Design Study of a Novel Positron Emission Tomography System for Plant Imaging

Positron Emission Tomography is a non-disruptive and high-sensitive digital imaging technique which allows to measure in-vivo and non invasively the changes of metabolic and transport mechanisms in plants. When it comes to the early assessment of stress-induced alterations of plant functions, plant PET has the potential of a major breakthrough. The development of dedicated plant PET systems faces a series of technological and experimental difficulties, which make conventional clinical and preclinical PET systems not fully suitable to agronomy. First, the functional and metabolic mechanisms of plants depend on environmental conditions, which can be controlled during the experiment if the scanner is transported into the growing chamber. Second, plants need to be imaged vertically, thus requiring a proper Field Of View. Third, the transverse Field of View needs to adapt to the different plant shapes, according to the species and the experimental protocols. In this paper, we perform a simulation study, proposing a novel design of dedicated plant PET scanners specifically conceived to address these agronomic issues. We estimate their expected sensitivity, count rate performance and spatial resolution, and we identify these specific features, which need to be investigated when realizing a plant PET scanner. Finally, we propose a novel approach to the measurement and verification of the performance of plant PET systems, including the design of dedicated plant phantoms, in order to provide a standard evaluation procedure for this emerging digital imaging agronomic technology

Leaf Morphology, Taxonomy and Geometric Morphometrics: A Simplified Protocol for Beginners

Taxonomy relies greatly on morphology to discriminate groups. Computerized geometric morphometric methods for quantitative shape analysis measure, test and visualize differences in form in a highly effective, reproducible, accurate and statistically powerful way. Plant leaves are commonly used in taxonomic analyses and are particularly suitable to landmark based geometric morphometrics. However, botanists do not yet seem to have taken advantage of this set of methods in their studies as much as zoologists have done. Using free software and an example dataset from two geographical populations of sessile oak leaves, we describe in detailed but simple terms how to: a) compute size and shape variables using Procrustes methods; b) test measurement error and the main levels of variation (population and trees) using a hierachical design; c) estimate the accuracy of group discrimination; d) repeat this estimate after controlling for the effect of size differences on shape (i.e., allometry). Measurement error was completely negligible; individual variation in leaf morphology was large and differences between trees were generally bigger than within trees; differences between the two geographic populations were small in both size and shape; despite a weak allometric trend, controlling for the effect of size on shape slighly increased discrimination accuracy. Procrustes based methods for the analysis of landmarks were highly efficient in measuring the hierarchical structure of differences in leaves and in revealing very small-scale variation. In taxonomy and many other fields of botany and biology, the application of geometric morphometrics contributes to increase scientific rigour in the description of important aspects of the phenotypic dimension of biodiversity. Easy to follow but detailed step by step example studies can promote a more extensive use of these numerical methods, as they provide an introduction to the discipline which, for many biologists, is less intimidating than the often inaccessible specialistic literature