Effects of tree trunks on estimation of clumping index and LAI from HemiView and terrestrial LiDAR

Estimating clumping indices is important for determining the leaf area index (LAI) of forest canopies. The spatial distribution of the clumping index is vital for LAI estimation. However, the neglect of woody tissue can result in biased clumping index estimates when indirectly deriving them from the gap probability and LAI observations. It is difficult to effectively and automatically extract woody tissue from digital hemispherical photos. In this study, a method for the automatic detection of trunks from Terrestrial Laser Scanning (TLS) data was used. Between-crown and within-crown gaps from TLS data were separated to calculate the clumping index. Subsequently, we analyzed the gap probability, clumping index, and LAI estimates based on TLS and HemiView data in consideration of woody tissue (trunks). Although the clumping index estimated from TLS had better agreement (R-2 = 0.761) than that from HemiView, the change of angular distribution of the clumping index affected by the trunks from TLS data was more obvious than with the HemiView data. Finally, the exclusion of the trunks led to a reduction in the average LAI by similar to 19.6% and 8.9%, respectively, for the two methods. These results also showed that the detection of woody tissue was more helpful for the estimation of clumping index distribution. Moreover, the angular distribution of the clumping index is more important for the LAI estimate than the average clumping index value. We concluded that woody tissue should be detected for the clumping index estimate from TLS data, and 3D information could be used for estimating the angular distribution of the clumping index, which is essential for highly accurate LAI field measurements

White paper – On the use of LiDAR data at AmeriFlux sites

Our aim is to inform the AmeriFlux community on existing and upcoming LiDAR technologies (atmospheric Doppler or Raman LiDAR often deployed at flux sites are not considered here), how it is currently used at flux sites, and how we believe it could, in the future, further contribute to the AmeriFlux vision. Heterogeneity in vegetation and ground properties at various spatial scales is omnipresent at flux sites, and 3D mapping of canopy, understory, and ground surface can help move the science forward

Achieving improved leaf area index estimations from digital hemispherical imagery through destructive sampling methods

Destructive sampling of 20 trees of four tree species in a mixed New England conifer/hardwood stand shows that leaf area comprises 72, 77, and 78 percent of plant area as measured with digital hemispherical photography of the stand in (1) leaf-off, (2) leaf-out and pre-harvest, and (3) leaf-out and post-harvest conditions. Leaf area index values for the stand, estimated through destructive sampling, were 4.42, 5.98, and 5.08 respectively, documenting the progression of leaf growth through post-harvest. Terrestrial lidar scans (TLS) of the stand in (1) leaf-off and (2) leaf-out and pre-harvest conditions provided leaf area index values of 4.49 and 6.00 using the correction applied to observed plant area index, showing good agreement. The method relies on destructive sampling to relate the weight of foliage removed from sample trees to leaf area and fine twig area within the foliage as measured by a flatbed scanner. Two conifer species, eastern hemlock and white pine, and two deciduous species, red maple and red oak, in five diameter-size classes, were harvested from the 50 x 50-m stand in late summer. Leaf and twig areas of these trees provided species-specific allometric equations relating stem basal area to leaf and twig area, and a stand map provided species, counts and diameters of all trees in the plot. These data then allowed estimation of the leaf area of the stand as a whole for comparison with optical methods. The ratios of leaf to fine-branch area for each species vary, with values of 5.33, 25.38, 260.88 and 140.35 for eastern hemlock, white pine, red maple, and red oak respectively. This variance shows that woody-to-total area constants, which are used for calculating leaf area index from plant area index values determined by optical gap probability methods, will be quite dependent on stand composition and questions the common usage of literature constants for this purpose. This study shows how destructive sampling can lead to better estimation of forest leaf area index and wood area index from hemispherical photography and terrestrial lidar scanning, which has the potential to improve modeling of nutrient cycling and carbon balance in ecosystem models

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

Retrieving Leaf Area Index (LAI) Using Remote Sensing: Theories, Methods and Sensors

The ability to accurately and rapidly acquire leaf area index (LAI) is an indispensable component of process-based ecological research facilitating the understanding of gas-vegetation exchange phenomenon at an array of spatial scales from the leaf to the landscape. However, LAI is difficult to directly acquire for large spatial extents due to its time consuming and work intensive nature. Such efforts have been significantly improved by the emergence of optical and active remote sensing techniques. This paper reviews the definitions and theories of LAI measurement with respect to direct and indirect methods. Then, the methodologies for LAI retrieval with regard to the characteristics of a range of remotely sensed datasets are discussed. Remote sensing indirect methods are subdivided into two categories of passive and active remote sensing, which are further categorized as terrestrial, aerial and satellite-born platforms. Due to a wide variety in spatial resolution of remotely sensed data and the requirements of ecological modeling, the scaling issue of LAI is discussed and special consideration is given to extrapolation of measurement to landscape and regional levels

