Accurate and timely detection of weeds between and within crop rows in the early growth stage is considered one of the main challenges in site-specific weed management (SSWM). In this context, a ...robust and innovative automatic object-based image analysis (OBIA) algorithm was developed on Unmanned Aerial Vehicle (UAV) images to design early post-emergence prescription maps. This novel algorithm makes the major contribution. The OBIA algorithm combined Digital Surface Models (DSMs), orthomosaics and machine learning techniques (Random Forest, RF). OBIA-based plant heights were accurately estimated and used as a feature in the automatic sample selection by the RF classifier; this was the second research contribution. RF randomly selected a class balanced training set, obtained the optimum features values and classified the image, requiring no manual training, making this procedure time-efficient and more accurate, since it removes errors due to a subjective manual task. The ability to discriminate weeds was significantly affected by the imagery spatial resolution and weed density, making the use of higher spatial resolution images more suitable. Finally, prescription maps for in-season post-emergence SSWM were created based on the weed maps—the third research contribution—which could help farmers in decision-making to optimize crop management by rationalization of the herbicide application. The short time involved in the process (image capture and analysis) would allow timely weed control during critical periods, crucial for preventing yield loss.
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Precision viticulture has arisen in recent years as a new approach in grape production. It is based on assessing field spatial variability and implementing site-specific management strategies, which ...can require georeferenced information of the three dimensional (3D) grapevine canopy structure as one of the input data. The 3D structure of vineyard fields can be generated applying photogrammetric techniques to aerial images collected with Unmanned Aerial Vehicles (UAVs), although processing the large amount of crop data embedded in 3D models is currently a bottleneck of this technology. To solve this limitation, a novel and robust object-based image analysis (OBIA) procedure based on Digital Surface Model (DSM) was developed for 3D grapevine characterization. The significance of this work relies on the developed OBIA algorithm which is fully automatic and self-adaptive to different crop-field conditions, classifying grapevines, and row gap (missing vine plants), and computing vine dimensions without any user intervention. The results obtained in three testing fields on two different dates showed high accuracy in the classification of grapevine area and row gaps, as well as minor errors in the estimates of grapevine height. In addition, this algorithm computed the position, projected area, and volume of every grapevine in the field, which increases the potential of this UAV- and OBIA-based technology as a tool for site-specific crop management applications.
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Remote sensing applied in the digital transformation of agriculture and, more particularly, in precision viticulture offers methods to map field spatial variability to support site-specific ...management strategies; these can be based on crop canopy characteristics such as the row height or vegetation cover fraction, requiring accurate three-dimensional (3D) information. To derive canopy information, a set of dense 3D point clouds was generated using photogrammetric techniques on images acquired by an RGB sensor onboard an unmanned aerial vehicle (UAV) in two testing vineyards on two different dates. In addition to the geometry, each point also stores information from the RGB color model, which was used to discriminate between vegetation and bare soil. To the best of our knowledge, the new methodology herein presented consisting of linking point clouds with their spectral information had not previously been applied to automatically estimate vine height. Therefore, the novelty of this work is based on the application of color vegetation indices in point clouds for the automatic detection and classification of points representing vegetation and the later ability to determine the height of vines using as a reference the heights of the points classified as soil. Results from on-ground measurements of the heights of individual grapevines were compared with the estimated heights from the UAV point cloud, showing high determination coefficients (R² > 0.87) and low root-mean-square error (0.070 m). This methodology offers new capabilities for the use of RGB sensors onboard UAV platforms as a tool for precision viticulture and digitizing applications.
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Photodynamic therapy (PDT) is a therapeutic modality that has shown effectiveness in the inactivation of cancer cell lines and microorganisms. Treatment consists of activating the photosensitizer ...(PS) upon light irradiation of adequate wavelength. After reaching the excited state, the PS can handle the intersystem conversion through energy transfer to the molecular oxygen, generating reactive oxygen species. This especially applies to singlet oxygen (1O2), which is responsible for the selective destruction of the sick tissue. Photosensitizing compounds (chlorophylls and derivatives) existing in the spinach extract have applicability for PDT. This study aimed to develop and characterize the thermoresponsive bioadhesive system composed of Pluronic F127 20.0%- and Carbopol 934P 0.2% (w/w) (FC)-containing chlorophyll-based extract 0.5% (w/w) (FC-Chl). Mechanical and rheological properties, in vitro release, sol–gel transition temperature, and ex vivo permeability of the spinach extract PS components (through pig ear skin) were investigated. Furthermore, photodynamic activity of the system was accessed through uric acid and time-solved measurements. The sol–gel transition temperature obtained for the FC-Chl system was 28.8 ± 0.3 °C. Rheological and texture properties of the platform were suitable for use as a dermatological system, exhibiting easy application and good characteristics of retention in the place of administration. In vitro release studies showed the presence of two distinct mechanisms that reasonably obey the zero-order and first-order kinetics models. PS components presented skin permeability and reached a permeation depth of 830 μm (between the epidermis and dermis). The photodynamic evaluation of the FC-Chl system was effective in the degradation of uric acid. The quantum yield (ΦΔ 1O2) and life time (τ1O2) of singlet oxygen showed similar values for the spinach extract and the isolated chlorophyll a species in ethanol. These results allowed for the classification of the FC-Chl platform as potentially useful for the delivery of the chlorophyll-based extract in the topic PDT, suggesting that it is worthy for in vivo evaluation.
