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Identifying and characterizing vascular plants in time and space is required in various disciplines, e.g. in forestry, conservation and agriculture. Remote sensing emerged as a key technology revealing both spatial and temporal vegetation patterns. Harnessing the ever growing streams of remote sensing data for the increasing demands on vegetation assessments and monitoring requires efficient, accurate and flexible methods for data analysis. In this respect, the use of deep learning methods is trend-setting, enabling high predictive accuracy, while learning the relevant data features independently in an end-to-end fashion. Very recently, a series of studies have demonstrated that the deep learning method of Convolutional Neural Networks (CNN) is very effective to represent spatial patterns enabling to extract a wide array of vegetation properties from remote sensing imagery. This review introduces the principles of CNN and distils why they are particularly suitable for vegetation remote sensing. The main part synthesizes current trends and developments, including considerations about spectral resolution, spatial grain, different sensors types, modes of reference data generation, sources of existing reference data, as well as CNN approaches and architectures. The literature review showed that CNN can be applied to various problems, including the detection of individual plants or the pixel-wise segmentation of vegetation classes, while numerous studies have evinced that CNN outperform shallow machine learning methods. Several studies suggest that the ability of CNN to exploit spatial patterns particularly facilitates the value of very high spatial resolution data. The modularity in the common deep learning frameworks allows a high flexibility for the adaptation of architectures, whereby especially multi-modal or multi-temporal applications can benefit. An increasing availability of techniques for visualizing features learned by CNNs will not only contribute to interpret but to learn from such models and improve our understanding of remotely sensed signals of vegetation. Although CNN has not been around for long, it seems obvious that they will usher in a new era of vegetation remote sensing.

Xylella fastidiosa (Xf) is a harmful plant pathogenic bacterium, able to infect over 500 plant species worldwide. Successful eradication and containment strategies for harmful pathogens require large-scale monitoring techniques for the detection of infected hosts, even when they do not display visual symptoms. Although a previous study using airborne hyperspectral and thermal imagery has shown promising results for the early detection of Xf-infected olive (Olea europaea) trees, further work is needed when adopting these techniques for large scale monitoring using multispectral cameras on board airborne platforms and satellites. We used hyperspectral and thermal imagery collected during a two-year airborne campaign in a Xf-infected area in southern Italy to assess the performance of spectrally constrained machine-learning algorithms for this task. The algorithms were used to assess multispectral bandsets, selected from the original hyperspectral imagery, that were compatible with large-scale monitoring from unmanned platforms and manned aircraft. In addition, the contribution of solar–induced chlorophyll fluorescence (SIF) and the temperature-based Crop Water Stress Index (CWSI) retrieved from hyperspectral and thermal imaging, respectively, were evaluated to quantify their relative importance in the algorithms used to detect Xf infection. The detection performance using support vector machine algorithms decreased from ∼80% (kappa, κ = 0.42) when using the original full hyperspectral dataset including SIF and CWSI to ∼74% (κ = 0.36) when the optimal set of six spectral bands most sensitive to Xf infection were used in addition to the CWSI thermal indicator. When neither SIF nor CWSI were used, the detection yielded less than 70% accuracy (decreasing κ to very low performance, 0.29), revealing that tree temperature was more important than chlorophyll fluorescence for the Xf detection. This work demonstrates that large-scale Xf monitoring can be supported using airborne platforms carrying multispectral and thermal cameras with a limited number of spectral bands (e.g., six to 12 bands with 10 nm bandwidths) as long as they are carefully selected by their sensitivity to the Xf symptoms. More precisely, the blue (bands between 400 and 450 nm to derive the NPQI index) and thermal (to derive CWSI from tree temperature) were the most critical spectral regions for their sensitivity to Xf symptoms in olive., Data collection was partially supported by the European Union’s Horizon 2020 research and innovation program through grants to the POnTE (Pest Organisms threatening Europe; grant 635646 from European Union’s Horizon 2020 Framework Research Programme) and XF-ACTORS (Xylella fastidiosa Active Containment Through a Multidisciplinary-Oriented Research Strategy; grant 727987 from European Union’s Horizon 2020 Framework Research Programme) projects. A. Hornero was supported by a research fellowship DTC GEO 29 “Detection of global photosynthesis and forest health from space” from the Science Doctoral Training Centre (Swansea University, UK).

