Principal variable selection to explain grain yield variation in winter wheat from features extracted from UAV imagery

Background: Automated phenotyping technologies are continually advancing the breeding process. However, collecting various secondary traits throughout the growing season and processing massive amounts of data still take great efforts and time. Selecting a minimum number of secondary traits that have the maximum predictive power has the potential to reduce phenotyping efforts. The objective of this study was to select principal features extracted from UAV imagery and critical growth stages that contributed the most in explaining winter wheat grain yield. Five dates of multispectral images and seven dates of RGB images were collected by a UAV system during the spring growing season in 2018. Two classes of features (variables), totaling to 172 variables, were extracted for each plot from the vegetation index and plant height maps, including pixel statistics and dynamic growth rates. A parametric algorithm, LASSO regression (the least angle and shrinkage selection operator), and a non-parametric algorithm, random forest, were applied for variable selection. The regression coefficients estimated by LASSO and the permutation importance scores provided by random forest were used to determine the ten most important variables influencing grain yield from each algorithm. Results: Both selection algorithms assigned the highest importance score to the variables related with plant height around the grain filling stage. Some vegetation indices related variables were also selected by the algorithms mainly at earlier to mid growth stages and during the senescence. Compared with the yield prediction using all 172 variables derived from measured phenotypes, using the selected variables performed comparable or even better. We also noticed that the prediction accuracy on the adapted NE lines (r = 0.58–0.81) was higher than the other lines (r = 0.21–0.59) included in this study with different genetic backgrounds. Conclusions: With the ultra-high resolution plot imagery obtained by the UAS-based phenotyping we are now able to derive more features, such as the variation of plant height or vegetation indices within a plot other than just an averaged number, that are potentially very useful for the breeding purpose. However, too many features or variables can be derived in this way. The promising results from this study suggests that the selected set from those variables can have comparable prediction accuracies on the grain yield prediction than the full set of them but possibly resulting in a better allocation of efforts and resources on phenotypic data collection and processing

A Comparative Analysis of Phytovolume Estimation Methods Based on UAV-Photogrammetry and Multispectral Imagery in a Mediterranean Forest

Management and control operations are crucial for preventing forest fires, especially in Mediterranean forest areas with dry climatic periods. One of them is prescribed fires, in which the biomass fuel present in the controlled plot area must be accurately estimated. The most used methods for estimating biomass are time-consuming and demand too much manpower. Unmanned aerial vehicles (UAVs) carrying multispectral sensors can be used to carry out accurate indirect measurements of terrain and vegetation morphology and their radiometric characteristics. Based on the UAV-photogrammetric project products, four estimators of phytovolume were compared in a Mediterranean forest area, all obtained using the difference between a digital surface model (DSM) and a digital terrain model (DTM). The DSM was derived from a UAV-photogrammetric project based on the structure from a motion algorithm. Four different methods for obtaining a DTM were used based on an unclassified dense point cloud produced through a UAV-photogrammetric project (FFU), an unsupervised classified dense point cloud (FFC), a multispectral vegetation index (FMI), and a cloth simulation filter (FCS). Qualitative and quantitative comparisons determined the ability of the phytovolume estimators for vegetation detection and occupied volume. The results show that there are no significant differences in surface vegetation detection between all the pairwise possible comparisons of the four estimators at a 95% confidence level, but FMI presented the best kappa value (0.678) in an error matrix analysis with reference data obtained from photointerpretation and supervised classification. Concerning the accuracy of phytovolume estimation, only FFU and FFC presented differences higher than two standard deviations in a pairwise comparison, and FMI presented the best RMSE (12.3 m) when the estimators were compared to 768 observed data points grouped in four 500 m2 sample plots. The FMI was the best phytovolume estimator of the four compared for low vegetation height in a Mediterranean forest. The use of FMI based on UAV data provides accurate phytovolume estimations that can be applied on several environment management activities, including wildfire prevention. Multitemporal phytovolume estimations based on FMI could help to model the forest resources evolution in a very realistic way

