Search Results (14)

The precise extractions of tree components such as wood (i.e., trunk and branches) and leaves are fundamental prerequisites for obtaining the key attributes of trees, which will provide significant benefits for ecological and physiological studies and forest applications. Terrestrial laser scanning technology offers an efficient means for acquiring three-dimensional information on tree attributes, and has marked potential for extracting the detailed tree attributes of tree components. However, previous studies on wood–leaf separation exhibited limitations in unsupervised adaptability and robustness to complex tree architectures, while demonstrating inadequate performance in fine branch detection. This study proposes a novel unsupervised model (NE-PC) that synergizes geometric features with graph-based path analysis to achieve accurate wood–leaf classification without training samples or empirical parameter tuning. First, the boundary-preserved supervoxel segmentation (BPSS) algorithm was adapted to generate supervoxels for calculating geometric features and representative points for constructing the undirected graph. Second, a node expansion (NE) approach was proposed, with nodes with similar curvature and verticality expanded into wood nodes to avoid the omission of trunk points in path frequency detection. Third, a path concatenation (PC) approach was developed, which involves detecting salient features of nodes along the same path to improve the detection of tiny branches that are often deficient during path retracing. Tested on multi-station TLS point clouds from trees with complex leaf–branch architectures, the NE-PC model achieved a 94.1% mean accuracy and a 86.7% kappa coefficient, outperforming renowned TLSeparation and LeWos (ΔOA = 2.0–29.7%, Δkappa = 6.2–53.5%). Moreover, the NE-PC model was verified in two other study areas (Plot B, Plot C), which exhibited more complex and divergent branch structure types. It achieved classification accuracies exceeding 90% (Plot B: 92.8 ± 2.3%; Plot C: 94.4 ± 0.7%) along with average kappa coefficients above 80% (Plot B: 81.3 ± 4.2%; Plot C: 81.8 ± 3.2%), demonstrating robust performance across various tree structural complexities. Full article

Effective classification of wood and leaf points from terrestrial laser scanning (TLS) point clouds is critical for analyzing and estimating forest attributes such as diameter at breast height (DBH), above-ground biomass (AGB), and wood volume. To address this, we introduce the Wood–Leaf Classification Network (WLC-Net), a deep learning model derived from PointNet++, designed to differentiate between wood and leaf points within tree point clouds. WLC-Net enhances classification accuracy, completeness, and speed by incorporating linearity as an inherent feature, refining the input–output framework, and optimizing the centroid sampling technique. We trained and evaluated WLC-Net using datasets from three distinct tree species, totaling 102 individual tree point clouds, and compared its performance against five existing methods including PointNet++, DGCNN, Krishna Moorthy’s method, LeWoS, and Sun’s method. WLC-Net achieved superior classification accuracy, with overall accuracy (OA) scores of 0.9778, 0.9712, and 0.9508; the mean Intersection over Union (mIoU) scores of 0.9761, 0.9693, and 0.9141; and F1-scores of 0.8628, 0.7938, and 0.9019, respectively. The model also demonstrated high efficiency, processing an average of 102.74 s per million points. WLC-Net has demonstrated notable advantages in wood–leaf classification, including significantly enhanced classification accuracy, improved processing efficiency, and robust applicability across diverse tree species. These improvements stem from its innovative integration of linearity in the model architecture, refined input–output framework, and optimized centroid sampling technique. In addition, WLC-Net also exhibits strong applicability across various tree point clouds and holds promise for further optimization. Full article

Terrestrial LiDAR scanning (TLS) has the potential to revolutionize forestry by enabling the precise estimation of aboveground biomass, vital for forest carbon management. This study addresses the lack of comprehensive benchmarking for leaf-filtering algorithms used in TLS data processing and evaluates four widely recognized geometry-based leaf-filtering algorithms (LeWoS, TLSeparation, CANUPO, and a novel random forest model) across openly accessible TLS datasets from diverse global locations. Multiple evaluation dimensions are considered, including pointwise classification accuracy, volume comparisons using a quantitative structure model applied to wood points, computational efficiency, and visual validation. The random forest model outperformed the other algorithms in pointwise classification accuracy (overall accuracy = 0.95 ± 0.04), volume comparison (R-squared = 0.96, slope value of 0.98 compared to destructive volume), and resilience to reduced point cloud density. In contrast, TLSeparation exhibits the lowest pointwise classification accuracy (overall accuracy = 0.81 ± 0.10), while LeWoS struggles with volume comparisons (mean absolute percentage deviation ranging from 32.14 ± 29.45% to 49.14 ± 25.06%) and point cloud density variations. All algorithms show decreased performance as data density decreases. LeWoS is the fastest in terms of processing time. This study provides valuable insights for researchers to choose appropriate leaf-filtering algorithms based on their research objectives and forest conditions. It also hints at future possibilities for improved algorithm design, potentially combining radiometry and geometry to enhance forest parameter estimation accuracy. Full article

