scholarly journals Semiautomated 3D Root Segmentation and Evaluation Based on X-Ray CT Imagery

2021 ◽  
Vol 2021 ◽  
pp. 1-13
Author(s):  
Stefan Gerth ◽  
Joelle Claußen ◽  
Anja Eggert ◽  
Norbert Wörlein ◽  
Michael Waininger ◽  
...  
Keyword(s):  
Root System ◽  
Large Scale ◽  
Plant Phenotyping ◽  
Manual Segmentation ◽  
Volume Data ◽  
Storage Roots ◽  
Root Volume ◽  
Time Resolved ◽  
X Ray ◽  
Wide Range

Background. Computed X-ray tomography (CTX) is a high-end nondestructive approach for the visual assessment of root architecture in soil. Nevertheless, in order to evaluate high-resolution CTX data of root architectures, manual segmentation of the depicted root systems from large-scale volume data is currently necessary, which is both time consuming and error prone. The duration of such a segmentation is of importance, especially for time-resolved growth analysis, where several instances of a plant need to be segmented and evaluated. Specifically, in our application, the contrast between soil and root data varies due to different growth stages and watering situations at the time of scanning. Additionally, the root system itself is expanding in length and in the diameter of individual roots. Objective. For semiautomated and robust root system segmentation from CTX data, we propose the RootForce approach, which is an extension of Frangi’s “multi-scale vesselness” method and integrates a 3D local variance. It allows a precise delineation of roots with diameters down to several μm in pots with varying diameters. Additionally, RootForce is not limited to the segmentation of small below-ground organs, but is also able to handle storage roots with a diameter larger than 40 voxels. Results. Using CTX volume data of full-grown bean plants as well as time-resolved (3D+time) growth studies of cassava plants, RootForce produces similar (and much faster) results compared to manual segmentation of the regarded root architectures. Furthermore, RootForce enables the user to obtain traits not possible to be calculated before, such as total root volume (Vroot), total root length (Lroot), root volume over depth, root growth angles (θmin, θmean, and θmax), root surrounding soil density Dsoil, or form fraction F. Discussion. The proposed RootForce tool can provide a higher efficiency for the semiautomatic high-throughput assessment of the root architectures of different types of plants from large-scale CTX. Furthermore, for all datasets within a growth experiment, only a single set of parameters is needed. Thus, the proposed tool can be used for a wide range of growth experiments in the field of plant phenotyping.

scholarly journals ROOT PHENOTYPING FROM X-RAY COMPUTED TOMOGRAPHY: SKELETON EXTRACTION

2021 ◽  
Vol XLIII-B4-2021 ◽  
pp. 417-422
Author(s):  
M. Herrero-Huerta ◽  
V. Meline ◽  
A. S. Iyer-Pascuzzi ◽  
A. M. Souza ◽  
M. R. Tuinstra ◽  
...  
Keyword(s):  
Computed Tomography ◽  
Root System ◽  
High Throughput ◽  
Skeletal Structure ◽  
Plant Phenotyping ◽  
Skeleton Extraction ◽  
X Ray ◽  
Digital Twin ◽  
Three Samples ◽  
Root Phenotyping

Abstract. Breakthrough imaging technologies are a potential solution to the plant phenotyping bottleneck in marker-assisted breeding and genetic mapping. X-Ray CT (computed tomography) technology is able to acquire the digital twin of root system architecture (RSA), however, advances in computational methods to digitally model spatial disposition of root system networks are urgently required.We extracted the root skeleton of the digital twin based on 3D data from X-ray CT, which is optimized for high-throughput and robust results. Significant root architectural traits such as number, length, growth angle, elongation rate and branching map can be easily extracted from the skeleton. The curve-skeleton extraction is computed based on a constrained Laplacian smoothing algorithm. This skeletal structure drives the registration procedure in temporal series. The experiment was carried out at the Ag Alumni Seed Phenotyping Facility (AAPF) at Purdue University in West Lafayette (IN, USA). Three samples of tomato root at 2 different times and three samples of corn root at 3 different times were scanned. The skeleton is able to accurately match the shape of the RSA based on a visual inspection.The results based on a visual inspection confirm the feasibility of the proposed methodology, providing scalability to a comprehensive analysis to high throughput root phenotyping.

