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

Atlantic water circulation over the Mendeleev Ridge and Chikchi Borderland from thermohaline intrusions and water mass properties

Hydrographic and tracer data from 2002 illustrate Atlantic water pathways and variability in the Mendeleev Ridge and Chukchi Borderland (CBLMR) region of the Arctic Ocean. Thermohaline double diffusive intrusions (zigzags) dominate both the Fram Strait (FSBW) and Barents Sea Branch Waters (BSBW) in the region. We show that details of the zigzags’ temperature-salinity structure partially describe the water masses forming the intrusions. Furthermore, as confirmed by chemical tracers, the zigzags’ peaks contain the least altered water, allowing assessment of the temporal history of the Atlantic waters. Whilst the FSBW shows the 1990s warming and then a slight cooling, the BSBW has continuously cooled and freshened over a similar time period. The newest boundary current waters are found west of the Mendeleev Ridge in 2002. Additionally, we show the zigzag structures can fingerprint various water masses, including the boundary current. Using this, tracer data and the advection of the 1990s warming, we conclude the strongly topographically steered boundary current, order 50 km wide and found between the 1500 m and 2500 m isobaths, crosses the Mendeleev Ridge north of 80°N, loops south around the Chukchi Abyssal Plain and north around the Chukchi Rise, with the 1990s warming having reached the northern (but not the southern) Northwind Ridge by 2002. Pacific waters influence the Atlantic layers near the shelf and over the Chukchi Rise. The Northwind Abyssal Plain is comparatively stagnant, being ventilated only slowly from the north. There is no evidence of significant boundary current flow through the Chukchi Gap.Keywords: Arctic circulation, Arctic Ocean Boundary Current, double diffusive intrusions, Arctic change, Atlantic water circulationKeywords: Arctic circulation, Arctic Ocean Boundary Current, double diffusive intrusions, Arctic change, Atlantic water circulatio

Pacific ventilation of the Artic Ocean's lower halocline by upwelling and diapycnal mixing over the continental margin

Pacific winter waters, a major source of nutrients and buoyancy to the Arctic Ocean, are thought to ventilate the Arctic's lower halocline either by injection (isopycnal or penetrative) of cold saline shelf waters, or by cooling and freshening Atlantic waters upwelled onto the shelf. Although ventilation at salinity (S) > 34 psu has previously been attributed to hypersaline polynya waters, temperature, salinity, nutrient and tracer data suggest instead that much of the western Arctic's lower halocline is in fact influenced by a diapycnal mixing of Pacific winter waters (with S ~ 33.1 psu) and denser eastern Arctic halocline (Atlantic) waters, the mixing taking place possibly over the northern Chukchi shelf/slope. Estimates from observational data confirm that sufficient quantities of Atlantic water may be upwelled to mix with the inflowing Pacific waters, with volumes implying the halocline over the Chukchi Borderland region may be renewed on timescales of order a year.Keywords: Pacific ventilation, Arctic Ocean, diapycnal mixingKeywords: Pacific ventilation, Arctic Ocean, diapycnal mixin

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