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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    Estimation of spruce needle-leaf chlorophyll content based on DART and PARAS canopy reflectance models
    Yanez Rausell, L. ; Malenovsky, Z. ; Rautiainen, M. ; Clevers, J.G.P.W. ; Lukes, P. ; Hanus, J. ; Schaepman, M.E. - \ 2015
    IEEE Journal of Selected Topics in Applied Earth Observations and Remote Sensing 8 (2015)4. - ISSN 1939-1404 - p. 1534 - 1544.
    photon recollision probability - area index - spectral invariants - forest - prospect - stands - simulations - resolution - retrieval - lai-2000
    Needle-leaf chlorophyll content (Cab) of a Norway spruce stand was estimated from CHRIS-PROBA images using the canopy reflectance simulated by the PROSPECT model coupled with two canopy reflectance models: 1) discrete anisotropic radiative transfer model (DART); and 2) PARAS. The DART model uses a detailed description of the forest scene, whereas PARAS is based on the photon recollision probability theory and uses a simplified forest structural description. Subsequently, statistically significant empirical functions between the optical indices ANCB670-720 and ANMB670-720 and the needle-leaf Cab content were established and then applied to CHRIS-PROBA data. The Cab estimating regressions using ANMB670_720 were more robust than using ANCB670-720 since the latter was more sensitive to LAI, especially in case of PARAS. Comparison between Cab estimates showed strong linear correlations between PARAS and DART retrievals, with a nearly perfect one-to-one fit when using ANMB670-720 (slope = 1.1, offset = 11 µg · cm-2). Further comparison with Cab estimated from an AISA Eagle image of the same stand showed better results for PARAS (RMSE = 2.7 µg · cm-2 for ANCB670-720; RMSE = 9.5 µg · cm-2 for ANMB670_720) than for DART (RMSE = 7.5 µg · cm-2 for ANCB670-720; RMSE = 23 µg · cm-2 for ANMB670-720). Although these results show the potential for simpler models like PARAS in estimating needle-leaf Cab from satellite imaging spectroscopy data, further analyses regarding parameterization of radiative transfer models are recommended.
    Minimizing measurement uncertainties of coniferous needle-leaf optical properties, part II: experimental set-up and error analysis
    Yanez Rausell, L. ; Malenovsky, Z. ; Clevers, J.G.P.W. ; Schaepman, M.E. - \ 2014
    IEEE Journal of Selected Topics in Applied Earth Observations and Remote Sensing 7 (2014)2. - ISSN 1939-1404 - p. 406 - 420.
    leaves
    We present uncertainties associated with the measurement of coniferous needle-leaf optical properties (OPs) with an integrating sphere using an optimized gap-fraction (GF) correction method, where GF refers to the air gaps appearing between the needles of a measured sample. We used an optically stable artificial material simulating needle leaves to investigate the potential effects of: 1) the sample holder carrying the needles during measurements and 2) multiple scattering in between the measured needles. Our optimization of integrating sphere port configurations using the sample holder showed an underestimation of the needle transmittance signal of at least 2% in flat needles and 4% in nonflat needles. If the needles have a nonflat cross section, multiple scattering of the photons during the GF measurement led to a GF overestimation. In addition, the multiple scattering of photons during the optical measurements caused less accurate performance of the GF-correction algorithms, which are based on the assumption of linear relationship between the nonGF-corrected signal and increasing GF, resulting in transmittance overestimation of nonflat needle samples. Overall, the final deviation achieved after optimizing the method is about 1% in reflectance and 6% in transmittance if the needles are flat, and if they are nonflat, the error increases to 4%-6% in reflectance and 10%-12% in transmittance. These results suggest that formulae for measurements and computation of coniferous needle OPs require modification that includes also the phenomenon of multiple scattering between the measured needles.