Invasive plant species can pose major threats to biodiversity, ecosystem functioning and services. Satellite based remote sensing has evolved as an important technology to spatially map the occurrence of invasive species in space and time. With the new era of the Sentinel missions, Synthetic Aperture Radar (SAR) and multispectral data are now freely available and repeatedly acquired on a high spatial and temporal resolution for the entire globe. However, the high potential of such sensors for automatic mapping procedures cannot be fully harnessed without sufficient and appropriate reference data for model calibration. Reference data are commonly acquired in field surveys, which however, are often relatively expensive and affected by sampling and observer bias. Moreover, a direct transferability to the remote sensing perspective and scale is difficult. Accordingly, we firstly assess the potential of Unmanned Aerial Vehicles (UAV) for semi-automatic reference data acquisition on species cover of three woody invasive species Pinus radiata, Ulex europaeus and Acacia dealbata occurring in Chile. Secondly, we test the upscaling of the estimated species cover to the spatial scale of Sentinel-1 and Sentinel-2. The proposed workflow includes the visual sampling of respective canopies in UAV orthomosaics and the subsequent spatial extrapolations using MaxEnt with spectral (RGB, Hyperspectral), textural (2D) and canopy structural (3D) predictors derived from UAV-based photogrammetry. These UAV-based maps are then used to train random forest models with multitemporal Sentinel-1 and Sentinel-2 data to map the invasive species cover on large spatial scales. Our results show that the semi-automatic UAV-based mapping of the three invasive species results in accurate predictions. Depending on the predictor combination, the correlation was 0.70, 0.77 and 0.90 for Pinus radiatia, Ulex europaeus, Acacia dealbata, respectively. Among the three species, we observed clear differences in the model performance between the tested photogrammetric predictors and their combinations (spectral, 2D texture or 3D structure). For scaling up the UAV-based estimates to the satellite-scale, the Sentinel-2 data (multispectral) were more important than Sentinel-1 data (SAR). An independent validation revealed that the R2 of the upscaling accounted for 0.78 or higher for all species and RMSE lower than 12%. Our results hence demonstrate that UAV-based reference data acquisitions are a promising alternative to traditional field surveys if the target species are directly identifiable in the UAV data.

Grasslands are one of the ecosystems that have been strongly affected by anthropogenic impacts. The state-of-the-art in monitoring changes in grassland species composition is to conduct repeated plot-based vegetation surveys that assess the occurrence and cover of plants. These plot-based surveys are typically limited to comparably small areas and the quality of the cover estimates depends strongly on the experience and performance of the surveyors. Here, we investigate the possibility of a semi-automated, image-based method for cover estimates, by analyzing the applicability of very high spatial resolution hyperspectral data to classify grassland species at the level of individuals. This individual-oriented approach is seen as an alternative to community-oriented remote sensing depicting canopy reflectance as the total of mixed species reflectance. An AISA + imaging spectrometer mounted on a scaffold was used to scan 1 m 2 grassland plots and assess the impact of four sources of variation on the predicted species cover: (1) the spatial resolution of the scans, (2) complexity, i.e. species number and structural diversity, (3) the species cover and (4) the share of functional types (graminoids and forbs). Classifications were conducted using a support vector machine classification with a linear kernel, obtaining a median Kappa of ~ 0.8. Species cover estimations reached median r 2 and root mean square errors (RMSE) of ~ 0.6 and ~ 6.2% respectively. We found that the spatial resolution and diversity level (mainly structural diversity) were the most important sources of variation affecting the performance of the proposed approach. A spatial resolution below 1 cm produced relatively good models for estimating species-specific coverages (r 2 = ~ 0.6; RMSE = ~ 7.5%) while predictions using pixel sizes over that threshold failed in this individual-oriented approach (r 2 = ~ 0.17; RMSE = ~ 20.7%). Areas with low inter-species overlap were better suited than areas with frequent inter-species overlap. We conclude that the application of very high resolution hyperspectral remote sensing in environments with low structural heterogeneity is suited for individual-oriented mapping of grassland plant species.

