Categorizing Grassland Vegetation with Full-Waveform Airborne Laser Scanning: A Feasibility Study for Detecting Natura 2000 Habitat Types

Identifying Key Environmental Factors for Paulownia coreana Habitats: Implementing National On-Site Survey and Machine Learning Algorithms

Monitoring and preserving natural habitats has become an essential activity in many countries today. As a native tree species in Korea, Paulownia coreana has periodically been surveyed in national ecological surveys and was identified as an important target for conservation as well as habitat monitoring and management. This study explores habitat suitability models (HSMs) for Paulownia coreana in conjunction with national ecological survey data and various environmental factors. Together with environmental variables, the national ecological survey data were run through machine learning algorithms such as Artificial Neural Network and Decision Tree & Rules, which were used to identify the impact of individual variables and create HSMs for Paulownia coreana, respectively. Unlike other studies, which used remote sensing data to create HSMs, this study employed periodical on-site survey data for enhanced validity. Moreover, localized environmental resources such as topography, soil, and rainfall were taken into account to project habitat suitability. Among the environment variables used, the study identified critical attributes that affect the habitat conditions of Paulownia coreana. Therefore, the habitat suitability modelling methods employed in this study could play key roles in planning, monitoring, and managing plants species in regional and national levels. Furthermore, it could shed light on existing challenges and future research needs.

Functional Analysis for Habitat Mapping in a Special Area of Conservation Using Sentinel-2 Time-Series Data

The mapping and monitoring of natural and semi-natural habitats are crucial activities and are regulated by European policies and regulations, such as the 92/43/EEC. In the Mediterranean area, which is characterized by high vegetational and environmental diversity, the mapping and monitoring of habitats are particularly difficult and often exclusively based on in situ observations. In this scenario, it is necessary to automate the generation of updated maps to support the decisions of policy makers. At present, the availability of high spatiotemporal resolution data provides new possibilities for improving the mapping and monitoring of habitats. In this work, we present a methodology that, starting from remotely sensed time-series data, generates habitat maps using supervised classification supported by Functional Data Analysis. We constructed the methodology using Sentinel-2 data in the Mediterranean Special Area of Conservation “Gola di Frasassi” (Code: IT5320003). In particular, the training set uses 308 field plots with 11 target classes (five forests, two shrubs, one grassland, one mosaic, one extensive crop, and one urban land). Starting from vegetation index time-series data, Functional Principal Component Analysis was applied to derive FPCA scores and components. In particular, in the classification stage, the FPCA scores are considered as features. The obtained results out-performed a previous map derived from photo-interpretation by domain experts. We obtained an overall accuracy of 85.58% using vegetation index time-series, topography, and lithology data. The main advantages of the proposed approach are the capability to efficiently compress high dimensional data (dense remote-sensing time series) providing results in a compact way (e.g., FPCA scores and mean seasonal time profiles) that: (i) facilitate the link between remote sensing with habitat mapping and monitoring and their ecological interpretation and (ii) could be complementary to species-based approaches in plant community ecology and phytosociology.

Sentinel-2 Remote Sensed Image Classification with Patchwise Trained ConvNets for Grassland Habitat Discrimination

The present study focuses on the use of Convolutional Neural Networks (CNN or ConvNet) to classify a multi-seasonal dataset of Sentinel-2 images to discriminate four grassland habitats in the “Murgia Alta” protected site. To this end, we compared two approaches differing only by the first layer machinery, which, in one case, is instantiated as a fully-connected layer and, in the other case, results in a ConvNet equipped with kernels covering the whole input (wide-kernel ConvNet). A patchwise approach, tessellating training reference data in square patches, was adopted. Besides assessing the effectiveness of ConvNets with patched multispectral data, we analyzed how the information needed for classification spreads to patterns over convex sets of pixels. Our results show that: (a) with an F1-score of around 97% (5 × 5 patch size), ConvNets provides an excellent tool for patch-based pattern recognition with multispectral input data without requiring special feature extraction; (b) the information spreads over the limit of a single pixel: the performance of the network increases until 5 × 5 patch sizes are used and then ConvNet performance starts decreasing.

