scholarly journals In situ Phenotyping of Grapevine Root System Architecture by 2D or 3D Imaging: Advantages and Limits of Three Cultivation Methods

2021 ◽  
Vol 12 ◽  
Author(s):  
Yuko Krzyzaniak ◽  
Frédéric Cointault ◽  
Camille Loupiac ◽  
Eric Bernaud ◽  
Frédéric Ott ◽  
...  
Keyword(s):  
Root System ◽  
Adventitious Root ◽  
Production Systems ◽  
Imaging Techniques ◽  
Root Traits ◽  
Automated Analysis ◽  
Root System Architecture ◽  
Neutron Tomography

The root system plays an essential role in the development and physiology of the plant, as well as in its response to various stresses. However, it is often insufficiently studied, mainly because it is difficult to visualize. For grapevine, a plant of major economic interest, there is a growing need to study the root system, in particular to assess its resistance to biotic and abiotic stresses, understand the decline that may affect it, and identify new ecofriendly production systems. In this context, we have evaluated and compared three distinct growing methods (hydroponics, plane, and cylindric rhizotrons) in order to describe relevant architectural root traits of grapevine cuttings (mode of grapevine propagation), and also two 2D- (hydroponics and rhizotron) and one 3D- (neutron tomography) imaging techniques for visualization and quantification of roots. We observed that hydroponics tubes are a system easy to implement but do not allow the direct quantification of root traits over time, conversely to 2D imaging in rhizotron. We demonstrated that neutron tomography is relevant to quantify the root volume. We have also produced a new automated analysis method of digital photographs, adapted for identifying adventitious roots as a feature of root architecture in rhizotrons. This method integrates image segmentation, skeletonization, detection of adventitious root skeleton, and adventitious root reconstruction. Although this study was targeted to grapevine, most of the results obtained could be extended to other plants propagated by cuttings. Image analysis methods could also be adapted to characterization of the root system from seedlings.

scholarly journals Trait-Based Root Phenotyping as a Necessary Tool for Crop Selection and Improvement

Agronomy ◽  
2020 ◽  
Vol 10 (9) ◽  
pp. 1328
Author(s):  
Rebecca K. McGrail ◽  
David A. Van Sanford ◽  
David H. McNear
Keyword(s):  
Root System ◽  
System Architecture ◽  
Production Systems ◽  
Root Traits ◽  
Root System Architecture ◽  
Root Decomposition ◽  
Crop Breeding ◽  
Organic Acid Production ◽  
Nutritional Qualities ◽  
Chemical Traits

Most of the effort of crop breeding has focused on the expression of aboveground traits with the goals of increasing yield and disease resistance, decreasing height in grains, and improvement of nutritional qualities. The role of roots in supporting these goals has been largely ignored. With the increasing need to produce more food, feed, fiber, and fuel on less land and with fewer inputs, the next advance in plant breeding must include greater consideration of roots. Root traits are an untapped source of phenotypic variation that will prove essential for breeders working to increase yields and the provisioning of ecosystem services. Roots are dynamic, and their structure and the composition of metabolites introduced to the rhizosphere change as the plant develops and in response to environmental, biotic, and edaphic factors. The assessment of physical qualities of root system architecture will allow breeding for desired root placement in the soil profile, such as deeper roots in no-till production systems plagued with drought or shallow roots systems for accessing nutrients. Combining the assessment of physical characteristics with chemical traits, including enzymes and organic acid production, will provide a better understanding of biogeochemical mechanisms by which roots acquire resources. Lastly, information on the structural and elemental composition of the roots will help better predict root decomposition, their contribution to soil organic carbon pools, and the subsequent benefits provided to the following crop. Breeding can no longer continue with a narrow focus on aboveground traits, and breeding for belowground traits cannot only focus on root system architecture. Incorporation of root biogeochemical traits into breeding will permit the creation of germplasm with the required traits to meet production needs in a variety of soil types and projected climate scenarios.

Coherent electron nanodiffraction from clean silver nano particles in a UHV STEM

1993 ◽  
Vol 51 ◽  
pp. 1058-1059
Author(s):  
J. Liu ◽  
M. Pan ◽  
G. E. Spinnler
Keyword(s):  
Supported Catalysts ◽  
Imaging Techniques ◽  
Nano Particles ◽  
Metal Particles ◽  
Shape Structure ◽  
Dynamical Simulations ◽  
Small Metal Particles ◽  
Extract Information

Small metal particles have peculiar chemical and physical properties as compared to bulk materials. They are especially important in catalysis since metal particles are common constituents of supported catalysts. The structural characterization of small particles is of primary importance for the understanding of structure-catalytic activity relationships. The shape and size of metal particles larger than approximately 5 nm in diameter can be determined by several imaging techniques. It is difficult, however, to deduce the shape of smaller metal particles. Coherent electron nanodiffraction (CEND) patterns from nano particles contain information about the particle size, shape, structure and defects etc. As part of an on-going program of STEM characterization of supported catalysts we report some preliminary results of CEND study of Ag nano particles, deposited in situ in a UHV STEM instrument, and compare the experimental results with full dynamical simulations in order to extract information about the shape of Ag nano particles.