The estimation of various forest inventory attributes from high spatial resolution airborne remote sensing data has been widely examined and proved to be successful at the experimental level. Nevertheless, the operational use of these data in automated procedures to support forest inventories and forest management is still limited to a small number of cases. The reasons for this are high data costs, limited availability of remote sensing data over large areas and resistance from practitioners. In this review the main aim is to stimulate debate about spaceborne very high resolution stereo-imagery (VHRSI) as an alternative to airborne remote sensing data by presenting: (1) a case study on the retrieval of stand density, aboveground biomass and tree species using a set of easy-to-calculate variables obtained from VHRSI data combined with image processing and nonparametric classification and modelling approaches; and (2) the results of an expert opinion survey on the potential of VHRSI as compared with Light Detection and Ranging (LiDAR), hyperspectral and airborne digital imagery to derive a range of forest inventory attributes. In the case study, stand density was estimated with r² = 0.71 and RMSE = 156 trees (rel./norm. RMSE = 24.9 per cent/12.4 per cent), biomass with r² = 0.64 and RMSE of 36.7 t/ha (rel./norm. RMSE = 20.0 per cent/12.8 per cent) while tree species classifications with five species reached overall accuracies of 84.2 per cent (kappa = 0.81). These results were comparable to earlier studies in the same test site, obtained with more expensive airborne acquisitions. Expert opinions were more diverse for VHRSI and aerial photographs (Shannon index values of 0.94 and 0.97) than for LiDAR and hyperspectral data (Shannon index values 0.69 and 0.88). In our opinion, this reflects the current state-of-the-art in the application of VHRSI for automatically retrieving forest inventory attributes. The number of studies using these data is still limited, and the full potential of these datasets is not yet completely explored. Compared with LiDAR and hyperspectral data, which both mostly received high scores for forest inventory products matching the sensor systems’ strengths, VHRSI and aerial photographs received more homogeneous scores indicating their potential as multi-purpose instruments to collect forest inventory information. In summary, considering the simpler acquisition, reasonable price and the comparably easy data format and handling of VHRSI compared with other sensor types, we recommend further research on the application of these data for supporting operational forest inventories.

With consumer-grade unmanned aerial vehicles (UAVs) on the rise, which enable easy, time-flexible, and cost-effective acquisition of very high-resolution RGB data, the mapping of forest tree species using solely RGB imagery is of high interest, as it does not rely on sophisticated sensors, does not require extensive calibration and preprocessing and, therefore, enables the application by a wide audience. In combination with convolutional neural networks (CNNs), which particularly exploit spatial patterns and, therefore, highly benfit from very high-resolution remote sensing, this offers great potential for accurately mapping forest tree species.Here, we present the findings of our recent study, in which we used very high-resolution RGB imagery from UAVs in combination with CNNs for the mapping of forest tree species. In this study, we used multicopter UAVs to obtain very high-resolution (In this contribution, we will give an outlook on how the combination of UAV imagery and CNNs can be integrated with multitemporal satellite imagery (Sentinel-1 and Sentinel-2) in order to extrapolate the UAV-based tree species maps to larger areas.

With the advent of Sentinel-2, it is now possible to generate large-scale chlorophyll content maps with unprecedented spatial and temporal resolution, suitable for monitoring ecological processes such as vegetative stress and/or decline. However methodological gaps exist for adapting this technology to heterogeneous natural vegetation and for transferring it among vegetation species or plan functional types. In this study, we investigated the use of Sentinel-2A imagery for estimating needle chlorophyll (Ca+b) in a sparse pine forest undergoing significant needle loss and tree mortality. Sentinel-2A scenes were acquired under two extreme viewing geometries (June vs. December 2016) coincident with the acquisition of high-spatial resolution hyperspectral imagery, and field measurements of needle chlorophyll content and crown leaf area index. Using the high-resolution hyperspectral scenes acquired over 61 validation sites we found the CI chlorophyll index R750/R710 and Macc index (which uses spectral bands centered at 680 nm, 710 nm and 780 nm) had the strongest relationship with needle chlorophyll content from individual tree crowns (r2 = 0.61 and r2 = 0.59, respectively; p 0.7 for June and >0.4 for December; p

Spaceborne sensors allow for wide-scale assessments of forest ecosystems. Combining the products of multiple sensors is hypothesized to improve the estimation of forest biomass. We applied interferometric (Tandem-X) and photogrammetric (WorldView-2) based predictors, e.g. canopy height models, in combination with hyperspectral predictors (EO1-Hyperion) by using 4 different machine learning algorithms for biomass estimation in temperate forest stands near Karlsruhe, Germany. An iterative model selection procedure was used to identify the optimal combination of predictors. The most accurate model (Random Forest) reached a r 2 of 0.73 with a RMSE of 14.9% (29.4 t/ha). Further results revealed that the predictive accuracy depended highly on the statistical model and the area size of the field samples. We conclude that a fusion of canopy height and spectral information allows for accurate estimations of forest biomass from space.

We used spectral, textural and photogrammetric information from very-high resolution (VHR) stereo satellite data (Pleiades and WorldView-2) to estimate forest biomass across two test sites located in Chile and Germany. We compared Random Forest model performances of different predictor sets (spectral, textural, and photogrammetric), forest inventory designs and filter sizes (texture information). Best model performances were obtained with photogrammetric combined with either textural or spectral information and smaller, but more field plots. Stereo-VHR images showed a great potential for canopy height model (CHM) generation and could be an adequate alternative to LiDAR and InSAR techniques.

