3D Scanning System for Automatic High-Resolution Plant Phenotyping

Thin leaves, fine stems, self-occlusion, non-rigid and slowly changing structures make plants difficult for three-dimensional (3D) scanning and reconstruction -- two critical steps in automated visual phenotyping. Many current solutions such as laser scanning, structured light, and multiview stereo can struggle to acquire usable 3D models because of limitations in scanning resolution and calibration accuracy. In response, we have developed a fast, low-cost, 3D scanning platform to image plants on a rotating stage with two tilting DSLR cameras centred on the plant. This uses new methods of camera calibration and background removal to achieve high-accuracy 3D reconstruction. We assessed the system's accuracy using a 3D visual hull reconstruction algorithm applied on 2 plastic models of dicotyledonous plants, 2 sorghum plants and 2 wheat plants across different sets of tilt angles. Scan times ranged from 3 minutes (to capture 72 images using 2 tilt angles), to 30 minutes (to capture 360 images using 10 tilt angles). The leaf lengths, widths, areas and perimeters of the plastic models were measured manually and compared to measurements from the scanning system: results were within 3-4% of each other. The 3D reconstructions obtained with the scanning system show excellent geometric agreement with all six plant specimens, even plants with thin leaves and fine stems.Comment: 8 papes, DICTA 201

Genetic analysis of leaf rolling in wheat

Dissertação de mestrado em Química Farmacêutica Industrial, apresentada à Faculdade de Farmácia da Universidade de CoimbraAtualmente, as doenças neurodegenerativas como a isquemia cerebral, Alzheimer e Parkinson atacam em massa a população mundial. O acréscimo destas patologias crê-se estar relacionado com falhas na homeostase de zinco e de espécies reativas de oxigénio (ROS) no sistema nervoso central. Neste trabalho questões desta natureza foram investigadas nas sinapses das fibras musgosas da área CA3 do hipocampo de rato. Os estudos foram efetuados em fatias cerebrais utilizando sondas fluorescentes de zinco e de espécies reativas de oxigénio. Sinais intracelulares de zinco foram medidos utilizando o indicador Newport Green na forma permeante, que não complexa o zinco presente nas vesículas sinápticas e que é co-libertado com o glutamato. As variações de zinco foram induzidas por meio de despolarizações com KCl ou usando um meio extracelular com TEA e rico em cálcio. No primeiro caso verificou-se um aumento significativo dos sinais de fluorescência de zinco. Os resultados obtidos usando antagonistas de recetores de glutamato e um bloqueador de canais de cálcio dependentes do potencial, indicam que aqueles sinais têm origem na zona pós-sináptica. No meio com TEA e muito cálcio, usado para induzir quimicamente a potenciação de longa duração, que se considera representar uma forma de memorização ao nível celular, verificou-se uma diminuição reversível da intensidade de fluorescência. Este facto pode ser devido à activação, pelo zinco libertado, de canais de K/ATP pré-sinápticos, o que origina a hiperpolarização da membrana e uma diminuição na libertação de zinco. Alterações na formação de espécies reativas de oxigénio foram estudadas, por meio da sonda H2DCFDA permeante, que é sensível essencialmente aos radicais hidroxilo e peróxido de hidrogénio. Os resultados obtidos, induzidos de forma semelhante aos de zinco, têm dum modo geral um comportamento idêntico ao destes sinais Inúmeros avanços na indústria e na medicina prometem melhorias ao nível das patologias anteriormente mencionadas e outras. No entanto, existe o reverso da moeda, o aumento da industrialização e de fármacos disponíveis provoca um aumento da poluição em efluentes e águas residuais, tendo em conta que os processos usados nas estações de tratamento não são totalmente eficazes. III O sulfametoxazole (SMX) é um antibiótico largamente utilizado, que não é totalmente metabolizado pelo organismo, tendo por isso vindo a ser detetado em águas residuais. Os sinais de zinco medidos aumentam quando as fatias são expostas a esta sulfonamida, voltando ao nível inicial após a mudança para o meio extracelular normal. O efeito do sulfametoxazole nas espécies reativas de oxigénio também foi testado, tendo-se verificado um aumento daquelas espécies na presença de SMX. Os resultados mostram que a ação deste antibiótico não é reversível, por este motivo, as quantidades ambientais de SMX nas águas residuais assumem uma preocupação crescente. A observação de efeitos irreversíveis na formação de espécies reactivas de oxigénio durante actividade neuronal intensa, sugere que aquele fármaco pode contribuir para diversas patologias neurodegenerativas.Currently, neurodegenerative diseases such as cerebral ischemia, Alzheimer's and Parkinson's mass attack the world population. The increase of these diseases is believed to be related to failures in the homeostasis of zinc and of reactive oxygen species in the central nervous system. In this work such issues have been investigated in the mossy fiber synapses from area CA3 of the rat hippocampus. The studies were performed in brain slices using fluorescent probes of zinc and of reactive oxygen species. Intracellular zinc signals were measured using the indicator Newport Green in the permeant form, that does not complex the zinc present in the synaptic vesicles which is co-released with glutamate. The zinc changes were induced by KCl depolarization or applying an extracellular medium containing TEA and rich in calcium. In the first case a significant increase of the fluorescence zinc signals was observed. The results obtained using antagonists of glutamate receptors and one blocker of voltage-dependent calcium channels, indicate that those signals have a postsynaptic origin. In the medium containing TEA and high calcium, used to chemically induce long-term potentiation, which is considered to represent a way of memory formation at the cellular level, a reversible decrease of the fluorescence intensity was observed. This fact may be due to the activation, by released zinc, of presynaptic K / ATP channels, which leads to membrane hyperpolarization and to a decrease in zinc release. Changes in the formation of reactive oxygen species were studied by means of the permeant H2DCFDA probe, which is specially sensitive to the hydroxyl and hydrogen peroxide radicals. The results, induced in a similar way as for zinc, have in general an identical behaviour to that of these signals. Numerous advances in industry and medicine promise improvements in the above mentioned pathologies and others. However, there is the reverse of the coin, the increasing industrialization and availability of drugs results in increased pollution in waste waters and effluents, since the processes used in water treatment plants are not entirely effective. V Sulfamethoxazole (SMX) is a widely used antibiotic, which is not fully metabolized by the organism and, for this reason, is being detected in wastewaters. The measured zinc signals increase when the slices are exposed to this sulfonamide, returning to the initial level after changing to the normal extracellular medium. The effect of sulfamethoxazole in reactive oxygen species was also tested, having been observed an increase of those species in the presence of SMX. The results show that the action of this antibiotic is not reversible, therefore, their environmental quantities in wastewaters are of growing concern. The observation of irreversible effects on the formation of reactive oxygen species during intense neuronal activity, suggests that that pharmaceutical agent may contribute to various neurodegenerative pathologie

