Terrestrial laser scanning for forest monitoring

Remote sensing data worden beschouwd als één van de belangrijkste databronnen voor het observeren van uitgestrekte bosgebieden. Het belangrijkste doel van dit proefschrift is om het potentieel van terrestrische LiDAR voor het monitoren van bossen te onderzoeken en om methoden te ontwikkelen voor het afleiden van accurate in-situ referentiedata voor bos monitoring

Extracting individual trees from lidar point clouds using treeseg

Recent studies have demonstrated the potential of lidar-derived methods in plant ecology and forestry. One limitation to these methods is accessing the information content of point clouds, from which tree-scale metrics can be retrieved. This is currently undertaken through laborious and time-consuming manual segmentation of tree-level point clouds from larger-area point clouds, an effort that is impracticable across thousands of stems. 2. Here, we present treeseg, an open-source software to automate this task. This method utilises generic point cloud processing techniques including Euclidean clustering, principal component analysis, region-based segmentation, shape fitting and connectivity testing. This data-driven approach uses few a priori assumptions of tree architecture, and transferability across lidar instruments is constrained only by data quality requirements. 3. We demonstrate the treeseg algorithm here on data acquired from both a structurally simple open forest and a complex tropical forest. Across these data, we successfully automatically extract 96% and 70% of trees, respectively, with the remainder requiring some straightforward manual segmentation. 4. treeseg allows ready and quick access to tree-scale information contained in lidar point clouds. treeseg should help contribute to more wide-scale uptake of lidarderived methods to applications ranging from the estimation of carbon stocks through to descriptions of plant form and function

CICLAD: A Fast and Memory-efficient Closed Itemset Miner for Streams

Mining association rules from data streams is a challenging task due to the (typically) limited resources available vs. the large size of the result. Frequent closed itemsets (FCI) enable an efficient first step, yet current FCI stream miners are not optimal on resource consumption, e.g. they store a large number of extra itemsets at an additional cost. In a search for a better storage-efficiency trade-off, we designed Ciclad,an intersection-based sliding-window FCI miner. Leveraging in-depth insights into FCI evolution, it combines minimal storage with quick access. Experimental results indicate Ciclad's memory imprint is much lower and its performances globally better than competitor methods.Comment: KDD2

New perspectives on the ecology of tree structure and tree communities through terrestrial laser scanning

Terrestrial laser scanning (TLS) opens up the possibility of describing the three-dimensional structures of trees in natural environments with unprecedented detail and accuracy. It is already being extensively applied to describe how ecosystem biomass and structure vary between sites, but can also facilitate major advances in developing and testing mechanistic theories of tree form and forest structure, thereby enabling us to understand why trees and forests have the biomass and three-dimensional structure they do. Here we focus on the ecological challenges and benefits of understanding tree form, and highlight some advances related to capturing and describing tree shape that are becoming possible with the advent of TLS. We present examples of ongoing work that applies, or could potentially apply, new TLS measurements to better understand the constraints on optimization of tree form. Theories of resource distribution networks, such as metabolic scaling theory, can be tested and further refined. TLS can also provide new approaches to the scaling of woody surface area and crown area, and thereby better quantify the metabolism of trees. Finally, we demonstrate how we can develop a more mechanistic understanding of the effects of avoidance of wind risk on tree form and maximum size. Over the next few years, TLS promises to deliver both major empirical and conceptual advances in the quantitative understanding of trees and tree-dominated ecosystems, leading to advances in understanding the ecology of why trees and ecosystems look and grow the way they do

