Ash Tree Identification Based on the Integration of Hyperspectral Imagery and High-density Lidar Data

Monitoring and management of ash trees has become particularly important in recent years due to the heightened risk of attack from the invasive pest, the emerald ash borer (EAB). However, distinguishing ash from other deciduous trees can be challenging. Both hyperspectral imagery and Light detection and ranging (LiDAR) data are two valuable data sources that are often used for tree species classification. Hyperspectral imagery measures detailed spectral reflectance related to the biochemical properties of vegetation, while LiDAR data measures the three-dimensional structure of tree crowns related to morphological characteristics. Thus, the accuracy of vegetation classification may be improved by combining both techniques. Therefore, the objective of this research is to integrate hyperspectral imagery and LiDAR data for improving ash tree identification. Specifically, the research aims include: 1) using LiDAR data for individual tree crowns segmentation; 2) using hyperspectral imagery for extraction of relative pure crown spectra; 3) fusing hyperspectral and LiDAR data for ash tree identification. It is expected that the classification accuracy of ash trees will be significantly improved with the integration of hyperspectral and LiDAR techniques. Analysis results suggest that, first, 3D crown structures of individual trees can be reconstructed using a set of generalized geometric models which optimally matched LiDAR-derived raster image, and crown widths can be further estimated using tree height and shape-related parameters as independent variables and ground measurement of crown widths as dependent variables. Second, with constrained linear spectral mixture analysis method, the fractions of all materials within a pixel can be extracted, and relative pure crown-scale spectra can be further calculated using illuminated-leaf fraction as weighting factors for tree species classification. Third, both crown shape index (SI) and coefficient of variation (CV) can be extracted from LiDAR data as invariant variables in tree’s life cycle, and improve ash tree identification by integrating with pixel-weighted crown spectra. Therefore, three major contributions of this research have been made in the field of tree species classification:1) the automatic estimation of individual tree crown width from LiDAR data by combining a generalized geometric model and a regression model, 2) the computation of relative pure crown-scale spectral reflectance using a pixel-weighting algorithm for tree species classification, 3) the fusion of shape-related structural features and pixel-weighted crown-scale spectral features for improving of ash tree identification

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

Characterization of Acantharea-Phaeocystis photosymbioses: distribution, abundance, specificity, maintenance and host-control

Microbial eukaryotes (protists) are important contributors to marine biogeochemistry and play essential roles as both producers and consumers in marine ecosystems. Among protists, mixotrophs—those that use both heterotrophy and autotrophy to meet their energy requirements—are especially important to primary production in low-nutrient regions. Acantharian protists (clades E & F) accomplish mixotrophy by hosting ​Phaeocystis spp.​ as algal endosymbionts and are extremely abundant in subtropical low-nutrient regions where they form productivity hotspots. Despite their ecological importance, acantharians remain understudied due to their structural fragility and inability to survive in culture. In order to overcome these challenges and illuminate key aspects of acantharian biology and ecology—including distribution, abundance, and specificity and specialization of symbioses—single-cell RNA sequencing methods were developed for acantharians and used alongside environmental metabarcode sequencing and high-throughput, in-situ imaging. Major findings from this thesis were that i) acantharian cell (> 250 µm) concentrations decrease with depth, which correlates to patterns in relative sequence abundances for acantharian clades with known morphologies but not for those lacking known morphology, and that ii) while individual acantharians simultaneously harbor multiple symbiont species, intra-host symbiont communities do not match environmental communities, providing evidence for multiple uptake events but against continuous symbiont turnover, and that iii) photosynthesis genes are upregulated in symbiotic Phaeocystis​, reflecting enhanced productivity in symbiosis, but DNA replication and cell-cycle genes are downregulated, demonstrating that hosts suppress symbiont cell division. Moreover, storage carbohydrate and lipid biosynthesis and metabolism genes are downregulated in symbiotic ​Phaeocystis​, suggesting fixed carbon is relinquished to acantharian hosts. Gene expression patterns indicate that symbiotic ​Phaeocystis​ is not nutrient limited and likely benefits from host-supplied ammonium and urea, thus providing evidence for nutrient transfer between hosts and symbionts. Interestingly, genes associated with protein kinase signaling pathways that promote cell proliferation are downregulated in symbiotic ​Phaeocystis​. Deactivation of these genes may prevent symbionts from overgrowing hosts and therefore represents a key component of maintaining the symbiosis. This research contributes new insights into the ecologically relevant photosymbioses between Acantharea and ​Phaeocystis​ and illustrates the benefits of combining single-cell sequencing and imaging technologies to illuminate important microbial relationships in marine ecosystems.Okinawa Institute of Science and Technology Graduate Universit

