Structured Light-Based 3D Reconstruction System for Plants.

Camera-based 3D reconstruction of physical objects is one of the most popular computer vision trends in recent years. Many systems have been built to model different real-world subjects, but there is lack of a completely robust system for plants. This paper presents a full 3D reconstruction system that incorporates both hardware structures (including the proposed structured light system to enhance textures on object surfaces) and software algorithms (including the proposed 3D point cloud registration and plant feature measurement). This paper demonstrates the ability to produce 3D models of whole plants created from multiple pairs of stereo images taken at different viewing angles, without the need to destructively cut away any parts of a plant. The ability to accurately predict phenotyping features, such as the number of leaves, plant height, leaf size and internode distances, is also demonstrated. Experimental results show that, for plants having a range of leaf sizes and a distance between leaves appropriate for the hardware design, the algorithms successfully predict phenotyping features in the target crops, with a recall of 0.97 and a precision of 0.89 for leaf detection and less than a 13-mm error for plant size, leaf size and internode distance

Visualization of Tomato Growth Based on Dry Matter Flow

The visualization of tomato growth can be used in 3D computer games and virtual gardens. Based on the growth theory involving the respiration theory, the photosynthesis, and dry matter partition, a visual system is developed. The tomato growth visual simulation system is light-and-temperature-dependent and shows plausible visual effects in consideration of the continuous growth, texture map, gravity influence, and collision detection. In addition, the virtual tomato plant information, such as the plant height, leaf area index, fruit weight, and dry matter, can be updated and output in real time

High-throughput plant phenotyping: a role for metabolomics?

High-throughput (HTP) plant phenotyping approaches are developing rapidly and are already helping to bridge the genotype–phenotype gap. However, technologies should be developed beyond current physico-spectral evaluations to extend our analytical capacities to the subcellular level. Metabolites define and determine many key physiological and agronomic features in plants and an ability to integrate a metabolomics approach within current HTP phenotyping platforms has huge potential for added value. While key challenges remain on several fronts, novel technological innovations are upcoming yet under-exploited in a phenotyping context. In this review, we present an overview of the state of the art and how current limitations might be overcome to enable full integration of metabolomics approaches into a generic phenotyping pipeline in the near future.info:eu-repo/semantics/publishedVersio

Modelling and remote sensing of canopy light interception and plant stress in greenhouses