Vegetation Dynamics in Ecuador

Global forest cover has suffered a dramatic reduction during recent decades, especially in tropical regions, which is mainly due to human activities caused by enhanced population pressures. Nevertheless, forest ecosystems, especially tropical forests, play an important role in the carbon cycle functioning as carbon stocks and sinks, which is why conservation strategies are of utmost importance respective to ongoing global warming. In South America the highest deforestation rates are observed in Ecuador, but an operational surveillance system for continuous forest monitoring, along with the determination of deforestation rates and the estimation of actual carbon socks is still missing. Therefore, the present investigation provides a functional tool based on remote sensing data to monitor forest stands at local, regional and national scales. To evaluate forest cover and deforestation rates at country level satellite data was used, whereas LiDAR data was utilized to accurately estimate the Above Ground Biomass (AGB; carbon stocks) at catchment level. Furthermore, to provide a cost-effective tool for continuous forest monitoring of the most vulnerable parts, an Unmanned Aerial Vehicle (UAV) was deployed and equipped with various sensors (RBG and multispectral camera). The results showed that in Ecuador total forest cover was reduced by about 24% during the last three decades. Moreover, deforestation rates have increased with the beginning of the new century, especially in the Andean Highland and the Amazon Basin, due to enhanced population pressures and the government supported oil and mining industries, besides illegal timber extractions. The AGB stock estimations at catchment level indicated that most of the carbon is stored in natural ecosystems (forest and páramo; AGB ~98%), whereas areas affected by anthropogenic land use changes (mostly pastureland) lost nearly all their storage capacities (AGB ~2%). Furthermore, the LiDAR data permitted the detection of the forest structure, and therefore the identification of the most vulnerable parts. To monitor these areas, it could be shown that UAVs are useful, particularly when equipped with an RGB camera (AGB correlation: R² > 0.9), because multispectral images suffer saturation of the spectral bands over dense natural forest stands, which results in high overestimations. In summary, the developed operational surveillance systems respective to forest cover at different spatial scales can be implemented in Ecuador to promote conservation/ restoration strategies and to reduce the high deforestation rates. This may also mitigate future greenhouse gas emissions and guarantee functional ecosystem services for local and regional populations

Uumanned Aerial Vehicle Data Analysis For High-throughput Plant Phenotyping

The continuing population is placing unprecedented demands on worldwide crop yield production and quality. Improving genomic selection for breeding process is one essential aspect for solving this dilemma. Benefitted from the advances in high-throughput genotyping, researchers already gained better understanding of genetic traits. However, given the comparatively lower efficiency in current phenotyping technique, the significance of phenotypic traits has still not fully exploited in genomic selection. Therefore, improving HTPP efficiency has become an urgent task for researchers. As one of the platforms utilized for collecting HTPP data, unmanned aerial vehicle (UAV) allows high quality data to be collected within short time and by less labor. There are currently many options for customized UAV system on market; however, data analysis efficiency is still one limitation for the fully implementation of HTPP. To this end, the focus of this program was data analysis of UAV acquired data. The specific objectives were two-fold, one was to investigate statistical correlations between UAV derived phenotypic traits and manually measured sorghum biomass, nitrogen and chlorophyll content. Another was to conduct variable selection on the phenotypic parameters calculated from UAV derived vegetation index (VI) and plant height maps, aiming to find out the principal parameters that contribute most in explaining winter wheat grain yield. Corresponding, two studies were carried out. Good correlations between UAV-derived VI/plant height and sorghum biomass/nitrogen/chlorophyll in the first study suggested that UAV-based HTPP has great potential in facilitating genetic improvement. For the second study, variable selection results from the single-year data showed that plant height related parameters, especially from later season, contributed more in explaining grain yield. Advisor: Yeyin Sh

Advancements in Multi-temporal Remote Sensing Data Analysis Techniques for Precision Agriculture

L'abstract è presente nell'allegato / the abstract is in the attachmen

Assessing spring phenology of a temperate woodland : a multiscale comparison of ground, unmanned aerial vehicle and Landsat satellite observations

