High-Throughput System for the Early Quantification of Major Architectural Traits in Olive Breeding Trials Using UAV Images and OBIA Techniques

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

Country-wide retrieval of forest structure from optical and SAR satellite imagery with deep ensembles

Monitoring and managing Earth’s forests in an informed manner is an important requirement for addressing challenges like biodiversity loss and climate change. While traditional in situ or aerial campaigns for forest assessments provide accurate data for analysis at regional level, scaling them to entire countries and beyond with high temporal resolution is hardly possible. In this work, we propose a method based on deep ensembles that densely estimates forest structure variables at country-scale with 10-m resolution, using freely available satellite imagery as input. Our method jointly transforms Sentinel-2 optical images and Sentinel-1 syntheticaperture radar images into maps of five different forest structure variables: 95th height percentile, mean height, density, Gini coefficient, and fractional cover. We train and test our model on reference data from 41 airborne laser scanning missions across Norway and demonstrate that it is able to generalize to unseen test regions, achieving normalized mean absolute errors between 11% and 15%, depending on the variable. Our work is also the first to propose a variant of so-called Bayesian deep learning to densely predict multiple forest structure variables with well-calibrated uncertainty estimates from satellite imagery. The uncertainty information increases the trustworthiness of the model and its suitability for downstream tasks that require reliable confidence estimates as a basis for decision making. We present an extensive set of experiments to validate the accuracy of the predicted maps as well as the quality of the predicted uncertainties. To demonstrate scalability, we provide Norway-wide maps for the five forest structure variables.publishedVersio

Remote sensing image fusion on 3D scenarios: A review of applications for agriculture and forestry

Three-dimensional (3D) image mapping of real-world scenarios has a great potential to provide the user with a more accurate scene understanding. This will enable, among others, unsupervised automatic sampling of meaningful material classes from the target area for adaptive semi-supervised deep learning techniques. This path is already being taken by the recent and fast-developing research in computational fields, however, some issues related to computationally expensive processes in the integration of multi-source sensing data remain. Recent studies focused on Earth observation and characterization are enhanced by the proliferation of Unmanned Aerial Vehicles (UAV) and sensors able to capture massive datasets with a high spatial resolution. In this scope, many approaches have been presented for 3D modeling, remote sensing, image processing and mapping, and multi-source data fusion. This survey aims to present a summary of previous work according to the most relevant contributions for the reconstruction and analysis of 3D models of real scenarios using multispectral, thermal and hyperspectral imagery. Surveyed applications are focused on agriculture and forestry since these fields concentrate most applications and are widely studied. Many challenges are currently being overcome by recent methods based on the reconstruction of multi-sensorial 3D scenarios. In parallel, the processing of large image datasets has recently been accelerated by General-Purpose Graphics Processing Unit (GPGPU) approaches that are also summarized in this work. Finally, as a conclusion, some open issues and future research directions are presented.European Commission 1381202-GEU PYC20-RE-005-UJA IEG-2021Junta de Andalucia 1381202-GEU PYC20-RE-005-UJA IEG-2021Instituto de Estudios GiennesesEuropean CommissionSpanish Government UIDB/04033/2020DATI-Digital Agriculture TechnologiesPortuguese Foundation for Science and Technology 1381202-GEU FPU19/0010

Landscape scale mapping of tundra vegetation structure at ultra-high resolution using UAVs and computer vision

