for atmospheric effects, and, if needed, for adjacency, directional, or topographic effects are usually applied sequentially and independently. Physically, however, these effects are inter-related, and each correction introduces errors. These errors propagate to the TOC reflectance data, which are used to invert the canopy RT model. The performance of the TOC approach is therefore limited by the errors introduced in the data during the pre-processing steps. This thesis proposes to minimize these errors by directly using measured TOA radiance data. In such a TOA approach, the atmospheric RT model, which is normally inverted to perform the atmospheric correction, is coupled to the canopy RT model. The coupled canopy-atmosphere model is inverted directly using the measured radiance data. Adjacency, directional and topographic effects can then be included in the coupled RT model. The same regularization methods as used for TOC approaches can be applied to obtain stable and unique estimates. The TOA approach was tested using four case studies based on mono-temporal data. A) The performance of the TOA approach was compared to a TOC approach for three Norway spruce stands in the Czech Republic, using near-nadir Compact High Resolution Imaging Spectrometer (CHRIS) data. The coupled model included canopy directional effects and simulated the CHRIS radiance data with similar accuracy as the canopy model simulated the atmospherically-corrected CHRIS data. Local sensitivity analyses showed that the atmospheric parameters had much less influence on the simulations than the vegetation parameters, and that the sensitivity profiles of the latter were very similar for both TOC and TOA approaches. The dimensionality of the estimation problem was evaluated to be 3 for both approaches. Canopy cover (Cv), fraction of bark material (fB), Cab, and leaf dry matter content (Cdm) were estimated using look-up tables (LUT) with similar accuracy with both approaches. B) Regularization using multi-angular data was tested for the TOA approach, using four angular CHRIS datasets, for the same three stands as used in A). The coupled model provided good simulations for all angles. The dimensionality increased from 3 to 6 when using all four angles. Two LUTs were built for each stand: a 4-variable LUT with fB, Cv, Cdm, and Cab, and a 7-variable LUT where leaf brown pigment concentration (Cs), dissociation factor (D), and tree shape factor (Zeta) were added. The results did not fully match the expectation that the more angles used, the more accurate the estimates become. Although their exploitation remains challenging, multi-angular data have higher potential than mono-angular data at TOA level. C) A Bayesian object-based approach was developed and tested on at-sensor Airborne Prism Experiment (APEX) radiance data for an agricultural area in Switzerland. This approach consists of two steps. First, up to six variables were estimated for each crop field object using a Bayesian optimization algorithm, using a priori information. Second, a LUT was built for each object with only LAI and Cab as free variables, thus spatially constraining the values of all other variables to the values obtained in the first step. The Bayesian object-based approach estimated LAI more accurately than a LUT with a Bayesian cost function approach. This case study relied on extensive field data allowing defining the objects and a priori data. D) The Bayesian object-based approach proposed in C) was applied to a simulated TOA Sentinel-2 scene, covering the area around Zurich, Switzerland. The simulated scene was mosaicked using seven APEX flight lines, which allowed including all spatial and spectral characteristics of Sentinel-2. Automatic multi-resolution segmentation and classification of the vegetated objects in four levels of brightness in the visible domain enabled defining the objects and a priori data without field data, allowing successful implementation of the Bayesian object-based approach. The research conducted in this thesis contributes to the improvement of the use of regularization methods in ill-posed RT model inversions. Three major areas were identified for further research: 1) inclusion of adjacency and topography effects in the coupled model, 2) addition of temporal constraints in the inversion, and 3) better inclusion of observation and model uncertainties in the cost function. The TOA approach proposed here will facilitate the exploitation of multi-angular, multi-temporal and multi-sensor data, leading to more accurate RS vegetation products. These higher quality products will support many vegetation-related applications.</p

Estimation of FAPAR over croplands using MISR data and the Earth Observation Land Data Assimilation System (EO-LDAS)

The Fraction of Absorbed Photosynthetically-Active Radiation (FAPAR) is an important parameter in climate and carbon cycle studies. In this paper, we use the Earth Observation Land Data Assimilation System (EO-LDAS) framework to retrieve FAPAR from observations of directional surface reflectance measurements from the Multi-angle Imaging SpectroRadiometer(MISR) instrument. The procedure works by interpreting the reflectance data via the semi-discrete Radiative Transfer (RT) model, supported by a prior parameter distribution and a dynamic regularisation model and resulting in an inference of land surface parameters, such as effective Leaf Area Index (LAI), leaf chlorophyll concentration and fraction of senescent leaves, with full uncertainty quantification. The method is demonstrated over three agricultural FLUXNET sites, and the EO-LDAS results are compared with eight years of in situ measurements of FAPAR and LAI, resulting in a total of 24 site years. We additionally compare three other widely-used EO FAPAR products, namely the MEdium Resolution Imaging Spectrometer (MERIS) Full Resolution, the MISR High Resolution (HR) Joint Research Centre Two-stream Inversion Package (JRC-TIP) and MODIS MCD15 FAPAR products. The EO-LDAS MISR FAPAR retrievals show a high correlation with the ground measurements (r(2) > 0.8), as well as the lowest average RMSE (0.14), in line with the MODIS product. As the EO-LDAS solution is effectively interpolated, if only measurements that are coincident with MISR observations are considered, the correlation increases (r(2) > 0.85); the RMSE is lower by 4-5%; and the bias is 2% and 7%. The EO-LDAS MISR LAI estimates show a strong correlation with ground-based LAI (average r(2) = 0.76), but an underestimate of LAI for optically-thick canopies due to saturation (average RMSE = 2.23). These results suggest that the EO-LDAS approach is successful in retrieving both FAPAR and other land surface parameters. A large part of this success is based on the use of a dynamic regularisation model that counteracts the poor temporal sampling from the MISR instrument