PhD ThesisVegetation phenology is the study of plant natural life cycle stages. Plant phenological events are related to carbon, energy and water cycles within terrestrial ecosystems, operating from local to global scales. As plant phenology events are highly sensitive to climate fluctuations, the timing of these events has been used as an independent indicator of climate change. The monitoring of forest phenology in a cost-effective manner, at a fine spatial scale and over relatively large areas remains a significant challenge. To address this issue, unmanned aerial vehicles (UAVs) appear to be a potential new platform for forest phenology monitoring. The aim of this research is to assess the potential of UAV data to track the temporal dynamics of spring phenology, from the individual tree to woodland scale, and to cross-compare UAV results against ground and satellite observations, in order to better understand characteristics of UAV data and assess potential for use in validation of satellite-derived phenology. A time series of UAV data were acquired in tandem with an intensive ground campaign during the spring season of 2015, over Hanging Leaves Wood, Northumberland, UK. The radiometric quality of the UAV imagery acquired by two consumer-grade cameras was assessed, in terms of the ability to retrieve reflectance and Normalised Difference Vegetation Index (NDVI), and successfully validated against ground (0.84≤R2≥0.96) and Landsat (0.73≤R2≥0.89) measurements, but only NDVI resulted in stable time series. The start (SOS), middle (MOS) and end (EOS) of spring season dates were estimated at an individual tree-level using UAV time series of NDVI and Green Chromatic Coordinate (GCC), with GCC resulting in a clearer and stronger seasonal signal at a tree crown scale. UAV-derived SOS could be predicted more accurately than MOS and EOS, with an accuracy of less than 1 week for deciduous woodland and within 2 weeks for evergreen. The UAV data were used to map phenological events for individual trees across the whole woodland, demonstrating that contrasting canopy phenological events can occur within the extent of a single Landsat pixel. This accounted for the poor relationships found between UAV- and Landsat-derived phenometrics (R2<0.45) in this study. An opportunity is now available to track very fine scale land surface changes over contiguous vegetation communities, information which could improve characterization of vegetation phenology at multiple scales.The Science without Borders program, managed by CAPES-Brazil (Coordenação de Aperfeiçoamento de Pessoal de Nível Superior)

Remote Sensing in Agriculture: State-of-the-Art

The Special Issue on “Remote Sensing in Agriculture: State-of-the-Art” gives an exhaustive overview of the ongoing remote sensing technology transfer into the agricultural sector. It consists of 10 high-quality papers focusing on a wide range of remote sensing models and techniques to forecast crop production and yield, to map agricultural landscape and to evaluate plant and soil biophysical features. Satellite, RPAS, and SAR data were involved. This preface describes shortly each contribution published in such Special Issue

Unmanned Aerial Vehicles (UAVs) in environmental biology: A Review

Acquiring information about the environment is a key step during each study in the field of environmental biology&nbsp;at different levels, from an individual species to community and biome. However, obtaining information about the environment is frequently difficult because of, for example, the phenological timing, spatial distribution&nbsp;of a species or limited accessibility of a particular area for the field survey. Moreover, remote sensing&nbsp;technology, which enables the observation of the Earth’s surface and is currently very common in environmental&nbsp;research, has many limitations such as insufficient spatial, spectral and temporal resolution and a high cost of&nbsp;data acquisition. Since the 1990s, researchers have been exploring the potential of different types of unmanned&nbsp;aerial vehicles (UAVs) for monitoring Earth’s surface. The present study reviews recent scientific literature&nbsp;dealing with the use of UAV in environmental biology. Amongst numerous papers, short communications and&nbsp;conference abstracts, we selected 110 original studies of how UAVs can be used in environmental biology and&nbsp;which organisms can be studied in this manner. Most of these studies concerned the use of UAV to measure the&nbsp;vegetation parameters such as crown height, volume, number of individuals (14 studies) and quantification of&nbsp;the spatio-temporal dynamics of vegetation changes (12 studies). UAVs were also frequently applied to count&nbsp;birds and mammals, especially those living in the water. Generally, the analytical part of the present study was&nbsp;divided into following sections: (1) detecting, assessing and predicting threats on vegetation, (2) measuring&nbsp;the biophysical parameters of vegetation, (3) quantifying the dynamics of changes in plants and habitats and&nbsp;(4) population and behaviour studies of animals. At the end, we also synthesised all the information showing,&nbsp;amongst others, the advances in environmental biology because of UAV application. Considering that 33% of&nbsp;studies found and included in this review were published in 2017 and 2018, it is expected that the number and&nbsp;variety of applications of UAVs in environmental biology will increase in the future

Derivation of forest inventory parameters from high-resolution satellite imagery for the Thunkel area, Northern Mongolia. A comparative study on various satellite sensors and data analysis techniques.