Three Dimensional (3D) Reconstruction of Subterranean Clover

Three dimensional (3D) plant reconstructions, extended to four dimensions with the use of time series and accompanied by visual modelling, is being used for a number of purposes including the estimation of biovolume and as the basis for functional structural plant modelling (FSPM). This has been successfully applied to crop species such as cotton (Paproki et al. 2012). Measuring the growth pattern and arrangement of a pasture sward is a difficult task but can be used as an indirect measure of other variables of interest, such as growth rate, light interception, nutritional quality, herbivore intake, etc. (Laca and Lemaire 2000). Digital representation of individual plants in three dimensions is one way to determine sward structure. The High Resolution Plant Phenomics Centre (HRPPC) has developed PlantScan™ which combines robotics, image analysis and computing advances, to accelerate and automate the measurement of plant growth characteristics and allow discrimination of differences between individual plants within species. Image silhouettes and LiDAR (Light Detection And Ranging) are used and combined to digitise plant architecture in three dimensions with a high level of detail. Colour information, extracted from multispectral sensors, and thermal imaging from infra-red (IR) cameras are then overlaid on these 3D plant representations, thus providing a tool to link plant structure to plant function. Successful reconstructions using data collected by PlantScan™ in controlled conditions, have been conducted for a range of grasses such as wheat (Triticum aestivum), rice (Oryza sativa), corn (Zea mays) and broadleaf species such as canola (Brassica napus), cotton (Gossypium hirsutum) and tobacco (Nicotiana tabacum). This suggests that modelling the sward structure of grass and legume pasture species should be equally achievable. This study explores the use of PlantScanTM to reconstruct 3D images of the important and common pasture legume, subterranean clover (Trifolium subterraneum) with a view to analysing their 3D structure in-silico

Flexible scientific data management for plant phenomics research

In this paper, we expand on the design and implementation of the Phenomics Ontology Driven Data repository [1] (PODD) with respect to the capture, storage and retrieval of data and metadata gen- erated at the High Resolution Plant Phenomics Centre (Canberra, Aus- tralia). PODD is a schema-driven Semantic Web database which uses the Resource Description Framework (RDF) model to store semi-structured information. RDF allows PODD to process information about a range of phenomics experiments without needing to define a universal schema for all of the di ff erent structures. To illustrate the process, exemplar datasets were generated using a medium throughput, high resolution, three-dimensional digitisation system purposely built for studying plant structure and function simultaneously under specific environmental con- ditions. The High Performance Compute (HPC), storage and data collec- tion publication aspects of the workflow and their realisation in CSIRO infrastructure are also discussed along with their relationship to PODD