    Minimizing measurement uncertainties of coniferous needle-leaf optical properties, part I: methodological review
    Yanez Rausell, L. ; Schaepman, M.E. ; Clevers, J.G.P.W. ; Malenovsky, Z. - \ 2014
    IEEE Journal of Selected Topics in Applied Earth Observations and Remote Sensing 7 (2014)2. - ISSN 1939-1404 - p. 399 - 405.
    revised measurement methodology - chlorophyll content estimation - radiative-transfer model - reflectance spectra - hyperspectral data - bifacial leaf - boreal forest - leaves - light - absorption
    Optical properties (OPs) of non-flat narrow plant leaves, i.e., coniferous needles, are extensively used by the remote sensing community, in particular for calibration and validation of radiative transfer models at leaf and canopy level. Optical measurements of such small living elements are, however, a technical challenge and only few studies attempted so far to investigate and quantify related measurement errors. In this paper we review current methods and developments measuring optical properties of narrow leaves. We discuss measurement shortcomings and knowledge gaps related to a particular case of non-flat nonbifacial coniferous needle leaves, e.g., needles of Norway spruce (Picea abies (L.) Karst.).
    Review of optical-based remote sensing for plant trait mapping
    Homolova, L. ; Malenovsky, Z. ; Clevers, J.G.P.W. ; Garcia-Santos, G. ; Schaepman, M.E. - \ 2013
    Ecological Complexity 15 (2013). - ISSN 1476-945X - p. 1 - 16.
    leaf-area index - light-use efficiency - photochemical reflectance index - gross primary production - dry-matter content - terrestrial chlorophyll fluorescence - multiple linear-regression - forest canopy reflectance - fuel moisture-content - nitrogen concentratio
    Plant trait data have been used in various studies related to ecosystem functioning, community ecology, and assessment of ecosystem services. Evidences are that plant scientists agree on a set of key plant traits, which are relatively easy to measure and have a stable and strong predictive response to ecosystem functions. However, the field measurements of plant trait data are still limited to small area, to a certain moment in time and to certain number of species only. Therefore, remote sensing (RS) offers potential to complement or even replace field measurements of some plant traits. It offers instantaneous spatially contiguous information, covers larger areas and in case of satellite observations profits from their revisit capacity. In this review, we first introduce RS concepts of light–vegetation interactions, RS instruments for vegetation studies, RS methods, and scaling between field and RS observations. Further we discuss in detail current achievements and challenges of optical RS for mapping of key plant traits. We concentrate our discussion on three categorical plant traits (plant growth and life forms, flammability properties and photosynthetic pathways and activity) and on five continuous plant traits (plant height, leaf phenology, leaf mass per area, nitrogen and phosphorous concentration or content). We review existing literature to determine the retrieval accuracy of the continuous plant traits. The relative estimation error using RS ranged between 10% and 45% of measured mean value, i.e. around 10% for plant height of tall canopies, 20% for plant height of short canopies, 15% for plant nitrogen, 25% for plant phosphorus content/concentration, and 45% for leaf mass per area estimates. The potential of RS to map plant traits is particularly high when traits are related to leaf biochemistry, photosynthetic processes and canopy structure. There are also other plant traits, i.e. leaf chlorophyll content, water content and leaf area index, which can be retrieved from optical RS well and can be of importance for plant scientists. We underline the need that future assessments of ecosystem functioning using RS should require comprehensive and integrated measurements of various plant traits together with leaf and canopy spectral properties. By doing so, the interplay between plant structural, physiological, biochemical, phenological and spectral properties can be better understood.
    Measurement methods and variability assessment of the Norway spruce total leaf area: Implications for remote sensing
    Homolova, L. ; Lukes, P. ; Malenovsky, Z. ; Lhotakova, Z. ; Kaplan, V. ; Hanus, J. - \ 2013
    Trees-Structure and Function 27 (2013)1. - ISSN 0931-1890 - p. 111 - 121.