Ilmastomuutoksella on voimakkain vaikutus suurten leveysasteiden ekosysteemeissä, jotka ovat sopeutuneet viileään ilmastoon. Jotta suurella mittakaavalla havaittuja muutoksia tundrakasvillisuudessa ja niiden takaisinkytkentävaikutuksia ilmastoon voidaan ymmärtää ja ennustaa luotettavammin, on syytä tarkastella mitä tapahtuu pienellä mittakaavalla; jopa yksittäisissä kasveissa. Lähivuosikymmenten aikana tapahtunut teknologinen kehitys on mahdollistanut kustannustehokkaiden, kevyiden ja pienikokoisten miehittämättömien ilma-alusten (UAV) yleistymisen. Erittäin korkearesoluutioisten aineistojen (pikselikoko <10cm) lisääntyessä ja tullessa yhä helpommin saataville, ympäristön tarkastelussa käytetyt kaukokartoitusmenetelmät altistuvat paradigmanmuutokselle, kun konenäköön ja -oppimiseen perustuvat algoritmit ja analyysit yleistyvät. Menetelmien käyttöönotto on houkuttelevaa, koska ne mahdollistavat joustavan ja pitkälle automatisoidun aineistonkeruun ja erittäin tarkkojen kaukokartoitustuotteiden tuottamisen vaikeasti tavoitettavilta alueilta, kuten tundralla. Luotettavien tulosten saaminen vaatii kuitenkin huolellista suunnittelua sekä prosessointialgoritmien ja -parametrien pitkäjänteistä testaamista. Tässä tutkimuksessa tarkasteltiin, kuinka tarkasti tavallisella digitaalikameralla kerätyistä ilmakuvista johdetuilla muuttujilla voidaan kartoittaa kasvillisuuden rakennetta maisemamittakaavalla. Kilpisjärvellä Pohjois-Fennoskandiassa kerättiin dronella kolmensadan hehtaarin kokoiselta alueelta yhteensä noin 10 000 ilmakuvasta koostuva aineisto. Lisäksi alueella määritettiin 1183 pisteestä dominantti putkilokasvillisuus, sekä kasvillisuuden korkeus. Ilmakuvat prosessoitiin tiheiksi kolmiulotteisiksi pistepilviksi konenäköön ja fotogrammetriaan perustuvalla SfM (Structure from Motion) menetelmällä. Pistepilvien pohjalta interpoloitiin maastomalli sekä kasvillisuuden korkeusmalli. Lisäksi tuotettiin koko alueen kattava ilmakuvamosaiikki. Näiden aineistojen pohjalta laskettiin muuttujia, joita käytettiin yhdessä maastoreferenssiaineiston kanssa kasvillisuuden objektipohjaisessa analyysissä (GEOBIA, Geographical Object-Based Image Analysis). Suodatetut maanpintapisteet vastasivat luotettavasti todellista maanpinnan korkeutta koko alueella ja tuotetut korkeusmallit korreloivat voimakkaasti maastoreferenssiaineiston kanssa. Maastomallin virhe oli suurin alueilla, joilla oli korkeaa kasvillisuutta. Valaistusolosuhteissa ja kasvillisuudessa tapahtuneet muutokset ilmakuvien keruun aikana aiheuttivat haasteita objektipohjaisen analyysin molemmissa vaiheissa: segmentoinnissa ja luokittelussa. mutta kokonaistarkkuus parani 0,27:stä 0,,54:n kun luokitteluun lisättiin topografiaa, kasvillisuuden korkeutta ja tekstuuria kuvaavia muuttujia ja kohdeluokkien lukumäärää vähennettiin. Konenäköön ja –oppimiseen perustuvat menetelmät pystyvät tuottamaan tärkeää tietoa tundran kasvillisuuden rakenteesta, erityisesti kasvillisuuden korkeudesta, maisemassa. Lisää tutkimusta kuitenkin tarvitaan parhaiden algoritmien ja parametrien määrittämiseksi tundraympäristössä, jossa ympäristöolosuhteet muuttuvat nopeasti ja kasvillisuus on heterogeenistä ja sekoittunutta, mikä aiheuttaa eroja ilmakuvien välillä ja lisää vaikeuksia analyyseissä.Climate change has the strongest impact on high-latitude ecosystems that are adapted to cool climates. In order to better understand and predict the changes in tundra vegetation observed on large scales as well as their feedbacks onto climate, it is necessary to look at what is happening at finer scales; even in individual plants. Technological developments over the past few decades have enabled the spread of cost-effective, light and small unmanned aerial vehicles (UAVs). As very high-resolution data (pixel size <10cm) becomes more and more available, the remote sensing methods used in environmental analysis become subject to a paradigm shift as algorithms and analyzes based on machine vision and learning turn out to be more common. Harnessing new methods is attractive because they allow flexible and highly automated data collection and the production of highly accurate remote sensing products from hard-to-reach areas such as the tundra. However, obtaining reliable results requires careful planning and testing of processing algorithms and parameters. This study looked at how accurately variables derived from aerial images collected with an off-the-shelf digital camera can map the vegetation structure on a landscape scale. In Kilpisjärvi, northern Fennoscandia, a total of ~ 10,000 aerial photographs were collected by drone covering an area of three hundred hectares. In addition, dominant vascular plants were identified from 1183 points in the area, as well as vegetation height. Aerial images were processed into dense three-dimensional point clouds by using SfM (Structure from Motion) method, which is based on computer vision and digital photogrammetry. From the point clouds terrain models and vegetation height models were interpolated. In addition, image mosaic covering the entire area was produced. Based on these data, predictive variables were calculated, which were used together with the terrain reference data in Geographical Object-Based Image Analysis (GEOBIA). The filtered ground points corresponded to observations throughout the region, and the produced elevation models strongly correlated with the ground reference data. The terrain model error was greatest in areas with tall vegetation. Changes in lighting conditions and vegetation during aerial image surveys posed challenges in both phases of object-based analysis: segmentation and classification. but overall accuracy improved from 0.27 to 0.54 when topography, vegetation height and texture variables were added to the classifier and the number of target classes was reduced. Methods based on machine vision and learning can produce important information about vegetation structure, vegetation height, in a landscape. However, more research is needed to determine the best algorithms and parameters in a tundra environment where environmental conditions change rapidly and vegetation is heterogeneous and mixed, causing differences between aerial images and difficulties in analyses