Fusion of GF and MODIS Data for Regional-Scale Grassland Community Classification with EVI2 Time-Series and Phenological Features

Satellite-borne multispectral data are suitable for regional-scale grassland community classification owing to comprehensive coverage. However, the spectral similarity of different communities makes it challenging to distinguish them based on a single multispectral data. To address this issue, we proposed a support vector machine (SVM)–based method integrating multispectral data, two-band enhanced vegetation index (EVI2) time-series, and phenological features extracted from Chinese GaoFen (GF)-1/6 satellite with (16 m) spatial and (2 d) temporal resolution. To obtain cloud-free images, the Enhanced Spatial and Temporal Adaptive Reflectance Fusion Model (ESTARFM) algorithm was employed in this study. By using the algorithm on the coarse cloudless images at the same or similar time as the fine images with cloud cover, the cloudless fine images were obtained, and the cloudless EVI2 time-series and phenological features were generated. The developed method was applied to identify grassland communities in Ordos, China. The results show that the Caragana pumila Pojark, Caragana davazamcii Sanchir and Salix schwerinii E. L. Wolf grassland, the Potaninia mongolica Maxim, Ammopiptanthus mongolicus S. H. Cheng and Tetraena mongolica Maxim grassland, the Caryopteris mongholica Bunge and Artemisia ordosica Krasch grassland, the Calligonum mongolicum Turcz grassland, and the Stipa breviflora Griseb and Stipa bungeana Trin grassland are distinguished with an overall accuracy of 87.25%. The results highlight that, compared to multispectral data only, the addition of EVI2 time-series and phenological features improves the classification accuracy by 9.63% and 14.7%, respectively, and even by 27.36% when these two features are combined together, and indicate the advantage of the fine images in this study, compared to 500 m moderate-resolution imaging spectroradiometer (MODIS) data, which are commonly used for grassland classification at regional scale, while using 16 m GF data suggests a 23.96% increase in classification accuracy with the same extracted features. This study indicates that the proposed method is suitable for regional-scale grassland community classification.

Grassland Mowing Detection Using Sentinel-1 Time Series: Potential and Limitations

Grasslands encompass vast and diverse ecosystems that provide food, wildlife habitat and carbon storage. Their large range in land use intensity significantly impacts their ecological value and the balance between these goods and services. Mowing dates and frequencies are major aspects of grassland use intensity, which have an impact on their ecological value as habitats. Previous studies highlighted the feasibility of detecting mowing events based on remote sensing time series, a few of which using synthetic aperture radar (SAR) imagery. Although providing encouraging results, research on grassland mowing detection often lacks sufficient precise reference data for corroboration. The goal of the present study is to quantitatively and statistically assess the potential of Sentinel-1 C-band SAR for detecting mowing events in various agricultural grasslands, using a large and diverse reference data set collected in situ. Several mowing detection methods, based on SAR backscattering and interferometric coherence time series, were thoroughly evaluated. Results show that 54% of mowing events could be detected in hay meadows, based on coherence jumps. Grazing events were identified as a major confounding factor, as most false detections were made in pastures. Parcels with one mowing event in the summer were identified with the highest accuracy (71%). Overall, this study demonstrates that mowing events can be detected through Sentinel-1 coherence. However, the performances could probably be further enhanced by discriminating pastures beforehand and combining Sentinel-1 and Sentinel-2 data for mowing detection.

Intra-Annual Sentinel-2 Time-Series Supporting Grassland Habitat Discrimination

The present study aims to discriminate four semi-arid grassland habitats in a Mediterranean Natura 2000 site, Southern Italy, involving 6210/E1.263, 62A0/E1.55, 6220/E1.434 and X/E1.61-E1.C2-E1.C4 (according to Annex I of the European Habitat Directive/EUropean Nature Information System (EUNIS) taxonomies). For this purpose, an intra-annual time-series of 30 Sentinel-2 images, embedding phenology information, were investigated for 2018. The methodology adopted was based on a two-stage workflow employing a Support Vector Machine classifier. In the first stage only four Sentinel-2 multi-season images were analyzed, to provide an updated land cover map from where the grassland layer was extracted. The layer obtained was then used for masking the input features to the second stage. The latter stage discriminated the four grassland habitats by analyzing several input features configurations. These included multiple spectral indices selected from the time-series and the Digital Terrain Model. The results obtained from the different input configurations selected were compared to evaluate if the phenology information from time-series could improve grassland habitats discrimination. The highest F1 values (95.25% and 80.27%) were achieved for 6210/E1.263 and 6220/E1.434, respectively, whereas the results remained stable (97,33%) for 62A0/E1.55 and quite low (75,97%) for X/E1.61-E1.C2-E1.C4. However, since for all the four habitats analyzed no single configuration resulted effective, a Majority Vote algorithm was applied to achieve a reduction in classification uncertainty.

