Hyperspectral indices and model simulation for chlorophyll estimation in open-canopy tree crops

An investigation of the estimation of leaf biochemistry in open tree crop canopies using high-spatial hyperspectral remote sensing imagery is presented. Hyperspectral optical indices related to leaf chlorophyll content were used to test different radiative transfer modelling assumptions in open canopies where crown, soil and shadow components were separately targeted using 1 m spatial resolution ROSIS hyperspectral imagery. Methods for scaling-up of hyperspectral single-ratio indices such as R₇₅₀/R₇₁₀ and combined indices such as MCARI, TCARI and OSAVI were studied to investigate the effects of scene components on indices calculated from pure crown pixels and from aggregated soil, shadow and crown reflectance. Methods were tested on 1-m resolution hyperspectral ROSIS datasets acquired over two olive groves in southern Spain during the HySens 2002 campaign conducted by the German Aerospace Center (DLR). Leaf-level biochemical estimation using 1-m ROSIS data when targeting pure olive tree crowns employed PROSPECT-SAILH radiative transfer simulation. At lower spatial resolution, therefore with significant effects of soil and shadow scene components on the aggregated pixels, a canopy model to account for such scene components had to be used for a more appropriate estimation approach for leaf biochemical concentration. The linked models PROSPECT-SAILH-FLIM improved the estimates of chlorophyll concentration from these open tree canopies, demonstrating that crown-derived relationships between hyperspectral indices and biochemical constituents cannot be readily applied to hyperspectral imagery of lower spatial resolutions due to large soil and shadow effects. Predictive equations built on a MCARI/OSAVI scaled-up index through radiative transfer simulation minimized soil background variations in these open canopies, demonstrating superior performance compared to other single-ratio indices previously shown as good indicators of chlorophyll concentration in closed canopies. The MCARI/OSAVI index was demonstrated to be less affected than TCARI/OSAVI by soil background variations when calculated from the pure crown component even at the typically low LAI orchard and grove canopies.     

Monitoring canopy biophysical and biochemical parameters in ecosystem scale using satellite hyperspectral imagery: An application on a Phlomis fruticosa Mediterranean ecosystem using multiangular CHRIS/PROBA observations

This study focuses on the potential of satellite hyperspectral imagery to monitor vegetation biophysical and biochemical characteristics through narrow-band indices and different viewing angles. Hyperspectral images of the CHRIS/PROBA sensor in imaging mode 1 (5 observation angles, 62 bands, 410-1005 nm) were acquired throughout a two-year period for a Mediterranean ecosystem fully covered by the semi-deciduous shrub Phlomis fruticosa. During each acquisition, coincident ecophysiological field measurements were conducted. Leaf area index (LAI), leaf biochemical content (chlorophyll a, chlorophyll b, carotenoids) and leaf water potential were measured. The hyperspectral images were corrected for coherent noises, cloud and atmosphere, in order to produce ground reflectance images. The reflectance spectrum of each image was used to calculate a variety of vegetation indices (VIs) that are already published in relevant literature. Additionally, all combinations of the 62 bands were used in order to calculate Normalized Difference Spectral Indices (NDSI_(x,y)) and Simple Subtraction Indices (SSI_(x,y)). The above indices along with raw reflectance and reflectance derivatives were examined for linear relationship with the ground-measured variables and the strongest relationships were determined. It is concluded that higher observation angles are better for the extraction of biochemical indices. The first derivative of the reflectance spectra proved to be very useful in the prediction of all measured variables. In many cases, complex and improved spectral indices that are proposed in the literature do not seem to be more accurate than simple NDSIs such as NDVI. Even traditional broadband NDVI is proved to be adequate in LAI prediction, while green bands seem also very useful. However, in biochemical estimation narrow bands are necessary. Indices that incorporate red, blue and IR bands, such as PSRI, SIPI and mNDVI presented good performance in chlorophyll estimation, while CRI did not show any relevance to carotenoids and WI was poorly correlated to water potential. Moreover, analyses indicated that it is very important to use a near red-edge band (701 nm) for effective chlorophyll index design. SSIs that incorporate 701 nm with 511 or 605 nm showed best performance in chlorophyll determination. For carotenoid estimation, a band on the edge of carotenoid absorption (511 nm) combined with a red band performed best, while a normalized index of two water absorption bands (945, 971 nm) proved to be an effective water index. Finally, the attempt to investigate stress conditions through pigment ratios resulted in the use of the band centred at 701 nm.     

