Micron-scale phenotyping quantification and three-dimensional microstructure reconstruction of vascular bundles within maize stalks based on micro-CT scanning

2017 ◽  
Vol 44 (1) ◽  
pp. 10 ◽  
Author(s):  
Jianjun Du ◽  
Ying Zhang ◽  
Xinyu Guo ◽  
Liming Ma ◽  
Meng Shao ◽  
...  
Keyword(s):  
Spatial Distribution ◽  
Spatial Configuration ◽  
Three Dimensional ◽  
Ct Scanning ◽  
Phenotypic Traits ◽  
Vascular Bundles ◽  
Micro Computed Tomography ◽  
Cross Sectional ◽  
Imaging Device ◽  
Maize Stalks

Vascular bundles within maize (Zea mays L.) stalks play a key role in the mechanical support of plant architecture as well as in water and nutrient transportation. Convenient and accurate phenotyping of vascular bundles may help phenotypic identification of germplasm resources for breeding. Based on practical sample preparation procedures for maize stalks, we acquired serials of cross-sectional images using a micro-computed tomography (CT) imaging device. An image processing pipeline dedicated to the phenotyping of vascular bundles was also developed to automatically segment and validate vascular bundles from the cross-sectional images of maize stalks, from which phenotypic traits of vascular bundles, i.e. number, area, and spatial distribution, were calculated. More profound quantification of spatial distribution was given as area ratio of vascular bundles, which described the distribution of vascular bundles associated with the centroid of maize stalks. In addition, three-dimensional visualisation was performed to reveal the spatial configuration and distribution of vascular bundles. The proposed method significantly improves computation accuracy for the phenotypic traits of vascular bundles compared with previous methods, and is expected to be useful for illustrating relationships between phenotypic traits of vascular bundles and their function.

scholarly journals Petiole-Lamina Transition Zone: A Functionally Crucial but Often Overlooked Leaf Trait

Plants ◽  
2021 ◽  
Vol 10 (4) ◽  
pp. 774
Author(s):  
Max Langer ◽  
Thomas Speck ◽  
Olga Speck
Keyword(s):  
Transition Zone ◽  
Three Dimensional ◽  
Spatial Arrangement ◽  
Body Plan ◽  
The Body ◽  
Vascular Bundles ◽  
Cross Sectional ◽  
Thin Sections ◽  
Transition Zones ◽  
The Cross

Although both the petiole and lamina of foliage leaves have been thoroughly studied, the transition zone between them has often been overlooked. We aimed to identify objectively measurable morphological and anatomical criteria for a generally valid definition of the petiole–lamina transition zone by comparing foliage leaves with various body plans (monocotyledons vs. dicotyledons) and spatial arrangements of petiole and lamina (two-dimensional vs. three-dimensional configurations). Cross-sectional geometry and tissue arrangement of petioles and transition zones were investigated via serial thin-sections and µCT. The changes in the cross-sectional geometries from the petiole to the transition zone and the course of the vascular bundles in the transition zone apparently depend on the spatial arrangement, while the arrangement of the vascular bundles in the petioles depends on the body plan. We found an exponential acropetal increase in the cross-sectional area and axial and polar second moments of area to be the defining characteristic of all transition zones studied, regardless of body plan or spatial arrangement. In conclusion, a variety of terms is used in the literature for describing the region between petiole and lamina. We prefer the term “petiole–lamina transition zone” to underline its three-dimensional nature and the integration of multiple gradients of geometry, shape, and size.

scholarly journals Simulation of the Effect of Coal Microstructures on the Macroscopic Mechanical Behavior

2020 ◽  
Vol 2020 ◽  
pp. 1-14
Author(s):  
Yu Fu ◽  
Zhongliang Feng
Keyword(s):  
Spatial Distribution ◽  
Three Dimensional ◽  
Ct Scanning ◽  
Confining Pressure ◽  
Mineral Matter ◽  
Equivalent Diameter ◽  
Box Dimension ◽  
Distribution Characteristics ◽  
Two Phase ◽  
Mineral Structure

