Staff Publications

Staff Publications

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    'Staff publications' is the digital repository of Wageningen University & Research

    'Staff publications' contains references to publications authored by Wageningen University staff from 1976 onward.

    Publications authored by the staff of the Research Institutes are available from 1995 onwards.

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    Data supporting the research of: Estimating architecture-based metabolic scaling exponents of tropical trees using terrestrial LiDAR and 3D modelling
    Lau Sarmiento, A.I. ; Jackson, T. ; Raumonen, P. - \ 2019
    Wageningen University & Research
    architecture-based metabolic rate - destructive harvesting - quantitative structure models - terrestrial LiDAR - WBE plant scaling exponent
    Tree architecture influences physical and ecological processes within the tree. Prior work suggested the existence of general principles which govern these processes. Among these, the West, Brown and Enquist (WBE) theory is prominent; it holds that biological function has its origin in a tree's idealized branching system network; from which scaling exponents can be estimated. The scaling exponents of the WBE theory (branch radius scaling ratio, “a” and branch length scaling ratio “b”) can be derived from branch parameters and from these, metabolic scaling rate “ö” can be derived. Until now, branch parameter values are taken from direct measurements; either from standing trees or from harvested trees. Such measurements are time consuming, labour intensive and susceptible to subjective errors. Terrestrial LiDAR (TLS) is a promising alternative, being both less biased to error, scalable, and being able to collect large quantities of data without the need of destructive sampling the trees. In this thesis we estimated scaling exponents and derived metabolic rate from TLS and quantitative structure models (TreeQSM) models from nine trees in a tropical forest in Guyana. To validate these TLS-derived scaling exponents, we compared them with scaling exponents and derived metabolic rate from field measurements at three levels: branch-level, tree-level and plot-level. For that, we destructive sampled the scanned trees and measured all branches > 10 cm. Our results show that, with some limitations, radius, length scaling exponents and architecture-based metabolic rate can be derived from 3D data of tree point clouds. However, we found that only “ö” converged between our TreeQSM modelled and manually measured dataset at both, branch-level (0.59 and 0.50 for TreeQSM and manually measured exponent, respectively) and at tree-level (0.56 and 0.51). Our results did not support the same conclusion for “a” nor “b”- neither at branch-level nor at tree-level. The “a” diverged between TreeQSM and manually measured dataset at branch-level (0:45 and 0.63) and at the tree-level (0.46 and 0.64). The “b” was the exponent which most deviated between TreeQSM and manually measured dataset at branch-level (0.42 and 0.07) and at tree-level (0.41 and 0.05). At tree-level, we found that all estimated averaged exponents deviated significantly from metabolic scaling theory predictions (“a”=1/2 ; “b” =1/3 ; “ö”=3/4 ). Our study provides an alternative method to estimate scaling exponents variation at branch-level and tree-level in tropical forest trees without the need for destructive sampling. Although this approach is based on a limited sample of nine trees in Guyana, can be implemented for large-scale plant scaling assessments. This new data might improve our current understanding of metabolic scaling without harvesting trees.
    Geometric Tree Modelling with UAV-based Lidar
    Brede, B. ; Raumonen, Pasi ; Calders, Kim ; Lau Sarmiento, A.I. ; Bartholomeus, H.M. ; Herold, M. ; Kooistra, L. - \ 2018
    Assessing biomass and architecture of tropical trees with terrestrial laser scanning
    Lau Sarmiento, Alvaro Ivan - \ 2018
    Wageningen University. Promotor(en): M. Herold, co-promotor(en): H. Bartholomeus; K. Calders. - Wageningen : Wageningen University - ISBN 9789463434720 - 157

    Over the last two decades, terrestrial light detection and ranging (LiDAR), also known as terrestrial laser scanning (TLS) has become a valuable tool in assessing the woody structure of trees, in a method that is accurate, non-destructive, and replicable. This technique provides the ability to scan an area, and utilizes specialized software to create highly detailed 3D point cloud representations of its surroundings. Although the original usage of LiDAR was for precision survey applications, researchers have begun to apply LiDAR to forest research. Tree metrics can be extracted from TLS tree point clouds, and in combination with structure modelling, can be used to extract tree volume, aboveground biomass (AGB), growth, species, and to understand ecological questions such as tree mechanics, branching architecture, and surface area. TLS can provide a robust and rapid assessment of tree characteristics. These characteristics will improve current global efforts to measure forest carbon emissions, understand their uncertainties, and provide new insight into tropical forest ecology. Thus, the main objective of this PhD is to explore the use of 3D models from terrestrial laser scanning point clouds to estimate biomass and architecture of tropical trees. TLS-derived biomass and TLS-derived architecture can potentially be used to generate significant quality data for a better understanding of ecological challenges in tropical forests.