Leaf area index estimation with MODIS reflectance time series and model inversion during full rotations of Eucalyptus plantations

The leaf area index (LAI) of fast-growing Eucalyptus plantations is highly dynamic both seasonally and inter-annually, and is spatially variable depending on pedo-climatic conditions. LAI is very important in determining the carbon and water balance of a stand, but is difficult to measure during a complete stand rotation and at large scales. Remote-sensing methods allowing the retrieval of LAI time series with accuracy and precision are therefore necessary. Here, we tested two methods for LAI estimation from MODIS 250m resolution red and near-infrared (NIR) reflectance time series. The first method involved the inversion of a coupled model of leaf reflectance and transmittance (PROSPECT4), soil reflectance (SOILSPECT) and canopy radiative transfer (4SAIL2). Model parameters other than the LAI were either fixed to measured constant values, or allowed to vary seasonally and/or with stand age according to trends observed in field measurements. The LAI was assumed to vary throughout the rotation following a series of alternately increasing and decreasing sigmoid curves. The parameters of each sigmoid curve that allowed the best fit of simulated canopy reflectance to MODIS red and NIR reflectance data were obtained by minimization techniques. The second method was based on a linear relationship between the LAI and values of the GEneralized Soil Adjusted Vegetation Index (GESAVI), which was calibrated using destructive LAI measurements made at two seasons, on Eucalyptus stands of different ages and productivity levels. The ability of each approach to reproduce field-measured LAI values was assessed, and uncertainty on results and parameter sensitivities were examined. Both methods offered a good fit between measured and estimated LAI (R² = 0.80 and R² = 0.62 for model inversion and GESAVI-based methods, respectively), but the GESAVI-based method overestimated the LAI at young ages.     

Remote detection of Trichodesmium blooms in optically complex coastal waters: Examples with MODIS full-spectral data

Remote detection of the Trichodesmium spp. cyanobacteria blooms on the west Florida shelf (WFS) has been problematic due to optical complexity caused by sediment resuspension, coastal runoff, and bottom interference. By combining MODIS data measured by the ocean bands and land bands, an approach was developed to identify surface mats of Trichodesmium on the WFS. The approach first identifies possible bloom patches in MODIS FAI (floating algae index) 250 m resolution imagery derived from the Rayleigh-corrected reflectance at 667, 859, and 1240 nm. Then, spectral analysis examines the unique reflectance characteristics of Trichodesmium at 469, 488, 531, 551, and 555 nm due to specific optical properties (absorption, backscattering, and fluorescence) of the unusual pigments in Trichodesmium. These spectral characteristics (i.e., high-low-high-low-high reflectance at 469-488-531-551-555 nm, respectively) differentiate Trichodesmium mats unambiguously from other features observed in the FAI imagery, such as Sargassum spp. Tests in other coastal locations show that the approach is robust and applicable to other optically complex waters. Results shown here can help study Trichodesmium bloom dynamics (e.g., initiation and bloom formation) and may also help design future sensors to better detect and quantify Trichodesmium, an important N₂ fixer in the global oceans.     

Enhancing a leaf radiative transfer model to estimate concentrations and in vivo specific absorption coefficients of total carotenoids and chlorophylls a and b from single-needle reflectance and transmittance