Recursive Feature Elimination and Random Forest Classification of Natura 2000 Grasslands in Lowland River Valleys of Poland Based on Airborne Hyperspectral and LiDAR Data Fusion

The use of hyperspectral (HS) and LiDAR acquisitions has a great potential to enhance mapping and monitoring practices of endangered grasslands habitats, beyond conventional botanical field surveys. In this study we assess the potentiality of recursive feature elimination (RFE) in combination with random forest (RF) classification in extracting the main HS and LiDAR features needed to map selected Natura 2000 grasslands along Polish lowland river valleys, in particular alluvial meadows 6440, lowland hay meadows 6510, and xeric and calcareous grasslands 6120. We developed an automated RFE-RF system capable to combine the potentials of both techniques and applied it to multiple acquisitions. Several LiDAR-based products and different spectral indices (SI) were computed and used as input in the system, with the aim of shedding light on the best-to-use features. Results showed a remarkable increase in classification accuracy when LiDAR and SI products are added to the HS dataset, strengthening in particular the importance of employing LiDAR in combination with HS. Using only the 24 optimal features selection generalized over the three study areas, strongly linked to the highly heterogeneous characteristics of the habitats and landscapes investigated, it was possible to achieve rather high classification results (K around 0.7–0.77 and habitats F1 accuracy around 0.8–0.85), indicating that the selected Natura 2000 meadows and dry grasslands habitats can be automatically mapped by airborne HS and LiDAR data. Similar approaches might be considered for future monitoring activities in the context of habitats protection and conservation.

Detecting shrub encroachment in seminatural grasslands using UAS LiDAR

Shrub encroachment in seminatural grasslands threatens local biodiversity unless management is applied to reduce shrub density. Dense vegetation of Cytisus scoparius homogenizes the landscape negatively affecting local plant diversity. Detecting structural change (e.g., biomass) is essential for assessing negative impacts of encroachment. Hence, exploring new monitoring tools to achieve this task is important for effectively capturing change and evaluating management activities.This study combines traditional field-based measurements with novel Light Detection and Ranging (LiDAR) observations from an Unmanned Aircraft System (UAS). We investigate the accuracy of mapping C. scoparius in three dimensions (3D) and of structural change metrics (i.e., biomass) derived from ultrahigh-density point cloud data (>1,000 pts/m2). Presence-absence of 12 shrub or tree genera was recorded across a 6.7 ha seminatural grassland area in Denmark. Furthermore, 10 individuals of C. scoparius were harvested for biomass measurements. With a UAS LiDAR system, we collected ultrahigh-density spatial data across the area in October 2017 (leaf-on) and April 2018 (leaf-off). We utilized a 3D point-based classification to distinguish shrub genera based on their structural appearance (i.e., density, light penetration, and surface roughness).From the identified C. scoparius individuals, we related different volume metrics (mean, max, and range) to measured biomass and quantified spatial variation in biomass change from 2017 to 2018. We obtained overall classification accuracies above 86% from point clouds of both seasons. Maximum volume explained 77.4% of the variation in biomass.The spatial patterns revealed landscape-scale variation in biomass change between autumn 2017 and spring 2018, with a notable decrease in some areas. Further studies are needed to disentangle the causes of the observed decrease, for example, recent winter grazing and/or frost events. Synthesis and applications: We present a workflow for processing ultrahigh-density spatial data obtained from a UAS LiDAR system to detect change in C. scoparius. We demonstrate that UAS LiDAR is a promising tool to map and monitor grassland shrub dynamics at the landscape scale with the accuracy needed for effective nature management. It is a new tool for standardized and nonbiased evaluation of management activities initiated to prevent shrub encroachment.

The t-SNE Algorithm as a Tool to Improve the Quality of Reference Data Used in Accurate Mapping of Heterogeneous Non-Forest Vegetation