With the demise of the Soviet Union and the transition to a market economy starting in the 1990s, Mongolia has been experiencing dramatic changes resulting in social and economic disparities and an increasing strain on its natural resources. The situation is exacerbated by a changing climate, the erosion of forestry related administrative structures, and a lack of law enforcement activities. Mongolia’s forests have been afflicted with a dramatic increase in degradation due to human and natural impacts such as overexploitation and wildfire occurrences. In addition, forest management practices are far from being sustainable. In order to provide useful information on how to viably and effectively utilise the forest resources in the future, the gathering and analysis of forest related data is pivotal. Although a National Forest Inventory was conducted in 2016, very little reliable and scientifically substantiated information exists related to a regional or even local level. This lack of detailed information warranted a study performed in the Thunkel taiga area in 2017 in cooperation with the GIZ. In this context, we hypothesise that (i) tree species and composition can be identified utilising the aerial imagery, (ii) tree height can be extracted from the resulting canopy height model with accuracies commensurate with field survey measurements, and (iii) high-resolution satellite imagery is suitable for the extraction of tree species, the number of trees, and the upscaling of timber volume and basal area based on the spectral properties. The outcomes of this study illustrate quite clearly the potential of employing UAV imagery for tree height extraction (R2 of 0.9) as well as for species and crown diameter determination. However, in a few instances, the visual interpretation of the aerial photographs were determined to be superior to the computer-aided automatic extraction of forest attributes. In addition, imagery from various satellite sensors (e.g. Sentinel-2, RapidEye, WorldView-2) proved to be excellently suited for the delineation of burned areas and the assessment of tree vigour. Furthermore, recently developed sophisticated classifying approaches such as Support Vector Machines and Random Forest appear to be tailored for tree species discrimination (Overall Accuracy of 89%). Object-based classification approaches convey the impression to be highly suitable for very high-resolution imagery, however, at medium scale, pixel-based classifiers outperformed the former. It is also suggested that high radiometric resolution bears the potential to easily compensate for the lack of spatial detectability in the imagery. Quite surprising was the occurrence of dark taiga species in the riparian areas being beyond their natural habitat range. The presented results matrix and the interpretation key have been devised as a decision tool and/or a vademecum for practitioners. In consideration of future projects and to facilitate the improvement of the forest inventory database, the establishment of permanent sampling plots in the Mongolian taigas is strongly advised.2021-06-0

Sugarcane yields prediction at the row level using a novel cross-validation approach to multi-year multispectral images

Early prediction of sugarcane crop yield would benefit sugarcane growers and policymakers by allowing for timely decisions. The primary objective of this study was to reduce reliance on satellite images and improve early prediction of sugarcane yield at row level by using high-resolution multispectral Unmanned Aerial Vehicle (UAV) imagery. To our knowledge, no previous study has evaluated the performance of multispectral UAV-derived vegetation indices in sugarcane crops at the crop row level. In this study, we used UAV mapping on 48 rows of sugarcane at three main growth stages (early, middle, and mature) over three growing seasons. A secondary objective was to predict future sugarcane yields at the earliest possible stage of growth. The results showed that the optimal growth stage for all 23 VIs varied, but the middle stage, from mid-March to early May, was the most prevalent. Further detailed analysis in the middle stage revealed that March was the best month for predicting future sugarcane yields when compared to April and May. This result is approximately a month earlier than previous studies in the same region. Following two stages of feature selection, such as Pearson correlation analysis and stepwise feature selection, a novel cross-validation methodology based on a generalized linear model trained and tested the yield prediction models on various combinations of the VIs. This novel methodology improves model accuracy by avoiding overfitting and over complexity caused by interdependent VIs, and then validates the model generality using previously unseen data. The best performance was achieved by combining the Normalized Difference RedEdge (NDRE) and the Green–Red Normalized Difference Vegetation Index (GRNDVI) at March. These results help growers and decision-makers benefit from early row-level yield forecast, six months before harvest, if UAV mapping is available