Assessing the role of EO in biodiversity monitoring: options for integrating in-situ observations with EO within the context of the EBONE concept

The European Biodiversity Observation Network (EBONE) is a European contribution on terrestrial monitoring to GEO BON, the Group on Earth Observations Biodiversity Observation Network. EBONE’s aims are to develop a system of biodiversity observation at regional, national and European levels by assessing existing approaches in terms of their validity and applicability starting in Europe, then expanding to regions in Africa. The objective of EBONE is to deliver: 1. A sound scientific basis for the production of statistical estimates of stock and change of key indicators; 2. The development of a system for estimating past changes and forecasting and testing policy options and management strategies for threatened ecosystems and species; 3. A proposal for a cost-effective biodiversity monitoring system. There is a consensus that Earth Observation (EO) has a role to play in monitoring biodiversity. With its capacity to observe detailed spatial patterns and variability across large areas at regular intervals, our instinct suggests that EO could deliver the type of spatial and temporal coverage that is beyond reach with in-situ efforts. Furthermore, when considering the emerging networks of in-situ observations, the prospect of enhancing the quality of the information whilst reducing cost through integration is compelling. This report gives a realistic assessment of the role of EO in biodiversity monitoring and the options for integrating in-situ observations with EO within the context of the EBONE concept (cfr. EBONE-ID1.4). The assessment is mainly based on a set of targeted pilot studies. Building on this assessment, the report then presents a series of recommendations on the best options for using EO in an effective, consistent and sustainable biodiversity monitoring scheme. The issues that we faced were many: 1. Integration can be interpreted in different ways. One possible interpretation is: the combined use of independent data sets to deliver a different but improved data set; another is: the use of one data set to complement another dataset. 2. The targeted improvement will vary with stakeholder group: some will seek for more efficiency, others for more reliable estimates (accuracy and/or precision); others for more detail in space and/or time or more of everything. 3. Integration requires a link between the datasets (EO and in-situ). The strength of the link between reflected electromagnetic radiation and the habitats and their biodiversity observed in-situ is function of many variables, for example: the spatial scale of the observations; timing of the observations; the adopted nomenclature for classification; the complexity of the landscape in terms of composition, spatial structure and the physical environment; the habitat and land cover types under consideration. 4. The type of the EO data available varies (function of e.g. budget, size and location of region, cloudiness, national and/or international investment in airborne campaigns or space technology) which determines its capability to deliver the required output. EO and in-situ could be combined in different ways, depending on the type of integration we wanted to achieve and the targeted improvement. We aimed for an improvement in accuracy (i.e. the reduction in error of our indicator estimate calculated for an environmental zone). Furthermore, EO would also provide the spatial patterns for correlated in-situ data. EBONE in its initial development, focused on three main indicators covering: (i) the extent and change of habitats of European interest in the context of a general habitat assessment; (ii) abundance and distribution of selected species (birds, butterflies and plants); and (iii) fragmentation of natural and semi-natural areas. For habitat extent, we decided that it did not matter how in-situ was integrated with EO as long as we could demonstrate that acceptable accuracies could be achieved and the precision could consistently be improved. The nomenclature used to map habitats in-situ was the General Habitat Classification. We considered the following options where the EO and in-situ play different roles: using in-situ samples to re-calibrate a habitat map independently derived from EO; improving the accuracy of in-situ sampled habitat statistics, by post-stratification with correlated EO data; and using in-situ samples to train the classification of EO data into habitat types where the EO data delivers full coverage or a larger number of samples. For some of the above cases we also considered the impact that the sampling strategy employed to deliver the samples would have on the accuracy and precision achieved. Restricted access to European wide species data prevented work on the indicator ‘abundance and distribution of species’. With respect to the indicator ‘fragmentation’, we investigated ways of delivering EO derived measures of habitat patterns that are meaningful to sampled in-situ observations

