Andrew Burt

Nondestructive estimates of above‐ground biomass using terrestrial laser scanning

Summary: Allometric equations are currently used to estimate above-ground biomass (AGB) based on the indirect relationship with tree parameters. Terrestrial laser scanning (TLS) can measure the canopy structure in 3D with high detail. In this study, we develop an approach to estimate AGB from TLS data, which does not need any prior information about allometry. We compare these estimates against destructively harvested AGB estimates and AGB derived from allometric equations. We also evaluate tree parameters, diameter at breast height (DBH) and tree height, estimated from traditional field inventory and TLS data. Tree height, DBH and AGB data are collected through traditional forest inventory, TLS and destructive sampling of 65 trees in a native Eucalypt Open Forest in Victoria, Australia. Single trees are extracted from the TLS data and quantitative structure models are used to estimate the tree volume directly from the point cloud data. AGB is inferred from these volumes and basic density information and is then compared with the estimates derived from allometric equations and destructive sampling. AGB estimates derived from TLS show a high agreement with the reference values from destructive sampling, with a concordance correlation coefficient (CCC) of 0·98. The agreement between AGB estimates from allometric equations and the reference is lower (CCC = 0·68-0·78). Our TLS approach shows a total AGB overestimation of 9·68% compared to an underestimation of 36·57-29·85% for the allometric equations. The error for AGB estimates using allometric equations increases exponentially with increasing DBH, whereas the error for AGB estimates from TLS is not dependent on DBH. The TLS method does not rely on indirect relationships with tree parameters or calibration data and shows better agreement with the reference data compared to estimates from allometric equations. Using 3D data also enables us to look at the height distributions of AGB, and we demonstrate that 80% of the AGB at plot level is located in the lower 60% of the trees for a Eucalypt Open Forest. This method can be applied in many forest types and can assist in the calibration and validation of broad-scale biomass maps.s

Rapid characterisation of forest structure from TLS and 3D modelling

Raumonen et al.[1] have developed a new method for reconstructing topologically consistent tree architecture from TLS point clouds. This method generates a cylinder model of tree structure using a stepwise approach. Disney et al.[2] validated this method with a detailed 3D tree model where structure is known a priori, establishing a reconstruction relative error of less than 2%. Here we apply the same method to data acquired from Eucalyptus racemosa woodland, Banksia ameula low open woodland and Eucalyptus spp. open forest using a RIEGL VZ-400 instrument. Individual 3D tree models reconstructed from TLS point clouds are used to drive Monte Carlo ray tracing simulations of TLS with the same characteristics as those collected in the field. 3D reconstruction was carried out on the simulated point clouds so that errors and uncertainty arising from instrument sampling and reconstruction could be assessed directly. We find that total volume could be recreated to within a 10.8% underestimate. The greatest constraint to this approach is the accuracy to which individual scans can be globally registered. Inducing a 1cm registration error lead to a 8.8% total volumetric overestimation across the data set.

African Savanna-Forest Boundary Dynamics: A 20-Year Study

Recent studies show widespread encroachment of forest into savannas with important consequences for the global carbon cycle and land-atmosphere interactions. However, little research has focused on in situ measurements of the successional sequence of savanna to forest in Africa. Using long-term inventory plots we quantify changes in vegetation structure, above-ground biomass (AGB) and biodiversity of trees ≥10 cm diameter over 20 years for five vegetation types: savanna; colonising forest (F1), monodominant Okoume forest (F2); young Marantaceae forest (F3); and mixed Marantaceae forest (F4) in Lopé National Park, central Gabon, plus novel 3D terrestrial laser scanning (TLS) measurements to assess forest structure differences. Over 20 years no plot changed to a new stage in the putative succession, but F1 forests strongly moved towards the structure, AGB and diversity of F2 forests. Overall, savanna plots showed no detectable change in structure, AGB or diversity using this method, with zero trees ≥10 cm diameter in 1993 and 2013. F1 and F2 forests increased in AGB, mainly as a result of adding recruited stems (F1) and increased Basal Area (F2), whereas F3 and F4 forests did not change substantially in structure, AGB or diversity. Critically, the stability of the F3 stage implies that this stage may be maintained for long periods. Soil carbon was low, and did not show a successional gradient as for AGB and diversity. TLS vertical plant profiles showed distinctive differences amongst the vegetation types, indicating that this technique can improve ecological understanding. We highlight two points: (i) as forest colonises, changes in biodiversity are much slower than changes in forest structure or AGB; and (ii) all forest types store substantial quantities of carbon. Multi-decadal monitoring is likely to be required to assess the speed of transition between vegetation types.