Like trainer, like bot? Inheritance of bias in algorithmic content moderation

The internet has become a central medium through which `networked publics' express their opinions and engage in debate. Offensive comments and personal attacks can inhibit participation in these spaces. Automated content moderation aims to overcome this problem using machine learning classifiers trained on large corpora of texts manually annotated for offence. While such systems could help encourage more civil debate, they must navigate inherently normatively contestable boundaries, and are subject to the idiosyncratic norms of the human raters who provide the training data. An important objective for platforms implementing such measures might be to ensure that they are not unduly biased towards or against particular norms of offence. This paper provides some exploratory methods by which the normative biases of algorithmic content moderation systems can be measured, by way of a case study using an existing dataset of comments labelled for offence. We train classifiers on comments labelled by different demographic subsets (men and women) to understand how differences in conceptions of offence between these groups might affect the performance of the resulting models on various test sets. We conclude by discussing some of the ethical choices facing the implementers of algorithmic moderation systems, given various desired levels of diversity of viewpoints amongst discussion participants.Comment: 12 pages, 3 figures, 9th International Conference on Social Informatics (SocInfo 2017), Oxford, UK, 13--15 September 2017 (forthcoming in Springer Lecture Notes in Computer Science

Assessment of Bias in Pan-Tropical Biomass Predictions

Above-ground biomass (AGB) is an essential descriptor of forests, of use in ecological and climate-related research. At tree- and stand-scale, destructive but direct measurements of AGB are replaced with predictions from allometric models characterizing the correlational relationship between AGB, and predictor variables including stem diameter, tree height and wood density. These models are constructed from harvested calibration data, usually via linear regression. Here, we assess systematic error in out-of-sample predictions of AGB introduced during measurement, compilation and modeling of in-sample calibration data. Various conventional bivariate and multivariate models are constructed from open access data of tropical forests. Metadata analysis, fit diagnostics and cross-validation results suggest several model misspecifications: chiefly, unaccounted for inconsistent measurement error in predictor variables between in- and out-of-sample data. Simulations demonstrate conservative inconsistencies can introduce significant bias into tree- and stand-scale AGB predictions. When tree height and wood density are included as predictors, models should be modified to correct for bias. Finally, we explore a fundamental assumption of conventional allometry, that model parameters are independent of tree size. That is, the same model can provide predictions of consistent trueness irrespective of size-class. Most observations in current calibration datasets are from smaller trees, meaning the existence of a size dependency would bias predictions for larger trees. We determine that detecting the absence or presence of a size dependency is currently prevented by model misspecifications and calibration data imbalances. We call for the collection of additional harvest data, specifically under-represented larger trees

Innovations in Ground and Airborne Technologies as Reference and for Training and Validation: Terrestrial Laser Scanning (TLS)

The use of terrestrial laser scanning (TLS) to provide accurate estimates of 3D forest canopy structure and above-ground biomass (AGB) has developed rapidly. Here, we provide an overview of the state of the art in using TLS for estimating forest structure for AGB. We provide a general overview of TLS methods and then outline the advantages and limitations of TLS for estimating AGB. We discuss the specific type of measurements that TLS can provide, tools and methods that have been developed for turning TLS point clouds into quantifiable metrics of tree size and volume, as well as some of the challenges to improving these measurements. We discuss the role of TLS for enabling accurate calibration and validation (cal/val) of Earth observation (EO)-derived estimates of AGB from spaceborne lidar and RADAR missions. We give examples of the types of TLS equipment that are in use and how these might develop in future, and we show examples of where TLS has already been applied to measuring AGB in the tropics in particular. Comparing TLS with harvested AGB shows r2 > 0.95 for all studies thus far, with absolute agreement to within 10% at the individual tree level for all trees and to within 2% in the majority of cases. Current limitations to the uptake of TLS include the capital cost of some TLS equipment, processing complexity and the relatively small coverage that is possible. We argue that combining TLS measurements with the existing ground-based survey approaches will allow improved allometric models and better cal/val, resulting in improved regional and global estimates of AGB from space, with better-characterised, lower uncertainties. The development of new, improved equipment and methods will accelerate this process and make TLS more accessible

Benchmarking airborne laser scanning tree segmentation algorithms in broadleaf forests shows high accuracy only for canopy trees

