Bettina Wagner's research while affiliated with Swiss Federal Institute for Forest, Snow and Landscape Research WSL and other places

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Publications (4)


The point cloud data assessed with a terrestrial laser scanner a point cloud of a single 360° scan (average no. of points: 13,500,000) b close up of a single scan with one of the reference targets in the center c multiple scans (4–5) referenced with the Cyclone software d individual tree manually separated from the stand data (average no of points: 3,900,000)
Modeling procedure exemplarily shown for one Spruce stem a point cloud of a Spruce assessed by a terrestrial laser scanner b triangulated surface model of the tree stem generated in Geomagic studio c stem cross sections cut perpendicular to the tree stem and sanded for tree-ring measurements d the Matlab model combines tree-ring information with the outer shaper of the Geomagic surface model and interpolates cross sections at any point within the 3D model e by default 4 additional cross sections are interpolated between two input cross sections f example of interpolated cross section g example of interpolated 3D growth layer for one segment; Numbers shown in d–g represent Cartesian coordinates in meters
Annual tree-ring width plotted against annual volume accumulation of two Firs and three spruces
Annual tree-ring width plotted against the accumulated volume development of two Firs and three spruces
Annual height development of the five modeled trees per year and growth year
An annually-resolved stem growth tool based on 3D laser scans and 2D tree-ring data
  • Article
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February 2018

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266 Reads

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6 Citations

Trees

Bettina Wagner

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Key message The combination of terrestrial laser scans and tree-ring data allows for a highly precise reconstruction of annual stem growth, and thus complex tree-growth analyses independent of species and site characteristics. Abstract Reliable carbon pools data are needed to quantify the carbon stored in ecosystems and for effective forest management. Terrestrial laser scanning allows researchers to quickly acquire data about forest structure and to derive tree parameters and volume data automatically. However, accurate models of the development of tree volume over time are still lacking. In contrast to terrestrial laser scanning, tree-ring data show the annual growth development of trees, but do not contain information about tree volume. The fusion of terrestrial laser scanning and tree-ring data may, therefore, lead to reliable stem development data, and thus annually resolved models of volume increment of trees. The aim of this study is to combine these data and apply a root-development model to the aboveground part of trees. Three spruce trees (Picea abies) and two firs (Abies alba) which were part of a long-term forest monitoring survey were scanned using a terrestrial 3D-laser-scanner. Combining these data with tree-ring measurements, we were able to reconstruct stem volume at an annual resolution. Results provide robust annually resolved volume data along with ring-width measurements at any point within the modeled tree stem, which present great potential for complex growth analyses. Stem volume, estimated with a bole volume function, deviated between − 1.65 and 1.9% from our model for four out of five trees. For the fifth tree deviations of 13% were observed. The agreement between the function and our model demonstrates the robustness of the presented approach.

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Fig. 1 a Triangulated surface model, acquired with the Laser ScanArm and state of the model after integrating tree-ring radii (right) and entire tree-ring profiles (left) based on ring-width  
Fig. 6 Three reconstructed cross sections showing their spatial context, their mean chronologies and the deviations occurring between 3D and 2D interpolations  
Fig. 3 Schematic illustration of the interpolation steps (steps II–IV); a Calculating CS X from the scanner model (step II); b Defining C X of CS X (step III); c interpolation of ring profiles at CS X (step IV)  
Fig. 4 Schematic illustration of the volume computations (step V)  
A tool to model 3D coarse-root development with annual resolution

