Visualização de padrões temporais cíclicos em estudos de fenologia

Orientadores: Ricardo da Silva Torres, Leonor Patrícia Cerdeira MorellatoTese (doutorado) - Universidade Estadual de Campinas, Instituto de ComputaçãoResumo: Em diversas aplicações, grandes volumes de dados multidimensionais têm sido gerados continuamente ao longo do tempo. Uma abordagem adequada para lidar com estas coleções consiste no uso de métodos de visualização de informação, a partir dos quais padrões de interesse podem ser identificados, possibilitando o entendimento de fenômenos temporais complexos. De fato, em diversos domínios, o desenvolvimento de ferramentas adequadas para apoiar análises complexas, por exemplo, aquelas baseadas na identificação de padrões de mudanças ou correlações existentes entre múltiplas variáveis ao longo do tempo é de suma importância. Em estudos de fenologia, por exemplo, especialistas observam as mudanças que ocorrem ao longo da vida de plantas e animais e investigam qual é a relação entre essas mudanças com variáveis ambientais. Neste cenário, especialistas em fenologia cada vez mais precisam de ferramentas para, adequadamente, visualizar séries temporais longas, com muitas variáveis e de diferentes tipos (por exemplo, texto e imagem), assim como identificar padrões temporais cíclicos. Embora diversas abordagens tenham sido propostas para visualizar dados que variam ao longo do tempo, muitas não são apropriadas ou aplicáveis para dados de fenologia, porque não são capazes de: (i) lidar com séries temporais longas, com muitas variáveis de diferentes tipos de dados e de uma ou mais dimensões; e (ii) permitir a identificação de padrões temporais cíclicos e drivers ambientais associados. Este trabalho aborda essas questões a partir da proposta de duas novas abordagens para apoiar a análise e visualização de dados temporais multidimensionais. Nossa primeira proposta combina estruturas visuais radiais com ritmos visuais. As estruturas radiais são usadas para fornecer informação contextual sobre fenômenos cíclicos, enquanto que o ritmo visual é usado para sumarizar séries temporais longas em representações compactas. Nós desenvolvemos, avaliamos e validamos nossa proposta com especialistas em fenologia em tarefas relacionadas à visualização de dados de observação direta da fenologia de plantas em nível tanto de indivíduos quanto de espécies. Nós também validamos a proposta usando dados temporais relacionados a imagens obtidas de sistemas de monitoramento de vegetação próxima à superfície. Nossa segunda abordagem é uma nova representação baseada em imagem, chamada Change Frequency Heatmap (CFH), usada para codificar mudanças temporais de dados numéricos multivariados. O método calcula histogramas de padrões de mudanças observados em sucessivos instantes de tempo. Nós validamos o uso do CFH a partir da criação de uma ferramenta de caracterização de mudanças no ciclo de vida de plantas de múltiplos indivíduos e espécies ao longo do tempo. Nós demonstramos o potencial do CFH para ajudar na identificação visual de padrões de mudanças temporais complexas, especialmente na identificação de variações entre indivíduos em estudos relacionados à fenologia de plantasAbstract: In several applications, large volumes of multidimensional data have been generated continuously over time. One suitable approach for handling those collections in a meaningful way consists in the use of information visualization methods, based on which patterns of interest can be identified, triggering the understanding of complex temporal phenomena. In fact, in several domains, the development of appropriate tools for supporting complex analysis based, for example, on the identification of change patterns in temporal data or existing correlations, over time, among multiple variables, is of paramount importance. In phenology studies, for instance, phenologists observe changes in the development of plants and animals throughout their lives and investigate what is the relationship between these changes with environmental changes. Therefore, phenologists increasingly need tools for visualizing appropriately long-term series with many variables of different data types, as well as for identifying cyclical temporal patterns. Although several approaches have been proposed to visualize data varying over time, most of them are not appropriate or applicable to phenology data, because they are not able: (i) to handle long-term series with many variables of different data types and one or more dimensions and (ii) to support the identification of cyclical temporal patterns and associated environmental drivers. This work addresses these shortcomings by presenting two new approaches to support the analysis and visualization of multidimensional temporal data. Our first proposal to visualize phenological data combines radial visual structures along with visual rhythms. Radial visual structures are used to provide contextual insights regarding cyclical phenomena, while the visual rhythm encoding is used to summarize long-term time series into compact representations. We developed, evaluated, and validated our proposal with phenology experts using plant phenology direct observational data both at individuals and species levels. Also we validated the proposal using image-related temporal data obtained from near-surface vegetation monitoring systems. Our second approach is a novel image-based representation, named Change Frequency Heatmap (CFH), used to encode temporal changes of multivariate numerical data. The method computes histograms of change patterns observed at successive timestamps. We validated the use of CFHs through the creation of a temporal change characterization tool to support complex plant phenology analysis, concerning the characterization of plant life cycle changes of multiple individuals and species over time. We demonstrated the potential of CFH to support visual identification of complex temporal change patterns, especially to decipher interindividual variations in plant phenologyDoutoradoCiência da ComputaçãoDoutora em Ciência da Computação162312/2015-62013/501550-0CNPQCAPESFAPES