Individual tree segmentation from airborne laser scanning data is a longstanding and important challenge in forest remote sensing. Tree segmentation algorithms are widely available, but robust intercomparison studies are rare due to the difficulty of obtaining reliable reference data. Here we provide a benchmark data set for temperate and tropical broadleaf forests generated from labelled terrestrial laser scanning data. We compared the performance of four widely used tree segmentation algorithms against this benchmark data set. All algorithms performed reasonably well on the canopy trees. The point cloud-based algorithm AMS3D (Adaptive Mean Shift 3D) had the highest overall accuracy, closely followed by the 2D raster based region growing algorithm Dalponte2016 +. However, all algorithms failed to accurately segment the understory trees. This result was consistent across both forest types. This study emphasises the need to assess tree segmentation algorithms directly using benchmark data, rather than comparing with forest indices such as biomass or the number and size distribution of trees. We provide the first openly available benchmark data set for tropical forests and we hope future studies will extend this work to other regions

Finite element analysis of trees in the wind based on terrestrial laser scanning data

Wind damage is an important driver of forest structure and dynamics, but it is poorly understood in natural broadleaf forests. This paper presents a new approach in the study of wind damage: combining terrestrial laser scanning (TLS) data and finite element analysis. Recent advances in tree reconstruction from TLS data allowed us to accurately represent the 3D geometry of a tree in a mechanical simulation, without the need for arduous manual mapping or simplifying assumptions about tree shape. We used this simulation to predict the mechanical strains produced on the trunks of 21 trees in Wytham Woods, UK, and validated it using strain data measured on these same trees. For a subset of five trees near the anemometer, the model predicted a five-minute time-series of strain with a mean cross-correlation coefficient of 0.71, when forced by the locally measured wind speed data. Additionally, the maximum strain associated with a 5 ms−1 or 15 ms-1 wind speed was well predicted by the model (N = 17, R2 = 0.81 and R2 = 0.79, respectively). We also predicted the critical wind speed at which the trees will break from both the field data and models and find a good overall agreement (N = 17, R2 = 0.40). Finally, the model predicted the correct trend in the fundamental frequencies of the trees (N = 20, R2 = 0.38) although there was a systematic underprediction, possibly due to the simplified treatment of material properties in the model. The current approach relies on local wind data, so must be combined with wind flow modelling to be applicable at the landscape-scale or over complex terrain. This approach is applicable at the plot level and could also be applied to open-grown trees, such as in cities or parks

Leaf and wood classification framework for terrestrial LiDAR point clouds

Methods in Ecology and Evolution published by John Wiley & Sons Ltd on behalf of British Ecological Society. Leaf and wood separation is a key step to allow a new range of estimates from Terrestrial LiDAR data, such as quantifying above-ground biomass, leaf and wood area and their 3D spatial distributions. We present a new method to separate leaf and wood from single tree point clouds automatically. Our approach combines unsupervised classification of geometric features and shortest path analysis. The automated separation algorithm and its intermediate steps are presented and validated. Validation consisted of using a testing framework with synthetic point clouds, simulated using ray-tracing and 3D tree models and 10 field scanned tree point clouds. To evaluate results we calculated accuracy, kappa coefficient and F-score. Validation using simulated data resulted in an overall accuracy of 0.83, ranging from 0.71 to 0.94. Per tree average accuracy from synthetic data ranged from 0.77 to 0.89. Field data results presented and overall average accuracy of 0.89. Analysis of each step showed accuracy ranging from 0.75 to 0.98. F-scores from both simulated and field data were similar, with scores from leaf usually higher than for wood. Our separation method showed results similar to others in literature, albeit from a completely automated workflow. Analysis of each separation step suggests that the addition of path analysis improved the robustness of our algorithm. Accuracy can be improved with per tree parameter optimization. The library containing our separation script can be easily installed and applied to single tree point cloud. Average processing times are below 10 min for each tree