Leaf and wood classification framework for terrestrial LiDAR point clouds

Leaf and wood separation is a key step to allow a new range of estimates from Terrestrial LiDAR data, such as quantifying above-ground biomass, leaf and wood area and their 3D spatial distributions. We present a new method to separate leaf and wood from single tree point clouds automatically. Our approach combines unsupervised classification of geometric features and shortest path analysis. The automated separation algorithm and its intermediate steps are presented and validated. Validation consisted of using a testing framework with synthetic point clouds, simulated using ray-tracing and 3D tree models and 10 field scanned tree point clouds. To evaluate results we calculated accuracy, kappa coefficient and F-score. Validation using simulated data resulted in an overall accuracy of 0.83, ranging from 0.71 to 0.94. Per tree average accuracy from synthetic data ranged from 0.77 to 0.89. Field data results presented and overall average accuracy of 0.89. Analysis of each step showed accuracy ranging from 0.75 to 0.98. F-scores from both simulated and field data were similar, with scores from leaf usually higher than for wood. Our separation method showed results similar to others in literature, albeit from a completely automated workflow. Analysis of each separation step suggests that the addition of path analysis improved the robustness of our algorithm. Accuracy can be improved with per tree parameter optimization. The library containing our separation script can be easily installed and applied to single tree point cloud. Average processing times are below 10min for each tree

Variability and bias in active and passive ground-based measurements of effective plant, wood and leaf area index

In situ leaf area index (LAI) measurements are essential to validate widely-used large-area or global LAI products derived, indirectly, from satellite observations. Here, we compare three common and emerging ground-based sensors for rapid LAI characterisation of large areas, namely digital hemispherical photography (DHP), two versions of a widely-used commercial LAI sensor (LiCOR LAI-2000 and 2200), and terrestrial laser scanning (TLS). The comparison is conducted during leaf-on and leaf-off conditions at an unprecedented sample size in a deciduous woodland canopy. The deviation between estimates of these three ground-based instruments yields differences greater than the 5% threshold goal set by the World Meteorological Organization. The variance at sample level is reduced when aggregated to plot scale (1 ha) or site scale (6 ha). TLS shows the lowest relative standard deviation in both leaf-on (11.78%) and leaf-off (13.02%) conditions. Whereas the relative standard deviation of effective plant area index (ePAI) derived from DHP relates closely to us in leaf-on conditions, it is as large as 28.14-29.74% for effective wood area index (eWAI) values in leaf-off conditions depending on the thresholding technique that was used. ePAI values of TLS and LAI-2x00 agree best in leaf-on conditions with a concordance correlation coefficient (CCC) of 0.796. In leaf-off conditions, eWAI values derived from DHP with Ridler and Calvard thresholding agrees best with TLS. Sample size analysis using Monte Carlo bootstrapping shows that TLS requires the fewest samples to achieve a precision better than 5% for the mean +/- standard deviation. We therefore support earlier studies that suggest that TLS measurements are preferential to measurements from instruments that are dependent on specific illumination conditions. A key issue with validation of indirect estimates of LAI is that the true values are not known. Since we cannot know the true values of LAI, we cannot quantify the accuracy of the measurements. Our radiative transfer simulations show that ePAI estimates are, on average, 27% higher than eLAI estimates. Linear regression indicated a linear relationship between eLAI and ePAI-eWAI (R-2 = 0.87), with an intercept of 0.552 and suggests that caution is required when using LAI estimates

Validating canopy clumping retrieval methods using hemispherical photography in a simulated Eucalypt forest

The so-called clumping factor (Ω) quantifies deviation from a random 3D distribution of material in a vegetation canopy and therefore characterises the spatial distribution of gaps within a canopy. Ω is essential to convert effective Plant or Leaf Area Index into actual LAI or PAI, which has previously been shown to have a significant impact on biophysical parameter retrieval using optical remote sensing techniques in forests, woodlands, and savannas. Here, a simulation framework was applied to assess the performance of existing in situ clumping retrieval methods in a 3D virtual forest canopy, which has a high degree of architectural realism. The virtual canopy was reconstructed using empirical data from a Box Ironbark Eucalypt forest in Eastern Australia. Hemispherical photography (HP) was assessed due to its ubiquity for indirect LAI and structure retrieval. Angular clumping retrieval method performance was evaluated using a range of structural configurations based on varying stem distribution and LAI. The CLX clumping retrieval method (Leblanc et al., 2005) with a segment size of 15° was the best performing clumping method, matching the reference values to within 0.05 Ω on average near zenith. Clumping error increased linearly with zenith angle to > 0.3 Ω (equivalent to a 30% PAI error) at 75° for all structural configurations. At larger zenith angles, PAI errors were found to be around 25–30% on average when derived from the 55–60° zenith angle. Therefore, careful consideration of zenith angle range utilised from HP is recommended. We suggest that plot or site clumping factors should be accompanied by the zenith angle used to derive them from gap size and gap size distribution methods. Furthermore, larger errors and biases were found for HPs captured within 1 m of unrepresentative large tree stems, so these situations should be avoided in practice if possible