The effect of cover crops on soil structure is mainly driven by root architecture

2021 ◽  
Author(s):  
Maik Lucas ◽  
Linh Nguyen ◽  
Andrey Guber ◽  
Alexandra Kravchenko
Keyword(s):  
Root System ◽  
Cover Crops ◽  
Soil Structure ◽  
Image Features ◽  
Small Scale ◽  
Pore Characteristics ◽  
Pore Connectivity ◽  
Imaging Protocol ◽  
X Ray ◽  
Wide Range

<p>Cover crops are known to increase macroporosity and pore connectivity, thus having a beneficial effect on soil hydraulic properties such as saturated hydraulic conductivity, However, cover crop species typically used encompass a variety of contrasting root architectures and their effects on small-scale pore properties are difficult to quantify.</p><p>Here we explore the influence of five different cover crops (annual ryegrass, Austrian winter pea, dwarf essex rapeseed, oats, and oilseed radish) on soil structure with X-ray µCT. Undisturbed samples were taken from an experiment with these cover crops on Kellogg Biological Station (Michigan, USA) in October 2019. Two soil columns with a diameter of 5 cm were taken in 5 - 10 cm depth from each of three replicated plots per plant species and scanned with X-ray µCT at a resolution of 18 µm.</p><p>These images will be used to characterize pore structure in terms of pore size distribution, pore connectivity. In addition, a new imaging protocol will be used, which combines existing ones with a random forest classifier to segment image features such as pores, biopores and roots simultaneously.</p><p>First, the results reveal that different cover crops indeed result in different pore characteristics.  The fibrous root system of oats leads to the highest volume of narrow macropores and increased their connectivity, while the tap root system of dwarf essex rapeseed mainly effected wide macropores.  The highly diverse root system of Australian winter pea increased a wide range of pore sizes and thus resulted in the highest visible porosity.</p><p>The current study is funded by a grant from USDA Organic Transition program</p>

scholarly journals Time-Resolved X-Ray Microscopy for Materials Science

2019 ◽  
Vol 49 (1) ◽  
pp. 389-415 ◽  
Author(s):  
Haidan Wen ◽  
Mathew J. Cherukara ◽  
Martin V. Holt
Keyword(s):  
Large Scale ◽  
Materials Science ◽  
Time Resolved ◽  
X Ray ◽  
X Ray Imaging ◽  
Materials Research ◽  
Microscopic Studies ◽  
Nanoscale Imaging ◽  
Indispensable Tool ◽  
The Time Domain

X-ray microscopy has been an indispensable tool to image nanoscale properties for materials research. One of its recent advances is extending microscopic studies to the time domain to visualize the dynamics of nanoscale phenomena. Large-scale X-ray facilities have been the powerhouse of time-resolved X-ray microscopy. Their upgrades, including a significant reduction of the X-ray emittance at storage rings (SRs) and fully coherent ultrashort X-ray pulses at free-electron lasers (FELs), will lead to new developments in instrumentation and will open new scientific opportunities for X-ray imaging of nanoscale dynamics with the simultaneous attainment of unprecedentedly high spatial and temporal resolutions. This review presents recent progress in and the outlook for time-resolved X-ray microscopy in the context of ultrafast nanoscale imaging and its applications to condensed matter physics and materials science.

scholarly journals Short X-ray pulses from third-generation light sources

2016 ◽  
Vol 23 (1) ◽  
pp. 141-151 ◽  
Author(s):  
A. G. Stepanov ◽  
C. P. Hauri
Keyword(s):  
Large Scale ◽  
Light Sources ◽  
Third Generation ◽  
Time Duration ◽  
Pulse Emission ◽  
Time Resolved ◽  
High Brightness ◽  
X Ray ◽  
Synchrotron Light ◽  
Synchrotron Light Sources

High-brightness X-ray radiation produced by third-generation synchrotron light sources (TGLS) has been used for numerous time-resolved investigations in many different scientific fields. The typical time duration of X-ray pulses delivered by these large-scale machines is about 50–100 ps. A growing number of time-resolved studies would benefit from X-ray pulses with two or three orders of magnitude shorter duration. Here, techniques explored in the past for shorter X-ray pulse emission at TGLS are reviewed and the perspective towards the realisation of picosecond and sub-picosecond X-ray pulses are discussed.

scholarly journals Approach of Serial Crystallography

Crystals ◽  
2020 ◽  
Vol 10 (10) ◽  
pp. 854
Author(s):  
Ki Hyun Nam
Keyword(s):  
Radiation Damage ◽  
Room Temperature ◽  
Time Resolved ◽  
X Ray ◽  
X Ray Crystallography ◽  
The Past ◽  
Wide Range ◽  
Experimental Limitation ◽  
Serial Crystallography ◽  
Collection Strategies

Radiation damage and cryogenic sample environment are an experimental limitation observed in the traditional X-ray crystallography technique. However, the serial crystallography (SX) technique not only helps to determine structures at room temperature with minimal radiation damage, but it is also a useful tool for profound understanding of macromolecules. Moreover, it is a new tool for time-resolved studies. Over the past 10 years, various sample delivery techniques and data collection strategies have been developed in the SX field. It also has a wide range of applications in instruments ranging from the X-ray free electron laser (XFEL) facility to synchrotrons. The importance of the various approaches in terms of the experimental techniques and a brief review of the research carried out in the field of SX has been highlighted in this editorial.