Advances in measuring forest structure by terrestrial laser scanning with the Dual Wavelength ECHIDNA® LIDAR (DWEL)

Leaves in forests assimilate carbon from the atmosphere and woody components store the net production of that assimilation. Separate structure measurements of leaves and woody components advance the monitoring and modeling of forest ecosystem functions. This dissertation provides a method to determine, for the first time, the 3-D spatial arrangement and the amount of leafy and woody materials separately in a forest by classification of lidar returns from a new, innovative, lidar scanner, the Dual-Wavelength Echidna® Lidar (DWEL). The DWEL uses two lasers pulsing simultaneously and coaxially at near-infrared (1064 nm) and shortwave-infrared (1548 nm) wavelengths to locate scattering targets in 3-D space, associated with their reflectance at the two wavelengths. The instrument produces 3-D bispectral "clouds" of scattering points that reveal new details of forest structure and open doors to three-dimensional mapping of biophysical and biochemical properties of forests. The three parts of this dissertation concern calibration of bispectral lidar returns; retrieval of height profiles of leafy and woody materials within a forest canopy; and virtual reconstruction of forest trees from multiple scans to estimate their aboveground woody biomass. The test area was a midlatitude forest stand within the Harvard Forest, Petersham, Massachusetts, scanned at five locations in a 1-ha site in leaf-off and leaf-on conditions in 2014. The model for radiometric calibration assigned accurate values of spectral apparent reflectance, a range-independent and instrument-independent property, to scattering points derived from the scans. The classification of leafy and woody points, using both spectral and spatial context information, achieved an overall accuracy of 79±1% and 75±2% for leaf-off and leaf-on scans, respectively. Between-scan variation in leaf profiles was larger than wood profiles in leaf-off seasons but relatively similar to wood profiles in leaf-on seasons, reflecting the changing spatial heterogeneity within the stand over seasons. A 3-D structure-fitting algorithm estimated wood volume by modeling stems and branches from point clouds of five individual trees with cylinders. The algorithm showed the least variance for leaf-off, woody-points-only data, validating the value of separating leafy and woody points to the direct biomass estimates through the structure modeling of individual trees

A Density-Based Approach for Leaf Area Index Assessment in a Complex Forest Environment Using a Terrestrial Laser Scanner

Forests are an important part natural ecosystems, by for example providing food, fiber, habitat, and biodiversity, all of which contribute to stable natural systems. Assessing and modeling the structure and characteristics of forests, e.g., Leaf Area Index (LAI), volume, biomass, etc., can lead to a better understanding and management of these resources. In recent years, Terrestrial Laser Scanning (TLS) has been recognized as a tool that addresses many of the limitations of manual and traditional forest data collection methods. In this study, we propose a density-based approach for estimating the LAI in a structurally-complex forest environment, which contains variable and diverse structural attributes, e.g., non-circular stem forms, dense canopy and below-canopy vegetation cover, and a diverse species composition. In addition, 242 TLS scans were collected using a portable low-cost scanner, the Compact Biomass Lidar (CBL), in the Hawaii Volcanoes National Park (HAVO), Hawaii Island, USA. LAI also was measured for 242 plots in the site, using an AccuPAR LP-80 ceptometer. The first step after cleaning the point cloud involved detecting the higher forest canopy in the light detection and ranging (lidar) point clouds, using normal change rate assessment. We then estimated Leaf Area Density (LAD), using a voxel-based approach, and divided the canopy point cloud into five layers in the Z (vertical) direction. These five layers subsequently were divided into voxels in the X direction, where the size of these voxels were obtained based on inter-quartile analysis and the number of points in each voxel. We hypothesized that the intensity returned to the lidar system from woody materials, like branches, would be higher than from leaves, due to the liquid water absorption feature of the leaves and higher reflectance for woody material at the 905 nm laser wavelength. We also differentiated between foliar and woody materials using edge detection in the images from projected point clouds and evaluated the density of these regions to support our hypothesis. Density of points, or the number of points divided by the volume of a grid, in a 3D grid size of 0.1 m, was calculated for each of the voxels. The grid size was determined by investigating the size of the branches in the lower portion of the canopy. Subsequently, we fitted a Kernel Density Estimator (KDE) to these values, with the threshold set based on half of the area under the curve in each of the density distributions. All the grids with a density below the threshold were labeled as leaves, while those grids above the threshold were identified as non-leaves. Finally, we modeled LAI using the point densities derived from the TLS point clouds and the listed analysis steps. This model resulted in an R 2 value of 0.88. We also estimated the LAI directly from lidar data using the point densities and calculating LAD, which is defined as the total one-sided leaf area per unit volume. LAI can be obtained as the sum of the LAD values in all the voxels. The accuracy of LAI estimation was 90%, with an RMSE value of 0.31, and an average overestimation of 9% in TLS-derived LAI, when compared to field-measured LAI. Algorithm performance mainly was affected by the vegetation density and complexity of the canopy structures. It is worth noting that, since the LAI values cannot be considered spatially independent throughout all the plots in this site, we performed semivariogram analysis on the field-measured LAI data. This analysis showed that the LAI values can be assumed to be independent in plots that are at least 30 m apart. As a result, we divided the data into six subsets in which the plots were 30 m spaced. The R 2 values for these subsets, based on modeling of the field-measured LAI using leaf point density values, ranged between 0.84–0.96. The results bode well for using this method for efficient, automatic, and accurate/precise estimation of LAI values in complex forest environments, using a low-cost, rapid-scan TLS

