Staff Publications

Staff Publications

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    'Staff publications' is the digital repository of Wageningen University & Research

    'Staff publications' contains references to publications authored by Wageningen University staff from 1976 onward.

    Publications authored by the staff of the Research Institutes are available from 1995 onwards.

    Full text documents are added when available. The database is updated daily and currently holds about 240,000 items, of which 72,000 in open access.

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    Retrieval of spruce leaf chlorophyll content from airborne image data using continuum removal and radiative transfer
    Malenovsky, Z. ; Homolova, L. ; Zurita-Milla, R. ; Lukes, P. ; Kaplan, V. ; Hanus, J. ; Gastellu-Etchegorry, J.P. ; Schaepman, M.E. - \ 2013
    Remote Sensing of Environment 131 (2013). - ISSN 0034-4257 - p. 85 - 102.
    canopy reflectance models - optical-properties model - area index - hyperspectral data - forest canopies - precision agriculture - vegetation canopies - red - band - absorption
    We investigate combined continuum removal and radiative transfer (RT) modeling to retrieve leaf chlorophyll a & b content (Cab) from the AISA Eagle airborne imaging spectrometer data of sub-meter (0.4 m) spatial resolution. Based on coupled PROSPECT-DART RT simulations of a Norway spruce (Picea abies (L.) Karst.) stand, we propose a new Cab sensitive index located between 650 and 720 nm and termed ANCB650–720. The performance of ANCB650–720 was validated against ground-measured Cab of ten spruce crowns and compared with Cab estimated by a conventional artificial neural network (ANN) trained with continuum removed RT simulations and also by three previously published chlorophyll optical indices: normalized difference between reflectance at 925 and 710 nm (ND925&710), simple reflectance ratio between 750 and 710 nm (SR750/710) and the ratio of TCARI/OSAVI indices. Although all retrieval methods produced visually comparable Cab spatial patterns, the ground validation revealed that the ANCB650–720 and ANN retrievals are more accurate than the other three chlorophyll indices (R2 = 0.72 for both methods). ANCB650–720 estimated Cab with an RMSE = 2.27 µg cm- 2 (relative RRMSE = 4.35%) and ANN with an RMSE = 2.18 µg cm- 2 (RRMSE = 4.18%), while SR750/710 with an RMSE = 4.16 µg cm- 2 (RRMSE = 7.97%), ND925&710 with an RMSE = 9.07 µg cm- 2 (RRMSE = 17.38%) and TCARI/OSAVI with an RMSE = 12.30 µg cm- 2 (RRMSE = 23.56%). Also the systematic RMSES was lower than the unsystematic one only for the ANCB650–720 and ANN retrievals. Our results indicate that the newly proposed index can provide the same accuracy as ANN except for Cab values below 30 µg cm- 2, which are slightly overestimated (RMSE = 2.42 µg cm- 2). The computationally efficient ANCB650–720 retrieval provides accurate high spatial resolution airborne Cab maps, considerable as a suitable reference data for validating satellite-based Cab products.
    Canopy bidirectional reflectance calculation based on Adding method and SAIL formalism: AddingS / AddingSD
    Kallel, A. ; Verhoef, W. ; Hegarat-Mascle, S. Le; Ottle, C. ; Hubert-Moy, L. - \ 2008
    Remote Sensing of Environment 112 (2008)9. - ISSN 0034-4257 - p. 3639 - 3655.
    radiative-transfer - vegetation canopies - light-scattering - model - simulation
    The SAIL model (proposed by Verhoef) is largely used in the remote sensing community to calculate the canopy Bidirectional Reflectance Distribution Function. The simulation results appear acceptable compared to observations especially for not very dense planophile vegetation. However, for erectophile dense crops (e.g. corn) the simulations appear less accurate. This inadequacy is due to the assumption that the multiple scattered fluxes are isotropically distributed. The SAIL parameters are interpretable at the level of elementary layer components. Now, the Adding method (initially proposed by Van de Hulst) provides a good framework to model the radiative transfer inside a vegetation layer, but its parameter estimation lies on very simple geometric modeling of the canopy. In this paper, we first propose an adaptation of the Adding method using the SAIL model canopy representation in the turbid case: it is called AddingS model. Such an approach allows to overcome the isotropy assumption. Second, AddingS is extended to the Discrete case: defining the AddingSDmodel. It allows to take into account the multi hot spot effect. Moreover, the AddingS and AddingSD models allow to check the energy conservation in respectively turbid and discrete cases. Finally, in order to keep reasonable time performance, a fast computation method was developed.