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Almond is an emerging crop due to the health benefits of almond consumption including nutritional, anti-inflammatory, and hypocholesterolaemia properties. Traditional almond producers were ...concentrated in California, Australia, and Mediterranean countries. However, almond is currently present in more than 50 countries due to breeding programs have modernized almond orchards by developing new varieties with improved traits related to late flowering (to reduce the risk of damage caused by late frosts) and tree architecture. Almond tree architecture and flowering are acquired and evaluated through intensive field labour for breeders. Flowering detection has traditionally been a very challenging objective. To our knowledge, there is no published information about monitoring of the tree flowering dynamics of a crop at the field scale by using color information from photogrammetric 3D point clouds and OBIA. As an alternative, a procedure based on the generation of colored photogrammetric point clouds using a low cost (RGB) camera on-board an unmanned aerial vehicle (UAV), and an semi-automatic object based image analysis (OBIA) algorithm was created for monitoring the flower density and flowering period of every almond tree in the framework of two almond phenotypic trials with different planting dates.
Our method was useful for detecting the phenotypic variability of every almond variety by mapping and quantifying every tree height and volume as well as the flowering dynamics and flower density. There was a high level of agreement among the tree height, flower density, and blooming calendar derived from our procedure on both fields with the ones created from on-ground measured data. Some of the almond varieties showed a significant linear fit between its crown volume and their yield.
Our findings could help breeders and researchers to reduce the gap between phenomics and genomics by generating accurate almond tree information in an efficient, non-destructive, and inexpensive way. The method described is also useful for data mining to select the most promising accessions, making it possible to assess specific multi-criteria ranking varieties, which are one of the main tools for breeders.
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The need for the olive farm modernization have encouraged the research of more efficient crop management strategies through cross-breeding programs to release new olive cultivars more suitable for ...mechanization and use in intensive orchards, with high quality production and resistance to biotic and abiotic stresses. The advancement of breeding programs are hampered by the lack of efficient phenotyping methods to quickly and accurately acquire crop traits such as morphological attributes (tree vigor and vegetative growth habits), which are key to identify desirable genotypes as early as possible. In this context, an UAV-based high-throughput system for olive breeding program applications was developed to extract tree traits in large-scale phenotyping studies under field conditions. The system consisted of UAV-flight configurations, in terms of flight altitude and image overlaps, and a novel, automatic, and accurate object-based image analysis (OBIA) algorithm based on point clouds, which was evaluated in two experimental trials in the framework of a table olive breeding program, with the aim to determine the earliest date for suitable quantifying of tree architectural traits. Two training systems (intensive and hedgerow) were evaluated at two very early stages of tree growth: 15 and 27 months after planting. Digital Terrain Models (DTMs) were automatically and accurately generated by the algorithm as well as every olive tree identified, independently of the training system and tree age. The architectural traits, specially tree height and crown area, were estimated with high accuracy in the second flight campaign, i.e. 27 months after planting. Differences in the quality of 3D crown reconstruction were found for the growth patterns derived from each training system. These key phenotyping traits could be used in several olive breeding programs, as well as to address some agronomical goals. In addition, this system is cost and time optimized, so that requested architectural traits could be provided in the same day as UAV flights. This high-throughput system may solve the actual bottleneck of plant phenotyping of "linking genotype and phenotype," considered a major challenge for crop research in the 21st century, and bring forward the crucial time of decision making for breeders.
The geometric features, such as canopy area, tree height and crown volume, of agricultural trees provide useful information to elucidate plantation status and to design input prescription maps ...adjusted to real crop needs. This work presents an innovative procedure for computing the 3-dimensional (3D) geometric features of almond trees by applying two phases: 1) generation of photogrammetric point clouds with unmanned aerial vehicle (UAV) technology, and 2) analysis of the point clouds using object-based image analysis (OBIA) techniques. To test this approach, a UAV with a visible-RGB (low-cost) sensor was flown over three experimental almond groves at different phenological stages for two years, and the validation field method consisted of registering the height of a total of 325 trees in the two fields. The OBIA algorithm developed in this study achieved successful results: i) the individual and overall similarity measures between manually delineated and automatically detected almond tree crowns were above 0.9, and ii) the validation assessment conducted to estimate tree height from the UAV-derived algorithm produced an R2 = 0.94, an overall root mean square error (RMSE) of 0.39 m. The information derived from the OBIA algorithm was used for generating 3D maps for every tree volume and volume growth, which would be useful to understand the linkages between tree and crop management operations in the context of precision agriculture, with relevant agro-environmental implications. Our findings show that an RGB, low-cost sensor on-board a UAV provided dense 3D point clouds can be used for accurately characterising almond tree architecture.