Growth rings in tropical trees : role of functional traits, environment, and phylogeny

Acknowledgments Financial support of the Centre National de la Recherche Scientifique (USR 3330), France, and from the Rufford Small Grants Foundation (UK) is acknowledged. We thank the private farmers and coffee plantation companies of Kodagu for providing permissions and logistical support for this project. We are grateful to N. Barathan for assistance with slide preparation and data entry, S. Aravajy for botanical assistance, S. Prasad and G. Orukaimoni for technical inputs, and A. Prathap, S. Shiva, B. Saravana, and P. Shiva for field assistance. The corresponding editor and three anonymous reviewers provided insightful comments that improved the manuscript.Peer reviewedPostprin

Study of Various Techniques for Medicinal Plant Identification

Ayurveda, the Indian ancient medicinal system, has gained importance because of its effectiveness in treating diseases. Medicinal plants are used in Ayurvedic medicines since ancient times. It is necessary to classify these plants so that it would be easy to select the right plant for the medicinal preparation or to study more about its characteristics. Identification is the pre-condition of classification of medicinal plant. In this paper, we have reviewed Image processing Near-Infrared Spectroscopy (NIRS), taxonomic key repository, neural network and DeoxyriboNucleic Acid (DNA) barcoding. The study shows that image processing is leading domain in identification of medicinal plant. The results are improved when multiple methods are used together in a sequence to identify a medicinal plant. Apart from that none of these methods are using geographical information to identify medicinal plants and we can use geographical Information System (GIS) information to improve its accuracy further

Leaf Phenology of Cassia Sieberiana L. in KSUSTA Campus of Kebbi State, Nigeria

The Aliero local government area is located at approximate latitudes 110 03\u27 S, 120 47\u27N and longitudes 30 6\u27W and 40 27\u27E. In kebbi state, north western part of Nigeria, It also has a total area of 412 square kilometers and is bordered in the east by Tambuwal Local government area of Sokoto state in the North West by Birnin Kebbi local government area in the South West by Jega local government area. The study was carried out in Aliero local government area, Kebbi state Nigeria. Leaf exchange is crucial in the lifecycle patterns of a tree species, these also includes leaf fall, leaf emergence, leaf flush, death or senescence (leaf onset and leaf offset). The study of leaf dynamics is termed leaf Phenology. Phonological phases are reoccurring biological events that signal changes in climate, environmental conditions, and genetic factors during the developmental growth of plants. Cassia sieberiana L trees maintained significant foliage was recorded in March in individuals which did not become leafless

Role of semiochemical in host finding, oviposition and sexual communication in Guatemalan potato moth Tecia solanivora