Laser scanning applications in fluvial studies

Peer reviewe

Estimation of forest variables using airborne laser scanning

Airborne laser scanning can provide three-dimensional measurements of the forest canopy with high efficiency and precision. There are presently a large number of airborne laser scanning instruments in operation. The aims of the studies reported in this thesis were, to develop and validate methods for estimation of forest variables using laser data, and to investigate the influence of laser system parameters on the estimates. All studies were carried out in hemi-boreal forest at a test area in southwestern Sweden (lat. 58°30’N, long. 13°40’ E). Forest variables were estimated using regression models. On plot level, the Root Mean Square Error (RMSE) for mean tree height estimations ranged between 6% and 11% of the average value for different datasets and methods. The RMSE for stem volume estimations ranged between 19% and 26% of the average value for different datasets and methods. On stand level (area 0.64 ha), the RMSE was 3% and 11% of the average value for mean tree height and stem volume estimations, respectively. A simulation model was used to investigate the effect of different scanning angles on laser measurement of tree height and canopy closure. The effect of different scanning angles was different within different simulated forest types, e.g., different tree species. High resolution laser data were used for detection of individual trees. In total, 71% of the field measurements were detected representing 91% of the total stem volume. Height and crown diameter of the detected trees could be estimated with a RMSE of 0.63 m and 0.61 m, respectively. The magnitude of the height estimation errors was similar to what is usually achieved using field inventory. Using different laser footprint diameters (0.26 to 3.68 m) gave similar estimation accuracies. The tree species Norway spruce (Picea abies L. Karst.) and Scots pine (Pinus sylvestris L.) were discriminated at individual tree level with an accuracy of 95%. The results in this thesis show that airborne laser scanners are useful as forest inventory tools. Forest variables can be estimated on tree level, plot level and stand level with similar accuracies as traditional field inventories

Complexity and Dynamics of Semi-Arid Vegetation Structure, Function and Diversity Across Spatial Scales from Full Waveform Lidar

Semi-arid ecosystems cover approximately 40% of the earth’s terrestrial landscape and show high dynamicity in ecosystem structure and function. These ecosystems play a critical role in global carbon dynamics, productivity, and habitat quality. Semi-arid ecosystems experience a high degree of disturbance that can severely alter ecosystem services and processes. Understanding the structure-function relationships across spatial extents are critical in order to assess their demography, response to disturbance, and for conservation management. In this research, using state-of-the-art full waveform lidar (airborne and spaceborne) and field observations, I developed a framework to assess the complexity and dynamics of vegetation structure, function and diversity across spatial scales in a semi-arid ecosystem. Difficulty in differentiating low stature vegetation from bare ground is the key remote sensing challenge in semi-arid ecosystems. In this study, I developed a workflow to differentiate key plant functional types (PFTs) using both structural and biophysical variables derived from the full waveform lidar and an ensemble random forest technique. The results revealed that waveform lidar pulse width can clearly distinguish shrubs from bare ground. The models showed PFT classification accuracy of 0.81–0.86% and 0.60–0.70% at 10 m and 1 m spatial resolutions, respectively. I found that structural variables were more important than the biophysical variables to differentiate the PFTs in this study area. The study further revealed an overlap between the structural features of different PFTs (e.g. shrubs from trees). Using structural features, I derived three main functional traits (canopy height, plant area index and foliage height diversity) of shrubs and trees that describe canopy architecture and light use efficiency of the ecosystem. I evaluated the trends and patterns of functional diversity and their relationship with non-climatic abiotic factors and fire disturbance. In addition to the fine resolution airborne lidar, I used simulated large footprint spaceborne lidar representing the newly launched Global Ecosystem Dynamics Investigation system (GEDI, a lidar sensor on the International Space Station) to evaluate the potential of capturing functional diversity trends of semi-arid ecosystems at global scales. The consistency of diversity trends between the airborne lidar and GEDI confirmed GEDI’s potential to capture functional diversity. I found that the functional diversity in this ecosystem is mainly governed by the local elevation gradient, soil type, and slope. All three functional diversity indices (functional richness, functional evenness and functional divergence) showed a diversity breakpoint near elevations of 1500 m – 1700 m. Functional diversity of fire-disturbed areas revealed that the fires in our study area resulted in a more even and less divergent ecosystem state. Finally, I quantified aboveground biomass using the structural features derived from both the airborne lidar and GEDI data. Regional estimates of biomass can indicate whether an ecosystem is a net carbon sink or source as well as the ecosystem’s health (e.g. biodiversity). Further, the potential of large footprint lidar data to estimate biomass in semi-arid ecosystems are not yet fully explored due to the inherent overlapping vegetation responses in the ground signals that can be affected by the ground slope. With a correction to the slope effect, I found that large footprint lidar can explain 42% of variance of biomass with a RMSE of 351 kg/ha (16% RMSE). The model estimated 82% of the study area with less than 50% uncertainty in biomass estimates. The cultivated areas and the areas with high functional richness showed the highest uncertainties. Overall, this dissertation establishes a novel framework to assess the complexity and dynamics of vegetation structure and function of a semi-arid ecosystem from space. This work enhances our understanding of the present state of an ecosystem and provides a foundation for using full waveform lidar to understand the impact of these changes to ecosystem productivity, biodiversity and habitat quality in the coming decades. The methods and algorithms in this dissertation can be directly applied to similar ecosystems with relevant corrections for the appropriate sensor. In addition, this study provides insights to related NASA missions such as ICESat-2 and future NASA missions such as NISAR for deriving vegetation structure and dynamics related to disturbance