Estimation of above-ground biomass of large tropical trees with Terrestrial LiDAR

1. Tropical forest biomass is a crucial component of global carbon emission estimations. However, calibration and validation of such estimates require accurate and effective methods to estimate in situ above-ground biomass (AGB). Present methods rely on allometric models that are highly uncertain for large tropical trees. Terrestrial laser scanning (TLS) tree modelling has demonstrated to be more accurate than these models to infer forest AGB. Nevertheless, applying TLS methods on tropical large trees is still challenging. We propose a method to estimate AGB of large tropical trees by three-dimensional (3D) tree modelling of TLS point clouds. 2. Twenty-nine plots were scanned with a TLS in three study sites (Peru, Indonesia and Guyana). We identified the largest tree per plot (mean diameter at breast height of 73.5cm), extracted its point cloud and calculated its volume by 3D modelling its structure using quantitative structure models (QSM) and converted to AGB using species-specific wood density. We also estimated AGB using pantropical and local allometric models. To assess the accuracy of our and allometric methods, we harvest the trees and took destructive measurements. 3. AGB estimates by the TLS-QSM method showed the best agreement in comparison to destructive harvest measurements (28.37% coefficient of variation of root mean square error [CV-RMSE] and concordance correlation coefficient [CCC] of 0.95), outperforming the pantropical allometric models tested (35.6%-54.95% CV-RMSE and CCC of 0.89-0.73). TLS-QSM showed also the lowest bias (overall underestimation of 3.7%) and stability across tree size range, contrasting with the allometric models that showed a systematic bias (overall underestimation ranging 15.2%-35.7%) increasing linearly with tree size. The TLS-QSM method also provided accurate tree wood volume estimates (CV RMSE of 23.7%) with no systematic bias regardless the tree structural characteristics. 4. Our TLS-QSM method accounts for individual tree biophysical structure more effectively than allometric models, providing more accurate and less biased AGB estimates for large tropical trees, independently of their morphology. This non-destructive method can be further used for testing and calibrating new allometric models, reducing the current under-representation of large trees in and enhancing present and past estimates of forest biomass and carbon emissions from tropical forests.

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).

Weighing trees with lasers : advances, challenges and opportunities

Terrestrial laser scanning (TLS) is providing exciting new ways to quantify tree and forest structure, particularly above-ground biomass (AGB). We show how TLS can address some of the key uncertainties and limitations of current approaches to estimating AGB based on empirical allometric scaling equations (ASEs) that underpin all large-scale estimates of AGB. TLS provides extremely detailed non-destructive measurements of tree form independent of tree size and shape. We show examples of three-dimensional (3D) TLS measurements from various tropical and temperate forests and describe how the resulting TLS point clouds can be used to produce quantitative 3D models of branch and trunk size, shape and distribution. These models can drastically improve estimates of AGB, provide new, improved large-scale ASEs, and deliver insights into a range of fundamental tree properties related to structure. Large quantities of detailed measurements of individual 3D tree structure also have the potential to open new and exciting avenues of research in areas where difficulties of measurement have until now prevented statistical approaches to detecting and understanding underlying patterns of scaling, form and function. We discuss these opportunities and some of the challenges that remain to be overcome to enable wider adoption of TLS methods.