The relative concentrations of different pigments within a leaf have significant physiological and spectral consequences. Photosynthesis, light use efficiency, mass and energy exchange, and stress response are dependent on relationships among an ensemble of pigments. This ensemble also determines the visible characteristics of a leaf, which can be measured remotely and used to quantify leaf biochemistry and structure. But current remote sensing approaches are limited in their ability to resolve individual pigments. This paper focuses on the incorporation of three pigments—chlorophyll a, chlorophyll b, and total carotenoids—into the LIBERTY leaf radiative transfer model to better understand relationships between leaf biochemical, biophysical, and spectral properties.Pinus ponderosa and Pinus jeffreyi needles were collected from three sites in the California Sierra Nevada. Hemispheric single-leaf visible reflectance and transmittance and concentrations of chlorophylls a and b and total carotenoids of fresh needles were measured. These data were input to the enhanced LIBERTY model to estimate optical and biochemical properties of pine needles. The enhanced model successfully estimated reflectance (RMSE = 0.0255, BIAS = 0.00477, RMS%E = 16.7%), had variable success estimating transmittance (RMSE = 0.0442, BIAS = 0.0294, RMS%E = 181%), and generated very good estimates of carotenoid concentrations (RMSE = 2.48 µg/cm², BIAS = 0.143 µg/cm², RMS%E = 20.4%), good estimates of chlorophyll a concentrations (RMSE = 10.7 µg/cm², BIAS = − 0.992 µg/cm², RMS%E = 21.1%), and fair estimates of chlorophyll b concentrations (RMSE = 7.49 µg/cm², BIAS = − 2.12 µg/cm², RMS%E = 43.7%). Overall root mean squared errors of reflectance, transmittance, and pigment concentration estimates were lower for the three-pigment model than for the single-pigment model. The algorithm to estimate three in vivo specific absorption coefficients is robust, although estimated values are distorted by inconsistencies in model biophysics. The capacity to invert the model from single-leaf reflectance and transmittance was added to the model so it could be coupled with vegetation canopy models to estimate canopy biochemistry from remotely sensed data.     

Normalized difference spectral indices for estimating photosynthetic efficiency and capacity at a canopy scale derived from hyperspectral and CO2 flux measurements in rice

We explored simple and useful spectral indices for estimating photosynthetic variables (radiation use efficiency and photosynthetic capacity) at a canopy scale based on seasonal measurements of hyperspectral reflectance, ecosystem CO₂ flux, and plant and micrometeorological variables. An experimental study was conducted over the simple and homogenous ecosystem of an irrigated rice field. Photosynthetically active radiation absorbed by the canopy (APAR), the canopy absorptivity of APAR (fAPAR), net ecosystem exchange of CO₂ (NEE_CO2) gross primary productivity (GPP), photosynthetic capacity at the saturating APAR (P_max), and three parameters of radiation use efficiency (ε_N: NEE_CO2/APAR; ε_G: GPP/APAR; φ: quantum efficiency) were derived from the data set. Based on the statistical analysis of relationships between these ecophysiological variables and reflectance indicators such as normalized difference spectral indices (NDSI[i,j]) using all combinations of two wavelengths (i and j nm), we found several new indices that would were more effective than conventional spectral indices such as photochemical reflectance index (PRI) and normalized difference vegetation index (NDVI = NDSI[near-infrared, red]). ε_G was correlated well with NDSI[710, 410], NDSI[710, 520], and NDSI[530, 550] derived from nadir measurements. φ was best correlated with NDSI[450, 1330]. NDSI[550, 410] and NDSI[720, 420] had a consistent linear relationships with fAPAR throughout the growing season, whereas conventional indices such as NDVI showed very different relationships before and after heading. Off-nadir measurements were more closely related to the efficiency parameters than nadir measurements. Our results provide useful insights for assessing plant productivity and ecosystem CO₂ exchange, using a wide range of available spectral data as well as useful information for designing future sensors for ecosystem observations.     

Spectral sensing of foliar water conditions in two co-occurring conifer species: Pinus edulis and Juniperus monosperma