•UAV derived photogrammetric point clouds were generated in 3 almond orchards.•An automatic OBIA algorithm was developed for analyzing the point clouds.•Automatic almond crown delineation and height estimation achieved high accuracies.•Maps for almond tree volume and volume growth were generated.
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Self-propelled swimmers such as bacteria agglomerate into clusters as a result of their persistent motion. In 1D, those clusters do not coalesce macroscopically and the stationary cluster size ...distribution (CSD) takes an exponential form. We develop a minimal lattice model for active particles in narrow channels to study how clustering is affected by the interplay between self-propulsion speed diversity and confinement. A mixture of run-and-tumble particles with a distribution of self-propulsion speeds is simulated in 1D. Particles can swap positions at rates proportional to their relative self-propulsion speed. Without swapping, we find that the average cluster size
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's, unlike the case of tumbling-rate diversity previously studied. Effectively, the mixture is thus equivalent to a system of identical particles whose self-propulsion speed is the harmonic mean self-propulsion speed of the mixture. With swapping, particles escape more quickly from clusters. As a consequence,
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decreases with swapping rates and depends less strongly on diversity. We derive a dynamical equilibrium theory for the CSDs of binary and fully polydisperse systems. Similarly to the clustering behaviour of one-component models, our qualitative results for mixtures are expected to be universal across active matter. Using literature experimental values for the self-propulsion speed diversity of unicellular swimmers known as choanoflagellates, which naturally differentiate into slower and faster cells, we predict that the error in estimating their
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one-component models which use the conventional arithmetic mean self-propulsion speed is around 30%.
Mixtures of active particles with more diverse swim speeds form smaller persistence-induced clusters. Their average cluster size is equal to that of one-component systems whose swim speed is the harmonic mean of the swim speeds of the mixture.
Canopy management operations, such as shoot thinning, leaf removal, and shoot trimming, are among the most relevant agricultural practices in viticulture. However, the supervision of these tasks ...demands a visual inspection of the whole vineyard, which is time-consuming and laborious. The application of photogrammetric techniques to images acquired with an Unmanned Aerial Vehicle (UAV) has proved to be an efficient way to measure woody crops canopy. Consequently, the objective of this work was to determine whether the use of UAV photogrammetry allows the detection of canopy management operations. A UAV equipped with an RGB digital camera was used to acquire images with high overlap over different canopy management experiments in four vineyards with the aim of characterizing vine dimensions before and after shoot thinning, leaf removal, and shoot trimming operations. The images were processed to generate photogrammetric point clouds of every vine that were analyzed using a fully automated object-based image analysis algorithm. Two approaches were tested in the analysis of the UAV derived data: (1) to determine whether the comparison of the vine dimensions before and after the treatments allowed the detection of the canopy management operations; and (2) to study the vine dimensions after the operations and assess the possibility of detecting these operations using only the data from the flight after them. The first approach successfully detected the canopy management. Regarding the second approach, significant differences in the vine dimensions after the treatments were detected in all the experiments, and the vines under the shoot trimming treatment could be easily and accurately detected based on a fixed threshold.
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The gene expression landscape of pine seedling tissues Cañas, Rafael A.; Li, Zhen; Pascual, M. Belén ...
The Plant journal : for cell and molecular biology,
September 2017, 2017-Sep, 2017-09-00, 20170901, Volume:
91, Issue:
6
Journal Article
Peer reviewed
Open access
Summary
Conifers dominate vast regions of the Northern hemisphere. They are the main source of raw materials for timber industry as well as a wide range of biomaterials. Despite their inherent ...difficulties as experimental models for classical plant biology research, the technological advances in genomics research are enabling fundamental studies on these plants. The use of laser capture microdissection followed by transcriptomic analysis is a powerful tool for unravelling the molecular and functional organization of conifer tissues and specialized cells. In the present work, 14 different tissues from 1‐month‐old maritime pine (Pinus pinaster) seedlings have been isolated and their transcriptomes analysed. The results increased the sequence information and number of full‐length transcripts from a previous reference transcriptome and added 39 841 new transcripts. In total, 2376 transcripts were ubiquitously expressed in all of the examined tissues. These transcripts could be considered the core ‘housekeeping genes’ in pine. The genes have been clustered in function to their expression profiles. This analysis reduced the number of profiles to 38, most of these defined by their expression in a unique tissue that is much higher than in the other tissues. The expression and localization data are accessible at ConGenIE.org (http://v22.popgenie.org/microdisection/). This study presents an overview of the gene expression distribution in different pine tissues, specifically highlighting the relationships between tissue gene expression and function. This transcriptome atlas is a valuable resource for functional genomics research in conifers.
Significance Statement
In the present work, a gene expression atlas from tissues of maritime pine was generated using laser capture microdissection and next generation sequencing. The main results are accessible at ConGenIE.org (http://congenie.org/). This public information will facilitate future studies in conifer genomics.
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