The role of aerodynamic resistance in thermal remote sensing-based evapotranspiration models

Aerodynamic resistance (hereafter ra) is a preeminent variable in evapotranspiration (ET) modelling. The accurate quantification of ra plays a pivotal role in determining the performance and consistency of thermal remote sensing-based surface energy balance (SEB) models for estimating ET at local to regional scales. Atmospheric stability links ra with land surface temperature (LST) and the representation of their interactions in the SEB models determines the accuracy of ET estimates. The present study investigates the influence of ra and its relation to LST uncertainties on the performance of three structurally different SEB models. It used data from nine Australian OzFlux eddy covariance sites of contrasting aridity in conjunction with MODIS Terra and Aqua LST and leaf area index (LAI) products. Simulations of the sensible heat flux (H) and the latent heat flux (LE, the energy equivalent of ET in W/m2) from the SPARSE (Soil Plant Atmosphere and Remote Sensing Evapotranspiration), SEBS (Surface Energy Balance System) and STIC (Surface Temperature Initiated Closure) models forced with MODIS LST, LAI, and in-situ meteorological datasets were evaluated against flux observations in water-limited (arid and semi-arid) and energy-limited (mesic) ecosystems from 2011 to 2019. Our results revealed an overestimation tendency of instantaneous LE by all three models in the water-limited shrubland, woodland and grassland ecosystems by up to 50% on average, which was caused by an underestimation of H. Overestimation of LE was associated with discrepancies in ra retrievals under conditions of high atmospheric instability, during which uncertainties in LST (expressed as the difference between MODIS LST and in-situ LST) apparently played a minor role. On the other hand, a positive difference in LST coincided with low ra (high wind speeds) and caused a slight underestimation of LE at the water-limited sites. The impact of ra on the LE residual error was found to be of the same magnitude as the influence of LST uncertainties in the semi-arid ecosystems as indicated by variable importance in projection (VIP) coefficients from partial least squares regression above unity. In contrast, our results for the mesic forest ecosystems indicated minor dependency on ra for modelling LE (VIP \u3c 0.4), which was due to a higher roughness length and lower LST resulting in the dominance of mechanically generated turbulence, thereby diminishing the importance of buoyancy production for the determination of ra

Insights into the aerodynamic versus radiometric surface temperature debate in thermal-based evaporation modeling

Global evaporation monitoring from Earth observation thermal infrared satellite missions is historically challenged due to the unavailability of any direct measurements of aerodynamic temperature. State-of-the-art one-source evaporation models use remotely sensed radiometric surface temperature as a substitute for the aerodynamic temperature and apply empirical corrections to accommodate for their inequality. This introduces substantial uncertainty in operational drought mapping over complex landscapes. By employing a non-parametric model, we show that evaporation can be directly retrieved from thermal satellite data without the need of any empirical correction. Independent evaluation of evaporation in a broad spectrum of biome and aridity yielded statistically significant results when compared with eddy covariance observations. While our simplified model provides a new perspective to advance spatio-temporal evaporation mapping from any thermal remote sensing mission, the direct retrieval of aerodynamic temperature also generates the highly required insight on the critical role of biophysical interactions in global evaporation research

Insights Into the Aerodynamic Versus Radiometric Surface Temperature Debate in Thermal-Based Evaporation Modeling

Global evaporation monitoring from Earth observation thermal infrared satellite missions is historically challenged due to the unavailability of any direct measurements of aerodynamic temperature. State-of-the-art one-source evaporation models use remotely sensed radiometric surface temperature as a substitute for the aerodynamic temperature and apply empirical corrections to accommodate for their inequality. This introduces substantial uncertainty in operational drought mapping over complex landscapes. By employing a non-parametric model, we show that evaporation can be directly retrieved from thermal satellite data without the need of any empirical correction. Independent evaluation of evaporation in a broad spectrum of biome and aridity yielded statistically significant results when compared with eddy covariance observations. While our simplified model provides a new perspective to advance spatio-temporal evaporation mapping from any thermal remote sensing mission, the direct retrieval of aerodynamic temperature also generates the highly required insight on the critical role of biophysical interactions in global evaporation research

Exploring the potential of DSCOVR EPIC data to retrieve clumping index in Australian terrestrial ecosystem research network observing sites