    chlorophyll-a - light-interception - hyperspectral data - picea-abies - imaging spectroscopy - conifer needles - surface-area - gas-exchange - canopy - biochemistry
    Estimation of total leaf area (LAT) is important to express biochemical properties in plant ecology and remote sensing studies. A measurement of LAT is easy in broadleaf species, but it remains challenging in coniferous canopies. We proposed a new geometrical model to estimate Norway spruce LAT and compared its accuracy with other five published methods. Further, we assessed variability of the total to projected leaf area conversion factor (CF) within a crown and examined its implications for remotely sensed estimates of leaf chlorophyll content (Cab). We measured morphological and biochemical properties of three most recent needle age classes in three vertical canopy layers of a 30 and 100-year-old spruce stands. Newly introduced geometrical model and the parallelepiped model predicted spruce LAT with an error >5 % of the average needle LAT, whereas two models based on an elliptic approximation of a needle shape underestimated LAT by up to 60 %. The total to projected leaf area conversion factor varied from 2. 5 for shaded to 3. 9 for sun exposed needles and remained invariant with needle age class and forest stand age. Erroneous estimation of an average crown CF by 0. 2 introduced an error of 2-3 µg cm-2 into the crown averaged Cab content. In our study, this error represents 10-15 % of observed crown averaged Cab range (33-53 µg cm-2). Our results demonstrate the importance of accurate LAT estimates for validation of remotely sensed estimates of Cab content in Norway spruce canopies.
    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.
    Sentinels for science: Potential of Sentinel-1, -2, and -3 missions for scientific observations of ocean, cryosphere, and land
    Malenovsky, Z. ; Rott, H. ; Cihlar, J. ; Schaepman, M.E. ; Garcia-Santos, G. ; Fernandes, R. ; Berger, M. - \ 2012
    Remote Sensing of Environment 120 (2012). - ISSN 0034-4257 - p. 91 - 101.
    The Sentinel-1, -2, and -3 satellite missions can meet various observational needs for spatially explicit physical, biogeophysical, and biological variables of the ocean, cryosphere, and land research activities. The currently known observational requirements were extracted from documents produced by major international scientific projects and programs. The summarized observational needs were then cross-referenced with the capabilities of the planned sensors aboard of the first three Sentinels. A comparative analysis, also incorporating scientific challenges of the ESA Living Planet Programme and the Essential Climate Variables (ECVs), resulted in a preliminary scientific priority assessment of the reviewed environmental variables. Results of these activities, discussed and consolidated in March 2011 at the Sentinels for Science (SEN4SCI) scientific workshop, demonstrate the high potential of the Sentinel-1, -2, and -3 missions for systematic, long-term observations of the Earth system.
    A note on upscaling coniferous needle spectra to shoot spectral albedo
    Rautiainen, M. ; Mottus, M. ; Yanez Rausell, L. ; Homolova, L. ; Malenovsky, Z. ; Schaepman, M.E. - \ 2012
    Remote Sensing of Environment 117 (2012). - ISSN 0034-4257 - p. 469 - 474.
    leaf-area index - scots pine - optical-properties - silhouette area - radiation - canopies - light - stands - model - simulations
    Mutual shading of needles in coniferous shoots and small-scale variations in needle area density both within and between shoots violate conventional assumptions used in the definition of the elementary volume in radiative transfer models. In this paper, we test the hypothesis if it is possible to scale needle spectral albedo up to shoot spectral albedo using only one structural parameter: the spherically averaged shoot silhouette to total area ratio (STAR). To test the hypothesis, we measured both structural and spectral properties of ten Scots pine (Pinus sylvestris) shoots and their needles. Our results indicate that it is possible to upscale from needle to shoot spectral albedo using STAR. The upscaling model performed best in the VIS and SWIR regions, and for shoots with high STAR values. As STAR is linearly related to photon recollision probability, it is also possible to apply the upscaling model as integral part of radiative transfer models.
    Estimation of plant functional biochemical traits of subalpine and alpine grasslands from airborne images of high spatial and spectral resolution
    Homolova, L. ; Malenovsky, Z. ; Schaepman, M.E. ; Clevers, J.G.P.W. - \ 2011
    Influence of gap fraction on coniferous needle optical properties measurements
    Yanez Rausell, L. ; Malenovsky, Z. ; Schaepman, M.E. - \ 2011
    Scaling spectroscopic approaches – from leaf albedo to ecosystems mapping
    Schaepman, M.E. ; Kneubühler, M. ; Bartholomeus, H. ; Malenovsky, Z. ; Damm, A. ; Schaepman-Strub, G. ; Hueni, A. - \ 2010
    - p. 1 - 19.