Unmanned aerial vehicle (UAV) derived structure-from-motion photogrammetry point clouds for oil palm (Elaeis guineensis) canopy segmentation and height estimation

This is the author accepted manuscript. The final version is available from Taylor & Francis via the DOI in this record.The vast size of oil palm (Elaeis guineensis) plantations has led to lightweight unmanned aerial vehicles (UAVs) being identified as cost effective tools to generate inventories for improved plantation management, with proximal aerial data capable of resolving single palm canopies at potentially, centimetric resolution. If acquired with sufficient overlap, aerial data from UAVs can be processed within structure-from-motion (SfM) photogrammetry workflows to yield volumetric point cloud representations of the scene. Point cloud-derived structural information on individual palms can benefit not only plantation management but is also of great environmental research interest, given the potential to deliver spatially contiguous quantifications of aboveground biomass, from which carbon can be accounted. Using lightweight UAVs we captured data over plantation plots of varying ages (2, 7 and 10 years) at peat soil sites in Sarawak, Malaysia, and we explored the impact of changing spatial resolution and image overlap on spatially variable uncertainties in SfM derived point clouds for the ten year old plot. Point cloud precisions were found to be in the decimetre range (mean of 26.7 31 cm) for a 10 year old plantation plot surveyed at 100 m flight altitude and >75% image overlap. Derived canopy height models were used and evaluated for automated palm identification using local height maxima. Metrics such as maximum canopy height and stem height, derived from segmented single palm point clouds were tested relative to ground validation data. Local maximum identification performed best for palms which were taller than surrounding undergrowth but whose fronds did not overlap significantly (98.2% mapping accuracy for 7 year old plot of 776 palms). Stem heights could be predicted from point cloud derived metrics with root-mean-square errors (RMSEs) of 0.27 m (R2= 0.63) for 7 year old and 0.45 m (R2=0.69) for 10 year old palms. It was also found that an acquisition designed to yield the minimal required overlap between images (60%) performed almost as well as higher overlap acquisitions (>75%) for palm identification and basic height metrics which is promising for operational implementations seeking to maximise spatial coverage and minimise processing costs. We conclude that UAV-based SfM can provide reliable data not only for oil palm inventory generation but allows the retrieval of basic structural parameters which may enable per-palm above-ground biomass estimations.European CommissionMarie Skłodowska-Curi

Biodiversity beyond species census: assessing organisms' traits and functional attributes using computer vision

César Herrera studied the functions of intertidal crabs in estuarine mudflats in Townsville. He developed a novel workflow and software that use computer vision to monitor crab movement and behaviour. His analytical framework is more effective than traditional sampling techniques, and it will help ecologists to gather more and better ecological information on crabs

Geographic Information Systems and Science

Geographic information science (GISc) has established itself as a collaborative information-processing scheme that is increasing in popularity. Yet, this interdisciplinary and/or transdisciplinary system is still somewhat misunderstood. This book talks about some of the GISc domains encompassing students, researchers, and common users. Chapters focus on important aspects of GISc, keeping in mind the processing capability of GIS along with the mathematics and formulae involved in getting each solution. The book has one introductory and eight main chapters divided into five sections. The first section is more general and focuses on what GISc is and its relation to GIS and Geography, the second is about location analytics and modeling, the third on remote sensing data analysis, the fourth on big data and augmented reality, and, finally, the fifth looks over volunteered geographic information.info:eu-repo/semantics/publishedVersio

Vegetation shadow casts impact remotely sensed reflectance from permafrost thaw ponds in the subarctic forest-tundra zone

Thermokarst lakes and ponds are a common landscape feature resulting from permafrost thaw, but their intense greenhouse gas emissions are still poorly constrained as a feedback mechanism for global warming because of their diversity, abundance, and remoteness. Thermokarst waterbodies may be small and optically diverse, posing specifc challenges for optical remote sensing regarding detection, classifcation, and monitoring. This is especially relevant when accounting for external factors that afect water refectance, such as scattering and vegetation shadow casts. In this study, we evaluated the efects of shadowing across optically diverse waterbodies located in the forest–tundra zone of northern Canada. We used ultra-high spatial resolution multispectral data and digital surface models obtained from unmanned aerial systems for modeling and analyzing shadow efects on water refectance at Earth Observation satellite overpass time. Our results show that shadowing causes variations in refectance, reducing the usable area of remotely sensed pixels for waterbody analysis in small lakes and ponds. The efects were greater on brighter and turbid inorganic thermokarst lakes embedded in post-glacial silt–clay marine deposits and littoral sands, where the mean refectance decrease was from -51 to -70%, depending on the wavelength. These efects were also dependent on lake shape and vegetation height and were amplifed in the cold season due to low solar elevations. Remote sensing will increasingly play a key role in assessing thermokarst lake responses and feedbacks to global change, and this study shows the magnitude and sources of optical variations caused by shading that need to be considered in future analyses.info:eu-repo/semantics/publishedVersio

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