Integrating remote sensing datasets into ecological modelling: a Bayesian approach

Process-based models have been used to simulate 3-dimensional complexities of forest ecosystems and their temporal changes, but their extensive data requirement and complex parameterisation have often limited their use for practical management applications. Increasingly, information retrieved using remote sensing techniques can help in model parameterisation and data collection by providing spatially and temporally resolved forest information. In this paper, we illustrate the potential of Bayesian calibration for integrating such data sources to simulate forest production. As an example, we use the 3-PG model combined with hyperspectral, LiDAR, SAR and field-based data to simulate the growth of UK Corsican pine stands. Hyperspectral, LiDAR and SAR data are used to estimate LAI dynamics, tree height and above ground biomass, respectively, while the Bayesian calibration provides estimates of uncertainties to model parameters and outputs. The Bayesian calibration contrasts with goodness-of-fit approaches, which do not provide uncertainties to parameters and model outputs. Parameters and the data used in the calibration process are presented in the form of probability distributions, reflecting our degree of certainty about them. After the calibration, the distributions are updated. To approximate posterior distributions (of outputs and parameters), a Markov Chain Monte Carlo sampling approach is used (25 000 steps). A sensitivity analysis is also conducted between parameters and outputs. Overall, the results illustrate the potential of a Bayesian framework for truly integrative work, both in the consideration of field-based and remotely sensed datasets available and in estimating parameter and model output uncertainties

Mapping Species Composition of Forests and Tree Plantations in Northeastern Costa Rica with an Integration of Hyperspectral and Multitemporal Landsat Imagery

An efficient means to map tree plantations is needed to detect tropical land use change and evaluate reforestation projects. To analyze recent tree plantation expansion in northeastern Costa Rica, we examined the potential of combining moderate-resolution hyperspectral imagery (2005 HyMap mosaic) with multitemporal, multispectral data (Landsat) to accurately classify (1) general forest types and (2) tree plantations by species composition. Following a linear discriminant analysis to reduce data dimensionality, we compared four Random Forest classification models: hyperspectral data (HD) alone; HD plus interannual spectral metrics; HD plus a multitemporal forest regrowth classification; and all three models combined. The fourth, combined model achieved overall accuracy of 88.5%. Adding multitemporal data significantly improved classification accuracy (p less than 0.0001) of all forest types, although the effect on tree plantation accuracy was modest. The hyperspectral data alone classified six species of tree plantations with 75% to 93% producer's accuracy; adding multitemporal spectral data increased accuracy only for two species with dense canopies. Non-native tree species had higher classification accuracy overall and made up the majority of tree plantations in this landscape. Our results indicate that combining occasionally acquired hyperspectral data with widely available multitemporal satellite imagery enhances mapping and monitoring of reforestation in tropical landscapes

The Assessment of habitat condition and consevation status of lowland British woodlands using earth observation techniques.

The successful implementation of habitat preservation and management demands regular and spatially explicit monitoring of conservation status at a range of scales based on indicators. Woodland condition can be described in terms of compositional and structural attributes (e.g. overstorey, understorey, ground flora), evidence of natural turnover (e.g. deadwood and tree regeneration), andanthropogenic influences (e.g.disturbance, damage). Woodland condition assessments are currently conducted via fieldwork, which is hampered by cost, spatial coverage, objectiveness and repeatability.This projectevaluates the ability of airborne remote sensing (RS) techniques to assess woodland condition, utilising a sensor-fusion approach to survey a foreststudy site and develop condition indicators. Here condition is based on measures of structural and compositional diversity in the woodland vertical profile, with consideration of the presence of native species, deadwood, and tree regeneration. A 22 km2 study area was established in the New Forest, Hampshire, UK, which contained a variety of forest types, including managed plantation, semi-ancient coniferous and deciduous woodland. Fieldwork was conducted in 41 field plots located across this range of forest types, each with varying properties. The field plots were 30x30m in size and recorded a total of 39 forest metrics relating to individual elements of condition as identified in the literature. Airborne hyperspectral data (visible and near-infrared) and small footprint LiDAR capturing both discrete-return (DR) and full-waveform (FW) data were acquired simultaneously, under both leaf-on and leaf-off conditions in 2010. For the combined leaf-on and leaf-off datasets a total of 154 metrics were extracted from the hyperspectral data, 187 metrics from the DR LiDAR and 252 metrics from the FW LiDAR. This comprised both area-based and individual tree crown metrics. These metrics were entered into two statistical approaches, ordinary least squares and Akaike information criterion regression, in order to estimate each of the 39 field plot-level forest variables. These estimated variables were then used as inputs to six forest condition assessment approaches identified in the literature. In total, 35 of the 39 field plot-level forest variables could be estimated with a validated NRMSE value below 0.4 using RS data (23 of these models had NRMSE values below 0.3). Over half of these models involved the use of FW LiDAR data on its own or combined with hyperspectral data, demonstrating this to be single most able dataset. Due to the synoptic coverage of the RS data, each of these field plot variables could be estimated and mapped continuously over the entire study site at the 30x30m resolution (i.e. field plot-level scale). The RS estimated field variables were then used as inputs to six forest condition assessment approaches identified in the literature.Three of the derived condition indices were successful based on correspondence with field validation data and woodlandcompartment boundaries. The three successful condition assessment methods were driven primarily by tree size and tree size variation. The best technique for assessing woodland condition was a score-based method which combined seventeen inputs which relate to tree species composition, tree size and variability, deadwood, and understory components; all of whichwere shown to be derived successfully from the appropriate combination of airborne hyperspectral and LiDAR datasets. The approach demonstrated in this project therefore shows that conventional methods of assessing forest condition can be applied with RS derived inputs for woodland assessment purposes over landscape-scale areas