September 2011

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182 Reads

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21 Citations

Plant and Soil

Dynamic root-development models are indispensable for biomechanical and biomass allocation studies, and also play an important role in understanding slope stability. There are few root-development models in the literature, and there is a specific lack of dynamic models. Therefore, the aim of this study is to develop a 3D growth-development model for coarse roots, which is species independent, as long as annual rings are formed. In order to implement this model, the objectives are (I) to interpolate annual growth layers, and (II) to evaluate the interpolations and annual volume computations. The model developed is a combination of 3D laser scans and 2D tree-ring data. A FARO laser ScanArm is used to acquire the coarse-root structure. A MATLAB program then integrates the ring-width measurements into the 3D model. A weighted interpolation algorithm is used to compute cross sections at any point within the model to obtain growth layers. The algorithm considers both the root structure and the ring-width data. The model reconstructed ring profiles with a mean absolute error for mean ring chronologies of <9% and for single radii of <20%. The interpolation accuracy was dependent on the number of input sections and root curvature. Total volume computations deviated by 3.5–6.6% from the reference model. A new robust root-modelling tool was developed which allows for annual volume computations and sophisticated root-development analyses. KeywordsAllocation–Laser scanning–Root growth–Tree rings–Volume


Fig. 2 Point cloud representation of a root segment (left) and resulting surface models based on triangulation (center) and non rational b-splines (NURBS, right) 
Fig. 3 Automatic ( a , b , e ) and semi-automatic ( c , d , f ) hole filling techniques applied to different hole sizes ( a , b , e ), with different curvature degree ( f ) and carrying skeleton technique ( c , d ) 
Fig. 4 ( a ) Root disc and position of the four radii for the detailed WinDENDRO measurements of ( b ) ring-width and distance of the radii ’ s starting points; ( c ) model cross section indicating ideal starting points and directions ( arrows ) of radii and ( d ) trigonometric parameters to calculate the intersection point P I and starting points P3-P4 based on real measurements 
Fig. 5 ( a ) real cross section and position of radii; ( b ) radii integrated into the model cross section based on trigonometric parameters (compare Fig. 5) with two starting points intersecting the segment line; ( c , d ) possible, but not optimized positions of 
Fig. 6 Automated positioning of radii within the model cross section exemplarily shown for two cross sections. Upper part: Calculated standard deviation for all positions possible (left: 476; right: 1,225) in the respective cross section. Black line = max/min values of all computed constellations; blue star = 
Incorporating 2D tree-ring data in 3D laser scans of coarse-root systems

September 2010

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239 Reads

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26 Citations

Plant and Soil

In times of global change biomass calculations and the carbon cycle is gaining in importance. Forests act as carbon sinks and hence, play a crucial role in worlds and forests carbon budgets. Unfortunately, growth models and biomass calculations existing so far mainly concentrate on the above-ground part of trees. For this reason, the aim of the present study is to develop an annually resolved 3D growth model for tree roots, which allows for reliable biomass calculations and can later be combined with above-ground models. A FARO scan arm was used to measure the surface of a tree-root segment. In addition, ring-width measurements were performed manually on sampled cross sections using WinDENDRO. The main goal of this study is to model root growth on an annual scale by combining these data sets. In particular, a laser scan arm was tested as a device for the realistic reproduction of tree-root architecture, although the first evaluation has been performed for a root segment rather than for an entire root system. Deviations in volume calculations differed between 5% and 7% from the actual volume and varied depending on the used modeling technique. The model with the smallest deviations represented the structure of the root segment in a realistic way and distances and diameter of cross sections were acceptable approximations of the real values. However, the volume calculations varied depending on object complexity, modeling technique and order of modeling steps. In addition, it was possible to merge tree-ring borders as coordinates into the surface model and receive age information in connection with the spatial allocation. The scan arm was evaluated as an innovative and applicable device with high potential for root modeling. Nevertheless, there are still many problems connected with the scanning technique which have an influence on the accuracy of the model but are expected to improve with technical progress.