An open-set recognition scheme for tree leaves based on deep learning feature extraction is presented in this study. Deep learning algorithms are used to extract leaf features for different wood species, and the leaf set of a wood species is divided into two datasets: the leaf set of a known wood species and the leaf set of an unknown species. The deep learning network (CNN) is trained on the leaves of selected known wood species, and the features of the remaining known wood species and all unknown wood species are extracted using the trained CNN. Then, the single-class classification is performed using the weighted SVDD algorithm to recognize the leaves of known and unknown wood species. The features of leaves recognized as known wood species are fed back to the trained CNN to recognize the leaves of known wood species. The recognition results of a single-class classifier for known and unknown wood species are combined with the recognition results of a multi-class CNN to finally complete the open recognition of wood species. We tested the proposed method on the publicly available Swedish Leaf Dataset, which includes 15 wood species (5 species used as known and 10 species used as unknown). The test results showed that, with F1 scores of 0.7797 and 0.8644, mixed recognition rates of 95.15% and 93.14%, and Kappa coefficients of 0.7674 and 0.8644 under two different data distributions, the proposed method outperformed the state-of-the-art open-set recognition algorithms in all three aspects. And, the more wood species that are known, the better the recognition. This approach can extract effective features from tree leaf images for open-set recognition and achieve wood species recognition without compromising tree material. Full article

To investigate forest resources, it is necessary to identify the tree species. However, it is a challenge to identify tree species using 3D point clouds of trees collected by light detection and ranging (LiDAR). PointNet++, a point cloud deep learning network, can effectively classify 3D objects. It is important to establish high-quality individual tree point cloud datasets when applying PointNet++ to identifying tree species. However, there are different data processing methods to produce sample datasets, and the processes are tedious. In this study, we suggest how to select the appropriate method by designing comparative experiments. We used the backpack laser scanning (BLS) system to collect point cloud data for a total of eight tree species in three regions. We explored the effect of tree height on the classification accuracy of tree species by using different point cloud normalization methods and analyzed the effect of leaf point clouds on classification accuracy by separating the leaves and wood of individual tree point clouds. Five downsampling methods were used: farthest point sampling (FPS), K-means, random, grid average sampling, and nonuniform grid sampling (NGS). Data with different sampling points were designed for the experiments. The results show that the tree height feature is unimportant when using point cloud deep learning methods for tree species classification. For data collected in a single season, the leaf point cloud has little effect on the classification accuracy. The two suitable point cloud downsampling methods we screened were FPS and NGS, and the deep learning network could provide the most accurate tree species classification when the number of individual tree point clouds was in the range of 2048–5120. Our study further illustrates that point-based end-to-end deep learning methods can be used to classify tree species and identify individual tree point clouds. Combined with the low-cost and high-efficiency BLS system, it can effectively improve the efficiency of forest resource surveys. Full article

