SilviLaser 2012, Sept.

16-19 September 2012 Vancouver, Canada

Automatic extraction of tree stem models from single terrestrial lidar scans in structurally heterogeneous forest environments
David Kelbe1, Paul Romanczyk1, Jan van Aardt1, Kerry Cawse-Nicholson1 & Keith Krause2
1

Rochester Institute of Technology, 54 Lomb Memorial Drive, Rochester, NY djk2312@cis.rit.edu 2 National Ecological Observatory Network

Keywords: terrestrial laser scanning, single scan, tree stem models, DBH Paper ID: SL2012-031 Abstract
An important application of terrestrial laser scanning is the extraction of tree stem models for diameter at breast height (DBH) assessment and forest inventory. Much work has been done to automate this process using adjacent co-registered lidar scans. Existing studies, however, have focused on pre-registered point clouds obtained from commercial lidar systems. We envision an affordable and efficient portable lidar hardware-software alternative for forest structural assessment. For such systems, point cloud registration software may not be available. Therefore we have developed automatic tree stem and DBH modelling approaches for single lidar scans collected from an off-the-shelf SICK LMS-151 lidar system. We assessed visual and quantitative accuracy for automatic tree extraction in a dense, heterogeneous, 20m x 20m forest site. We found that modelling tapered cylinders to the lidar point distribution of tree stems presents a viable algorithm for our single-scan lidar system, even in cluttered heterogeneous forest environments. This work demonstrates the potential for forest inventory using affordable, off-the-shelf lidar systems, and offers suggestions for future research.

1. Introduction
Terrestrial laser scanning (light detection and ranging; lidar) has become an increasingly important tool for forest structure assessment in recent years. Laser scanning technology records the return trip time, from laser emission to target backscatter to final detection, of a backscattered laser pulse for a series of scan mirror positions. Range distance to the object is computed based on the speed of light, and as a result, a dense 3D point cloud is generated. This rich data source holds the possibility of extracting many forest structure parameters, including those that would be unfeasible to collect using traditional field methods (e.g., stem volume, sweep, flexuosity, and branch structure) (Gorte and Pfeifer, 2004; Othmani et al., 2011). Yet, due to the complexity of segmentation in forested environments, most studies so far have focused on the extraction of individual tree diameter-at-breast-height (DBH) and corresponding stem densities (Simonse et al., 2003; Aschoff et al., 2004; Maas et al., 2008; Othmani et al., 2011). Significant advances have been made in recent years to automatically measure and extract tree DBH on an operational scale. However, most algorithms rely on expensive commercial lidar systems and associated proprietary software. Furthermore, the data acquisition time of most commercial systems prohibits large-scale inventory. We envision an affordable and efficient terrestrial lidar hardware and software solution that can be utilized for forest inventory and assessment outside the domain of research and academia. Such a product-algorithm suite could
1