AUTOMATED TREE-LEVEL FOREST QUANTIFICATION USING AIRBORNE LIDAR

Traditional forest management relies on a small field sample and interpretation of aerial photography that not only are costly to execute but also yield inaccurate estimates of the entire forest in question. Airborne light detection and ranging (LiDAR) is a remote sensing technology that records point clouds representing the 3D structure of a forest canopy and the terrain underneath. We present a method for segmenting individual trees from the LiDAR point clouds without making prior assumptions about tree crown shapes and sizes. We then present a method that vertically stratifies the point cloud to an overstory and multiple understory tree canopy layers. Using the stratification method, we modeled the occlusion of higher canopy layers with respect to point density. We also present a distributed computing approach that enables processing the massive data of an arbitrarily large forest. Lastly, we investigated using deep learning for coniferous/deciduous classification of point cloud segments representing individual tree crowns. We applied the developed methods to the University of Kentucky Robinson Forest, a natural, majorly deciduous, closed-canopy forest. 90% of overstory and 47% of understory trees were detected with false positive rates of 14% and 2% respectively. Vertical stratification improved the detection rate of understory trees to 67% at the cost of increasing their false positive rate to 12%. According to our occlusion model, a point density of about 170 pt/m² is needed to segment understory trees located in the third layer as accurately as overstory trees. Using our distributed processing method, we segmented about two million trees within a 7400-ha forest in 2.5 hours using 192 processing cores, showing a speedup of ~170. Our deep learning experiments showed high classification accuracies (~82% coniferous and ~90% deciduous) without the need to manually assemble the features. In conclusion, the methods developed are steps forward to remote, accurate quantification of large natural forests at the individual tree level

lidR : an R package for analysis of Airborne Laser Scanning (ALS) data

Airborne laser scanning (ALS) is a remote sensing technology known for its applicability in natural resources management. By quantifying the three-dimensional structure of vegetation and underlying terrain using laser technology, ALS has been used extensively for enhancing geospatial knowledge in the fields of forestry and ecology. Structural descriptions of vegetation provide a means of estimating a range of ecologically pertinent attributes, such as height, volume, and above-ground biomass. The efficient processing of large, often technically complex datasets requires dedicated algorithms and software. The continued promise of ALS as a tool for improving ecological understanding is often dependent on user-created tools, methods, and approaches. Due to the proliferation of ALS among academic, governmental, and private-sector communities, paired with requirements to address a growing demand for open and accessible data, the ALS community is recognising the importance of free and open-source software (FOSS) and the importance of user-defined workflows. Herein, we describe the philosophy behind the development of the lidR package. Implemented in the R environment with a C/C++ backend, lidR is free, open-source and cross-platform software created to enable simple and creative processing workflows for forestry and ecology communities using ALS data. We review current algorithms used by the research community, and in doing so raise awareness of current successes and challenges associated with parameterisation and common implementation approaches. Through a detailed description of the package, we address the key considerations and the design philosophy that enables users to implement user-defined tools. We also discuss algorithm choices that make the package representative of the ‘state-of-the-art' and we highlight some internal limitations through examples of processing time discrepancies. We conclude that the development of applications like lidR are of fundamental importance for developing transparent, flexible and open ALS tools to ensure not only reproducible workflows, but also to offer researchers the creative space required for the progress and development of the discipline