Comparison of forest attributes derived from two terrestrial lidar systems.

Abstract Terrestrial lidar (TLS) is an emerging technology for deriving forest attributes, including conventional inventory and canopy characterizations. However, little is known about the influence of scanner specifications on derived forest parameters. We compared two TLS systems at two sites in British Columbia. Common scanning benchmarks and identical algorithms were used to obtain estimates of tree diameter, position, and canopy characteristics. Visualization of range images and point clouds showed clear differences, even though both scanners were relatively high-resolution instruments. These translated into quantifiable differences in impulse penetration, characterization of stems and crowns far from the scan location, and gap fraction. Differences between scanners in estimates of effective plant area index were greater than differences between sites. Both scanners provided a detailed digital model of forest structure, and gross structural characterizations (including crown dimensions and position) were relatively robust; but comparison of canopy density metrics may require consideration of scanner attributes

Remote Sensing of Biophysical Parameters

Vegetation plays an essential role in the study of the environment through plant respiration and photosynthesis. Therefore, the assessment of the current vegetation status is critical to modeling terrestrial ecosystems and energy cycles. Canopy structure (LAI, fCover, plant height, biomass, leaf angle distribution) and biochemical parameters (leaf pigmentation and water content) have been employed to assess vegetation status and its dynamics at scales ranging from kilometric to decametric spatial resolutions thanks to methods based on remote sensing (RS) data.Optical RS retrieval methods are based on the radiative transfer processes of sunlight in vegetation, determining the amount of radiation that is measured by passive sensors in the visible and infrared channels. The increased availability of active RS (radar and LiDAR) data has fostered their use in many applications for the analysis of land surface properties and processes, thanks to their insensitivity to weather conditions and the ability to exploit rich structural and texture information. Optical and radar data fusion and multi-sensor integration approaches are pressing topics, which could fully exploit the information conveyed by both the optical and microwave parts of the electromagnetic spectrum.This Special Issue reprint reviews the state of the art in biophysical parameters retrieval and its usage in a wide variety of applications (e.g., ecology, carbon cycle, agriculture, forestry and food security)

Developing a dual-wavelength full-waveform terrestrial laser scanner to characterise forest canopy structure

The development of a dual-wavelength full-waveform terrestrial laser scanner to measure the three-dimensional structure of forest canopies is described, and field measurements used to evaluate and test the instrument measurement characteristics. The Salford Advanced Laser Canopy Analyser (SALCA) measures the full-waveform of backscattered radiation at two laser wavelengths, one in the near-infrared (1063 nm) and one in the shortwave infrared (1545 nm). The instrument is field-portable and measures up to nine million waveforms, at the two wavelengths, across a complete hemisphere above the instrument. SALCA was purpose-built to measure structural characteristics of forest canopies and this paper reports the first results of field-based data collection using the instrument. Characteristics of the waveforms, and waveform data processing are outlined, applications of dual wavelength measurements are evaluated, and field deployment of the instrument at a forest test site described. Preliminary instrument calibration results are presented and challenges in extracting useful information on forest structure are highlighted. Full-waveform multiple-wavelength terrestrial laser scanners are likely to provide more detailed and more accurate forest structural measurement in the future. This research demonstrates how SALCA provides a key step to develop, test and apply this new technology in a range of forest-related problems