    The third RAdiation transfer Model Intercomparison (RAMI) exercise: Documenting progress in canopy reflectance models
    Widlowski, J.L. ; Taberner, M. ; Pinty, B. ; Bruniquel-Pinel, V. ; Disney, M.I. ; Fernandes, R. ; Gastellu-Etchegorry, J.P. ; Gobron, N. ; Kuusk, A. ; Lavergne, T. ; LeBlanc, S. ; Lewis, P.E. ; Martin, E. ; Mõttus, M. ; North, P.R.J. ; Qin, W. ; Robustelli, M. ; Rochdi, N. ; Ruiloba, R. ; Thompson, R. ; Verhoef, W. ; Verstraete, M.M. ; Xie, D. - \ 2007
    Journal of Geophysical Research: Atmospheres 112 (2007). - ISSN 2169-897X
    digital hemispherical photography - vegetation canopies - leaf orientation - solar-radiation - plant canopies - scattering - project - surface - validation - absorption
    [1] The Radiation Transfer Model Intercomparison ( RAMI) initiative benchmarks canopy reflectance models under well-controlled experimental conditions. Launched for the first time in 1999, this triennial community exercise encourages the systematic evaluation of canopy reflectance models on a voluntary basis. The first phase of RAMI focused on documenting the spread among radiative transfer (RT) simulations over a small set of primarily 1-D canopies. The second phase expanded the scope to include structurally complex 3-D plant architectures with and without background topography. Here sometimes significant discrepancies were noted which effectively prevented the definition of a reliable "surrogate truth,'' over heterogeneous vegetation canopies, against which other RT models could then be compared. The present paper documents the outcome of the third phase of RAMI, highlighting both the significant progress that has been made in terms of model agreement since RAMI-2 and the capability of/need for RT models to accurately reproduce local estimates of radiative quantities under conditions that are reminiscent of in situ measurements. Our assessment of the self-consistency and the relative and absolute performance of 3-D Monte Carlo models in RAMI-3 supports their usage in the generation of a "surrogate truth'' for all RAMI test cases. This development then leads ( 1) to the presentation of the "RAMI Online Model Checker'' (ROMC), an open-access web-based interface to evaluate RT models automatically, and ( 2) to a reassessment of the role, scope, and opportunities of the RAMI project in the future.
    Coupled soil-leaf-canopy and atmosphere radiative transfer modeling to simulate hyperspectral multi-angular surface reflectance and TOA radiance data
    Verhoef, W. ; Bach, H. - \ 2007
    Remote Sensing of Environment 109 (2007)2. - ISSN 0034-4257 - p. 166 - 182.
    photosynthetically active radiation - light interaction-model - vegetation canopies - plant-canopy - sail model - scattering - inversion - prospect - spectra - indexes
    Coupling radiative transfer models for the soil background and vegetation canopy layers is facilitated by means of the four-stream flux interaction concept and use of the adding method. Also the coupling to a state-of-the-art atmospheric radiative transfer model like MODTRAN4 can be established in this way, thus enabling the realistic simulation of top-of-atmosphere radiances detected by space-borne remote sensing instruments. Possible applications of coupled modeling vary from mission design to parameter retrieval and data assimilation. This paper introduces a modified Hapke soil BRDF model, a robust version of the PROSPECT leaf model, and a modernized canopy radiative transfer model called 4SAIL2. The latter is a hybrid two-layer version of SAIL accommodating horizontal and vertical heterogeneities, featuring improved modeling of the hot spot effect and output of canopy absorptances. The integrated model is simply called SLC (soil¿leaf-canopy) and has been implemented as a speed-optimized Windows DLL which allows efficient use of computer resources even when simulating massive amounts of hyperspectral multi-angular observations. In this paper various examples of possible model output are shown, including simulated satellite image products. First validation results have been obtained from atmospherically corrected hyperspectral multi-angular CHRIS-PROBA data of the Upper Rhine Valley in Germany.
    Coupled carbon-water exchange of the Amazon rain forest. I. Model description, parameterization and sensitivity analysis
    Simon, E. ; Meixner, F.X. ; Ganzeveld, L.N. ; Kesselmeier, J. - \ 2005
    Biogeosciences 2 (2005)3. - ISSN 1726-4170 - p. 231 - 253.