A Review on Deep Learning in UAV Remote Sensing

Deep Neural Networks (DNNs) learn representation from data with an impressive capability, and brought important breakthroughs for processing images, time-series, natural language, audio, video, and many others. In the remote sensing field, surveys and literature revisions specifically involving DNNs algorithms' applications have been conducted in an attempt to summarize the amount of information produced in its subfields. Recently, Unmanned Aerial Vehicles (UAV) based applications have dominated aerial sensing research. However, a literature revision that combines both "deep learning" and "UAV remote sensing" thematics has not yet been conducted. The motivation for our work was to present a comprehensive review of the fundamentals of Deep Learning (DL) applied in UAV-based imagery. We focused mainly on describing classification and regression techniques used in recent applications with UAV-acquired data. For that, a total of 232 papers published in international scientific journal databases was examined. We gathered the published material and evaluated their characteristics regarding application, sensor, and technique used. We relate how DL presents promising results and has the potential for processing tasks associated with UAV-based image data. Lastly, we project future perspectives, commentating on prominent DL paths to be explored in the UAV remote sensing field. Our revision consists of a friendly-approach to introduce, commentate, and summarize the state-of-the-art in UAV-based image applications with DNNs algorithms in diverse subfields of remote sensing, grouping it in the environmental, urban, and agricultural contexts.Comment: 38 pages, 10 figure

Optical remote sensing of aboveground forest biomass and carbon stocks in resource-constrained African environments.

Ph. D. University of KwaZulu-Natal, Pietermaritzburg 2015.No abstract available

Do airborne laser scanning biomass prediction models benefit from Landsat time series, hyperspectral data or forest classification in tropical mosaic landscapes?

Airborne laser scanning (ALS) is considered as the most accurate remote sensing data for the predictive modelling of AGB. However, tropical landscapes experiencing land use changes are typically heterogeneous mosaics of various land cover types with high tree species richness and trees outside forests, making them challenging environments even for ALS. Therefore, combining ALS data with other remote sensing data, or stratification by land cover type could be particularly beneficial in terms of modelling accuracy in such landscapes. Our objective was to test if spectral-temporal metrics from the Landsat time series (LTS), simultaneously acquired hyperspectral (HS) data, or stratification to the forest and non-forest classes improves accuracy of the AGB modelling across an Afromontane landscape in Kenya. The combination of ALS and HS data improved the cross-validated RMSE from 51.5 Mg ha−1 (42.7%) to 47.7 Mg ha−1 (39.5%) in comparison to the use of ALS data only. Furthermore, the combination of ALS data with LTS and HS data improved accuracies of the models for the forest and non-forest classes, and the overall best results were achieved when using ALS and HS data with stratification (RMSE 40.0 Mg ha−1, 33.1%). We conclude that ALS data alone provides robust models for AGB mapping across tropical mosaic landscapes, even without stratification. However, ALS and HS data together, and additional forest classification for stratification, can improve modelling accuracy considerably in similar, tree species rich areas.Peer reviewe

Using Sentinel-2 and canopy height models to derive a landscape-level biomass map covering multiple vegetation types

Vegetation biomass is a globally important climate-relevant terrestrial carbon pool and also drives local hydrological systems via evapotranspiration. Vegetation biomass of individual vegetation types has been successfully estimated from active and passive remote sensing data. However, for many tasks, landscape-level biomass maps across several vegetation types are more suitable than biomass maps of individual vegetation types. For example, the validation of ecohydrological models and carbon budgeting typically requires spatially continuous biomass estimates, independent from vegetation type. Studies that derive biomass estimates across multiple vegetation or land-cover types to merge them into a single landscape-level biomass map are still scarce, and corresponding workflows must be developed. Here, we present a workflow to derive biomass estimates on landscape-level for a large watershed in central Chile. Our workflow has three steps: First, we combine field plotbased biomass estimates with spectral and structural information collected from Sentinel-2, TanDEM-X and airborne LiDAR data to map grassland, shrubland, native forests and pine plantation biomass using random forest regressions with an automatic feature selection. Second, we predict all models to the entire landscape. Third, we derive a land-cover map including the four considered vegetation types. We then use this land-cover map to assign the correct vegetation type-specific biomass estimate to each pixel according to one of the four considered vegetation types. Using a single repeatable workflow, we obtained biomass predictions comparable to earlier studies focusing on only one of the four vegetation types (Spearman correlation between 0.80 and 0.84; normalized-RMSE below 16 % for all vegetation types). For all woody vegetation types, height metrics were amongst the selected predictors, while for grasslands, only Sentinel-2 bands were selected. The land-cover was also mapped with high accuracy (OA = 83.1 %). The final landscape-level biomass map spatially agrees well with the known biomass distribution patterns in the watershed. Progressing from vegetation-type specific maps towards landscape-level biomass maps is an essential step towards integrating remote-sensing based biomass estimates into models for water and carbon management