The accurate separation between leaf and woody components from terrestrial laser scanning (TLS) data is vital for the estimation of leaf area index (LAI) and wood area index (WAI). Here, we present the application of deep learning time series separation of leaves and wood from TLS point clouds collected from broad-leaved trees. First, we use a multiple radius nearest neighbor approach to obtain a time series of the geometric features. Second, we compare the performance of Fully Convolutional Neural Network (FCN), Long Short-Term Memory Fully Convolutional Neural Network (LSTM-FCN), and Residual Network (ResNet) on leaf and wood classification. We also compare the effect of univariable (UTS) and multivariable (MTS) time series on classification accuracy. Finally, we explore the utilization of a class activation map (CAM) to reduce the black-box effect of deep learning. The average overall accuracy of the MTS method across the training data is 0.96, which is higher than the UTS methods (0.67 to 0.88). Meanwhile, ResNet spent much more time than FCN and LSTM-FCN in model development. When testing our method on an independent dataset, the MTS models based on FCN, LSTM-FCN, and ResNet all demonstrate similar performance. Our method indicates that the CAM can explain the black-box effect of deep learning and suggests that deep learning algorithms coupled with geometric feature time series can accurately separate leaf and woody components from point clouds. This provides a good starting point for future research into estimation of forest structure parameters. Full article

Tree skeletons play an important role in tree structure analysis and 3D model reconstruction. However, it is a challenge to extract a skeleton from a tree point cloud with complex branches. In this paper, an automatic and fast tree skeleton extraction method (FTSEM) based on voxel thinning is proposed. In this method, a wood–leaf classification algorithm was introduced to filter leaf points for the reduction of the leaf interference on tree skeleton generation, tree voxel thinning was adopted to extract a raw tree skeleton quickly, and a breakpoint connection algorithm was used to improve the skeleton connectivity and completeness. Experiments were carried out in Haidian Park, Beijing, in which 24 trees were scanned and processed to obtain tree skeletons. The graph search algorithm (GSA) was used to extract tree skeletons based on the same datasets. Compared with the GSA method, the FTSEM method obtained more complete tree skeletons. The time cost of the FTSEM method was evaluated using the runtime and time per million points (TPMP). The runtime of FTSEM was from 1.0 s to 13.0 s, and the runtime of GSA was from 6.4 s to 309.3 s. The average value of TPMP was 1.8 s for FTSEM and 22.3 s for GSA, respectively. The experimental results demonstrate that the proposed method is feasible, robust, and fast with good potential for tree skeleton extraction. Full article

Grapevine virus A (GVA), the type species of the Vitivirus genus, is one of the causal agents of the Kober stem grooving disease of the rugose wood complex and one of the most frequently detected viruses in grapevine. There is little information on GVA gene(s) marker useful for phylogenetic analysis. To this aim, a total of 403 leaf samples were collected from vineyards of East and West Azarbaijan provinces in the Northwestern provinces of Iran during 2014–2016 and tested by DAS-ELISA and RT-PCR using ORF5-specific primers. GVA was detected in 56 symptomatic samples, corresponding to 14% of infection, while it was not detected in asymptomatic samples. The ORF5 (p10) protein sequence of eight Iranian isolates was compared to other vitiviruses, showing that the most conserved region resides in the N-terminus, carrying an arginine-rich motif followed by a zinc-finger motif. Next, to define a robust phylogenetic marker representative of the whole genome sequence suitable for phylogenetic and evolutionary studies, phylogenetic trees based on the full genome sequences of all the available GVA isolates and on individual genomic regions were constructed and compared. ORF1, which encodes the RNA-dependent RNA polymerase, was found to be the best phylogenetic marker for GVA classification and evolution studies. These results can be used for further research on phylogenetic analyses, evolution history, epidemiology, and etiology of rugose wood complex, and to identify control measures against GVA and other vitiviruses. Full article

The coffee plant Coffea spp. offers much more than the well-known drink made from the roasted coffee bean. During its cultivation and production, a wide variety of by-products are accrued, most of which are currently unused, thermally recycled, or used as animal feed. The modern, ecologically oriented society attaches great importance to waste reduction, so it makes sense to not dispose of the by-products of coffee production but to bring them into the value chain. The aim of this presentation is to provide an updated overview of novel coffee products in the food sector and their current legal classification in the European Union (EU). Coffee flowers, leaves, cascara, coffee cherry spirit, silver skin, and coffee wood are among the materials considered in this article. Some of these products may have, at least, an indirect history of consumption in Europe (silver skin), while others have already been used as traditional foods in non-EU-member countries (coffee leaves, flowers, cascara, and coffee cherry spirit). Of these, coffee leaf tea and cascara have already been approved by the European Commission. Following a consultation with EU member states, spent coffee grounds were determined as being not novel. For the other products, toxicity and/or safety data need to be gathered to further advance novel food applications. Full article