    nitrogen-use efficiency - leaf-area index - stomatal conductance - photosynthetic capacity - biochemical-properties - vegetation canopies - vapor exchange - boundary-layer - c-3 plants - co2
    Detailed one-dimensional multilayer biosphere-atmosphere models, also referred to as CANVEG models, are used for more than a decade to describe coupled water-carbon exchange between the terrestrial vegetation and the lower atmosphere. Within the present study, a modified CANVEG scheme is described. A generic parameterization and characterization of biophysical properties of Amazon rain forest canopies is inferred using available field measurements of canopy structure, in-canopy profiles of horizontal wind speed and radiation, canopy albedo, soil heat flux and soil respiration, photosynthetic capacity and leaf nitrogen as well as leaf level enclosure measurements made on sunlit and shaded branches of several Amazonian tree species during the wet and dry season. The sensitivity of calculated canopy energy and CO2 fluxes to the uncertainty of individual parameter values is assessed. In the companion paper, the predicted seasonal exchange of energy, CO2, ozone and isoprene is compared to observations. A bi-modal distribution of leaf area density with a total leaf area index of 6 is inferred from several observations in Amazonia. Predicted light attenuation within the canopy agrees reasonably well with observations made at different field sites. A comparison of predicted and observed canopy albedo shows a high model sensitivity to the leaf optical parameters for near-infrared short-wave radiation (NIR). The predictions agree much better with observations when the leaf reflectance and transmission coefficients for NIR are reduced by 25¿40%. Available vertical distributions of photosynthetic capacity and leaf nitrogen concentration suggest a low but significant light acclimation of the rain forest canopy that scales nearly linearly with accumulated leaf area. Evaluation of the biochemical leaf model, using the enclosure measurements, showed that recommended parameter values describing the photosynthetic light response, have to be optimized. Otherwise, predicted net assimilation is overestimated by 30¿50%. Two stomatal models have been tested, which apply a well established semi-empirical relationship between stomatal conductance and net assimilation. Both models differ in the way they describe the influence of humidity on stomatal response. However, they show a very similar performance within the range of observed environmental conditions. The agreement between predicted and observed stomatal conductance rates is reasonable. In general, the leaf level data suggests seasonal physiological changes, which can be reproduced reasonably well by assuming increased stomatal conductance rates during the wet season, and decreased assimilation rates during the dry season. The sensitivity of the predicted canopy fluxes of energy and CO2 to the parameterization of canopy structure, the leaf optical parameters, and the scaling of photosynthetic parameters is relatively low (1¿12%), with respect to parameter uncertainty. In contrast, modifying leaf model parameters within their uncertainty range results in much larger changes of the predicted canopy net fluxes (5¿35%)
    On Lagrangian dispersion of 222Rn, H2O and CO2 within the Amazon rain forest
    Simon, E. ; Lehmann, B. ; Ammann, C. ; Ganzeveld, L.N. ; Rummel, U. ; Meixner, F.X. ; Nobre, A.D. ; Araujo, A. de; Kesselmeier, J. - \ 2005
    Agricultural and Forest Meteorology 132 (2005)3-4. - ISSN 0168-1923 - p. 286 - 340.
    atmospheric boundary-layers - net ecosystem exchange - model-plant canopy - douglas-fir forest - carbon-dioxide - tropical forest - turbulence statistics - source distributions - vegetation canopies - scalar dispersion
    The present study focuses on the description of the vertical dispersion of trace gases within the Amazon rain forest. A Lagrangian approach is parameterised using in-canopy turbulence measurements made at a site in Rondônia (Reserva Jaru). In contrast to common scaling schemes that solely depend on friction parameters measured above the canopy, a combined scaling that also includes night-time free convective mixing in the lower part of dense vegetation canopies is proposed here. 222Rn concentration profiles and soil flux measurements made at a second site near Manaus (Reserva Cuieiras) are used to evaluate the derived parameterisation and the uncertainties of the forward (prediction of concentration profiles) and inverse (prediction of vertical source/sink distributions) solution of the transfer equations. Averaged day- and night-time predictions of the forward solution agree with the observations within their uncertainty range. During night-time, a weak, but effective free convective mixing process in the lower canopy ensures a relatively high flushing rate with residence times of
    Estimation of sensible heat flux using the Surface Energy Balance System (SEBS) and ATSR measurements
    Jia, L. ; Su, Z. ; Hurk, B. van den; Menenti, M. ; Moene, A.F. ; Bruin, H.A.R. de; Baselga Yrisarry, J.J. ; Ibanez, M. ; Cuesta, A. - \ 2003
    Physics and Chemistry of the Earth 28 (2003). - ISSN 1474-7065 - p. 75 - 88.