Mapping alpine treeline with high resolution imagery and LiDAR data in North Cascades National Park, Washington

We evaluated several approaches for the automated detection and mapping of trees and treeline in an alpine environment. Using multiple remote sensing platforms and software programs, we evaluated both pixel-based and object-based classification approaches in combination with high-resolution multispectral imagery and LiDAR-derived tree height data. The study area in North Cascades National Park included over 10,000 hectares of some of the most rugged terrain in the conterminous U.S. Through the use of the Normalized Difference Vegetation Index (NDVI), differences in illumination conditions created by steep slopes and tall trees were minimized. Data fusion of the multispectral imagery, NDVI, and LiDAR-derived tree height data produced the highest percent accuracies using both the pixel-based (88.4%) and the object-based classifications (92.9%). These results demonstrate that either method will produce an acceptable level of accuracy, and that the availability of a near-infrared band to calculate NDVI is extremely important. The NDVI used in conjunction with the multispectral imagery helped to minimize issues with shadows caused by rugged terrain. Furthermore, LiDAR-derived tree heights were used to augment classification routines to achieve even greater accuracy; where shadows were too dark to produce meaningful NDVI values, the LiDAR-derived tree height data was instrumental in helping to distinguish trees from other land cover types. Both the pixel-based and the object-based approaches hold considerable promise for automated mapping and monitoring of the treeline ecotone; however, the pixel-based approach may be superior because it is more straightforward and easily replicable compared to the object-based approach. These treeline mapping efforts will enhance future ecological treeline research by producing more accurate detections of trees and estimations of treeline position, and will be instrumental in building time series of imagery for future scientists conducting change detection studies at treeline

Tree Classification with Fused Mobile Laser Scanning and Hyperspectral Data

Mobile Laser Scanning data were collected simultaneously with hyperspectral data using the Finnish Geodetic Institute Sensei system. The data were tested for tree species classification. The test area was an urban garden in the City of Espoo, Finland. Point clouds representing 168 individual tree specimens of 23 tree species were determined manually. The classification of the trees was done using first only the spatial data from point clouds, then with only the spectral data obtained with a spectrometer, and finally with the combined spatial and hyperspectral data from both sensors. Two classification tests were performed: the separation of coniferous and deciduous trees, and the identification of individual tree species. All determined tree specimens were used in distinguishing coniferous and deciduous trees. A subset of 133 trees and 10 tree species was used in the tree species classification. The best classification results for the fused data were 95.8% for the separation of the coniferous and deciduous classes. The best overall tree species classification succeeded with 83.5% accuracy for the best tested fused data feature combination. The respective results for paired structural features derived from the laser point cloud were 90.5% for the separation of the coniferous and deciduous classes and 65.4% for the species classification. Classification accuracies with paired hyperspectral reflectance value data were 90.5% for the separation of coniferous and deciduous classes and 62.4% for different species. The results are among the first of their kind and they show that mobile collected fused data outperformed single-sensor data in both classification tests and by a significant margin

Sub-canopy terrain modelling for archaeological prospecting in forested areas through multiple-echo discrete-pulse laser ranging: a case study from Chopwell Wood, Tyne & Wear