Many fundamental ecosystem properties and dynamics are determined by plant water stress, particularly in dryland ecosystems where water is usually limiting. Indeed, under severe drought, plant water stress and associated insect infestations can produce landscape-scale mortality. Despite the fundamental importance of plant water stress in determining properties and dynamics at ecosystem and landscape scales, approaches for remotely sensing plant water stress are largely lacking, particularly for conifers. We evaluated the remotely sensed detection of foliar drought stress in two conifer species, Pinus edulis and Juniperus monosperma, which are co-dominants of extensive-juniper woodlands in North America, the first of which experienced extensive mortality in association with a recent drought. Needle spectra were made on these species in the field using an integrating sphere and portable spectrometer. Two indices of foliar water condition, plant water content (% of dry mass) and plant water potential, were compared to five spectral analyses: continuum removal of the 970 and 1200 nm water absorption features, the Normalized Difference Water Index (NDWI), the Normalized Difference Vegetation Index (NDVI), and the red edge wavelength position. For P. edulis, plant water content was significantly correlated with four of the five indices: NDVI (R²=0.71) and NDWI (R²=0.68) which exhibited stronger relationships than 970 nm continuum removal (R²=0.57) or red edge position (R²=0.45). All five indices were significantly correlated with P. edulis water content when trees undergoing mortality were included in analyses (R²=0.60-0.93). Although the correlations were weaker than for plant water content, plant water potential was significantly correlated with NDWI (R²=0.49), 970 nm (R²=0.44), NDVI (R²=0.35), and red edge (R²=0.34); again all five indices had significant relationships when trees undergoing mortality were included (R²=0.51-0.86). The relationships were weaker for J. monosperma: water content was significantly related to 970 nm (R²=0.50) and 1200 nm (R²=0.37) continuums and NDVI (R²=0.33), while water potential was related only to 1200 nm (R²=0.40). Our results demonstrate a critical link between plant physiological characteristics tied to water stress and associated spectral signatures for two extensive co-occurring conifer species.     

Assessing the effect of hydrocarbon oil type and thickness on a remote sensing signal: A sensitivity study based on the optical properties of two different oil types and the HYMAP and Quickbird sensors

We measured the light absorption properties of two naturally occurring Australian hydrocarbon oils, a Gippsland light crude oil and a North West Shelf light condensate. Using the results from these measurements in conjunction with estimated sensor environmental noise thresholds, the theoretical minimum limit of detectability of each oil type (as a function of oil thickness) was calculated for both the hyperspectral HYMAP and multispectral Quickbird sensors. The Gippsland crude oil is discernable at layer thickness of 20 µm or more in the Quickbird green channel. The HYMAP sensor was found to be theoretically capable of detecting a layer of Gippsland crude oil with a thickness of 10 µm in approximately six sensor channels. By contrast, the North West Shelf light condensate was not able to be detected by either sensor for any thickness up to 200 µm. Optical remote sensing is therefore not applicable for detecting diagnostic absorption features associated with this light condensate oil type, which is typical of the chemistry of many hydrocarbon oils found in the Australian Northwest Shelf area and condensates world wide. We conclude that oil type is critical to the applicability of optical remote sensing for natural oil slick detection and identification. We recommend that a sensor- and oil-specific sensitivity study should be conducted prior to applying optical remote sensors for oil exploration.The oil optical properties were obtained using two different laboratory methods, a reflectance-based approach and transmittance-based approach. The reflectance-based approach was relatively complex to implement, but was chosen in order to replicate as closely as possible real world remote sensing measurement conditions of an oil film on water. The transmittance-based approach, based upon standard laboratory spectrophotometric measurements was found to generate results in good agreement with the reflectance-based approach. Therefore, for future oil- and sensor-specific sensitivity studies, we recommend the relatively accessible transmittance-based approach, which is detailed in this paper.     

On intra-annual EVI variability in the dry season of tropical forest: A case study with MODIS and hyperspectral data