Vegetation foliage clumping significantly alters the radiation environment and affects vegetation growth as well as water, carbon cycles. The clumping index (CI) is useful in ecological and meteorological models because it provides new structural information in addition to the effective leaf area index. Previously generated CI maps using a diverse set of Earth Observation multi-angle datasets across a wide range of scales have all relied on the single approach of using the normalized difference hotspot and darkspot (NDHD) method. We explore an alternative approach to estimate CI from space using the unique observing configuration of the Deep Space Climate Observatory Earth Polychromatic Imaging Camera (DSCOVR EPIC) and associated products at 10 km resolution. The performance was evaluated with in situ measurements in five sites of the Australian Terrestrial Ecosystem Research Network comprising a diverse range of canopy structure from short and sparse to dense and tall forest. The DSCOVR EPIC data can provide meaningful CI retrievals at the given spatial resolution. Independent but comparable CI retrievals obtained with a completely different sensor and new approach were encouraging for the general validity and compatibility of the foliage clumping information retrievals from space. We also assessed the spatial representativeness of the five TERN sites with respect to a particular point in time (field campaigns) for satellite retrieval validation. Our results improve our understanding of product uncertainty both in terms of the representativeness of the field data collected over the TERN sites and its relationship to Earth Observation data at different spatial resolutions.Published versio

Environment-sensitivity functions for gross primary productivity in light use efficiency models

The sensitivity of photosynthesis to environmental changes is essential for understanding carbon cycle responses to global climate change and for the development of modeling approaches that explains its spatial and temporal variability. We collected a large variety of published sensitivity functions of gross primary productivity (GPP) to different forcing variables to assess the response of GPP to environmental factors. These include the responses of GPP to temperature; vapor pressure deficit, some of which include the response to atmospheric CO2 concentrations; soil water availability (W); light intensity; and cloudiness. These functions were combined in a full factorial light use efficiency (LUE) model structure, leading to a collection of 5600 distinct LUE models. Each model was optimized against daily GPP and evapotranspiration fluxes from 196 FLUXNET sites and ranked across sites based on a bootstrap approach. The GPP sensitivity to each environmental factor, including CO2 fertilization, was shown to be significant, and that none of the previously published model structures performed as well as the best model selected. From daily and weekly to monthly scales, the best model's median Nash-Sutcliffe model efficiency across sites was 0.73, 0.79 and 0.82, respectively, but poorer at annual scales (0.23), emphasizing the common limitation of current models in describing the interannual variability of GPP. Although the best global model did not match the local best model at each site, the selection was robust across ecosystem types. The contribution of light saturation and cloudiness to GPP was observed across all biomes (from 23% to 43%). Temperature and W dominates GPP and LUE but responses of GPP to temperature and W are lagged in cold and arid ecosystems, respectively. The findings of this study provide a foundation towards more robust LUE-based estimates of global GPP and may provide a benchmark for other empirical GPP products.publishersversionpublishe

Monitoring the regional impact of forest loss and gain on carbon uptake with solar-induced fluorescence measurements from the GOME-2A and TROPOMI sensors

Reliable and robust monitoring tools are crucial to assess the effectiveness of land mitigation techniques (LMTs) in enhancing carbon uptake, enabling informed decision-making by policymakers. This study, addressing one of the scientific goals of the EU H2020 LANDMARC project, examines the feasibility of using satellite solar-induced fluorescence (SIF), in combination with other satellite data, as a monitoring proxy to evaluate the effects of LMTs on carbon uptake. Two distinct cases are explored: (1) instantaneous vegetation destruction caused by a 2019 Eucalyptus wildfire in south-east Australia, and, (2) gradual forest gain resulting from reforestation efforts in northern China over 2007–2012. The cases are monitored using TROPOMI and GOME-2A SIF, respectively. Comparing the temporal variability in SIF across the affected and nearby reference areas reveals that vegetation dynamics changed as a consequence of the land use changes in both cases. Specifically, in the Australia case, TROPOMI demonstrated an immediate reduction in SIF signal of 0.6 mW m−2 sr−1 nm−1 (−72 %) over the Eucalypt Forest right after the fire. Exploiting the strong correspondence between TROPOMI SIF and gross primary productivity (GPP) at the nearby eddy-covariance Tumbarumba site and through the FluxSat product, we estimate that the fire led to a loss in GPP of 130–200 GgC in the first eight months after the fire. Over the northern Chinese provinces of Gansu, Shaanxi, Sichuan, Chongqing and Shanxi, we report an increase in GOME-2A summertime SIF of 0.1–0.2 mW m−2 sr−1 nm−1 coinciding with reforestation efforts between 2007 and 2012. This increase in SIF signal is likely driven by a combination of increasingly favourable natural conditions and the reforestation effort itself. A multivariate model that takes into account growth factors such as water availability and maximum temperature as well as satellite-derived forest cover data explains the observed variability in GOME-2A SIF in the Chinese case reasonably well (R2=0.72). The model suggests that both increases in forest cover as well as in soil moisture have led, in step, to the observed increase in vegetation activity over northern China. In that region, for every 100 km2 of additional forest cover, SIF increases by 0.1 mW m−2 sr−1 nm−1 between 2007 and 2012. Our study highlights that the combined use of satellite-based SIF, together with supporting in situ, modelled and satellite-data, allows to monitor the impact of LMT implementation on regional carbon uptake as long as the scale of the LMT is of sufficient spatial extent