A greenhouse crop can be approached as an open system that can be affected by a number of parameters such as light, climate or nutrient supply. In the last decades efforts have been made to understand the functioning of this system and the interaction between the different parameters. The intensive nature of greenhouse cultivation combined with the economic necessity to enlarge the farm size makes the development of decision support systems (DSS) imperative to help the growers in managing their farms efficiently. The foundation of DSS are plant models and in order to work more efficiently they should be able to receive information in real time from sensors that measure different plant parameters such as light interception, leaf area index and photosynthetic stress in a non-destructive way. In order to develop functional DSS it is imperative to develop accurate models and monitoring techniques applied in the specific greenhouse environment. The aim of this thesis was to explore different techniques to simulate and monitor light interception and photosynthesis by a greenhouse grown tomato canopy. Since photosynthesis is directly linked to light absorption we opted to develop a three dimensional model that takes into account the explicit plant architecture. Different methodologies to monitor these physiological properties online by means of remote sensing were also explored. A number of physiological tomato models have been proposed the last decades, their main challenge being the correct simulation of fruit yield. For this, an accurate simulation of light interception, and thus photosynthesis, is of primary importance. At present most process-based models and the majority of three dimensional models, include simplifications of plant architecture that can compromise the accuracy of light interception simulations and, accordingly, canopy photosynthesis. In Chapter 2.1 the first steps towards the development of the model are presented. Light interception is highly dependent on the canopy structure, which is affected, among others, by the distance between plant rows, the distance of plants within the row, leaf pruning and crop variety. The model was used to test different crop planting scenarios on their effect on light interception. Light interception from the planting scenarios was then compared with results of a totally homogeneous canopy. Also analysis of differences between manual measurements of leaf length, width, elevation angle and leaf orientation was conducted. Changes of leaf elevation angles at two different times of the day were also measured. In tomato differences in leaf length, width and elevation angle of the leaves were mainly observed in the upper 90cm of the plant, in the still developing zone. Changes of the architectural characteristics of structural plant characteristics affected directly light interception by the crop canopy. Nevertheless even if plant structure stayed the same, light penetration could easily be manipulated by changing the row spacing in the crop, thus affecting light interception and potentially plant production. In Chapter 2.2 the development and calibration of a functional-structural tomato model is fully described. The model was used to investigate the canopy heterogeneity of an explicitly described tomato canopy in relation to temporal dynamics of horizontal and vertical light distribution and photosynthesis under direct and diffuse light conditions. The model consists of an architectural static virtual plant coupled with a nested radiosity model for light absorption and a leaf photosynthesis module. Different scenarios for horizontal and vertical distributions of light interception, incident light and photosynthesis were investigated under diffuse and direct light conditions. Simulated light interception showed a good correspondence to the measured values. Explicitly described leaf elevation angles resulted in higher light interception in the middle of the plant canopy compared to fixed and ellipsoidal leaf elevation angle distribution models, although the total light interception remained the same. The fraction of light intercepted at a north-south orientation of rows differed from an east-west orientation by 10% in winter and 23% on summer days. The horizontal distribution of photosynthesis differed significantly between the top, middle and lower canopy layer. Taking into account the vertical variation of leaf photosynthetic parameters in the canopy, led to ca. 8% increase on simulated canopy photosynthesis. Manipulation of plant structure can strongly affect light distribution in the canopy and photosynthesis. In Chapter 2.3 the idea of identifying different plant ideotypes for optimization of light absorption and photosynthesis was explored. Using the functional-structural tomato model presented in the previous chapters, a range of different plant architectural characteristics were tested for two different seasons in order to find the optimal architecture with respect to light absorption and photosynthesis. Sensitivity analyses were carried out for leaf elevation angle, leaf phyllotaxis, leaflet angle, leaf shape, leaflet arrangement and internode length. From the results of this analysis two possible ideotypes were proposed. Increasing light absorption in the top part of the canopy by 25 %, without changing light absorption of the canopy as a whole, augmented photosynthesis by 6 % in winter and decreased it by 7 % in summer. The measured plant structure was already optimal with respect to leaf elevation angle, leaflet angle and leaflet arrangement for both light absorption and photosynthesis while phyllotaxis had no effect. Increasing the length-to-width ratio of leaves by 1.5 or increasing internode length from 7 to 12 cm led to an increase of 7 – 10 % for light absorption and photosynthesis. The most important architectural traits found were the internode length and the leaf shape as they affect vertical light distribution in the canopy distinctly. A new plant ideotype with more spacious canopy architecture due to long internodes and long and narrow leaves led to an increase in photosynthesis of up to 10 %. In Chapter 3.1 ways to monitor on-line LAI and PAR interception of the canopy, under greenhouse conditions, through reflectance measurements, were explored. LAI and PAR interception were measured at the same moments as reflectance at six wavelengths in different developmental stages of tomato and sweet pepper plants. Normalized Difference Vegetation Index (NDVI) was calculated. Relationships between the measured parameters were established in experimental greenhouses and subsequently these were tested in commercial greenhouses. The best estimation for LAI and PAR interception was obtained from reflectance at 460nm for both tomato and sweet pepper. The goodness of the fit was validated with data from the commercial greenhouses and was also tested in this study. The divergence of the results from the ones reported from field experiments can be traced back to the special greenhouse environment, where more sources of reflectance are added due to construction parts and a white plastic covered background. Reflectance measurements offer a non- destructive way to estimate PAR interception and LAI (up to the value of 3) in greenhouse production systems. The relationship established between reflectance at 460 nm, PAR interception and LAI for both tomato and sweet pepper, can become a good tool for crop online monitoring in greenhouse conditions. Furthermore if information from reflectance sensors is used as input directly into the crop models, new opportunities for decision support systems in greenhouse production could be opened up. Photosynthetic stress induced by water deprivation in plants affects a number of physiological processes such as photosynthetic rate, stomatal conductance as well as the operating efficiency of PSII and non- photochemical quenching. Photochemical Reflectance Index (PRI) is reported to be sensitive to changes of xanthophyll cycle that occur during stress and could possibly be used to monitor changes in the physiological parameters mentioned before. In Chapter 3.2 the use of PRI as an early photosynthetic stress indicator was evaluated. A water stress treatment was imposed on a greenhouse tomato crop. CO2 assimilation, stomatal conductance, light and dark adapted fluorescence as well as PRI and relative water content of the rooting medium RWCs% where repeatedly measured. The same measurements were also performed on well-irrigated plants that acted as a reference. The experiment was repeated in four consecutive weeks. Results showed that PRI can be used as an early stress indicator only when light intensity at crop level was above 700μmol m-2 s-1. At lower values of light intensity the relationship of PRI to RWCs% was poor in comparison to photosynthesis or fluorescence parameters that showed a high correlation to RWCs%. For that reason we can conclude that PRI as water stress indicator cannot be independent of the ambient light conditions and its use can make sense only under conditions of high light. Finally in Chapter 4 the main achievements and limitations of this study are discussed and directions for future research are proposed. </p

Architectural and non-architectural effects of salinity on canopy structure, light interception and dry mass production on greenhouse cucumber and tomato

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