Supervised classification methods, used for many applications, including vegetation mapping require accurate “ground truth” to be effective. Nevertheless, it is common for the quality of this data to be poorly verified prior to it being used for the training and validation of classification models. The fact that noisy or erroneous parts of the reference dataset are not removed is usually explained by the relatively high resistance of some algorithms to errors. The objective of this study was to demonstrate the rationale for cleaning the reference dataset used for the classification of heterogeneous non-forest vegetation, and to present a workflow based on the t-distributed stochastic neighbor embedding (t-SNE) algorithm for the better integration of reference data with remote sensing data in order to improve outcomes. The proposed analysis is a new application of the t-SNE algorithm. The effectiveness of this workflow was tested by classifying three heterogeneous non-forest Natura 2000 habitats: Molinia meadows (Molinion caeruleae; code 6410), species-rich Nardus grassland (code 6230) and dry heaths (code 4030), employing two commonly used algorithms: random forest (RF) and AdaBoost (AB), which, according to the literature, differ in their resistance to errors in reference datasets. Polygons collected in the field (on-ground reference data) in 2016 and 2017, containing no intentional errors, were used as the on-ground reference dataset. The remote sensing data used in the classification were obtained in 2017 during the peak growing season by a HySpex sensor consisting of two imaging spectrometers covering spectral ranges of 0.4–0.9 μm (VNIR-1800) and 0.9–2.5 μm (SWIR-384). The on-ground reference dataset was gradually cleaned by verifying candidate polygons selected by visual interpretation of t-SNE plots. Around 40–50% of candidate polygons were ultimately found to contain errors. Altogether, 15% of reference polygons were removed. As a result, the quality of the final map, as assessed by the Kappa and F1 accuracy measures as well as by visual evaluation, was significantly improved. The global map accuracy increased by about 6% (in Kappa coefficient), relative to the baseline classification obtained using random removal of the same number of reference polygons.

Multitemporal Hyperspectral Data Fusion with Topographic Indices—Improving Classification of Natura 2000 Grassland Habitats

Accurately identifying Natura 2000 habitat areas with the support of remote sensing techniques is becoming increasingly feasible. Various data types and methods are used for this purpose, and the fusion of data from various sensors and temporal periods (terms) within the phenological cycle allows natural habitats to be precisely identified. This research was aimed at selecting optimal datasets to classify three grassland Natura 2000 habitats (codes 6210, 6410 and 6510) in the Ostoja Nidziańska Natura 2000 site in Poland based on hyperspectral imagery and botanical on-ground reference data acquired in three terms during one vegetative period in 2017 (May, July and September), as well as a digital terrain model (DTM) obtained by airborne laser scanning (ALS). The classifications were carried out using a random forest (RF) algorithm on minimum noise fraction (MNF) transform output bands obtained for single terms, as well as data fusion combining the topographic indices (TOPO) calculated from the DTM, multitemporal hyperspectral data, or a combination of the two. The classification accuracy statistics were analysed in various combinations based on the datasets and their terms of acquisition. Topographic indices improved the classification accuracy of habitats 6210 and 6410, with the greatest impact noted in increased classification accuracy of xerothermic grasslands. The best terms for identifying specific habitats were autumn for 6510 and summer for 6210 and 6410, while the best results overall were obtained by combining data from all terms. The highest obtained values of the F1 coefficient were 84.5% for habitat 6210, 83.2% for habitat 6410, and 69.9% for habitat 6510. Comparing the data fusion results for habitats 6210 and 6410, greater accuracy was obtained by adding topographic indices to multitemporal hyperspectral data, while for habitat 6510, greater accuracy was obtained by fusing only multitemporal hyperspectral data.

Light detection and ranging explains diversity of plants, fungi, lichens, and bryophytes across multiple habitats and large geographic extent

Effective planning and nature management require spatially accurate and comprehensive measures of the factors important for biodiversity. Light detection and ranging (LIDAR) can provide exactly this, and is therefore a promising technology to support future nature management and related applications. However, until now studies evaluating the potential of LIDAR for this field have been highly limited in scope. Here, we assess the potential of LIDAR to estimate the local diversity of four species groups in multiple habitat types, from open grasslands and meadows over shrubland to forests and across a large area (~43,000 km2 ), providing a crucial step toward enabling the application of LIDAR in practice, planning, and policy-making. We assessed the relationships between the species richness of macrofungi, lichens, bryophytes, and plants, respectively, and 25 LIDAR-based measures related to potential abiotic and biotic diversity drivers. We used negative binomial generalized linear modeling to construct 19 different candidate models for each species group, and leave-one-region-out cross validation to select the best models. These best models explained 49%, 31%, 32%, and 28% of the variation in species richness (R2 ) for macrofungi, lichens, bryophytes, and plants, respectively. Three LIDAR measures, terrain slope, shrub layer height and variation in local heat load, were important and positively related to the richness in three of the four species groups. For at least one of the species groups, four other LIDAR measures, shrub layer density, medium-tree layer density, and variations in point amplitude and in relative biomass, were among the three most important. Generally, LIDAR measures exhibited strong associations to the biotic environment, and to some abiotic factors, but were poor measures of spatial landscape and temporal habitat continuity. In conclusion, we showed how well LIDAR alone can predict the local biodiversity across habitats. We also showed that several LIDAR measures are highly correlated to important biodiversity drivers, which are notoriously hard to measure in the field. This opens up hitherto unseen possibilities for using LIDAR for cost-effective monitoring and management of local biodiversity across species groups and habitat types even over large areas.