Estimation of FAPAR over Croplands Using MISR Data and the Earth Observation Land Data Assimilation System (EO-LDAS)

The Fraction of Absorbed Photosynthetically-Active Radiation (FAPAR) is an important parameter in climate and carbon cycle studies. In this paper, we use the Earth Observation Land Data Assimilation System (EO-LDAS) framework to retrieve FAPAR from observations of directional surface reflectance measurements from the Multi-angle Imaging SpectroRadiometer(MISR) instrument. The procedure works by interpreting the reflectance data via the semi-discrete Radiative Transfer (RT) model, supported by a prior parameter distribution and a dynamic regularisation model and resulting in an inference of land surface parameters, such as effective Leaf Area Index (LAI), leaf chlorophyll concentration and fraction of senescent leaves, with full uncertainty quantification. The method is demonstrated over three agricultural FLUXNET sites, and the EO-LDAS results are compared with eight years of in situ measurements of FAPAR and LAI, resulting in a total of 24 site years. We additionally compare three other widely-used EO FAPAR products, namely the MEdium Resolution Imaging Spectrometer (MERIS) Full Resolution, the MISR High Resolution (HR) Joint Research Centre Two-stream Inversion Package (JRC-TIP) and MODIS MCD15 FAPAR products. The EO-LDAS MISR FAPAR retrievals show a high correlation with the ground measurements ( r 2 &gt; 0.8), as well as the lowest average R M S E (0.14), in line with the MODIS product. As the EO-LDAS solution is effectively interpolated, if only measurements that are coincident with MISR observations are considered, the correlation increases ( r 2 &gt; 0.85); the R M S E is lower by 4–5%; and the bias is 2% and 7%. The EO-LDAS MISR LAI estimates show a strong correlation with ground-based LAI (average r 2 = 0.76), but an underestimate of LAI for optically-thick canopies due to saturation (average R M S E = 2.23). These results suggest that the EO-LDAS approach is successful in retrieving both FAPAR and other land surface parameters. A large part of this success is based on the use of a dynamic regularisation model that counteracts the poor temporal sampling from the MISR instrument

Estimation of FAPAR over croplands using MISR data and the Earth Observation Land Data Assimilation System (EO-LDAS)

The fraction of photosynthetically active radiation (FAPAR) is an important parameter in climate and carbon cycle studies. In this paper, we use the Earth Observation Land Data Assimilation System (EO-LDAS) framework to retrieve FAPAR from observations of directional surface reflectance measurements from the Multi-angle Imaging SpectroRadiometer (MISR) instrument. The procedure works by interpreting the reflectance data via the semi-discrete radiative transfer (RT) model, supported by a prior parameter distribution and a dynamic regularisation model, and resulting in an inference of land surface parameters, such as effective leaf area index (LAI), leaf chlorophyll concentration and fraction of senescent leaves, with full uncertainty quantification. The method is demonstrated over three agricultural FLUXNET sites, and the EO-LDAS results are compared with 8 years of in situ measurements of FAPAR and LAI, resulting in a total of 24 site years. We additionally compare three other widely used EO FAPAR products, namely the MEdium Resolution Imaging Spectrometer (MERIS) Full Resolution, theMISR High Resolution (HR) Joint Research Centre Two-stream Inversion Package (JRC-TIP) and MODIS MCD15 FAPAR products. The EO-LDAS MISR FAPAR retrievals show a high correlation with the ground measurements (r2>0.8), as well as the lowest average RMSE (0.14), in line with the MODIS product. As the EO-LDAS solution is effectively interpolated, if only measurements that are coincident with MISR observations are considered, the correlation increases (r2>0.85), the RMSE is lower by 4-5%, and the bias is 2 and 7%. The EO-LDAS MISR LAI estimates show a strong correlation with ground based LAI (average r2=0.76), but an underestimate of LAI for optically thick canopies due to saturation (average RMSE=2.23). These results suggest that the EO-LDAS approach is successful in retrieving both FAPAR and other land surface parameters. A large part of this success is based on the use of a dynamic regularisation model that counteracts the poor temporal sampling from the MISR instrument.JRC.D.6-Knowledge for Sustainable Development and Food Securit