Terrestrial laser scanning (TLS) can obtain tree point clouds with high precision and high density. The efficient classification of wood points and leaf points is essential for the study of tree structural parameters and ecological characteristics. Using both intensity and geometric information, we present an automated wood–leaf classification with a three-step classification and wood point verification. The tree point cloud was classified into wood points and leaf points using intensity threshold, neighborhood density and voxelization successively, and was then verified. Twenty-four willow trees were scanned using the RIEGL VZ-400 scanner. Our results were compared with the manual classification results. To evaluate the classification accuracy, three indicators were introduced into the experiment: overall accuracy (OA), Kappa coefficient (Kappa), and Matthews correlation coefficient (MCC). The ranges of OA, Kappa, and MCC of our results were from 0.9167 to 0.9872, 0.7276 to 0.9191, and 0.7544 to 0.9211, respectively. The average values of OA, Kappa, and MCC were 0.9550, 0.8547, and 0.8627, respectively. The time costs of our method and another were also recorded to evaluate the efficiency. The average processing time was 1.4 s per million points for our method. The results show that our method represents a potential wood–leaf classification technique with the characteristics of automation, high speed, and good accuracy. Full article

Optical remote sensing can contribute to biodiversity monitoring and species composition mapping in tropical forests. Inferring ecological information from canopy reflectance is complex and data availability suitable to such a task is limiting, which makes simulation tools particularly important in this context. We explored the capability of the 3D radiative transfer model DART (Discrete Anisotropic Radiative Transfer) to simulate top of canopy reflectance acquired with airborne imaging spectroscopy in a complex tropical forest, and to reproduce spectral dissimilarity within and among species, as well as species discrimination based on spectral information. We focused on two factors contributing to these canopy reflectance properties: the horizontal variability in leaf optical properties (LOP) and the fraction of non-photosynthetic vegetation (NPVf). The variability in LOP was induced by changes in leaf pigment content, and defined for each pixel based on a hybrid approach combining radiative transfer modeling and spectral indices. The influence of LOP variability on simulated reflectance was tested by considering variability at species, individual tree crown and pixel level. We incorporated NPVf into simulations following two approaches, either considering NPVf as a part of wood area density in each voxel or using leaf brown pigments. We validated the different scenarios by comparing simulated scenes with experimental airborne imaging spectroscopy using statistical metrics, spectral dissimilarity (within crowns, within species, and among species dissimilarity) and supervised classification for species discrimination. The simulation of NPVf based on leaf brown pigments resulted in the closest match between measured and simulated canopy reflectance. The definition of LOP at pixel level resulted in conservation of the spectral dissimilarity and expected performances for species discrimination. Therefore, we recommend future research on forest biodiversity using physical modeling of remote-sensing data to account for LOP variability within crowns and species. Our simulation framework could contribute to better understanding of performances of species discrimination and the relationship between spectral variations and taxonomic and functional dimensions of biodiversity. This work contributes to the improved integration of physical modeling tools for applications, focusing on remotely sensed monitoring of biodiversity in complex ecosystems, for current sensors, and for the preparation of future multispectral and hyperspectral satellite missions. Full article