"Rolled-upness": phenotyping leaf rolling in cereals using computer vision and functional data analysis approaches

BACKGROUND: The flag leaf of a wheat (Triticum aestivum L.) plant rolls up into a cylinder in response to drought conditions and then unrolls when leaf water relations improve. This is a desirable trait for extending leaf area duration and improving grain size particularly under drought. But how do we quantify this phenotype so that different varieties of wheat or different treatments can be compared objectively since this phenotype can easily be confounded with inter-genotypic differences in root-water uptake and/or transpiration at the leaf level if using traditional methods? RESULTS: We present a new method to objectively test a range of lines/varieties/treatments for their propensity of leaves to roll. We have designed a repeatable protocol and defined an objective measure of leaf curvature called “rolled-upness” which minimises confounding factors in the assessment of leaf rolling in grass species. We induced leaf rolling by immersing leaf strips in an osmoticum of known osmotic pressure. Using micro-photographs of individual leaf cross-sections at equilibrium in the osmoticum, two approaches were used to quantify leaf rolling. The first was to use some properties of the convex hull of the leaf cross-section. The second was to use cubic smoothing splines to approximate the transverse leaf shape mathematically and then use a statistic derived from the splines for comparison. Both approaches resulted in objective measurements that could differentiate clearly between breeding lines and varieties contrasting genetically in their propensity for leaf rolling under water stress. The spline approach distinguished between upward and downward curvature and allowed detailed properties of the rolling to be examined, such as the position on the strip where maximum curvature occurs. CONCLUSIONS: A method applying smoothing splines to skeletonised images of transverse wheat leaf sections enabled objective measurements of inter-genotypic variation for hydronastic leaf rolling in wheat. Mean-curvature of the leaf cross-section was the measure selected to discriminate between genotypes, as it was straightforward to calculate and easily construed. The method has broad applicability and provides an avenue to genetically dissect the trait in cereals.We thank the Grains Research and Development Corporation of Australia for funding a PhD scholarship for Xavier Sirault

Phenomenal: a software framework for model-assisted analysis of high throughput plant phenotyping data

International audiencePlant high-throughput phenotyping aims at capturing the genetic variability of plant response to environmental factors for thousands of plants, hence identifying heritable traits for genomic selection and predicting the genetic values of allelic combinations in different environment. This first implies the automation of the measurement of a large number of traits to characterize plant growth, plant development and plant functioning. It also requires a fluent and versatile interaction between data and continuously evolving plant response models, that are essential in the analysis of the marker x environment interaction and in the integration of processes for predicting crop performance [1]. In the frame of the Phenome high throughput phenotyping infrastructure, we develop Phenomenal: a software framework dedicated to the analysis of high throughput phenotyping data and models. It is based on the OpenAlea platform [2] that provides methods and softwares for the modelling of plants, together with a user-friendly interface for the design and execution of scientific workflows. OpenAlea is also part of the InfraPhenoGrid infrastructure that allows high throughput computation and recording of provenance during the execution [3]. Figure 1: The 3D plant reconstruction and segmentation pipeline. Muti-view plants images from PhenoArch are binarised and used to reconstruct plants in3D. The 3D skeleton is extracted and separated into stem (central vertical elements) and leaves. 3D voxels are segmented by propagating skeleton segmentation

Grapevine varieties exhibiting differences in stomatal response to water deficit

Abstract. Knowledge on variety traits and physiological responses to stress is still scarce in Vitis vinifera L., limiting the optimisation of irrigation and breeding for high water use efficiency. We have characterised five grapevine varieties using thermal imaging, leaf gas exchange, leaf morphology and carbon isotope composition. Plants of the varieties Aragonez, Trincadeira, Cabernet Sauvignon, Syrah and Touriga Nacional were grown in field conditions. Two experiments were performed. In Experiment I (2006), vines of Aragonez and Trincadeira were either well irrigated (WI, 80% ETc), nonirrigated but rain fed (NI) or subjected to regulated deficit irrigation (RDI, 40% ETc) and studied along the summer season. In Experiment II (2006 and 2007), vines of the five varieties were subjected to RDI (30–40% ETc) and studied at veraison. In Experiment I, leaf temperature (Tleaf) correlated negatively with stomatal conductance (gs) and leaf water potential (Ypd). The inverse relationship between gs and Tleaf was highly significant in the afternoon. In Experiment II, the different genotypes showed different Tleaf for similar Ypd. Stomatal density did not correlate with gs suggesting that varieties have different stomatal control. Our results show that combined measurements of canopy temperature and Ypd can aid in better understanding of stomatal regulation in different grapevine varieties. Such variation in stomatal regulation should be taken into account in determining irrigation strategie