scholarly journals XMM-Newton observations of elliptical galaxies in the local universe

2009 ◽  
Vol 5 (H15) ◽  
pp. 273-273
Author(s):  
Ginevra Trinchieri
Keyword(s):  
Globular Clusters ◽  
Large Scale ◽  
Spectral Characteristics ◽  
Large Field ◽  
Specific Class ◽  
Early Type ◽  
X Ray ◽  
Compact Source ◽  
Wide Range ◽  
The Individual

XMM-Newton is well suited to the study of the X-ray properties of early-type galaxies: the wide energy band allows a characterization of the different components of the X-ray emission in galaxies, separating the gas from the compact source component through their spectral characteristics, and identifying low-luminosity absorbed AGNs; the large field of view allows a proper understanding of the large scale emission, and the separation between the galaxy and the surrounding group. Nonetheless, in spite of the much improved understanding of the X-ray characteristics of this class of sources, much of the original questions on the global X-ray properties of early-type galaxies remain. One in particular: how can we predict how much gas is there in any given galaxy? We have learned that the individual sources are tightly linked to the stellar component, both field stars and relative frequency of globular clusters. We have also learned that the central group galaxies, brighter and more extended, might represent a specific class of early-type galaxies, rather than the population as a whole. Yet we have not learned how to predict, from the stellar properties, how much hot gas a galaxy will have. Even a well selected class of sources, namely early type galaxies in isolation, where we can exclude the influence of the environment, appear to retain different amounts of the hot ISM produced by the stellar population, and display a wide range of Lx for their gaseous component for a relative narrow range of Lb, or mass [measured through LK], as shown by Fig. 1.

In Situ Time-Resolved X-Ray Diffraction Investigation of the ω→ψ Transition in Al-Cu-Fe Quasicrystal-Forming Alloys

2007 ◽  
Vol 558-559 ◽  
pp. 943-947 ◽  
Author(s):  
E. Otterstein ◽  
R. Nicula ◽  
J. Bednarčík ◽  
M. Stir ◽  
E. Burkel
Keyword(s):  
Large Scale ◽  
Applied Pressure ◽  
High Temperature Phase ◽  
Temperature Phase ◽  
X Ray Diffraction ◽  
Time Resolved ◽  
X Ray ◽  
In Situ Xrd ◽  
Kinetics Of

Quasicrystals are aperiodic long-range ordered solids with a high potential for many modern applications. Interest is nowadays paid to the development of economically viable large-scale synthesis procedures of quasicrystalline materials involving solid-state transformations. The kinetics of the high-temperature phase transition from the complex ω-phase to the icosahedral quasicrystalline (iQC) ψ-phase in AlCuFe nanopowders was here examined by in-situ time-resolved X-ray diffraction experiments using synchrotron radiation. In-situ XRD experiments will allow insight on the influence of uniaxial applied pressure on the kinetics of phase transitions leading to the formation of single-phase QC nanopowders and further contribute to the optimization of sintering procedures for nano-quasicrystalline AlCuFe alloy powders.

The SAXS/WAXS software system of the DUBBLE CRG beamline at the ESRF

2001 ◽  
Vol 34 (4) ◽  
pp. 519-522 ◽  
Author(s):  
E. Homan ◽  
M. Konijnenburg ◽  
C. Ferrero ◽  
R. E. Ghosh ◽  
I. P. Dolbnya ◽  
...  
Keyword(s):  
Integrated System ◽  
Software System ◽  
Test Bed ◽  
Time Resolved ◽  
X Ray ◽  
Standard Data ◽  
Data Formats ◽  
X Ray Scattering ◽  
Angle Scattering ◽  
Wide Range

The small/wide-angle X-ray scattering (SAXS/WAXS) system on the DUBBLE CRG beamline at the ESRF is used for both static and time-resolved measurements. The integrated system developed for control and data reduction deals effectively with the high rates of incoming data from the different detector systems, as well as the presentation of results for the user. To ensure that the data may be used directly by a wide range of packages, they may be recorded in a number of output formats, thus serving as a practical test bed where developing standards may be compared and contrasted. The software system implements proposals raised at the canSAS meetings to promote a limited set of standard data formats for small-angle scattering studies. The system presented can cope with a volume of results in excess of 10 Gbytes of data per experiment and shows the advantages achieved by minimizing the dependence on raw-data formats.