Dead wood such as coarse dead wood debris (CWD) is an important component in natural forests since it increases the diversity of plants, fungi, and animals. It serves as habitat, provides nutrients and is conducive to forest regeneration, ecosystem stabilization and soil protection. In commercially operated forests, dead wood is often unwanted as it can act as an originator of calamities. Accordingly, efficient CWD monitoring approaches are needed. However, due to the small size of CWD objects satellite data-based approaches cannot be used to gather the needed information and conventional ground-based methods are expensive. Unmanned aerial systems (UAS) are becoming increasingly important in the forestry sector since structural and spectral features of forest stands can be extracted from the high geometric resolution data they produce. As such, they have great potential in supporting regular forest monitoring and inventory. Consequently, the potential of UAS imagery to map CWD is investigated in this study. The study area is located in the center of the Hainich National Park (HNP) in the federal state of Thuringia, Germany. The HNP features natural and unmanaged forest comprising deciduous tree species such as Fagus sylvatica (beech), Fraxinus excelsior (ash), Acer pseudoplatanus (sycamore maple), and Carpinus betulus (hornbeam). The flight campaign was controlled from the Hainich eddy covariance flux tower located at the Eastern edge of the test site. Red-green-blue (RGB) image data were captured in March 2019 during leaf-off conditions using off-the-shelf hardware. Agisoft Metashape Pro was used for the delineation of a three-dimensional (3D) point cloud, which formed the basis for creating a canopy-free RGB orthomosaic and mapping CWD. As heavily decomposed CWD hardly stands out from the ground due to its low height, it might not be detectable by means of 3D geometric information. For this reason, solely RGB data were used for the classification of CWD. The mapping task was accomplished using a line extraction approach developed within the object-based image analysis (OBIA) software eCognition. The achieved CWD detection accuracy can compete with results of studies utilizing high-density airborne light detection and ranging (LiDAR)-based point clouds. Out of 180 CWD objects, 135 objects were successfully delineated while 76 false alarms occurred. Although the developed OBIA approach only utilizes spectral information, it is important to understand that the 3D information extracted from our UAS data is a key requirement for successful CWD mapping as it provides the foundation for the canopy-free orthomosaic created in an earlier step. We conclude that UAS imagery is an alternative to laser data in particular if rapid update and quick response is required. We conclude that UAS imagery is an alternative to laser data for CWD mapping, especially when a rapid response and quick reaction, e.g., after a storm event, is required. Full article

Grapevine wood fungal diseases such as esca are among the biggest threats in vineyards nowadays. The lack of very efficient preventive (best results using commercial products report 20% efficiency) and curative means induces huge economic losses. The study presented in this paper is centered around the in-field detection of foliar esca symptoms during summer, exhibiting a typical “striped” pattern. Indeed, in-field disease detection has shown great potential for commercial applications and has been successfully used for other agricultural needs such as yield estimation. Differentiation with foliar symptoms caused by other diseases or abiotic stresses was also considered. Two vineyards from the Bordeaux region (France, Aquitaine) were chosen as the basis for the experiment. Pictures of diseased and healthy vine plants were acquired during summer 2017 and labeled at the leaf scale, resulting in a patch database of around 6000 images (224 × 224 pixels) divided into red cultivar and white cultivar samples. Then, we tackled the classification part of the problem comparing state-of-the-art SIFT encoding and pre-trained deep learning feature extractors for the classification of database patches. In the best case, 91% overall accuracy was obtained using deep features extracted from MobileNet network trained on ImageNet database, demonstrating the efficiency of simple transfer learning approaches without the need to design an ad-hoc specific feature extractor. The third part aimed at disease detection (using bounding boxes) within full plant images. For this purpose, we integrated the deep learning base network within a “one-step” detection network (RetinaNet), allowing us to perform detection queries in real time (approximately six frames per second on GPU). Recall/Precision (RP) and Average Precision (AP) metrics then allowed us to evaluate the performance of the network on a 91-image (plants) validation database. Overall, 90% precision for a 40% recall was obtained while best esca AP was about 70%. Good correlation between annotated and detected symptomatic surface per plant was also obtained, meaning slightly symptomatic plants can be efficiently separated from severely attacked plants. Full article

Many biophysical forest properties such as wood volume and leaf area index (LAI) require prior knowledge on either photosynthetic or non-photosynthetic components. Laser scanning appears to be a helpful technique in nondestructively quantifying forest structures, as it can acquire an accurate three-dimensional point cloud of objects. In this study, we propose an unsupervised geometry-based method named Dynamic Segment Merging (DSM) to identify non-photosynthetic components of trees by semantically segmenting tree point clouds, and examining the linear shape prior of each resulting segment. We tested our method using one single tree dataset and four plot-level datasets, and compared our results to a supervised machine learning method. We further demonstrated that by using an optimal neighborhood selection method that involves multi-scale analysis, the results were improved. Our results showed that the overall accuracy ranged from 81.8% to 92.0% with an average value of 87.7%. The supervised machine learning method had an average overall accuracy of 86.4% for all datasets, on account of a collection of manually delineated representative training data. Our study indicates that separating tree photosynthetic and non-photosynthetic components from laser scanning data can be achieved in a fully unsupervised manner without the need of training data and user intervention. Full article