Airborne Light Detection and Ranging (LiDAR) technology is assessed for its effectiveness as a tool for measuring terrain under forest canopy. To evaluate the capability of multiple-return discrete-pulse airborne laser ranging for detecting and resolving sub-canopy archaeological features, LiDAR data were collected from a helicopter over a forest near Gateshead in July 2009. Coal mining and timber felling have characterised Chopwell Wood, a mixed coniferous and deciduous woodland of 360 hectares, since the Industrial Revolution. The state-of-the-art Optech ALTM 3100EA LiDAR system operated at 70,000 pulses per second and raw data were acquired over the study area at a point density of over 30 points per square metre. Reference terrain elevation data were acquired on-site to ‘train’ the progressive densification filtering algorithm of Axelsson (1999; 2000) to identify laser reflections from the terrain surface. A number of sites, offering a variety of tree species, variable terrain roughness & gradient and understorey vegetation cover of varying density, were identified in the wood to assess the accuracy of filtered LiDAR terrain data. Results showed that the laser scanner over-estimated the elevation of reference terrain data by 13±17 cm under deciduous canopy and 23±18 cm under coniferous canopy. Terrain point density was calculated as 4.1 and 2.4 points per square metre under deciduous and coniferous forest, respectively. Classified terrain points were modelled with the kriging interpolation technique and topographic archaeological features, such as coal tubways (transportation routes) and areas of subsidence over relic mine shafts, were identified in digital terrain models (DTMs) using advanced exaggeration and artificial illumination techniques. Airborne LiDAR is capable of recording high quality terrain data even under the most dense forest canopy, but the accuracy and density of terrain data are controlled by a combination of tree species, forest management practices and understorey vegetation

Individual Tree Species Classification from Airborne Multisensor Imagery Using Robust PCA

Remote sensing of individual tree species has many applications in resource management, biodiversity assessment, and conservation. Airborne remote sensing using light detection and ranging (LiDAR) and hyperspectral sensors has been used extensively to extract biophysical traits of vegetation and to detect species. However, its application for individual tree mapping remains limited due to the technical challenges of precise coalignment of images acquired from different sensors and accurately delineating individual tree crowns (ITCs). In this study, we developed a generic workflow to map tree species at ITC level from hyperspectral imagery and LiDAR data using a combination of well established and recently developed techniques. The workflow uses a nonparametric image registration approach to coalign images, a multiclass normalized graph cut method for ITC delineation, robust principal component analysis for feature extraction, and support vector machine for species classification. This workflow allows us to automatically map tree species at both pixel- and ITC-level. Experimental tests of the technique were conducted using ground data collected from a fully mapped temperate woodland in the UK. The overall accuracy of pixel-level classification was 91%, while that of ITC-level classification was 61%. The test results demonstrate the effectiveness of the approach, and in particular the use of robust principal component analysis to prune the hyperspectral dataset and reveal subtle difference among species.Department for Environment, Food and Rural AffairsThis is the author accepted manuscript. The final version is available from IEEE via http://dx.doi.org/10.1109/JSTARS.2016.256940

