Ground Filtering Algorithms for Airborne LiDAR Data: A Review of Critical Issues

This paper reviews LiDAR ground filtering algorithms used in the process of creating Digital Elevation Models. We discuss critical issues for the development and application of LiDAR ground filtering algorithms, including filtering procedures for different feature types, and criteria for study site selection, accuracy assessment, and algorithm classification. This review highlights three feature types for which current ground filtering algorithms are suboptimal, and which can be improved upon in future studies: surfaces with rough terrain or discontinuous slope, dense forest areas that laser beams cannot penetrate, and regions with low vegetation that is often ignored by ground filters

Hierarchical watershed segmentation of canopy height model for multi-scale forest inventory

ABSTRACT: Canopy Height Model (CHM) is a standard LiDAR-derived product for deriving relevant forest inventory information, among which individual tree identification is a crucial task. The watershed algorithm from markers is the typical procedure applied to CHMs for delineation of crowns. However, for low-quality CHMs or under certain canopy conditions, segmentation at individual tree level is not practical, e.g., due to grouped trees in dense forests. In this study, we investigated the feasibility of a hierarchical watershed transform (HWT) algorithm to segment CHMs at both individual tree levels and scales above that. As compared to the results by the variable-window filtering for individual trees, HWT allows more flexibilities in removing nontreetop maxima by referring to the "dynamic" attributes of the potential treetops (i.e., local maxima). It is also found that the choice of filters for smoothing CHM has significant influences on the detection of treetops. Beyond individual tree level, the segmentation by HWT was compared with a commercial package eCognition, and both give similar segmentation results, though with minor differences. Due to the lack of fieldmeasured trees matched with LiDAR-detected ones, no quantitative evaluation of accuracy is provided in this study. Nevertheless, the results of this study reveal that HWT is a viable procedure that could be applied for multilevel segmentation of CHM

Enhanced Understanding of Infectious Diseases by Fusing Multiple Datasets: A Case Study on Malaria in the Western Brazilian Amazon Region

BACKGROUND: A common challenge to the study of several infectious diseases consists in combining limited cross-sectional survey data, collected with a more sensitive detection method, with a more extensive (but biased) syndromic sentinel surveillance data, collected with a less sensitive method. Our article describes a novel modeling framework that overcomes this challenge, resulting in enhanced understanding of malaria in the Western Brazilian Amazon. METHODOLOGY/PRINCIPAL FINDINGS: A cohort of 486 individuals was monitored using four cross-sectional surveys, where all participants were sampled regardless of symptoms (aggressive-active case detection), resulting in 1,383 microscopy and 1,400 polymerase chain reaction tests. Data on the same individuals were also obtained from the local surveillance facility (i.e., passive and active case detection), totaling 1,694 microscopy tests. Our model accommodates these multiple pathogen and case detection methods. This model is shown to outperform logistic regression in terms of interpretability of its parameters, ability to recover the true parameter values, and predictive performance. We reveal that the main infection determinant was the extent of forest, particularly during the rainy season and in close proximity to water bodies, and participation on forest activities. We find that time residing in Acrelandia (as a proxy for past malaria exposure) decreases infection risk but surprisingly increases the likelihood of reporting symptoms once infected, possibly because non-naïve settlers are only susceptible to more virulent Plasmodium strains. We suggest that the search for asymptomatic carriers should focus on those at greater risk of being infected but lower risk of reporting symptoms once infected. CONCLUSIONS/SIGNIFICANCE: The modeling framework presented here combines cross-sectional survey data and syndromic sentinel surveillance data to shed light on several aspects of malaria that are critical for public health policy. This framework can be adapted to enhance inference on infectious diseases whenever asymptomatic carriers are important and multiple datasets are available

Seasonal variability of multiple leaf traits captured by leaf spectroscopy at two temperate deciduous forests

Author Posting. © The Author(s), 2015. This is the author's version of the work. It is posted here for personal use, not for redistribution. The definitive version was published in Remote Sensing of Environment 179 (2016): 1-12, doi:10.1016/j.rse.2016.03.026.Understanding the temporal patterns of leaf traits is critical in determining the seasonality and magnitude of terrestrial carbon and water fluxes. However, robust and efficient ways to monitor the temporal dynamics of leaf traits are lacking. Here we assessed the potential of using leaf spectroscopy to predict leaf traits across their entire life cycle, forest sites, and light environments (sunlit vs. shaded) using a weekly sampled dataset across the entire growing season at two temperate deciduous forests. The dataset includes field measured leaf-level directional-hemispherical reflectance/transmittance together with seven important leaf traits [total chlorophyll (chlorophyll a and b), carotenoids, mass-based nitrogen concentration (Nmass), mass-based carbon concentration (Cmass), and leaf mass per area (LMA)]. All leaf properties, including leaf traits and spectra, varied significantly throughout the growing season, and displayed trait-specific temporal patterns. We used a Partial Least Square Regression (PLSR) analysis to estimate leaf traits from spectra, and found a significant capability of PLSR to capture the variability across time, sites, and light environment of all leaf traits investigated (R2=0.6~0.8 for temporal variability; R2=0.3~0.7 for cross-site variability; R2=0.4~0.8 for variability from light environments). We also tested alternative field sampling designs and found that for most leaf traits, biweekly leaf sampling throughout the growing season enabled accurate characterization of the leaf trait seasonal patterns. Increasing the sampling frequency improved in the estimation of Nmass, Cmass and LMA comparing with foliar pigments. Our results, based on the comprehensive analysis of spectra-trait relationships across time, sites and light environments, highlight the capacity and potential limitations to use leaf spectra to estimate leaf traits with strong seasonal variability, as an alternative to time-consuming traditional wet lab approaches.This research was supported by the Brown University–Marine Biological Laboratory graduate program in Biological and Environmental Sciences, and Marine Biological Laboratory start-up funding for JT. JT was also partially supported by the U.S. Department of Energy (U.S. DOE) Office of Biological and Environmental Research grant DE-SC0006951 and the National Science Foundation grants DBI-959333 and AGS-1005663. SPS was supported in part by the U.S. DOE contract No. DE-SC00112704 to Brookhaven National Laboratory. JW was supported by the NASA Earth and Space Science Fellowship (NESSF2014)