Semiochemicals are important cues in the interaction between plant and insects and between conspecific insects. Volatile compounds emitted by plants provide herbivorous insects with cues for host finding, selection and discrimination. In moths, female emitted sex pheromones enable conspecific males to find them for mating. This thesis investigated the role of semiochemicals in the behaviour of the Guatemalan potato moth Tecia solanivora (Lepidoptera: Gelechiidae), a pest insect of potato. Identification of odours of foliage, flowers, and tubers of potato, Solanum tuberosum, were done with coupled gas chromatography-mass spectrometry and with high-performance liquid chromatography for non-volatile compounds in tubers. Antennal activity of potato volatiles was tested with electroantennographic recordings. Attraction of T. solanivora to potato volatile compounds was investigated through olfactometer, wind tunnel and field bioassays. Male behavior towards two different synthetic pheromone blends was similarly tested, to clarify their mode of action in mating disruption management. Potato emits structure-specific volatile blends that change during the development of the plant. Tuberization stage was the preferred stage for oviposition while foliage released deterrent compounds. A three-component flower-odour mimic attracted males and females, virgin and mated, and enhanced the number of eggs laid. Female oviposition in the soil, during the tuberization stage might be guided by odours from spatially separated flowers, as an indication of suitable host vicinity. Larval survival was low in tubers with high concentrations of glycoalkaloids. This study demonstrates that odours from qualitatively different sites guide female to oviposit on tubers with high suitability for larval performance. Mating disruption was obtained with pheromone-permeated air with the two blends, but the disruption mechanism were different between them. This first study on chemical communication between T. solanivora and its host plant showed that potato volatile compounds are perceived by the moth and act as cues in host location and oviposition. It highlights the possibility of using semiochemicals to manipulate the behavior of the moths and provides a base for further investigation and development of odour-based pest management

Deep learning in plant phenological research: A systematic literature review

Climate change represents one of the most critical threats to biodiversity with far-reaching consequences for species interactions, the functioning of ecosystems, or the assembly of biotic communities. Plant phenology research has gained increasing attention as the timing of periodic events in plants is strongly affected by seasonal and interannual climate variation. Recent technological development allowed us to gather invaluable data at a variety of spatial and ecological scales. The feasibility of phenological monitoring today and in the future depends heavily on developing tools capable of efficiently analyzing these enormous amounts of data. Deep Neural Networks learn representations from data with impressive accuracy and lead to significant breakthroughs in, e.g., image processing. This article is the first systematic literature review aiming to thoroughly analyze all primary studies on deep learning approaches in plant phenology research. In a multi-stage process, we selected 24 peer-reviewed studies published in the last five years (2016–2021). After carefully analyzing these studies, we describe the applied methods categorized according to the studied phenological stages, vegetation type, spatial scale, data acquisition- and deep learning methods. Furthermore, we identify and discuss research trends and highlight promising future directions. We present a systematic overview of previously applied methods on different tasks that can guide this emerging complex research field

RadialPheno: A tool for near-surface phenology analysis through radial layouts

Premise Increasingly, researchers studying plant phenology are exploring novel technologies to remotely observe plant changes over time. The increasing use of phenocams to monitor leaf phenology, based on the analysis of indices extracted from sequences of daily digital vegetation images, has demanded the development of appropriate tools for data visualization and analysis. Here, we describe RadialPheno, a tool that uses radial layouts to represent time series from digital repeat photographs, and applies them to the analysis of leafing patterns and leaf exchange strategies of different vegetations. Methods and Results We developed a web tool, RadialPheno, provided with the R and Shiny environments, which uses radial visual structures to represent cyclical multidimensional temporal data associated with digital image time series. We demonstrate the application of our methods and tool for a savanna vegetation phenology in the Brazilian Cerrado. We visually represented the greenness index extracted from sequential imagery using the RadialPheno tool. Conclusions RadialPheno was successfully applied for the visualization and interpretation of individual, species, and community long-term leafing phenology data associated with near-surface phenological observations of Cerrado vegetation. RadialPheno was also effective for intercomparisons of ground-based direct visual observations and camera-derived phenology observations

Spatio-Temporal Vegetation Pixel Classification by Using Convolutional Networks

Plant phenology studies rely on long-term monitoring of life cycles of plants. High-resolution unmanned aerial vehicles (UAVs) and near-surface technologies have been used for plant monitoring, demanding the creation of methods capable of locating, and identifying plant species through time and space. However, this is a challenging task given the high volume of data, the constant data missing from temporal dataset, the heterogeneity of temporal profiles, the variety of plant visual patterns, and the unclear definition of individuals' boundaries in plant communities. In this letter, we propose a novel method, suitable for phenological monitoring, based on convolutional networks (ConvNets) to perform spatio-temporal vegetation pixel classification on high-resolution images. We conducted a systematic evaluation using high-resolution vegetation image datasets associated with the Brazilian Cerrado biome. Experimental results show that the proposed approach is effective, overcoming other spatio-temporal pixel-classification strategies