Using spectral diversity and heterogeneity measures to map habitat mosaics: An example from the Classical Karst

Questions: Can we map complex habitat mosaics from remote-­sensing data? In doing this, are measures of spectral heterogeneity useful to improve image classification performance? Which measures are the most important? How can multitemporal data be integrated in a robust framework? Location: Classical Karst (NE Italy). Methods: First, a habitat map was produced from field surveys. Then, a collection of 12 monthly Sentinel-­2 images was retrieved. Vegetation and spectral heterogeneity (SH) indices were computed and aggregated in four combinations: (1) monthly layers of vegetation and SH indices; (2) seasonal layers of vegetation and SH indices; (3) yearly layers of SH indices computed across the months; and (4) yearly layers of SH indices computed across the seasons. For each combination, a Random Forest clas- sification was performed, first with the complete set of input layers and then with a subset obtained by recursive feature elimination. Training and validation points were independently extracted from field data. Results: The maximum overall accuracy (0.72) was achieved by using seasonally ag- gregated vegetation and SH indices, after the number of vegetation types was re- duced by aggregation from 26 to 11. The use of SH measures significantly increased the overall accuracy of the classification. The spectral β-­diversity was the most im- portant variable in most cases, while the spectral α-­diversity and Rao's Q had a low relative importance, possibly because some habitat patches were small compared to the window used to compute the indices. Conclusions: The results are promising and suggest that image classification frame- works could benefit from the inclusion of SH measures, rarely included before. Habitat mapping in complex landscapes can thus be improved in a cost-­and time-­effective way, suitable for monitoring applications

An updated survey on the use of geospatial technologies in New Zealand’s plantation forestry sector

Background: Geospatial technologies have developed rapidly in recent decades and can provide detailed, accurate data to support forest management. Knowledge of the uptake of geospatial technologies, as well as barriers to adoption, in New Zealand’s plantation forest management sector is limited and would be beneficial to the industry. This study provides an update to the 2013 benchmark study by Morgenroth and Visser. Methods: An online survey was sent to 29 companies that own or manage plantation forests in New Zealand. The survey was split into seven sections, composed of multiple-choice and open-ended questions, on the topics of: demographic information, data portals and datasets, global navigation satellite system (GNSS) receivers, and four remote-sensing technologies. These included aerial imagery, multispectral imagery, hyperspectral imagery, and light detection and ranging (LiDAR). Each section included questions relating to the acquisition, application and products created from each remote-sensing technology. Questions were also included that related to the barriers preventing the uptake of technologies. To determine the progression in the uptake of these technologies the results were compared to Morgenroth and Visser's study conducted five years' earlier. Results: Twenty-three companies responded to the survey and together, those companies managed approximately 1,172,000 ha (or 69% of New Zealand’s 1.706 million ha plantation forest estate (NZFOA, 2018)). The size of the estates managed by individual companies ranged from 1,000 ha to 177,000 ha (quartile 1 = 19,000 ha, median = 33,000 ha, quartile 3 = 63,150 ha). All companies used GNSS receivers and acquired three-band, Red-Green-Blue, aerial imagery. Multispectral imagery, hyperspectral imagery and LiDAR data were acquired by 48%, 9% and 70% of companies, respectively. Common applications for the products derived from these technologies were forest mapping and description, harvest planning, and cutover mapping. The main barrier preventing companies from acquiring most remotely-sensed data was the lack of staff knowledge and training, though cost was the main barrier to LiDAR acquisition. The uptake of all remote-sensing technologies has increased since 2013. LiDAR had the largest progression in uptake, increasing from 17% to 70%. There has also been a change in the way companies acquired the data. Many of the companies used unpiloted aerial vehicles (UAV) to acquire aerial and multispectral imagery in 2018, while in 2013 no companies were using UAVs. ESRI ArcGIS continues to be the dominant geographic information system used by New Zealand’s forest management companies (91%), though 22% of companies now use free GIS software, like QGIS or GRASS. The use of specialised software (e.g. FUSION, LAStools) for LiDAR or photogrammetric point cloud analysis increased since 2013, but most forestry companies who are processing .las files into various products (e.g. digital terrain model) are using ArcGIS. Conclusions: This study showed that there had been a progression in the uptake of geospatial technologies in the New Zealand plantation forest management sector. However, there are still barriers preventing the full utilisation of these technologies. The results suggest that the industry could benefit from investing in more training relating to geospatial technologies