scholarly journals ChronoRoot: High-throughput phenotyping by deep segmentation networks reveals novel temporal parameters of plant root system architecture

2020 ◽  
Author(s):  
Nicolás Gaggion ◽  
Federico Ariel ◽  
Vladimir Daric ◽  
Éric Lambert ◽  
Simon Legendre ◽  
...  
Keyword(s):  
Deep Learning ◽  
Root System ◽  
High Throughput ◽  
System Architecture ◽  
Root Traits ◽  
Root System Architecture ◽  
Machine Intelligence ◽  
Reconstruction Process ◽  
High Throughput Phenotyping ◽  
3D Printed

ABSTRACTDeep learning methods have outperformed previous techniques in most computer vision tasks, including image-based plant phenotyping. However, massive data collection of root traits and the development of associated artificial intelligence approaches have been hampered by the inaccessibility of the rhizosphere. Here we present ChronoRoot, a system which combines 3D printed open-hardware with deep segmentation networks for high temporal resolution phenotyping of plant roots in agarized medium. We developed a novel deep learning based root extraction method which leverages the latest advances in convolutional neural networks for image segmentation, and incorporates temporal consistency into the root system architecture reconstruction process. Automatic extraction of phenotypic parameters from sequences of images allowed a comprehensive characterization of the root system growth dynamics. Furthermore, novel time-associated parameters emerged from the analysis of spectral features derived from temporal signals. Altogether, our work shows that the combination of machine intelligence methods and a 3D-printed device expands the possibilities of root high-throughput phenotyping for genetics and natural variation studies as well as the screening of clock-related mutants, revealing novel root traits.

Characterization of the bone-metal implant interface by Digital Volume Correlation of in-situ loading using neutron tomography

2017 ◽  
Vol 75 ◽  
pp. 271-278 ◽  
Author(s):  
Sophie Le Cann ◽  
Erika Tudisco ◽  
Christina Perdikouri ◽  
Ola Belfrage ◽  
Anders Kaestner ◽  
...  
Keyword(s):  
Digital Volume Correlation ◽  
Neutron Tomography ◽  
Metal Implant

scholarly journals FTIR, Raman and AFM characterization of the clinically valid biochemical parameters of the thrombi in acute ischemic stroke

2019 ◽  
Vol 9 (1) ◽  
Author(s):  
Aneta Blat ◽  
Jakub Dybas ◽  
Karolina Chrabaszcz ◽  
Katarzyna Bulat ◽  
Agnieszka Jasztal ◽  
...  
Keyword(s):  
Ischemic Stroke ◽  
Biochemical Parameters ◽  
Imaging Techniques ◽  
Quantitative Imaging ◽  
Automated Analysis ◽  
Force Microscopy ◽  
Atomic Force ◽  
Non Destructive ◽  
Histological Staining

Abstract The significance and utility of innovative imaging techniques in arterial clot analysis, which enable far more detailed and automated analysis compared to standard methods, are presented. The examination of two types of human thrombi is shown, representing the main ischemic stroke etiologies: fibrin–predominant clot of large vessel origin and red blood cells–rich clot of cardioembolic origin. The synergy effect of Fourier–transform infrared spectroscopy (FTIR), Raman spectroscopy (RS) and atomic force microscopy (AFM) techniques supported by chemometrics in comparison with reference histological staining was presented. The main advantage of such approach refers to free–label and non–destructive quantitative imaging of clinically valid, biochemical parameters in whole sample (FTIR–low resolution) and selected regions (RS–ultra–high resolution). We may include here analysis of lipid content, its distribution and total degree of unsaturation as well as analysis of protein content (mainly fibrin and hemoproteins). The AFM studies enhanced the vibrational data, showed clearly shape and thickness of clot features as well as visualized the fibrin framework. The extraordinary sensitivity of FTIR and RS imaging toward detection and discrimination of clinically valid parameters in clot confirms its applicability in assessment of thrombi origin.

scholarly journals Genetic Dissection of the Seminal Root System Architecture in Mediterranean Durum Wheat Landraces by Genome-Wide Association Study

Agronomy ◽  
2019 ◽  
Vol 9 (7) ◽  
pp. 364 ◽  
Author(s):  
Martina Roselló ◽  
Conxita Royo ◽  
Miguel Sanchez-Garcia ◽  
Jose Miguel Soriano
Keyword(s):  
Durum Wheat ◽  
Root System ◽  
System Architecture ◽  
Eastern Mediterranean Region ◽  
Root Traits ◽  
Root System Architecture ◽  
Seminal Root ◽  
Large Variability ◽  
Wheat Landraces ◽  
Durum Wheat Landraces