Land cover is of fundamental importance to many environmental applications and serves as critical baseline information for many large scale models e.g. in developing future scenarios of land use and climate change. Although there is an ongoing movement towards the development of higher resolution global land cover maps, medium resolution land cover products (e.g. GLC2000 and MODIS) are still very useful for modelling and assessment purposes. However, the current land cover products are not accurate enough for many applications so we need to develop approaches that can take existing land covers maps and produce a better overall product in a hybrid approach. This paper uses geographically weighted regression (GWR) and crowdsourced validation data from Geo-Wiki to create two hybrid global land cover maps that use medium resolution land cover products as an input. Two different methods were used: (a) the GWR was used to determine the best land cover product at each location; (b) the GWR was only used to determine the best land cover at those locations where all three land cover maps disagree, using the agreement of the land cover maps to determine land cover at the other cells. The results show that the hybrid land cover map developed using the first method resulted in a lower overall disagreement than the individual global land cover maps. The hybrid map produced by the second method was also better when compared to the GLC2000 and GlobCover but worse or similar in performance to the MODIS land cover product depending upon the metrics considered. The reason for this may be due to the use of the GLC2000 in the development of GlobCover, which may have resulted in areas where both maps agree with one another but not with MODIS, and where MODIS may in fact better represent land cover in those situations. These results serve to demonstrate that spatial analysis methods can be used to improve medium resolution global land cover information with existing products.

The presented work evaluates the potential of a Sentinel-2 time-series to detect Pinus radiata (Monterey Pine) invasions in endemic Nothofagus (Southern Beeches) forests in the Maule region, central Chile. Suitable cloud free images of the phenological cycle were selected from six Sentinel-2 scenes available for the years 2016. The scenes were unmixed using a non-negative least square (nnls) algorithm for different landcover components per pixel. The results were validated with a SVM classification of UAV-based hyperspectral mosaics acquired in March 2016. The results show that it is possible to map the coverage of the Pinus radiata class up to an accuracy of R2 ∼ 0.6 and RMSE of ∼ 10 %. Generally, a higher number of Sentinel-2 images increased the performance of the model, while there was no significant dependency on a specific acquisition date. However, the variability of the results is high, which indicates that a careful selection of multi-temporal endmembers is crucial to a successful unmixing of Pinus radiata.

Peatlands are key reservoirs of belowground carbon (C) and their monitoring is important to assess the rapid changes in the C cycle caused by climate change and direct anthropogenic impacts. Frequently, information of peatland area and vegetation type estimated by remote sensing has been used along with soil measurements and allometric functions to estimate belowground C stocks. Despite the accuracy of such approaches, there is still the need to find mappable proxies that enhance predictions with remote sensing data while reducing field and laboratory efforts. Therefore, we assessed the use of aboveground vegetation attributes as proxies to predict peatland belowground C stocks. First, the ecological relations between remotely detectable vegetation attributes (i.e. vegetation height, aboveground biomass, species richness and floristic composition of vascular plants) and belowground C stocks were obtained using structural equation modeling (SEM). SEM was formulated using expert knowledge and trained and validated using in-situ information. Second, the SEM latent vectors were spatially mapped using random forests regressions with UAV-based hyperspectral and structural information. Finally, this enabled us to map belowground C stocks using the SEM functions parameterized with the random forests derived maps. This SEM approach resulted in higher accuracies than a direct application of a purely data-driven random forests approach with UAV data, with improvements of r 2 from 0.39 to 0.54, normalized RMSE from 31.33% to 20.24% and bias from −0.73 to 0.05. Our case study showed that: (1) vegetation height, species richness and aboveground biomass are good proxies to map peatland belowground C stocks, as they can be estimated using remote sensing data and hold strong relationships with the belowground C gradient; and (2) SEM is facilitates to incorporate theoretical knowledge in empirical modeling approaches.