    In this thesis, a dataset of forest inventory with TLS point clouds and destructive tree harvesting were created from three tropical regions: Indonesia, Guyana, and Peru. A total of 1858 trees were traditionally inventoried, 135 trees were TLS scanned, and 55 trees were destructively harvested. In this thesis, procedures to estimate tree metrics such as tree height (H), diameter at breast height (D), crown diameter (CD), and the length and diameter of individual branches were developed using 3D point clouds and 3D modelling. From these tree metrics, I infer AGB, develop allometric models, and estimate metabolic plant scaling of individual tropical trees. All these metrics are validated against a traditional forest inventory data and destructively harvested trees.

    Chapter 2 presents a procedure to estimate tree volume and quantify AGB for large tropical trees based on estimates of tree volume and basic wood density. The accurate estimation of AGB of large tropical trees (diameter > 70 cm) is particularly relevant due to their major influence on tropical forest AGB variation. Nevertheless, current allometric models have large uncertainties for large tree AGB, partly due to the relative lack of large trees in the empirical datasets used to create them. The key result of this chapter is that TLS and 3D modelling are able to provide individual large tree volume and AGB estimates that are less likely to be biased by tree size or structural irregularities, and are more accurate than allometric models.

    Chapter 3 focuses on the development of accurate local allometric models to estimate tree AGB in Guyana based solely on TLS-based tree metrics (H, CD, and D) and validated against destructive measurements. Current tropical forest AGB estimates typically rely on pantropical allometric models that are developed with relatively few large trees. This leads to large uncertainties with increasing tree size and often results in an underestimation of AGB for large trees. I showed in Chapter 2 that AGB of individual large trees can be estimated regardless of their size and architecture. This chapter evaluates the performance of my local allometric models against existing pantropical models and evidenced that inclusion of TLS-based metrics to build allometric models provides as good as, or even better, AGB estimates than current pantropical models.

    Chapter 4 provides an insight into the architecture and branching structure of tropical trees. In Chapter 2, I demonstrated the potential of TLS to characterize woody tree structure as a function of tree volume, but little is known regarding their detailed architecture. Previous studies have quantitatively described tree architectural traits, but they are limited to the intensity of quantifying tree structure in-situ with enough detail. Here, I analysed the length and diameter of individual branches, and compared them to reference measurements. I demonstrated that basic tree architecture parameters could be reconstructed from large branches (> 40 cm diameter) with sufficient accuracy. I also discuss the limitations found when modelling small branches and how future studies could use my results as a basis for understanding tree architecture.

    Chapter 5 describes an alternative approach to estimating metabolic scaling exponents using the branching architecture derived from TLS point clouds. This approach does not rely on destructive sampling and can help to increase data collection. A theory on metabolic scaling, the West, Brown & Enquist (WBE) theory, suggests that metabolic rate and other biological functions have their origins in an optimal branching system network (among other assumptions). This chapter demonstrates that architecture-based metabolic scaling can be estimated for big branches of tropical trees with some limitations and provides an alternative method that can be implemented for large-scale assessments and provides better understanding of metabolic scaling.

    The results from this thesis provide a scientific contribution to the current development of new methods using terrestrial LiDAR and 3D modelling in tropical forests. The results can potentially be used to generate significant quality data for a better understanding of ecological challenges in tropical forests. I encourage further testing of my work using more samples including other types of forests to reduce inherent uncertainties.