Multiple Flights or Single Flight Instrument Fusion of Hyperspectral and ALS Data? A Comparison of their Performance for Vegetation Mapping

Fusion of remote sensing data often improves vegetation mapping, compared to using data from only a single source. The effectiveness of this fusion is subject to many factors, including the type of data, collection method, and purpose of the analysis. In this study, we compare the usefulness of hyperspectral (HS) and Airborne Laser System (ALS) data fusion acquired in separate flights, Multiple Flights Data Fusion (MFDF), and during a single flight through Instrument Fusion (IF) for the classification of non-forest vegetation. An area of 6.75 km2 was selected, where hyperspectral and ALS data was collected during two flights in 2015 and one flight in 2017. This data was used to classify three non-forest Natura 2000 habitats i.e., Xeric sand calcareous grasslands (code 6120), alluvial meadows of river valleys of the Cnidion dubii (code 6440), species-rich Nardus grasslands (code 6230) using a Random Forest classifier. Our findings show that it is not possible to determine which sensor, HS, or ALS used independently leads to a higher classification accuracy for investigated Natura 2000 habitats. Concurrently, increased stability and consistency of classification results was confirmed, regardless of the type of fusion used; IF, MFDF and varied information relevance of single sensor data. The research shows that the manner of data collection, using MFDF or IF, does not determine the level of relevance of ALS or HS data. The analysis of fusion effectiveness, gauged as the accuracy of the classification result and time consumed for data collection, has shown a superiority of IF over MFDF. IF delivered classification results that are more accurate compared to MFDF. IF is always cheaper than MFDF and the difference in effectiveness of both methods becomes more pronounced when the area of aerial data collection becomes larger.

Classification of Expansive Grassland Species in Different Growth Stages Based on Hyperspectral and LiDAR Data

Expansive species classification with remote sensing techniques offers great support for botanical field works aimed at detection of their distribution within areas of conservation value and assessment of the threat caused to natural habitats. Large number of spectral bands and high spatial resolution allows for identification of particular species. LiDAR (Light Detection and Ranging) data provide information about areas such as vegetation structure. Because the species differ in terms of features during the growing season, it is important to know when their spectral responses are unique in the background of the surrounding vegetation. The aim of the study was to identify two expansive grass species: Molinia caerulea and Calamagrostis epigejos in the Natura 2000 area in Poland depending on the period and dataset used. Field work was carried out during late spring, summer and early autumn, in parallel with remote sensing data acquisition. Airborne 1-m resolution HySpex images and LiDAR data were used. HySpex images were corrected geometrically and atmospherically before Minimum Noise Fraction (MNF) transformation and vegetation indices calculation. Based on a LiDAR point cloud generated Canopy Height Model, vegetation structure from discrete and full-waveform data and topographic indexes were generated. Classifications were performed using a Random Forest algorithm. The results show post-classification maps and their accuracies: Kappa value and F1 score being the harmonic mean of producer (PA) and user (UA) accuracy, calculated iteratively. Based on these accuracies and botanical knowledge, it was possible to assess the best identification date and dataset used for analysing both species. For M. caerulea the highest median Kappa was 0.85 (F1 = 0.89) in August and for C. epigejos 0.65 (F1 = 0.73) in September. For both species, adding discrete or full-waveform LiDAR data improved the results. We conclude that hyperspectral (HS) and LiDAR airborne data could be useful to identify grassland species encroaching into Natura 2000 habitats and for supporting their monitoring.

Consolidating new paradigms in large-scale monitoring and assessment of forest ecosystems

Forests provide a wide range of ecosystem services from which people benefit, and upon which all life depends. However, any rational decision related to the maintenance and enhancement of the multiple functions provided by the forests needs to be based on objective, reliable information. As such, forest monitoring and assessment are rapidly evolving as new information needs arise or new techniques and tools become available. Global change issues and utilities from ecosystem management are distinctively to be considered, so that forest inventory and mapping are broadening their scope towards multipurpose resources surveys. Recent changes in forest management perspective have promoted the consideration of forests as complex adaptive systems, thereby highlighting the need to account that such approaches actually work: forest monitoring and assessment are then expected to address and fully incorporate this perspective at global scale, seeking to support planning and management decisions that are evidence-based. This contribution provides selected considerations on the above mentioned issues, in the form of a commented discussion with examples from the literature produced in the last decade.