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serve as an alternative to traditional forest inventory techniques. As such we have integrated a SICK LMS-151 laser scanning system with a rotation stage and portable computer, at a cost of under US$ 10,000. Our system allows rapid and economical forest structure data acquisition. It is our goal to draw upon the tools developed for tree structure extraction, specifically DBH, to expand our system functionality towards automatically extracting tree stem models. Specifically, we hope to investigate the extension of DBH extraction techniques to single lidar scans. The majority of previous studies focus on modelling tree stems from multiple, pre-registered scans of a central location (Simonse et al., 2003; Aschoff et al., 2004; Maas et al., 2008; Othmani et al., 2011). Emphasis on multiple-scan algorithms has so far been motivated by the decreased measurement error due to fewer occlusions of the laser beam by understory (Watt and Donoghue, 2005). In other words, adjacent scans may provide a view of the target that was otherwise obscured in the single scan. Traditional terrestrial lidar-based DBH-approximation methods consider points from a 5cm thick horizontal z-slice centred at 1.3m above ground. A single circle is fitted to the 2D-projection of these points. Operationally, this procedure may be applied at varying heights above ground (Othmani et al., 2011; van Leeuwen et al., 2011). In contrast, relatively few studies have considered tree stem characterization from a single scan. The challenges introduced by single scans are several: First, a singular scan position causes obscuration radially outward from each intercepted object. Second, point density and resolution decrease radially due to the laser beam divergence. In one pilot study, the rate of tree detection from single scans was less than half that for multiple scans (Thies and Spiecker, 2004). However, despite the challenges introduced from single scan algorithms, there are advantages: It is clear that a single panoramic scan is preferable economically (Thies and Spiecker, 2004). A robust single-scan algorithm could vastly increase operational efficiency for field crews. We suggest that a balance can be achieved between efficiency and accuracy, by taking advantage of the full structural information available from a single laser scan: Instead of fitting points to a circle at 1.3m, we will utilize the full set of points between 0.3m and 1.3m above ground and fit tapered cylinders. Here we present preliminary results of algorithm development for single-scan tree stem modelling by modelling tapered cylinders to the hemi-cylindrical point distribution on individual tree boles.

2. Method
2.1 Study area Our study area is a 10ha section of the Hemlock-Canadice State Forest, located at 42.7377 N, 77.6061 W, in upstate New York (Figure 1). The Hemlock-Canadice State Forest lies adjacent to Hemlock Lake, the water source for the city of Rochester. The forests history traces back to the early 1900s when tracts of land in the watershed of Hemlock Lake were acquired by the city to protect the public water supply. Most of the land was agricultural at the time. In order to protect the quality of the water, aggressive tree planting began shortly after. Planted species included Scots pine (Pinus sylvestris), white pine (Pinus strobus), red pine (Pinus resinosa), and Norway spruce (Picea abies), while pockets are naturally forested. In 1929, spread of a fungal disease prompted the underplanting of stressed conifers with hardwood seedlings, in order to retain forest cover should the conifers die. 2.1.1 Site establishment We established 20 sites on the west-facing shore of Hemlock Lake, in the Hemlock-Canadice

SilviLaser 2012, Sept. 16-19 September 2012 Vancouver, Canada

State Forest. Site centres are separated by approximately 70-90m, depending on restrictive characteristics, such as extreme slopes at site centres. Each site is 20m x 20m in dimension. For this work a single site was selected using a pseudo-random number generator to investigate the challenges of automatically extracting tree stem models from a single lidar scan. Our site (Site #6) is a natural mixture of young deciduous and coniferous trees on variable terrain (Figure 2). Many conifer branches are present under 2m, resulting in significant visual occlusion and clutter.

Figure 1: Our site was randomly selected from 20 marked sites on the west-facing slopes of Hemlock-Canadice State Forest, located in upstate New York (a). The site is a natural mixture of deciduous and coniferous trees (b). (map: Google Maps)

2.1.2 Data Lidar data were collected in April 2012 during the leaf-off season using the SICK LMS-151 lidar system. This system has a maximum vertical field of view of 270, an angular step width of 0.25 and a scanning frequency of 50Hz. The instrument is mounted on a rotation stage to provide 360 field of view in azimuth at a 0.25 step width. The lidar beam diverges to give an effective beam size of 15.8cm at 10m. The system is then mounted on a tripod and tethered to a computer and power supply, which can be carried by the operator in an external frame backpack (Figure 3). This allows rapid data acquisition at the rate of 25-scans/half-hour. In addition, we measured the DBH and stem location, using a compass and tape measure from plot centre, of each tree over 5cm DBH within the site.

SilviLaser 2012, Sept. 16-19 September 2012 Vancouver, Canada

Figure 2: Our mobile lidar system allows rapid forest structure inventory at approximately 25 scans/half-hour.