KLASIFIKACIJA VRSTA DRVEĆA U PRIRODNOJ URBANOJ ŠUMI KORISTEĆI WORLDVIEW-2 SATELITSKE SNIMKE I LIDAR

A detailed tree species inventory is needed to sustainably manage a natural, mixed, heterogeneous urban forest. An object-based image analysis of a combination of high-resolution WorldView-2 multi-spectral satellite imagery and airborne laser scanning (LiDAR) data was tested for classification of individual tree crowns of five different tree species. The model training data were obtained from a systematic grid of plots in the forest. In total, 304 coniferous (Norway spruce and Scots pine) and 270 deciduous (European beech, Sessile and Pedunculate oak (combined), and Sweet chestnut) trees were identified in the field. The classification was performed by applying the support vector machine model. An accuracy assessment was performed by calculating a confusion matrix to evaluate the accuracy of the classification output by comparing the classification result to the independent test data. The overall accuracy of the classification was 58 %.Osnovni zadatak gospodarenja šumama je provedba inventure drveća. Posebno se to odnosi na blisko prirodi gospodarene urbane šume. Cilj ovog istraživanja je provjeriti može li se metoda analize snimaka (tzv. object-based image analysis – OBIA) kombinacijom WorldView-2 multispektralnih satelitskih snimaka visoke prostorne rezulocije i laserskog skeniranja (LiDAR-a) koristiti za uspješnu klasifikaciju krošanja pojedinačnih stabala različitih vrsta drveća u prirodnim, mješovitim i heterogenim urbanim šumama u Ljubljani (Slika 1).Terenska klasifikacija vrsta drveća provedena je postavljanjem mreže kružnih ploha (100x100 m) veličine od 2000 m2. Na svakoj od 332 plohe, registrirana su stabla iz dominantnog i kodominantnog sloja drveća. Ukupno je za analizu izdvojeno 574 stabala, od čega 304 stabla četinjača (obična smreka, obični bor) i 270 stabala listača (obična bukva, hrast lužnjak i kitnjak, pitomi kesten). Polovica uzorkovanih stabala tj. njihovih krošanja korišteno je kao probni set podataka u nadgledanoj klasifikaciji, dok je druga polovica uzorkovanih stabala korištena za ocjenu točnosti provedene klasifikacije (tzv. testni podaci).Za klasifikaciju su korištene WorldView-2 multispektralne satelitske snimke (8-kanalne), tzv. ‘Red-Edge’ normalizirani razlikovni vegetacijski indeks (NDVI) izračunat pomoću rubnog crvenog i crvenog spektralnog kanala te digitalni model krošanja (tzv. Digital Canopy Model – DCM) dobiven iz LiDAR podataka. Prostorna rezolucija WorldView-2 satelitskih snimaka iznosila je 1 m.Klasifikacija je provedena pomoću Exelis ENVI 5 kompjuterskog programa, primjenjujući tzv. pomoćni vektorski model. Preciznost procjene izračunata je na temelju izračunate matrice pogreške, uspoređujući rezultate klasifikacije s testnim podacima. Također je provedena analiza glavnih komponenata, koja je pokazala da je najveća varijabilnost (oko 85 %) objašnjena pomoću rubnog crvenog spektralnog kanala (705–745 nm), bližeg infracrvenog kanala – 1 (770–895 nm) te bližeg infracrvenog spektralnog kanala – 2 (860–1040 nm) WorldView-2 snimaka.Metoda analize snimaka (OBIA) kombinacijom WorldView-2 satelitskih snimaka I LiDAR podataka korištena u ovom istraživanju pokazala je obećavajuće rezultate pri klasifikaciji vrsta drveća u gustim, mješovitim i heterogenim prirodnim urbanim šumama, u kojima često dolazi do isprepletanja krošanja. Najpouzdaniji dobiveni rezultati odnose se na razlikovanje četinjača i listača. Kod sastojina s gustim krošnjama, posebice kod listača kod kojih je teško napraviti delineaciju krošanja, otežana je i manualna i automatska delineacija (segmentacija) krošanja. Ovo istraživanje novi je dokaz kako se primjenom podataka dobivenih metodama daljinskih istraživanja pruža mogućnost uštede u vremenu pri inventarizaciji vrsta drveća.Ukupna preciznost identifikacije iznosila je 58 %, a Kappa koeficijent je iznosio 0.421 (Tablica 4). Za svaku vrstu drveća izračunata je preciznost na osnovi razlike između preciznosti koju navodi proizvođač (postotak točno identificiranih piksela u odnosu na ukupan broj piksela na probnim podacima) i preciznosti korisnika. Rezultati tako dobivene preciznosti iznosili su 80 % za smreku, 70 % za hrastove lužnjak i kitnjak, 50 % za obični bor, 38 % za bukvu, te manje od 1 % za pitomi kesten

Determining successional stage of temperate coniferous forests with Landsat satellite data

Thematic Mapper (TM) digital imagery was used to map forest successional stages and to evaluate spectral differences between old-growth and mature forests in the central Cascade Range of Oregon. Relative sun incidence values were incorporated into the successional stage classification to compensate for topographic induced variation. Relative sun incidence improved the classification accuracy of young successional stages, but did not improve the classification accuracy of older, closed canopy forest classes or overall accuracy. TM bands 1, 2, and 4; the normalized difference vegetation index (NDVI); and TM 4/3, 4/5, and 4/7 band ratio values for old-growth forests were found to be significantly lower than the values of mature forests (P less than or equal to 0.010). Wetness and the TM 4/5 and 4/7 band ratios all had low correlations to relative sun incidence (r(exp 2) less than or equal to 0.16). The TM 4/5 band ratio was named the 'structural index' (SI) because of its ability to distinguish between mature and old-growth forests and its simplicity