    Performance of the PROSPECT leaf radiative transfer model version 4 for Norway spruce needles
    Yanez Rausell, L. ; Malenovsky, Z. ; Clevers, J.G.P.W. ; Schaepman, M.E. - \ 2010
    In: Proceedings Hyperspectral 2010 Workshop (SP-683), Frascati, Italy, 17-19 March 2010. - Frascati, Italy : ESA - p. 4 - 4.
    Effects of woody elements on simulated canopy reflectance: implications for forest chlorophyll content retrieval
    Verrelst, J. ; Schaepman, M.E. ; Malenovsky, Z. ; Clevers, J.G.P.W. - \ 2010
    Remote Sensing of Environment 114 (2010)3. - ISSN 0034-4257 - p. 647 - 656.
    leaf optical-properties - light-use efficiency - resolution satellite imagery - radiative-transfer models - high-spatial-resolution - spectral reflectance - imaging spectroscopy - vegetation indexes - hyperspectral reflectance - sensitivity-analysis
    An important bio-indicator of actual plant health status, the foliar content of chlorophyll a and b (Cab), can be estimated using imaging spectroscopy. For forest canopies, however, the relationship between the spectral response and leaf chemistry is confounded by factors such as background (e.g. understory), canopy structure, and the presence of non-photosynthetic vegetation (NPV, e.g. woody elements)—particularly the appreciable amounts of standing and fallen dead wood found in older forests. We present a sensitivity analysis for the estimation of chlorophyll content in woody coniferous canopies using radiative transfer modeling, and use the modeled top-of-canopy reflectance data to analyze the contribution of woody elements, leaf area index (LAI), and crown cover (CC) to the retrieval of foliar Cab content. The radiative transfer model used comprises two linked submodels: one at leaf level (PROSPECT) and one at canopy level (FLIGHT). This generated bidirectional reflectance data according to the band settings of the Compact High Resolution Imaging Spectrometer (CHRIS) from which chlorophyll indices were calculated. Most of the chlorophyll indices outperformed single wavelengths in predicting Cab content at canopy level, with best results obtained by the Maccioni index ([R780 - R710] / [R780 - R680]). We demonstrate the performance of this index with respect to structural information on three distinct coniferous forest types (young, early mature and old-growth stands). The modeling results suggest that the spectral variation due to variation in canopy chlorophyll content is best captured for stands with medium dense canopies. However, the strength of the up-scaled Cab signal weakens with increasing crown NPV scattering elements, especially when crown cover exceeds 30%. LAI exerts the least perturbations. We conclude that the spectral influence of woody elements is an important variable that should be considered in radiative transfer approaches when retrieving foliar pigment estimates in heterogeneous stands, particularly if the stands are partly defoliated or long-lived
    Algorithm theoretical basis document
    Huber, S. ; Schaepman, M.E. ; Clevers, J.G.P.W. ; Malenovsky, Z. ; Carrère, V. ; Gamba, P. ; Zagajewski, B. - \ 2009
    Wageningen : Wageningen University (Hyper-i-net technical report D6.1) - 117 p.
    Scientific and technical challenges in remote sensing of plant canopy reflectance and fluorescence
    Malenovsky, Z. ; Mishra, K.B. ; Zemek, F. ; Rascher, U. ; Nedbal, L. - \ 2009
    Journal of Experimental Botany 60 (2009)11. - ISSN 0022-0957 - p. 2987 - 3004.