3. Algorithm
Tree stem modelling was performed by iteratively querying a subset of points within the region between 0.4 and 1.3m above ground. Each subset of points represents a candidate stem for cylinder model fitting. A 1.3m height threshold was chosen to exclude the majority of branch and lower canopy returns. Points within the subset were then fitted to models of either lines or tapered cylinders, based on the number of points within the subset. The DBH was computed as a function of modelled parameters; the algorithm is discussed in the following sections. 3.1 DTM extraction The digital terrain model (DTM) describes the height of the ground with respect to the lidar coordinate system origin. The DTM gives a reference from which DBH can be measured. To derive the DTM, a search window is applied to find local minima points. The search window size is radially dependent to account for decreasing point density with range. Outlier points are detected and eliminated based on a slope threshold, pre-determined from knowledge of scene terrain. The remaining points are interpolated using Delaunay triangulation. The final grid product is inpainted (Matlab; Bertalmio et al., 2000) to ensure DTM coverage over the entire sample area. 3.2 Line fitting Lidar points are fit to a line if fewer than 150 points are located within the subset. In order to estimate the principal direction of the line, e.g., the tree stem growth angle, we find the direction of maximum variance using principal component analysis (PCA). The position of the stem tree centre is computed from the intersection of this vector with the DTM. The stem diameter is estimated from the standard deviation of points in the direction orthogonal to both the principal direction of growth and the line of sight vector to the lidar scanner. 3.3 Cylinder fitting Lidar points are fitted to a tapered cylinder if more than 150 points are contained in the subset. A two-stage approach is used to a) derive an initial estimate and then b) iteratively adjust that estimate to optimize model parameters.

SilviLaser 2012, Sept. 16-19 September 2012 Vancouver, Canada

3.3.1 Initial Estimate The success of optimization routines is improved when an adequate initial estimate is supplied. We derive an initial estimate for the cylinders principal direction by calculating the direction of maximum variance using eigen analysis. The stem location is again computed as the intersection of the shifted eigenvector with the DTM. The radius is estimated from the distribution of points projected onto the vector orthogonal to both the first eigenvector and the vector to the origin. Their density distribution is fitted to a SuperGaussian with free parameters n and . Fitting to a SuperGaussian allows consistent stem diameter estimation for tree stems with and without branch returns. An initial estimate of the taper is fixed according to the Ormerod taper equation (Ormerod, 1973). 3.3.2 Optimization Modelled tree stem parameters are iteratively adjusted using Trust-Region-Reflective Optimization (Coleman and Li, 1996). We establish our model as follows: The task is to minimize the distance of points from the surface of a tapered cylinder A (Figure 5), with arbitrary location (x0, y0, z0), direction of growth (,,), base radius (r0), and taper angle (). In order to derive a functional form for the error, we transform the points to a vertical stem centred at the origin (Figure 5, cylinder B). The transformation matrix is derived from the current estimate of (,,) and (x0, y0, z0).

Figure 3: A schematic that shows the cylinder fitting process

The problem is then recast as minimizing

sum{( x )2 +( y )2 - ( r0 + z * tan())2}

(1)

where (x,y,z) are the observed lidar points. This process is iterated for all candidate tree stems within the lidar point cloud. The result is a list of parameterized tree stem models. Each model is defined by an (x,y,z) coordinate denoting the intersection of the tree bole with the DEM, the angular orientation or direction of growth, (,,), the taper angle (), and the diameter at breast height (computed). Additionally, the indices of the inlier points to the model are stored for point classification (e.g., ground, bole, etc.).

SilviLaser 2012, Sept. 16-19 September 2012 Vancouver, Canada

4. Results and Discussion

4.1 Visual Analysis To visualize the results of automatic tree stem extraction, we generated a 2D panoramic image from the lidar point cloud (Figure 4). Columns correspond to sampled steps in azimuth angle, and rows correspond to sampled steps in elevation angle. The intensity of each pixel was derived from the backscattered 905nm intensity for the appropriate intercepted object. Point classification was performed to provide a visual analysis of stem detection. Unclassified points are grey. Ground points, derived from the DTM, are blue. Stem points, derived from cylinder fitting, are orange. Note that only points used in the cylinder-fitting model (0.4m to 1.3m above ground) are classified. Good visual classification is achieved even under partial occlusion, varying terrain, branch structure, and object distance.