    vegetation canopies - evapotranspiration models - bidirectional reflectance - physical model - land-surface - temperature - radiation - area - resistance - scattering
    This paper describes a modified version of the Surface Energy Balance System (SEBS) as regards the use of radiometric data from space and presents the results of a large area validation study on estimated sensible heat flux, extended over several months. The improvements were made possible by the characteristics of the Along Track Scanning Radiometer (ATSR-2) on board the European Remote Sensing satellite (ERS-2) and relate to: (a) the use of bi-angular radiometric data in two thermal infrared channels to estimate column atmospheric water vapor: (b) the use of bi-angular radiometric data in four spectral channels in the 550-1600 nm spectral regions to estimate aerosols optical depth: (c) determination of bottom of atmosphere (BOA) spectral reflectance using column water vapor, aerosols optical depth and a two-stream radiative transfer scheme to relate BOA spectral reflectance to top of atmosphere spectral radiance (d) direct and inverse modeling of radiative transfer in a vegetation canopy to relate BOA spectral reflectance to canopy properties, such as spectrally integrated hemispherical reflectance (albedo). A parameterization of the aerodynamic resistance for heat transfer (in term of kB(-1)) was applied for the first time at large spatial scales. For such large area analyses SEBS requires wind speed, potential temperature and humidity of air at an appropriate reference height. The latter was taken as being the height of the planetary boundary layer (PBL) and the data used were fields generated by an advanced numerical weather prediction model, i.e. regional atmospheric climate model (RACMO), integrated over the PBL. Validation of estimated sensible heat flux H obtained with the ATSR radiometric data was done using long-range, line-averaged measurements of H done with large aperture scintillometers (LAS) located at three sites in Spain and operated continuously between April and September 1999. The root mean square deviation of SEBS H estimates from LAS H measurements was 25.5 W m(-2). (C) 2003 Elsevier Science Ltd. All rights reserved.
    Modelling kinetics of plant canopy architecture: concepts and applications
    Birch, C.J. ; Andrieu, B. ; Fournier, C. ; Vos, J. ; Room, P. - \ 2003
    European Journal of Agronomy 19 (2003). - ISSN 1161-0301 - p. 519 - 533.
    maize zea-mays - atmospheric carbon-dioxide - root-system architecture - leaf-area - hydraulic architecture - vegetation canopies - radiative-transfer - climate change - grain-sorghum - epic model
    Most crop models simulate the crop canopy as an homogeneous medium. This approach enables modelling of mass and energy transfer through relatively simple equations, and is useful for understanding crop production. However, schematisation of an homogeneous medium cannot address the heterogeneous nature of canopies and interactions between plants or plant organs, and errors in calculation of light interception may occur. Moreover, conventional crop models do not describe plant organs before they are visible externally e.g. young leaves of grasses. The conditions during early growth of individual organs are important determinants of final organ size, causing difficulties in incorporating effects of environmental stresses in such models. Limited accuracy in describing temporal source-sink relationships also contributes to difficulty in modelling dry matter distribution and paramaterisation of harvest indices. Functional-architectural modelling aims to overcome these limitations by (i) representing crops as populations of individual plants specified in three dimensions and (ii) by modelling whole plant growth and development from the behaviour of individual organs, based on models of organs such as leaves and internodes. Since individual plants consist of numerous organs, generic models of organ growth applicable across species are desirable. Consequently, we are studying the development of individual organs, and pararneterising it in terms of environmental variables and plant characteristics. Models incorporating plant architecture are currently applied in education, using dynamic visual representation for teaching growth and development. In research, the 3D representation of plants addresses issues presented above and new applications including modelling of pesticide distribution, fungal spore dispersal through splashing and plant to plant heterogeneity. (C) 2003 Elsevier Science B.V. All rights reserved.
    Cloud and rain processes in a biosphere-atmosphere interaction context in the Amazon Region
    Silva Dias, M.A.F. ; Rutledge, S. ; Kabat, P. ; Silva Dias, P.L. ; Nobre, C. ; Fisch, G. ; Dolman, A.J. ; Zipser, E. ; Garstang, M. ; Manzi, A.O. ; Fuentes, J.D. ; Rocha, H.R. ; Marengo, J. ; Plana-Fattori, A. ; Sá, L.D.A. ; Alvalá, R.C.S. ; Andreae, M.O. ; Artaxo, P. ; Gielow, R. ; Gatti, L. - \ 2002
    Journal of Geophysical Research: Atmospheres 107 (2002)D20. - ISSN 2169-897X - p. 8072 - 8072.
    boundary-layer experiment - ice-scattering signature - zero-plane displacement - coastal squall lines - dry season - vegetation canopies - tropical atmosphere - tall vegetation - coherent eddies - wet season
    This paper presents an overview of the results from the first major mesoscale atmospheric campaign of the Large-Scale Biosphere-Atmosphere Experiment in Amazonia (LBA) Program. The campaign, collocated with a Tropical Rainfall Measuring Mission (TRMM) satellite validation campaigns, was conducted in southwest Rondônia in January and February 1999 during the wet season. Highlights on the interaction between clouds, rain, and the underlying landscape through biospheric processes are presented and discussed.
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