Roots are crucial for adaptation to drought stress. However, phenotyping root systems is a difficult and time-consuming task due to the special feature of the traits in the process of being analyzed. Correlations between root system architecture (RSA) at the early stages of development and in adult plants have been reported. In this study, the seminal RSA was analysed on a collection of 160 durum wheat landraces from 21 Mediterranean countries and 18 modern cultivars. The landraces showed large variability in RSA, and differences in root traits were found between previously identified genetic subpopulations. Landraces from the eastern Mediterranean region, which is the driest and warmest within the Mediterranean Basin, showed the largest seminal root size in terms of root length, surface, and volume and the widest root angle, whereas landraces from eastern Balkan countries showed the lowest values. Correlations were found between RSA and yield-related traits in a very dry environment. The identification of molecular markers linked to the traits of interest detected 233 marker-trait associations for 10 RSA traits and grouped them in 82 genome regions named marker-train association quantitative trait loci (MTA-QTLs). Our results support the use of ancient local germplasm to widen the genetic background for root traits in breeding programs.

Wheats developed for high yield on stored soil moisture have deep vigorous root systems

2016 ◽  
Vol 43 (2) ◽  
pp. 173 ◽  
Author(s):  
Sarah M. Rich ◽  
Anton P. Wasson ◽  
Richard A. Richards ◽  
Trushna Katore ◽  
Renu Prashar ◽  
...  
Keyword(s):  
Root System ◽  
Soil Water ◽  
Production Systems ◽  
System Development ◽  
Root Traits ◽  
Grain Filling ◽  
Root Systems ◽  
High Yield ◽  
Eastern Australia ◽  
Mature Root

Many rainfed wheat production systems are reliant on stored soil water for some or all of their water inputs. Selection and breeding for root traits could result in a yield benefit; however, breeding for root traits has traditionally been avoided due to the difficulty of phenotyping mature root systems, limited understanding of root system development and function, and the strong influence of environmental conditions on the phenotype of the mature root system. This paper outlines an international field selection program for beneficial root traits at maturity using soil coring in India and Australia. In the rainfed areas of India, wheat is sown at the end of the monsoon into hot soils with a quickly receding soil water profile; in season water inputs are minimal. We hypothesised that wheat selected and bred for high yield under these conditions would have deep, vigorous root systems, allowing them to access and utilise the stored soil water at depth around anthesis and grain-filling when surface layers were dry. The Indian trials resulted in 49 lines being sent to Australia for phenotyping. These lines were ranked against 41 high yielding Australian lines. Variation was observed for deep root traits e.g. in eastern Australia in 2012, maximum depth ranged from 118.8 to 146.3 cm. There was significant variation for root traits between sites and years, however, several Indian genotypes were identified that consistently ranked highly across sites and years for deep rooting traits.

scholarly journals In-situ diagnostic of femtosecond laser probe pulses for high resolution ultrafast imaging

2021 ◽  
Vol 10 (1) ◽  
Author(s):  
Chen Xie ◽  
Remi Meyer ◽  
Luc Froehly ◽  
Remo Giust ◽  
Francois Courvoisier
Keyword(s):  
Spatial Frequency ◽  
Probe Pulse ◽  
Imaging Techniques ◽  
Frame Rate ◽  
Pulse Front ◽  
Pump Probe ◽  
Ultrafast Imaging ◽  
Probe Delay

AbstractUltrafast imaging is essential in physics and chemistry to investigate the femtosecond dynamics of nonuniform samples or of phenomena with strong spatial variations. It relies on observing the phenomena induced by an ultrashort laser pump pulse using an ultrashort probe pulse at a later time. Recent years have seen the emergence of very successful ultrafast imaging techniques of single non-reproducible events with extremely high frame rate, based on wavelength or spatial frequency encoding. However, further progress in ultrafast imaging towards high spatial resolution is hampered by the lack of characterization of weak probe beams. For pump–probe experiments realized within solids or liquids, because of the difference in group velocities between pump and probe, the determination of the absolute pump–probe delay depends on the sample position. In addition, pulse-front tilt is a widespread issue, unacceptable for ultrafast imaging, but which is conventionally very difficult to evaluate for the low-intensity probe pulses. Here we show that a pump-induced micro-grating generated from the electronic Kerr effect provides a detailed in-situ characterization of a weak probe pulse. It allows solving the two issues of absolute pump–probe delay determination and pulse-front tilt detection. Our approach is valid whatever the transparent medium with non-negligible Kerr index, whatever the probe pulse polarization and wavelength. Because it is nondestructive and fast to perform, this in-situ probe diagnostic can be repeated to calibrate experimental conditions, particularly in the case where complex wavelength, spatial frequency or polarization encoding is used. We anticipate that this technique will enable previously inaccessible spatiotemporal imaging in a number of fields of ultrafast science at the micro- and nanoscale.

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