scholarly journals The obscured X-ray binaries V404 Cyg, Cyg X–3, V4641 Sgr, and GRS 1915+105

2020 ◽  
Vol 639 ◽  
pp. A13 ◽  
Author(s):  
K. I. I. Koljonen ◽  
J. A. Tomsick
Keyword(s):  
Large Scale ◽  
Surrounding Medium ◽  
The Other ◽  
Opening Angle ◽  
Spectral Evolution ◽  
Time Resolved ◽  
Orbital Inclination ◽  
X Ray ◽  
Geometrical Change ◽  
X Ray Binaries

Aims. V404 Cyg, Cyg X–3, V4641 Sgr, and GRS 1915+105 are among the brightest X-ray binaries and display complex behavior in their multiwavelength emission. Except for Cyg X–3, the other three sources have large accretion disks, and there is evidence of a high orbital inclination. Therefore, any large-scale geometrical change in the accretion disk can cause local obscuration events. On the other hand, Cyg X–3 orbits its Wolf-Rayet companion star inside the heavy stellar wind obscuring the X-ray source. We study here whether the peculiar X-ray spectra observed from all four sources can be explained by local obscuration events. Methods. We used spectra obtained with the Nuclear Spectroscopic Telescope Array and Rossi X-ray Timing Explorer to study the spectral evolution of the four luminous hard X-ray sources. We fit the time-averaged spectra, and also time-resolved spectra in case of V404 Cyg, with two physically motivated models describing either a scenario where all the intrinsic emission is reprocessed in the surrounding matter or where the emitter is surrounded by a thick torus with variable opening angle. Results. We show that the X-ray spectra during specific times are very similar in all four sources, likely arising from the high-density environments where they are embedded. The fitted models suggest that a low-luminosity phase preceding an intense flaring episode in the 2015 outburst of V404 Cyg is heavily obscured, but intrinsically very bright (super-Eddington) accretion state. Similar spectral evolution to that of V404 Cyg is observed from the recent X-ray state of GRS 1915+105 that presented unusually low luminosity. The modeling results point to a geometry change in the (outflowing) obscuring matter in V404 Cyg and GRS 1915+105, which is also linked to the radio (jet) evolution. Within the framework of the models, all sources display obscured X-ray emission, but with different intrinsic luminosities ranging from lower than 1% of the Eddington luminosity up to the Eddington limit. This indicates that different factors cause the obscuration. This work highlights the importance of taking the reprocessing of the X-ray emission in the surrounding medium into account in modeling the X-ray spectra. This may well take place in other sources as well.

scholarly journals Bent It Like FRs: Extended Radio AGN in the COSMOS Field and Their Large-Scale Environment

Galaxies ◽  
2021 ◽  
Vol 9 (4) ◽  
pp. 93
Author(s):  
Eleni Vardoulaki ◽  
Franco Vazza ◽  
Eric F. Jiménez-Andrade ◽  
Ghassem Gozaliasl ◽  
Alexis Finoguenov ◽  
...  
Keyword(s):  
Large Scale ◽  
Ambient Medium ◽  
Adaptive Mesh ◽  
Radio Structure ◽  
X Ray ◽  
Galaxy Groups ◽  
Extended Radio ◽  
Wide Range ◽  
Jet Interactions ◽  
Host Properties

A fascinating topic in radio astronomy is how to associate the complexity of observed radio structures with their environment in order to understand their interplay and the reason for the plethora of radio structures found in surveys. In this project, we explore the distortion of the radio structure of Fanaroff–Riley (FR)-type radio sources in the VLA-COSMOS Large Project at 3 GHz and relate it to their large-scale environment. We quantify the distortion by using the angle formed between the jets/lobes of two-sided FRs, namely bent angle (BA). Our sample includes 108 objects in the redshift range 0.08<z<3, which we cross-correlate to a wide range of large-scale environments (X-ray galaxy groups, density fields, and cosmic web probes) in the COSMOS field. The median BA of FRs in COSMOS at zmed∼0.9 is 167.5−37.5+11.5 degrees. We do not find significant correlations between BA and large-scale environments within COSMOS covering scales from a few kpc to several hundred Mpc, nor between BA and host properties. Finally, we compare our observational data to magnetohydrodynamical (MHD) adaptive-mesh simulations ENZO-MHD of two FR sources at z = 0.5 and at z = 1. Although the scatter in BA of the observed data is large, we see an agreement between observations and simulations in the bent angles of FRs, following a mild redshift evolution with BA. We conclude that, for a given object, the dominant mechanism affecting the radio structures of FRs could be the evolution of the ambient medium, where higher densities of the intergalactic medium at lower redshifts as probed by our study allow more space for jet interactions.

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