Large-area virtual forests from terrestrial laser scanning data

Combining virtual forests with radiative transfer is a powerful tool to calibrate and validate ground-based, airborne and spaceborne sensors. In this set-up, we can control and calculate all aspects of the forest structure and the simulated signal, which would not be possible using measured data only. Terrestrial laser scanning (TLS) enables us to measure forest structure directly with high detail. We present a processing chain that uses TLS data as input data to assess the end-to-end traceability of various in situ LAI and fAPAR products via radiative transfer modelling. Tree reconstruction from TLS data is used to represent the explicit 3D forest structure in radiative transfer models.

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.

High density genetic mapping of Fusarium head blight resistance QTL in tetraploid wheat

Breeding for Fusarium head blight (FHB) resistance in durum wheat is complicated by the quantitative trait expression and narrow genetic diversity of available resources. High-density mapping of the FHB resistance quantitative trait loci (QTL), evaluation of their co-localization with plant height and maturity QTL and the interaction among the identified QTL are the objectives of this study. Two doubled haploid (DH) populations, one developed from crosses between Triticum turgidum ssp. durum lines DT707 and DT696 and the other between T. turgidum ssp. durum cv. Strongfield and T. turgidum ssp. carthlicum cv. Blackbird were genotyped using the 90K Infinium iSelect chip and evaluated phenotypically at multiple field FHB nurseries over years. A moderate broad-sense heritability indicated a genotype-by-environment interaction for the expression of FHB resistance in both populations. Resistance QTL were identified for the DT707 × DT696 population on chromosomes 1B, 2B, 5A (two loci) and 7A and for the Strongfield × Blackbird population on chromosomes 1A, 2A, 2B, 3A, 6A, 6B and 7B with the QTL on chromosome 1A and those on chromosome 5A being more consistently expressed over environments. FHB resistance co-located with plant height and maturity QTL on chromosome 5A and with a maturity QTL on chromosome 7A for the DT707 × DT696 population. Resistance also co-located with plant height QTL on chromosomes 2A and 3A and with maturity QTL on chromosomes 1A and 7B for the Strongfield × Blackbird population. Additive × additive interactions were identified, for example between the two FHB resistance QTL on chromosome 5A for the DT707 × DT696 population and the FHB resistance QTL on chromosomes 1A and 7B for the Strongfield × Blackbird population. Application of the Single Nucleotide Polymorphic (SNP) markers associated with FHB resistance QTL identified in this study will accelerate combining genes from the two populations.

Tropical forest canopies and their relationships with climate and disturbance: results from a global dataset of consistent field-based measurements

BackgroundCanopy structure, defined by leaf area index (LAI), fractional vegetation cover (FCover) and fraction of absorbed photosynthetically active radiation (fAPAR), regulates a wide range of forest functions and ecosystem services. Spatially consistent field-measurements of canopy structure are however lacking, particularly for the tropics.MethodsHere, we introduce the Global LAI database: a global dataset of field-based canopy structure measurements spanning tropical forests in four continents (Africa, Asia, Australia and the Americas). We use these measurements to test for climate dependencies within and across continents, and to test for the potential of anthropogenic disturbance and forest protection to modulate those dependences.ResultsUsing data collected from 887 tropical forest plots, we show that maximum water deficit, defined across the most arid months of the year, is an important predictor of canopy structure, with all three canopy attributes declining significantly with increasing water deficit. Canopy attributes also increase with minimum temperature, and with the protection of forests according to both active (within protected areas) and passive measures (through topography). Once protection and continent effects are accounted for, other anthropogenic measures (e.g. human population) do not improve the model.ConclusionsWe conclude that canopy structure in the tropics is primarily a consequence of forest adaptation to the maximum water deficits historically experienced within a given region. Climate change, and in particular changes in drought regimes may thus affect forest structure and function, but forest protection may offer some resilience against this effect.