Photosynthesis is essential for life on earth as it, inter alia, influences the composition of the atmosphere and is the driving mechanism of primary production. Photosynthesis is particularly controlled by leaf pigments such as chlorophyll, carotenoids or anthocyanins. Incoming solar radiation is mainly captured by chlorophyll, whereas plant organs are also protected from excess radiation by carotenoids and anthocyanins. Current and upcoming optical earth observation sensors are sensitive to these radiative processes and thus feature a high potential for mapping the spatial and temporal variation of these photosynthetic pigments. In the context of remote sensing, leaf pigments are either quantified as leaf area-based content [μg/cm2] or as leaf mass-based concentration [g/g or %]. However, these two metrics are fundamentally different, and until now there has been neither an in-depth discussion nor a consensus on which metric to choose. This is notable considering the amount of studies that do not explicitly differentiate between pigment content and concentration. We therefore seek to outline the differences between both metrics and thus show that the remote sensing of leaf pigment concentration [%] is unsubstantial. This is due to the fact that, firstly, pigment concentration is likely to primarily reflect variation in leaf mass per area and not pigments itself. Second, the radiative transfer in plant leaves is especially determined by the absolute content of pigments in a leaf and not its relative concentration to other leaf constituents. And third, as a ratio, pigment concentration is an ambiguous metric, which further complicates the quantification of leaf pigments at the canopy scale. Given these issues related to the use of chlorophyll concentration, we thus conclude that remote sensing of leaf pigments should be primarily performed on an area basis [μg/cm2]., The project was funded by the German Aerospace Center (DLR) on behalf of the Federal Ministry of Economics and Technology (BMWi), FKZ50EE 1347.

For reasons of documentation, management and certification there is a high interest in efficient inventories of palm plantations on the single plant level. Recent developments in unmanned aerial vehicle (UAV) technology facilitate spatial and temporal flexible acquisition of high resolution 3D data. Common single tree detection approaches are based on Very High Resolution (VHR) satellite or Airborne Laser Scanning (ALS) data. However, VHR data is often limited to clouds and does commonly not allow for height measurements. VHR and in particualar ALS data are characterized by high relatively high acquisition costs. Sperlich et al. (2013) already demonstrated the high potential of UAV-based photogrammetric point clouds for single tree detection using pouring algorithms. This approach was adjusted and improved for an application on palm plantation. The 9.4ha test site on Tarawa, Kiribati, comprised densely scattered growing palms, as well as abundant undergrowth and trees. Using a standard consumer grade camera mounted on an octocopter two flight campaigns at 70m and 100m altitude were performed to evaluate the effect Ground Sampling Distance (GSD) and image overlap. To avoid comission errors and improve the terrain interpolation the point clouds were classified based on the geometric characteristics of the classes, i.e. (1) palm, (2) other vegetation (3) and ground. The mapping accuracy amounts for 86.1 % for the entire study area and 98.2 % for dense growing palm stands. We conclude that this flexible and automatic approach has high capabilities for operational use.

In both ecology and forestry, there is a high demand for structural information of forest stands. Forest structures, due to their heterogeneity and density, are often difficult to assess. Hence, a variety of technologies are being applied to account for this "difficult to come by" information. Common techniques are aerial images or ground- and airborne-Lidar. In the present study we evaluate the potential use of unmanned aerial vehicles (UAVs) as a platform for tree stem detection in open stands. A flight campaign over a test site near Freiburg, Germany covering a target area of 120 × 75 [m2] was conducted. The dominant tree species of the site is oak (quercus robur) with almost no understory growth. Over 1000 images with a tilt angle of 45° were shot. The flight pattern applied consisted of two antipodal staggered flight routes at a height of 55 [m] above the ground. We used a Panasonic G3 consumer camera equipped with a 14–42 [mm] standard lens and a 16.6 megapixel sensor. The data collection took place in leaf-off state in April 2013. The area was prepared with artificial ground control points for transformation of the structure-from-motion (SFM) point cloud into real world coordinates. After processing, the results were compared with a terrestrial laser scanner (TLS) point cloud of the same area. In the 0.9 [ha] test area, 102 individual trees above 7 [cm] diameter at breast height were located on in the TLS-cloud. We chose the software CMVS/PMVS-2 since its algorithms are developed with focus on dense reconstruction. The processing chain for the UAV-acquired images consists of six steps: a. cleaning the data: removing of blurry, under- or over exposed and off-site images; b. applying the SIFT operator [Lowe, 2004]; c. image matching; d. bundle adjustment; e. clustering; and f. dense reconstruction. In total, 73 stems were considered as reconstructed and located within one meter of the reference trees. In general stems were far less accurate and complete as in the TLS-point cloud. Only few stems were considered to be fully reconstructed. From the comparison of reconstruction achievement with respect to height above ground, we can state that reconstruction accuracy decreased in the crown layer of the stand. In addition we were cutting 50 [cm] slices in z-direction and applied a robust cylinder fit to the stem slices. Radii of the TLS-cloud and the SFM-cloud surprisingly correlated well with a Pearson's correlation coefficient of r = 0.696. This first study showed promising results for UAV-based forest structure modelling. Yet, there is a demand for additional research with regard to vegetation stages, flight pattern, processing setup and the utilisation of spectral information.