    Monitoreo climático: herramienta al servicio de la caficultura Colombiana
    Sarmiento, Ninibeth ; Ramírez, Carolina ; Jaramillo, Álvaro ; Restrepo, Alexander ; García López, Juan Carlos ; Wolters, W. ; Miguel Ayala, L. - \ 2018
    Bogota : APC Columbia - ISBN 9789588490298 - 110
    Tropical forest canopies and their relationships with climate and disturbance: results from a global dataset of consistent field-based measurements
    Pfeifer, Marion ; Gonsamo, Alemu ; Woodgate, William ; Cayuela, Luis ; Marshall, Andrew R. ; Ledo, Alicia ; Paine, Timothy C.E. ; Marchant, Rob ; Burt, Andrew ; Calders, Kim ; Courtney-mustaphi, Colin ; Cuni-sanchez, Aida ; Deere, Nicolas J. ; Denu, Dereje ; Gonzalez De Tanago Meñaca, J. ; Hayward, Robin ; Lau Sarmiento, A.I. ; Macía, Manuel J. ; Olivier, Pieter I. ; Pellikka, Petri ; Seki, Hamidu ; Shirima, Deo ; Trevithick, Rebecca ; Wedeux, Beatrice ; Wheeler, Charlotte ; Munishi, Pantaleo K.T. ; Martin, Thomas ; Mustari, Abdul ; Platts, Philip J. - \ 2018
    Forest Ecosystems 5 (2018). - ISSN 2095-6355 - 14 p.
    Background: Canopy 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. Methods: Here, 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. Results: Using 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. Conclusions: We 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.
    Capturing forest structure and change – 5 years of laser scanning and future perspectives using UAV based LiDAR
    Bartholomeus, H.M. ; Lau Sarmiento, A.I. ; Gonzalez de Tanago Meñaca, J. ; Herold, M. ; Brede, B. ; Kooistra, L. ; Calders, Kim - \ 2017
    In: SilviLaser 2017 Program. - Blacksburg : Virginia Tech - p. 61 - 62.
    Above-ground biomass assessment of tropical trees with Terrestrial LiDAR and 3D architecture models
    Lau Sarmiento, A.I. ; Gonzalez de Tanago Meñaca, J. ; Bartholomeus, H.M. ; Herold, M. ; Avitabile, V. ; Raumonen, Pasi ; Martius, Christopher ; Goodman, R.C. ; Disney, Mathias ; Manuri, Solichin ; Burt, Andrew ; Calders, Kim - \ 2017
    In: SilviLaser 2017 Program. - Blacksburg : Virginia Tech - p. 123 - 124.
    Capturing forest structure using UAV based LiDAR
    Bartholomeus, H.M. ; Brede, B. ; Lau Sarmiento, A.I. ; Kooistra, L. - \ 2017
    - 2 p.
    Comparing RIEGL RiCOPTER UAV LiDAR Derived Canopy Height and DBH with Terrestrial LiDAR
    Brede, Benjamin ; Lau Sarmiento, A.I. ; Bartholomeus, Harm ; Kooistra, Lammert - \ 2017
    Sensors 17 (2017)10. - ISSN 1424-8220 - 16 p.
    In recent years, LIght Detection And Ranging (LiDAR) and especially Terrestrial Laser Scanning (TLS) systems have shown the potential to revolutionise forest structural characterisation by providing unprecedented 3D data. However, manned Airborne Laser Scanning (ALS) requires costly campaigns and produces relatively low point density, while TLS is labour intense and time demanding. Unmanned Aerial Vehicle (UAV)-borne laser scanning can be the way in between. In this study, we present first results and experiences with the RIEGL RiCOPTER with VUX ®
    ®
    -1UAV ALS system and compare it with the well tested RIEGL VZ-400 TLS system. We scanned the same forest plots with both systems over the course of two days. We derived Digital Terrain Model (DTMs), Digital Surface Model (DSMs) and finally Canopy Height Model (CHMs) from the resulting point clouds. ALS CHMs were on average 11.5 cm
    cm
    higher in five plots with different canopy conditions. This showed that TLS could not always detect the top of canopy. Moreover, we extracted trunk segments of 58 trees for ALS and TLS simultaneously, of which 39 could be used to model Diameter at Breast Height (DBH). ALS DBH showed a high agreement with TLS DBH with a correlation coefficient of 0.98 and root mean square error of 4.24 cm
    cm
    . We conclude that RiCOPTER has the potential to perform comparable to TLS for estimating forest canopy height and DBH under the studied forest conditions. Further research should be directed to testing UAV-borne LiDAR for explicit 3D modelling of whole trees to estimate tree volume and subsequently Above-Ground Biomass (AGB).
    Data acquisition considerations for Terrestrial Laser Scanning of forest plots
    Wilkes, Phil ; Lau Sarmiento, Alvaro ; Disney, Mathias ; Calders, Kim ; Burt, Andrew ; Gonzalez De Tanago Meñaca, J. ; Bartholomeus, Harm ; Brede, Benjamin ; Herold, Martin - \ 2017