Fig. 1. Principle of data acquisition by the laser beam and shadowing effect caused by obstacles between laser and object. a) Sphere to be scanned; b) Scan image of the sphere (scan view) and c) seen from the top, showing the measurement range (40°) and the shadowing effect of the scanner.
Fig. 2. Perspective view of the scatter-plot resulting from one scan. White areas within the scan range represent the shadowing effects caused by the laser scanner and the masking of roots, resulting in no data. Black arrow: Scan view direction.
Fig. 3. Three-dimensional scatter-plot of the spruce root system composed of 16 single scans. View from three different angles, each scene consisting of approx. 10 million x/y/z-coordinates.
Fig. 4. Illustration of composed 3D-slices of the root system (Microstation). The single volumetric bodies were created by using the plane section area and the height of the section. Single bodies are then combined to represent the whole system or special parts of interest. (Source: GÄRTNER and DENIER 2006)
3D-laser scanning: A new method to analyze coarse tree root systems

January 2009

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2,194 Reads

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28 Citations

Forest Snow and Landscape Research

Details about the spatiotemporal development of root systems and their influence on ring-width variations in tree stems are still unknown. Furthermore, their size, spread and architecture play an important role in studying tree stability and their stabilizing effect on slopes. A major problem in this regard is the detailed 3D-data acquisition and modeling of its complex structure. The appli -cation of a laser scanner is a step towards the solution of this problem. Scanning the root system of a mature spruce tree facilitated creating a 3D scatter-plot of the root structure (resolution: 2 mm). The subsequent modeling of the structure allowed an automated replication of the coarse root structure down to a size of 0.5 cm of single roots. The resulting model of the root system facilitates cutting the roots for ring-width analysis while tagging the sample points in the model as a base for the further analysis of the root system's development.

Citations (4)


... Luterbacher et al. (2004)), and expectation maximization approaches (Schneider 2001;Rutherford et al. 2005;Mann et al. 2007). Advances in random forest reconstructions ( Athey et al. 2019;Wagner et al. 2018), neural networks ( Gholami et al. 2018;Woodhouse 1999), and paleoclimate data assimilation ( Acevedo et al. 2017), to name a few, are also expanding the potential applications of tree-ring data. Over nearly a century of statistical and numerical pioneering, many early dendrochronological limitations have been overcome by a combination of increased computing power and decreased computational costs and the development of advanced programming languages for analyses of large data sets. ...

Reference:

New frontiers in tree-ring research
An annually-resolved stem growth tool based on 3D laser scans and 2D tree-ring data

Trees

... Laser scanning results in huge point clouds with more than one hundred thousand data points for a whole plant or ten to thirty thousand points per plant organ [16], and it has the advantages of high-precision and strong disturbance resistance. This technique has been used in various studies for plant analysis widely [27], but Light Detection and Ranging is still rarely used in detecting crop phenotypes. Jin et al. [28] proposed an advanced technique for maize stalk and leaf segmentation and phenotypic trait extraction using ground-based LiDAR data. ...

3D-laser scanning: A new method to analyze coarse tree root systems

Forest Snow and Landscape Research

... Changes in root morphology indicate the effect of ecological factors (Bohm, 1979;Coutts, 1987). In ecological studies, assessment of root morphological parameters, including root architecture, provides data on ecological conditions of root growth (Chiatante et al., 2002;Ostonen et al., 2007;Jagodziński and Kałucka, 2011;Jagodzinski et al., 2016;Wagner et al., 2010Wagner et al., , 2011). An understanding of root diameter growth provides insight into the relationship between soil pore size and the ability of roots to penetrate the soil (Wiersum, 1957;Bohm, 1979). ...

Incorporating 2D tree-ring data in 3D laser scans of coarse-root systems

Plant and Soil

... While RootBox does not allow for direct root thickening, this feature was added by modifying the parameters to create a root-thickening proxy (Leitner et al. 2010a). However, current simulations only allow for young roots to grow with the same diameter they will have at the end of the simulation, whereas root thickening is a characteristic found in older trees (Coutts 1987;Wagner et al. 2011). Root-Box does not have a feature for creating a root collar, which is important for determining the final radius of the ZRT and total root spread. ...

A tool to model 3D coarse-root development with annual resolution

Plant and Soil