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

Analyzing high resolution topography for advancing the understanding of mass and energy transfer through landscapes: A review

International audienceThe study of mass and energy transfer across landscapes has recently evolved to comprehensive considerations acknowledging the role of biota and humans as geomorphic agents, as well as the importance of small-scale landscape features. A contributing and supporting factor to this evolution is the emergence over the last two decades of technologies able to acquire high resolution topography (HRT) (meter and sub-meter resolution) data. Landscape features can now be captured at an appropriately fine spatial resolution at which surface processes operate; this has revolutionized the way we study Earth-surface processes. The wealth of information contained in HRT also presents considerable challenges. For example, selection of the most appropriate type of HRT data for a given application is not trivial. No definitive approach exists for identifying and filtering erroneous or unwanted data, yet inappropriate filtering can create artifacts or eliminate/distort critical features. Estimates of errors and uncertainty are often poorly defined and typically fail to represent the spatial heterogeneity of the dataset, which may introduce bias or error for many analyses. For ease of use, gridded products are typically preferred rather than the more information-rich point cloud representations. Thus many users take advantage of only a fraction of the available data, which has furthermore been subjected to a series of operations often not known or investigated by the user. Lastly, standard HRT analysis work-flows are yet to be established for many popular HRT operations, which has contributed to the limited use of point cloud data.In this review, we identify key research questions relevant to the Earth-surface processes community within the theme of mass and energy transfer across landscapes and offer guidance on how to identify the most appropriate topographic data type for the analysis of interest. We describe the operations commonly performed from raw data to raster products and we identify key considerations and suggest appropriate work-flows for each, pointing to useful resources and available tools. Future research directions should stimulate further development of tools that take advantage of the wealth of information contained in the HRT data and address the present and upcoming research needs such as the ability to filter out unwanted data, compute spatially variable estimates of uncertainty and perform multi-scale analyses. While we focus primarily on HRT applications for mass and energy transfer, we envision this review to be relevant beyond the Earth-surface processes community for a much broader range of applications involving the analysis of HRT

An experimental investigation into ALS uncertainty and its impact on environmental applications

This study takes an experimental approach to investigating the reliability and repeatability of an airborne laser scanning (ALS) survey. The ability to characterise an area precisely in 3-D using ALS is essential for multi-temporal analysis where change detection is an important application. The reliability and consistency between two ALS datasets is discussed in the context of uncertainty within a single epoch and in the context of well known point- and grid-based descriptors and metrics. The implications of repeatability, verifiability and reliability are discussed in the context of environmental applications, specifically concerning forestry where high resolution ALS surveys are commonly used for forest mensuration over large areas. The study used a regular 10-by-10 layout of standard school tables and decreased the separation from 2.5 metres apart to 0.5 metres in order to evaluate the effects of object separation on their detection. Each configuration was scanned twice using the same ALS scanning parameters and the difference between the datasets is investigated and discussed. The results quantify uncertainty in the ability of ALS to characterise objects, estimate vertical heights and interpret features / objects with certainty. The results show that repeat scanning of the same features under the same conditions result in a laser point cloud with different properties. Objects that are expected to be present in 40 points per metre2 laser point cloud are absent, and the investigation reveals that irregular point spacing and lack of consideration of the ALS footprint size and the interaction with the object of interest are significant factors in the detection and characterisation of features. The results strongly suggest that characterisation of error is important and relevant to environmental applications that use multi-epoch ALS or data with high resolution / point density for object detection and characterisatio