    laser-induced fluorescence - leaf-area index - light-use efficiency - induced chlorophyll fluorescence - blue-green fluorescence - photosynthetically active radiation - model inversion methods - vegetation biophysical parameters - rotational raman-scattering - net
    State-of-the-art optical remote sensing of vegetation canopies is reviewed here to stimulate support from laboratory and field plant research. This overview of recent satellite spectral sensors and the methods used to retrieve remotely quantitative biophysical and biochemical characteristics of vegetation canopies shows that there have been substantial advances in optical remote sensing over the past few decades. Nevertheless, adaptation and transfer of currently available fluorometric methods aboard air- and space-borne platforms can help to eliminate errors and uncertainties in recent remote sensing data interpretation. With this perspective, red and blue-green fluorescence emission as measured in the laboratory and field is reviewed. Remotely sensed plant fluorescence signals have the potential to facilitate a better understanding of vegetation photosynthetic dynamics and primary production on a large scale. The review summarizes several scientific challenges that still need to be resolved to achieve operational fluorescence based remote sensing approaches
    Structural parametrization of Norway spruce trees in radiative transfer of high spatial resolution
    Malenovsky, Z. ; Homolova, L. ; Hanus, J. ; Kaplan, V. ; Dolansky, T. ; Yanez, L. - \ 2008
    Towards remote sensing of physiological processes: Up-scaling the reflectance and fluorescence signals of vegetation
    Malenovsky, Z. ; Hanus, J. ; Ac, A. ; Homolova, L. ; Kaplan, V. ; Lukes, P. ; Pokorny, R. ; Cudlin, P. ; Schaepman, M.E. ; Marek, M.V. - \ 2008
    Towards remote sensing of vegetation processes
    Ac, A. ; Bandhu Mishra, K. ; Malenovsky, Z. ; Hanus, J. ; Trtílek, M. ; Nedbal, L. ; Marek, M.V. - \ 2008
    In: Proceedings of International Workshop Sensing a Changing World 2008/ CGI report CGI-08-005, Wageningen, the Netherlands, 19 - 21 November, 2008. - Wageningen : Wageningen University and Research Centre - p. 19 - 23.
    Geometrical and structural parametrization of forest canopy radiative transfer by LIDAR measurements
    Yanez, L. ; Homolova, L. ; Malenovsky, Z. ; Clevers, J.G.P.W. ; Schaepman, M.E. - \ 2008
    In: Intl. Archives of Photogrammetry, Remote Sensing and Spatial Information Sciences (ISPRS), Beijing, China, 3 - 11 July 2008. - Beijing : ISPRS - p. 45 - 50.
    Spectral analysis of coniferous foliage and possible links to soil chemistry: Are spectral chlorophyll indices related to forest floor dissolved organic C and N?
    Albrechtová, J. ; Seidl, Z. ; Aitkenhead Peterson, J. ; Lhotáková, Z. ; Rock, B.N. ; Alexander, J.E. ; Malenovsky, Z. ; McDowell, W.H. - \ 2008
    Science of the Total Environment 404 (2008)2-3. - ISSN 0048-9697 - p. 424 - 432.
    stream water - red spruce - nitrogen - matter - reflectance - carbon - polyphenols - ecosystems - dynamics - needles
    Dissolved organic matter in soils can be predicted from forest floor C:N ratio, which in turn is related to foliar chemistry. Little is known about the linkages between foliar constituents such as chlorophylls, lignin, and cellulose and the concentrations of water-extractable forest floor dissolved organic carbon and dissolved organic nitrogen. Lignin and cellulose are not mobile in foliage and thus may be indicative of growing conditions during prior years, while chlorophylls respond more rapidly to the current physiological status of a tree and reflect nutrient availability. The aim of this study was to examine potential links among spectral foliar data, and the organic C and N of forest soils. Two coniferous species (red spruce and balsam fir) were studied in the White Mountains of New Hampshire, USA. Six trees of each species were sampled at 5 watersheds (2 in the Hubbard Brook Experimental Forest, 3 in the Bartlett Experimental Forest). We hypothesized that in a coniferous forest, chemistry of old foliage would better predict the chemical composition of the forest floor litter layer than younger foliage, which is the more physiologically active and the most likely to be captured by remote sensing of the canopy. Contrary to our expectations, chlorophyll concentration of young needles proved to be most tightly linked to soil properties, in particular water-extractable dissolved organic carbon. Spectral indices related to the chlorophyll content of needles could be used to predict variation in forest floor dissolved organic carbon and dissolved organic nitrogen. Strong correlations were found between optical spectral indices based on chlorophyll absorption and forest floor dissolved organic carbon, with higher foliage chlorophyll content corresponding to lower forest floor dissolved organic carbon. The mechanisms behind these correlations are uncertain and need further investigation. However, the direction of the linkage from soil to tree via nutrient availability is hypothetized based on negative correlations found between foliar N and forest floor dissolved organic carbon.
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