Integrating LiDAR data and multi-temporal aerial imagery to map wetland inundation dynamics using Google Earth Engine

The Prairie Pothole Region of North America is characterized by millions of depressional wetlands, which provide critical habitats for globally significant populations of migratory waterfowl and other wildlife species. Due to their relatively small size and shallow depth, these wetlands are highly sensitive to climate variability and anthropogenic changes, exhibiting inter- and intra-annual inundation dynamics. Moderate-resolution satellite imagery (e.g., Landsat, Sentinel) alone cannot be used to effectively delineate these small depressional wetlands. By integrating fine spatial resolution Light Detection and Ranging (LiDAR) data and multi-temporal (2009–2017) aerial images, we developed a fully automated approach to delineate wetland inundation extent at watershed scales using Google Earth Engine. Machine learning algorithms were used to classify aerial imagery with additional spectral indices to extract potential wetland inundation areas, which were further refined using LiDAR-derived landform depressions. The wetland delineation results were then compared to the U.S. Fish and Wildlife Service National Wetlands Inventory (NWI) geospatial dataset and existing global-scale surface water products to evaluate the performance of the proposed method. We tested the workflow on 26 watersheds with a total area of 16,576 km2 in the Prairie Pothole Region. The results showed that the proposed method can not only delineate current wetland inundation status but also demonstrate wetland hydrological dynamics, such as wetland coalescence through fill-spill hydrological processes. Our automated algorithm provides a practical, reproducible, and scalable framework, which can be easily adapted to delineate wetland inundation dynamics at broad geographic scales

Regional scale cropland carbon budgets: Evaluating a geospatial agricultural modeling system using inventory data

Accurate quantification and clear understanding of regional scale cropland carbon (C) cycling is critical for designing effective policies and management practices that can contribute toward stabilizing atmospheric CO2 concentrations. However, extrapolating site-scale observations to regional scales represents a major challenge confronting the agricultural modeling community. This study introduces a novel geospatial agricultural modeling system (GAMS) exploring the integration of the mechanistic Environmental Policy Integrated Climate model, spatially-resolved data, surveyed management data, and supercomputing functions for cropland C budgets estimates. This modeling system creates spatiallyexplicit modeling units at a spatial resolution consistent with remotely-sensed crop identification and assigns cropping systems to each of them by geo-referencing surveyed crop management information at the county or state level. A parallel computing algorithm was also developed to facilitate the computationally intensive model runs and output post-processing and visualization. We evaluated GAMS against National Agricultural Statistics Service (NASS) reported crop yields and inventory estimated county-scale cropland C budgets averaged over 2000e2008. We observed good overall agreement, with spatial correlation of 0.89, 0.90, 0.41, and 0.87, for crop yields, Net Primary Production (NPP), Soil Organic C (SOC) change, and Net Ecosystem Exchange (NEE), respectively. However, we also detected notable differences in the magnitude of NPP and NEE, as well as in the spatial pattern of SOC change. By performing crop-specific annual comparisons, we discuss possible explanations for the discrepancies between GAMS and the inventory method, such as data requirements, representation of agroecosystem processes, completeness and accuracy of crop management data, and accuracy of crop area representation. Based on these analyses, we further discuss strategies to improve GAMS by updating input data and by designing more efficient parallel computing capability to quantitatively assess errors associated with the simulation of C budget components. The modularized design of the GAMS makes it flexible to be updated and adapted for different agricultural models so long as they require similar input data, and to be linked with socio-economic models to understand the effectiveness and implications of diverse C management practices and policies

Comparison of Small- and Large-Footprint Lidar Characterization of Tropical Forest Aboveground Structure and Biomass: A Case Study From Central Gabon

NASA's Global Ecosystem Dynamic Investigation (GEDI) mission has been designed to measure forest structure using lidar waveforms to sample the earth's vegetation while in orbit aboard the International Space Station. In this paper, we used airborne large-footprint (LF) lidar measurements to simulate GEDI observations from which we retrieved ground elevation, vegetation height, and aboveground biomass (AGB). GEDI-like product accuracy was then assessed by comparing them to similar products derived from airborne small-footprint (SF) lidar measurements. The study focused on tropical forests and used data collected during the NASA and European Space Agency (ESA) AfriSAR ground and airborne campaigns in the Lope National Park in Central Gabon. The measurements covered a gradient of successional stages of forest development with different height, canopy density, and topography. The comparison of the two sensors shows that LF lidar waveforms and simulated waveforms from SF lidar are equivalent in their ability to estimate ground elevation (RMSE = 0.5 m, bias = 0.29 m) and maximum forest height (RMSE = 2.99 m, bias = 0.24 m) over the study area. The difference in the AGB estimated from both lidar instruments at the 1-ha spatial scale is small over the entire study area (RMSE = 6.34 Mg·ha-1, bias = 11.27 Mg·ha-1) and the bias is attributed to the impact of ground slopes greater than 10–20° on the LF lidar measurements of forest height. Our results support the ability of GEDILF lidar to measure the complex structure of humid tropical forests and provide AGB estimates comparable to SF-derived ones