Measuring and modelling fAPAR for satellite product validation

This thesis presents a comprehensive approach to satellite Fraction of Absorbed Photosynthetically Active Radiation (fAPAR) product validation. This draws on 3D radiative transfer modelling and metrology to characterise the biases associated with a satellite fAPAR algorithm and the uncertainty associated with fAPAR estimates. This extends existing approaches which tend to assume that the in situ measurement technique produces the same fAPAR quantity as the satellite product. The validation procedure involves creating a closure experiment where every aspect of the satellite product definition and its associated assumptions can be tested from the perspective of the in situ and satellite sensors. The intrinsic differences created by the satellite product assumptions are also assessed, where a new reference is created. This is known as the “true” fAPAR since it is perfectly knowable within the context of the radiative transfer model used. Correction factors between the in situ and satellite-derived fAPAR are created to correct data collected over Wytham Woods. The results indicate that the corrections reduce differences of >10% to near zero. However, the uncertainty estimates for the satellite-derived fAPAR show that it does not meet the requirements given by Global Climate Observing System (GCOS) (≤(10% or 0.05)). The wider implications of the retrieved uncertainties are also presented showing that it is unlikely that the GCOS requirements associated with downstream applications that use satellite fAPAR can be met currently. This work represents an important step forward in the validation of satellitederived fAPAR because it is the first time that the absence of satellite and in situ data uncertainty and traceability, and satellite product definition differences have been addressed. This paves the way for the improvement of satellite fAPAR products because their uncertainties can now be quantified effectively and their validation conducted fairly, meaning there is now a benchmark to base improvements on

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

Realistic forest stand reconstruction from terrestrial LiDAR for radiative transfer modelling

Forest biophysical variables derived from remote sensing observations are vital for climate research. The combination of structurally and radiometrically accurate 3D virtual forests with radiative transfer (RT) models creates a powerful tool to facilitate the calibration and validation of remote sensing data and derived biophysical products by helping us understand the assumptions made in data processing algorithms. We present a workflow that uses highly detailed 3D terrestrial laser scanning (TLS) data to generate virtual forests for RT model simulations. Our approach to forest stand reconstruction from a co-registered point cloud is unique as it models each tree individually. Our approach follows three steps: (1) tree segmentation; (2) tree structure modelling and (3) leaf addition. To demonstrate this approach, we present the measurement and construction of a one hectare model of the deciduous forest in Wytham Woods (Oxford, UK). The model contains 559 individual trees. We matched the TLS data with traditional census data to determine the species of each individual tree and allocate species-specific radiometric properties. Our modelling framework is generic, highly transferable and adjustable to data collected with other TLS instruments and different ecosystems. The Wytham Woods virtual forest is made publicly available through an online repository

A new architectural perspective on wind damage in a natural forest

Wind damage is a significant driver of forest structure, ecology and carbon cycling in both temperate and tropical regions, but most of the literature on wind damage focusses on conifer plantations. Previous studies in broadleaf forests have been limited by a lack of data on tree architecture, a problem that is potentially overcome by terrestrial laser scanning (TLS). Here we apply novel approaches to estimate the critical wind speeds at which trees will break in a temperate, deciduous forest plot in Wytham Woods, UK, using a combination of field data and finite element analysis. Ash trees (Fraxinus excelsior) tend to have lower critical wind speeds than sycamores (Acer pseudoplatanus), while English oak (Quercus robur) are the most mechanically robust. This difference in critical wind speed (CWS) is driven by tree size and architecture, rather than material properties. We observe a trade-off between CWS and growth rate, both within and across species. Our estimates of critical wind speeds from field data are lower in summer than in winter, emphasizing the importance of the spring and autumn transition periods. Of the three species we studied, those with lower critical wind speeds drop their leaves earlier in autumn, suggesting that the timing of leaf shedding may be under selection pressure to minimize risk of tree damage from winter storms. These results are tentative, but also intriguing and intuitive

Using terrestrial laser scanning to constrain forest ecosystem structure and functions in the Ecosystem Demography model (ED2.2)

