Multiscale and multimodal spectral Imaging for mapping cell wall polymers in plant organs

Multiscale and Multimodal Spectral Imaging for Mapping Cell Wall Polymers in Plant Organs. 2nd International Plant Spectroscopy Conferenc

COMPUTATION OF MINKOWSKI MEASURES ON 2D AND 3D BINARY IMAGES

Minkowski functionals encompass standard geometric parameters such as volume, area, length and the Euler-Poincaré characteristic. Software tools for computing approximations of Minkowski functionals on binary 2D or 3D images are now available based on mathematical methods due to Serra, Lang and Ohser. Minkowski functionals can not be used to describe spatial heterogeneity of structures. This description can be performed by using Minkowski measures, which are local versions of Minkowski functionals. In this paper, we discuss how to extend the computation of Minkowski functionals to the computation of Minkowski measures. Approximations of Minkowski measures are computed using fltering and look-up table transformations. The final result is represented as a grey-level image. Approximation errors are investigated based on numerical examples. Convergence and non convergence of the measure approximations are discussed. The measure of surface area is used to describe spatial heterogeneity of a synthetic structure, and of an image of tomato pericarp

A Hitchhiker's guide through the bio-image analysis software universe

Modern research in the life sciences is unthinkable without computational methods for extracting, quantifying and visualising information derived from microscopy imaging data of biological samples. In the past decade, we observed a dramatic increase in available software packages for these purposes. As it is increasingly difficult to keep track of the number of available image analysis platforms, tool collections, components and emerging technologies, we provide a conservative overview of software that we use in daily routine and give insights into emerging new tools. We give guidance on which aspects to consider when choosing the platform that best suits the user's needs, including aspects such as image data type, skills of the team, infrastructure and community at the institute and availability of time and budget.Peer reviewe

Measurement of microfibril angle in plant fibres : Comparison between X-ray diffraction, second harmonic generation and transmission ellipsometry microscopies

The orientation of cellulose microfibrils within plant fibres is one of the main factors influencing their mechanical properties. As plant fibres are more and more used as reinforcement for agro-composites, their mechanical properties have a strong influence on the final composite properties. It is, therefore, of interest to obtain reliable information about the microfibril angle (MFA) to better support the choice of fibres depending on the product requirements. In the present study, the reliability and specificities of three non-destructive methods that allow analysis on the same fibre glued on a holder; X-ray diffraction (XRD), second harmonic generation (SHG) and transmission ellipsometry (TE) microscopy; are investigated. Three types of plant fibres, with both low (nettle), and high (cotton, sisal) MFA values, are compared and their geometry and biochemical composition are characterised. The results obtained on the same fibre confirm that MFA analysis remains tedious and that despite their limitations, the methods are complementary depending on the information requested. Indeed, SHG is recommended for direct, qualitative and plane-selective mapping of heterogeneities in macrofibril orientations at various depths. However, reliable quantitative results with SHG depend on the initial image quality and could benefit from further image processing refinement. On the contrary, XRD and TE measure MFAs over the entire fibre thickness and provide variations along the fibres if a sufficient optical/spatial resolution is reached. Regarding the characterization of intrinsic defects in plant fibres, both SHG and TE suffer from uncertainties induced by the disorganization of the microfibril network and the lack of symmetry between the front and back fibre walls. Finally, all techniques prove to be dependant on the initial fibre alignment and geometry (i.e. twisting, double fibre configuration or form factor) which vary along the fibre length and should be carefully taken into account.publishedVersionPeer reviewe

NucleusJ: an ImageJ plugin for quantifying 3D images of inter- phase nuclei

ABSTRACT Summary: NucleusJ is a simple and user-friendly ImageJ plugin dedicated to the characterization of nuclear morphology and chromatin organization in 3D. Starting from image stacks, the nuclear boundary is delimited by combining the Otsu segmentation method with optimization of nuclear sphericity. Chromatin domains are segmented by partitioning the nucleus using a 3D watershed algorithm and by thresholding a contrast measure over the resulting regions. As output, NucleusJ quantifies 15 parameters including shape and size of nuclei as well as intra-nuclear objects and their position within the nucleus. A step-by-step documentation is available for selftraining, together with data sets of nuclei with different nuclear organization. Availability: Data set of nuclei is available at https://www.gredclermont.fr/media/WorkDirectory.zip. NucleusJ is available at http://imagejdocu.tudor.lu/doku.php?id=plugin:stacks:nuclear_analysis_plugin:start