    Remote Sensing of Environment 196 (2017). - ISSN 0034-4257 - p. 140 - 153.
    The poor constraint of forest Above Ground Biomass (AGB) is responsible, in part, for large uncertainties in modelling future climate scenarios. Terrestrial Laser Scanning (TLS) can be used to derive unbiased and non-destructive estimates of tree structure and volume and can, therefore, be used to address key uncertainties in forest AGB estimates. Here we review our experience of TLS sampling strategies from 27 campaigns conducted over the past 5 years, across tropical and temperate forest plots, where data was captured with a RIEGL VZ-400 laser scanner. The focus is on strategies to derive Geometrical Modelling metrics (e.g. tree volume) over forest plots (≥1 ha) which require the accurate co-registration of 10s to 100s of individual point clouds. We recommend a 10 m × 10 m sampling grid as an approach to produce a point cloud with a uniform point distribution, that can resolve higher order branches (down to a few cm in diameter) towards the top of 30+ m canopies and can be captured in a timely fashion i.e. ∼3–6 days per ha. A data acquisition protocol, such as presented here, would facilitate data interoperability and inter-comparison of metrics between instruments/groups, from plot to plot and over time.
    Application of terrestrial LiDAR and modelling of tree branching structure for plant-scaling models in tropical forest trees
    Lau Sarmiento, A.I. ; Bartholomeus, H.M. ; Herold, M. ; Martius, Christopher ; Malhi, Yadvinder ; Bentley, Lisa Patrick ; Shenkin, Alexander ; Raumonen, P. - \ 2017
    Terrestrial LiDAR and 3D Reconstruction Models for Estimation of Large Tree Biomass in the Tropics
    Lau Sarmiento, A.I. ; Gonzalez de Tanago Meñaca, J. ; Bartholomeus, H.M. ; Herold, M. ; Raumonen, P. ; Avitabile, V. ; Martius, Christopher ; Goodman, R.M. ; Manuri, Solichin - \ 2016
    - 1 p.
    Terrestrial LiDAR and 3D Reconstruction Models for Large Individual Tree Biomass Estimation in Tropics
    Lau Sarmiento, A.I. ; Herold, M. ; Bartholomeus, H.M. ; Gonzalez de Tanago Meñaca, J. - \ 2016
    Application of Terrestrial LiDAR and Modelling of Tree Branching Structure for Plant-scaling Models in Tropical Forest Trees
    Lau Sarmiento, A.I. ; Bartholomeus, H.M. ; Herold, M. ; Martius, Christopher ; Malhi, Yadvinder ; Bentley, Lisa Patrick ; Shenkin, Alexander ; Raumonen, P. - \ 2016
    Quantification of Tropical Forest Biomass with Terrestrial LiDAR and 3D Tree Quantitative Structure Modelling
    Gonzalez deTanago Meñaca, J. ; Lau Sarmiento, A.I. ; Bartholomeus, H.M. ; Herold, M. ; Raumonen, P. ; Avitabile, V. ; Martius, Christopher ; Joseph, Shijo - \ 2016
    Terrestrial Laser Scanning for measuring forest biomass change
    Lau Sarmiento, A.I. ; Calders, K. ; Herold, M. ; Avitabile, V. ; Raumonen, P. ; Gonzalez De Tanago Meñaca, J. ; Bartholomeus, H.M. - \ 2015
    Application of terrestrial LiDAR and modelling of tree branching structure for plant-scaling models in tropical forest trees
    Lau Sarmiento, A.I. ; Bartholomeus, H.M. ; Herold, M. ; Martius, C. ; Malhi, Y. ; Bentley, L.P. ; Shenkin, A. ; Raumonen, P. - \ 2015
    In: Proceedings of the SilviLaser 2015 conference. - - p. 3 - 3.
    Terrestrial LiDAR and 3D tree reconstruction modeling for quantification of biomass loss and characterization of impacts of selective logging in tropical forest of Peruvian Amazon. Multi-sensor assessment, combining near and remote sensing
    Gonzalez De Tanago Meñaca, J. ; Joseph, Shijo ; Herold, M. ; Goodman, R.M. ; Bartholomeus, H.M. ; Avitabile, V. ; Raumonen, P. ; Calders, K. ; Lau Sarmiento, A.I. ; Janovec, J. - \ 2014
    Evaluation of different scan configurations for an effective field procedure on a terrestrial LiDAR scanner in tropical forest
    Lau Sarmiento, A.I. ; Bartholomeus, H.M. ; Gonzalez De Tanago Meñaca, J. - \ 2014
    Connecting Policy and Practice for the Conservation of Sacred Natural Sites
    Verschuuren, B. ; Wild, R. ; Verschoor, G.M. - \ 2014
    In: Indigenous Revival and Sacred Sites Conservation in the Americas / Sarmiento, F.O, Hitchner, S., New York : Berghahn Books (Environmental Anthropology and Ethnobiology ) - p. 26 - 61.
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