Terrestrial biosphere models (TBMs) are invaluable tools for studying plant-atmosphere interactions at multiple spatial and temporal scales, as well as how global change impacts ecosystems. Yet, TBM projections suffer from large uncertainties that limit their usefulness. Forest structure drives a significant part of TBM uncertainty as it regulates key processes such as the transfer of carbon, energy, and water between the land and the atmosphere, but it remains challenging to observe and reliably represent. The poor representation of forest structure in TBMs might actually result in simulations that reproduce observed land fluxes but fail to capture carbon pools, forest composition, and demography. Recent advances in terrestrial laser scanning (TLS) offer new opportunities to capture the three-dimensional structure of the ecosystem and to transfer this information to TBMs in order to increase their accuracy. In this study, we quantified the impacts of prescribing initial conditions (tree size distribution), constraining key model parameters with observations, as well as imposing structural observations of individual trees (namely tree height, leaf area, woody biomass, and crown area) derived from TLS on the state-of-the-art Ecosystem Demography model (ED2.2) of a temperate forest site (Wytham Woods, UK). We assessed the relative contributions of initial conditions, model structure, and parameters to the overall output uncertainty by running ensemble simulations with multiple model configurations. We show that forest demography and ecosystem functions as modelled by ED2.2 are sensitive to the imposed initial state, the model parameters, and the choice of key model processes. In particular, we show that: Parameter uncertainty drove the overall model uncertainty, with a mean contribution of 63 % to the overall variance of simulated gross primary production. Model uncertainty in the gross primary production was reduced fourfold when both TLS and trait data were integrated into the model configuration. Land fluxes and ecosystem composition could be simultaneously and accurately simulated with physically realistic parameters when appropriate constraints were applied to critical parameters and processes. We conclude that integrating TLS data can inform TBMs of the most adequate model structure, constrain critical parameters, and prescribe representative initial conditions. Our study also confirms the need for simultaneous observations of plant traits, structure, and state variables if we seek to improve the robustness of TBMs and reduce their overall uncertainties.Peer reviewe

TLS2trees: A scalable tree segmentation pipeline for TLS data

1. Above-ground biomass (AGB) is an important metric used to quantify the mass of carbon stored in terrestrial ecosystems. For forests, this is routinely estimated at the plot scale (typically 1 ha) using inventory measurements and allometry. In recent years, terrestrial laser scanning (TLS) has appeared as a disruptive technology that can generate a more accurate assessment of tree and plot scale AGB; however, operationalising TLS methods has had to overcome a number of challenges. One such challenge is the segmentation of individual trees from plot level point clouds that are required to estimate woody volume, this is often done manually (e.g. with interactive point cloud editing software) and can be very time consuming. / 2. Here we present TLS2trees, an automated processing pipeline and set of Python command line tools that aims to redress this processing bottleneck. TLS2trees consists of existing and new methods and is specifically designed to be horizontally scalable. The processing pipeline is demonstrated on 7.5 ha of TLS data captured across 10 plots of seven forest types; from open savanna to dense tropical rainforest. / 3. A total of 10,557 trees are segmented with TLS2trees: these are compared to 1281 manually segmented trees. Results indicate that TLS2trees performs well, particularly for larger trees (i.e. the cohort of largest trees that comprise 50% of total plot volume), where plot-wise tree volume bias is ±0.4 m3 and %RMSE is 60%. Segmentation performance decreases for smaller trees, for example where DBH ≤10 cm; a number of reasons are suggested including performance of semantic segmentation step. / 4. The volume and scale of TLS data captured in forest plots is increasing. It is suggested that to fully utilise this data for activities such as monitoring, reporting and verification or as reference data for satellite missions an automated processing pipeline, such as TLS2trees, is required. To facilitate improvements to TLS2trees, as well as modification for other laser scanning modes (e.g. mobile and UAV laser scanning), TLS2trees is a free and open-source software

Influence of levelling technique on the retrieval of canopy structural parameters from digital hemispherical photography