Prediction of permeability and formation factor of sandstone with hybrid lattice Boltzmann/finite element simulation on microtomographic images

In Fontainebleau sandstone, the evolution of transport properties with porosity is related to changes in both the size and connectivity of the pore space. Microcomputed tomography can be used to characterize the relevant geometric attributes, with the resolution that is sufficiently refined for realistic simulation of transport properties based on the 3D image. In this study, we adopted a hybrid computation scheme that is based on a hierarchical multi-scale approach. The specimen was partitioned into cubic sub-volumes for pore-scale simulation of hydraulic permeability and formation factor using the lattice Boltzmann method. The pore-scale results were then linked with finite element simulation in a homogenized scheme to compute and upscale the transport properties to specimen scale. The simulated permeability and formation factor have magnitude and anisotropy that are in good agreement with experimental rock physics data. Together with simulated and measured values of connected porosity and specific surface area, they provide useful insights into how pore geometry controls the evolution of the transport properties

Cortical contraction drives the 3D patterning of epithelial cell surfaces

Cellular protrusions create complex cell surface topographies, but biomechanical mechanisms regulating their formation and arrangement are largely unknown. To study how protrusions form, we focused on the morphogenesis of microridges, elongated actin-based structures that are arranged in maze-like patterns on the apical surfaces of zebrafish skin cells. Microridges form by accreting simple finger-like precursors. Live imaging demonstrated that microridge morphogenesis is linked to apical constriction. A nonmuscle myosin II (NMII) reporter revealed pulsatile contractions of the actomyosin cortex, and inhibiting NMII blocked apical constriction and microridge formation. A biomechanical model suggested that contraction reduces surface tension to permit the fusion of precursors into microridges. Indeed, reducing surface tension with hyperosmolar media promoted microridge formation. In anisotropically stretched cells, microridges formed by precursor fusion along the stretch axis, which computational modeling explained as a consequence of stretch-induced cortical flow. Collectively, our results demonstrate how contraction within the 2D plane of the cortex can pattern 3D cell surfaces

New Growth-Related Features of Wheat Grain Pericarp Revealed by Synchrotron-Based X-ray Micro-Tomography and 3D Reconstruction

Wheat (Triticum aestivum L.) is one of the most important crops as it provides 20% of calories and proteins to the human population. To overcome the increasing demand in wheat grain production, there is a need for a higher grain yield, and this can be achieved in particular through an increase in the grain weight. Moreover, grain shape is an important trait regarding the milling performance. Both the final grain weight and shape would benefit from a comprehensive knowledge of the morphological and anatomical determinism of wheat grain growth. Synchrotron-based phase-contrast X-ray microtomography (X-ray µCT) was used to study the 3D anatomy of the growing wheat grain during the first developmental stages. Coupled with 3D reconstruction, this method revealed changes in the grain shape and new cellular features. The study focused on a particular tissue, the pericarp, which has been hypothesized to be involved in the control of grain development. We showed considerable spatio-temporal diversity in cell shape and orientations, and in tissue porosity associated with stomata detection. These results highlight the growth-related features rarely studied in cereal grains, which may contribute significantly to the final grain weight and shape

localEstimation

Cet ensemble de fonctions Matlab permet de mesurer des paramètres géométriques (aire et périmètre en 2D, surface, épaisseur moyenne et volume en 3D...), et topologiques (caractéristique d'Euler-Poincaré) dans des images 2D et 3D. Les paramètres considérés sont : en 2D, la caractéristique d'Euler-Poincaré, le périmètre en 3D, la caractéristique d'Euler-Poincaré, la surface, et l'épaisseur moyenne Ces différents paramètres sont aussi appelés fonctionnelles de Minkowski, ou encore volumes intrinsèques. Plusieurs méthodes de mesures sont disponibles : mesure du paramètre de manière globale dans toute l'image calcul de la densité du paramètre ramenée à la taille de l'image calcul des contributions locales (pour chaque pixel ou voxel) des paramètres calcul des profils le long d'un axe de l'image La méthode utilisée ici est une discrétisation de la formule de Crofton. Il est possible d'utiliser différentes relations d'adjacence (4 et 8 connexité en 2D, 6 et 26 connexité en 3D), ainsi que des grilles avec des résolutions de taille variable

: Un ensemble de fonctions Matlab pour le traitement et l'analyse d'images

Un ensemble de fonctions Matlab pour le traitement et l'analyse d'images