Considerable controversy is associated with dry season increases in the Enhanced Vegetation Index (EVI), observed using the Moderate Resolution Imaging Spectroradiometer (MODIS), compared with field-based estimates of decreasing plant productivity. Here, we investigate potential causes of intra-annual variability by comparing EVI from mature forest with field-measured Leaf Area Index (LAI) to validate space-based observations. EVI was calculated from 19 nadir and off-nadir Hyperion images in the 2005 dry season, and inspected for consistency with MODIS observations from 2004 to 2009. The objective was to evaluate the possible influence of the view-illumination geometry and of canopy foliage and leaf flush on the EVI. Spectral mixture models were used to evaluate the relationship between EVI and the shade fraction, a measure that varies with pixel brightness. MODIS LAI values were compared with LAI estimated using hemispherical photographs taken in two field campaigns in the dry season. To keep LAI and leaf flush conditions as constant variables and vary solar illumination, we used airborne Hyperspectral Mapper (Hymap) data acquired over mature forest from another region on the same day but with two distinct solar zenith angles (SZA) (29° and 53°). Results showed that intra-annual variability in MODIS and nadir Hyperion EVI in the dry season of tropical forest were driven by solar illumination effects rather than changes in LAI. The reflectance of the MODIS and Hyperion blue, red and near infrared (NIR) bands was higher at the end of the dry season because of the predominance of sunlit canopy components for the sensors due to decreasing SZA from June (44°) to September (26°). Because EVI was highly correlated with the reflectance of the NIR band used to generate it (r of + 0.98 for MODIS and + 0.88 for Hyperion), this vegetation index followed the general NIR pattern, increasing with smaller SZA towards the end of the dry season. Hyperion EVI was inversely correlated with the shade fraction (r = − 0.93). Changes in canopy foliage detected from MODIS LAI data were not consistent with LAI estimates from hemispherical photographs. Although further research is necessary to measure the impact of leaf flush on intra-annual EVI variability in the Querência region, analysis of Hymap data with fixed LAI and leaf flush conditions confirmed the influence of the illumination effects on the EVI.     

Multi-scale linkages between topographic attributes and vegetation indices in a mountainous landscape

This paper addresses a few issues that are fundamental for the understanding of vegetation-topography relations: scale dependency, seasonal variability, and importance of observing individual properties. Particularly, it uses two statistical tools - Pearson's r and Moran's I - to define relationships of several topographic attributes with the Normalized Difference Vegetation Index (NDVI), the Normalized Difference Infrared Index (NDII), and their seasonal changes (from May to July and then September) in the Mediterranean-type landscape of the Santa Monica Mountains, California. The analyses are conducted at both the original data resolution and 20 aggregated resolutions, covering a total range of 30 m to 1500 m, so that topography-vegetation relationships can be compared at different scales. Large sample sizes have supported the significance of the following main findings for this landscape. First, elevation, slope, and southness are the most relevant primary topographic attributes among the tested attributes and their importance changes across seasons. Second, NDVI, NDII, and their seasonal variations have notably different relationships (including no relationship) with topography. Third, the observed topography-vegetation correlations (r) tend to change - typically increase - with the coarsening of spatial scale. Lastly, the spatial autocorrelation of vegetation variables and topographic attributes are often comparable, and the comparability is more apparent when topography-vegetation correlations are stronger. In all, the topography-NDVI/NDII relations defined in this paper may improve the understanding of the multi-scale and property-specific role that mountain topography plays in the formation and seasonal change of vegetation patterns.     

Red tide detection and tracing using MODIS fluorescence data: A regional example in SW Florida coastal waters

Near real-time data from the MODIS satellite sensor was used to detect and trace a harmful algal bloom (HAB), or red tide, in SW Florida coastal waters from October to December 2004. MODIS fluorescence line height (FLH in W m^− 2 μm^− 1 sr^− 1) data showed the highest correlation with near-concurrent in situ chlorophyll-a concentration (Chl in mg m^− 3). For Chl ranging between 0.4 to 4 mg m^− 3 the ratio between MODIS FLH and in situ Chl is about 0.1 W m^− 2 μm^− 1 sr^− 1 per mg m^− 3 chlorophyll (Chl = 1.255 (FLH × 10)^0.86, r = 0.92, n = 77). In contrast, the band-ratio chlorophyll product of either MODIS or SeaWiFS in this complex coastal environment provided false information. Errors in the satellite Chl data can be both negative and positive (3-15 times higher than in situ Chl) and these data are often inconsistent either spatially or temporally, due to interferences of other water constituents. The red tide that formed from November to December 2004 off SW Florida was revealed by MODIS FLH imagery, and was confirmed by field sampling to contain medium (10⁴ to 10⁵ cells L^− 1) to high (> 10⁵ cells L^− 1) concentrations of the toxic dinoflagellate Karenia brevis. The FLH imagery also showed that the bloom started in mid-October south of Charlotte Harbor, and that it developed and moved to the south and southwest in the subsequent weeks. Despite some artifacts in the data and uncertainty caused by factors such as unknown fluorescence efficiency, our results show that the MODIS FLH data provide an unprecedented tool for research and managers to study and monitor algal blooms in coastal environments.