Digital hemispherical photography is a simple, non-destructive method for estimating canopy biophysical parameters for ecological applications and validation of remote sensing products. Determination of optimum and repeatable acquisition procedures is well documented in the literature but so far this has not focused on evaluating the levelling procedure used to align the camera. In this paper, the standard recommendation that tripod levelling is a necessity is tested by comparing it with a hand-levelled procedure. The results show that the average difference between the two procedures is < 2% for effective plant area index and < 1% for gap fraction at the VALERI plot scale, which generally falls within the variance. Users implementing the hand-levelled technique can expect large reductions in data acquisition time, allowing many more samples to be collected without compromising the overall quality of the data retrieved

Development of robust quality assurance procedures for terrestrial essential climate variable data products derived from Earth Observation satellites

Data from Earth Observation (EO) satellites are increasingly used to monitor the environment, understand variability and change, inform evaluations of climate model simulations and forecasts and manage natural resources. Policy makers are progressively relying on information derived from EO data to make decisions on mitigating and adapting to climate change. These decisions should be evidence based, which requires complete confidence in satellite-derived products as well as the in situ measurements used to calibrate, validate or complement these data. This paper provides an overview of the components required to develop robust quality assurance procedures for terrestrial essential climate variable (ECV) data products derived from Earth Observation (EO) satellite datasets

An intensity, image-based method to estimate gap fraction, canopy openness and effective leaf area index from phase-shift terrestrial laser scanning

Accurate in situ estimates of leaf area index (LAI) are essential for a wide range of ecological studies and applications. Due to the destructiveness and impracticality of direct measurements, indirect optical methods have mostly been used in the field to derive estimates of LAI from gap fraction measurements. Terrestrial laser scanning (TLS) is strongly supporting use of this active technology, which possesses several advantages compared to passive sensors. However, edge effects and partial beam interceptions are significantly challenges for the accurate retrieval of gap fraction from 3D point cloud data available from TLS, particularly in phase-shift instruments, which in turns require point cloud filtering to correct erroneous point measurements. As the limitations above influences the point cloud, we proposed a new method which is based only on the laser return intensity (LRI) information derived from raw TLS data, which are used to generate 2D intensity images. The intensity image contains all the unfiltered LRI information captured by TLS, which is used to separate gap from non-gap pixels, using a procedure comparable to the standard image analysis processing of digital hemispherical images. This allows a theoretically consistent comparison between active and passive optical measurements of gap fraction across all the zenith angle range. The method was tested in real and simulated forests. Gap fraction, canopy openness and effective leaf area index derived from real and simulated intensity TLS images were compared with those obtained using digital hemispherical photography (DHP). Results indicated that the intensity, image-based method outperformed DHP, as the higher pixel resolution of the intensity images and the larger distance covered by TLS allowed detection of many small canopy elements, particularly at higher zenith angles (longer optical distance), which are not detected in DHP. The main findings support the reliability of the intensity, image-based method to standardize protocols for TLS phase-shift scan data processing and use of the produced canopy estimates as a benchmark for passive optical measurements

Evaluation of the Range Accuracy and the Radiometric Calibration of Multiple Terrestrial Laser Scanning Instruments for Data Interoperability

Terrestrial laser scanning (TLS) data provide 3-D measurements of vegetation structure and have the potential to support the calibration and validation of satellite and airborne sensors. The increasing range of different commercial and scientific TLS instruments holds challenges for data and instrument interoperability. Using data from various TLS sources will be critical to upscale study areas or compare data. In this paper, we provide a general framework to compare the interoperability of TLS instruments. We compare three TLS instruments that are the same make and model, the RIEGL VZ-400. We compare the range accuracy and evaluate the manufacturer's radiometric calibration for the uncalibrated return intensities. Our results show that the range accuracy between instruments is comparable and within the manufacturer's specifications. This means that the spatial XYZ data of different instruments can be combined into a single data set. Our findings demonstrate that radiometric calibration is instrument specific and needs to be carried out for each instrument individually before including reflectance information in TLS analysis. We show that the residuals between the calibrated reflectance panels and the apparent reflectance measured by the instrument are greatest for highest reflectance panels (residuals ranging from 0.058 to 0.312)