Figure 4: Point classification showing ground points (blue), stem points (orange), and unclassified points (grey), as projected onto a 2D panoramic image. Trees with >4cm DBH within a 10m x 10m site subset are labeled according to inventory number.

4.1 Quantitative Analysis Quantitative model accuracy was evaluated by (i) direct comparison to mapped and measured tree boles within a 10m x 10m site subset, and (ii) stem diameter distribution comparison within the full 20m x 20m site. For direct comparison between boles, the DBH of each tree greater than 4cm DBH was measured and mapped using a compass and tape measure. Measured DBH values were compared to the estimated DBH values for all trees within the 10m x 10m subset. Measurement error was calculated based on the lidar beam divergence. Beam divergence introduces measurement error due to the possibility of partially intercepted objects. At a distance x from the aperture, the lidar beam diverges to a width d according to Equation 2. d [m] = 008 [m] + 0.015 * x [m] (2)

In addition, a simple linear regression was calculated (Equation 3) relating measured and estimated DBH values (Figure 5). Estimated DBH = 0.071 + 0.805*Measured DBH (3)

SilviLaser 2012, Sept. 16-19 September 2012 Vancouver, Canada

Figure 5: Direct comparison between estimated and measured DBH.

The second method for model evaluation compared stem diameter distributions across the entire 20m x 20m site (Figure 6). In other words, the distribution of inventoried tree diameters was compared to that of the estimated tree diameters, without regard for location. This permitted model evaluation across the entire site when individual tree comparison was infeasible. It is expected that the lidar-derived stem counts should be lower than the actual stem counts, due to the occlusion of objects from a single lidar scan. This phenomenon should manifest itself in an estimated diameter distribution shifted below the actual diameter distribution (i.e., fewer trees detected at each DBH bin). However, Figure 6 shows a slight overestimation of stem counts. This reveals a high false alarm rate in tree detection that was difficult to visualize in the point classification image (Figure 4). False alarms may be difficult to visualize in the point classification image if only few pixels contribute to a computed tree stem model. Therefore, future work should additionally visualize tree stem models as objects in 3D space.

Figure 6: Stem DBH distribution comparison between estimated and measured values.

These analyses were derived from a single lidar scan collected from an affordable, off-the-shelf instrument. No proprietary pre-processing or registration software was needed, and scanning time was less than one minute. This work suggests the potential for efficient, large-scale forest inventory in the future, using economical lidar systems such as the SICK LMS-151.

5. Conclusion
An important application of terrestrial laser scanning is the extraction of tree stem models for

SilviLaser 2012, Sept. 16-19 September 2012 Vancouver, Canada

DBH assessment and forest inventory. We developed a method for single-scan stem detection based on existing methods for multiple-scan systems. We performed visual and quantitative assessment of automatic tree stem extraction. We found that modelling tapered cylinders to the lidar point distribution of tree stems presents a viable algorithm for our single-scan lidar system, even in cluttered heterogeneous forest environments. This has significant impact for future research, suggesting that off-the-shelf, single-scan lidar systems could extend the accessibility of forest structure assessment to cost-limited applications.

Acknowledgements
This material is based upon work supported by the National Science Foundation Accelerating Innovation Research (AIR) program and National Science Foundation Graduate Research Fellowship under Grant Nos. 1127728 and DGE-1102937, respectively. Any opinions, findings, and conclusions or recommendations expressed in this material are those of the author(s) and do not necessarily reflect the views of the National Science Foundation. The authors would also like to thank the NYS Department of Environmental Conservation, Region 8 for access to Hemlock-Canadice State Forest.

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