This paper investigates the influence of mineral structure on macromechanical behavior of coal under different loading conditions using X-ray CT scanning experimental and numerical methods. The three-dimensional (3D) reconstruction of coal was conducted to assess the spatial distribution characteristics of the mineral structure by AVIZO software. Based on fractal box dimension (BCD) and equivalent diameter, the mineral structures were quantitatively characterized. The 3D finite element models with three distribution characteristics of minerals were built, and the model was considered as a random heterogeneous two-phase material composed of coal matrix and mineral matter. The results show that the frequency of mineral structures decreases with the increase of equivalent diameter in the coal sample. The BCD of the original mineral structure in coal is greater than 2, but the BCD of each part of the minerals divided based on the screening principle is less than 2. Under uniaxial conditions, the elastic modulus, peak strength, and residual strength of coal are monotonically increasing with the size of the mineral structure. The larger the mineral structure size and the more complex the distribution are, the greater the area of stress concentration and the more uniformity the distribution will be. The failure (plasticity) first occurred at the interface between the matrix and the mineral, and the failure zone is significantly different due to the influence of different mineral structures. Under confining pressure, the presence of mineral structure decreases the brittleness of coal, and the variation of brittleness is related to the size and spatial distribution of mineral structures. The fitting relationship between confining pressure and brittleness index is linear, and the correlation coefficient exceeds 0.95.

StyroStone: A protocol for scanning and extracting three-dimensional meshes of stone artefacts using Micro-CT scanners v1

2021 ◽  
Author(s):  
Dominik Göldner ◽  
Fotios Alexandros Karakostis ◽  
Armando Falcucci
Keyword(s):  
Three Dimensional ◽  
Computation Time ◽  
Ct Scanning ◽  
3D Models ◽  
Stone Tools ◽  
Surface Model ◽  
Micro Ct ◽  
Ct Scanner ◽  
Micro Computed Tomography ◽  
Ct Scanners

This protocol presents the first detailed step-by-step pipeline for the 3D scanning and post processing of large batches of lithic artefacts using a micro-computed tomography (micro-CT) scanner (i.e., a Phoenix v-tome-x S model by General Electronics MCC, Boston MA) and an Artec Space Spider scanner (Artec Inc., Luxembourg). This protocol was used to scan and analyze ca. 700 lithic artefacts from the Protoaurignacian layers at Fumane Cave in north-eastern Italy (Falcucci et al., in preparation). For this study several costly scanners and proprietary software packages were employed. Although it is not easy to find a low-budget alternative for the scanners, it is possible to use free and open-source software programs, such as 3D-Slicer (https://www.slicer.org/) or MorphoDig (https://morphomuseum.com/morphodig), to process CT data as well as MeshLab (Cignoni et al. 2008) to interact with the 3D models in general. However, if alternative software is used, the steps and their order described in this protocol might diverge significantly. A cost-effective alternative to create 3D models is digital photogrammetry using commercial cameras and freely available software like Meshroom (https://alicevision.org). Although photogrammetry is an affordable technique to create accurate 3D models of objects, this method might not be useful when scanning large batches of artefacts, as it will require a lot of computation time and processing capacity. Likewise, it could be difficult to generate accurate 3D models of very small and/or detailed tool shapes using 3D surface scanners because stone tools are often much smaller than the recommended minimum field of view. Similarly, the resolution of conventional medical CT scanners might not be sufficient to capture minor details of stone tools, such as the outline or dorsal scars. Thus, high-resolution micro-CT technology is the only reliable way to accurately capture the overall morphology of small stone tools. This protocol aims at providing the first detailed procedure dedicated to the scanning of small lithic implements for further three-dimensional analysis. Note that some of the steps must be repeated at different working stages throughout this protocol. In cases where a task must be done in the exact same way as described in a previous step, a reference to that step is provided. When slight changes were made, the step was modified and reported entirely. This protocol contains a few red and green colours (e.g., arrows or within-program colours) which might be perceived differently by people with dyschromatopsia. However, the display of these colours has been kept to a minimum. We recommend the reader to go over the entire protocol carefully, even if only some specific parts are required. A few points are in fact interdependent, and some of them must be applied simultaneously. Content: Part 1 – Styrofoam preparation Part 2 – Micro-CT scanning Part 3 – 3D model extraction of CT scanned stone artifacts using Avizo Part 4 – Cropping extracted surface model to separate Face A and B in Artec Studio Part 5 – Cropping Face A to separate the lines in Artec Studio Part 6 – Cropping each stone artefact from the lines in Artec Studio Part 7 – Virtually control measurements in MeshLab Part 8 – Artec scanning of larger artifacts Part 9 – Export meshes as non-binary ply models for successive analysis in geomorph Three-dimensional example (in ply format) of the effectivity of the StyroStone Protocol: You can download an example of one Styrofoam line in 3D obtained using our protocol to appreciate the result that can be achieved. We have selected a line where objects are characterized by different metric and morphological attributes. Notice the retouching well visible in the last five smaller artifacts (counting from the left when artifact are oriented with the dorsal face in front of the observer and the butt down), as well as the platforms and bulbs of all artifacts. For more information and examples, feel free to contact us!

scholarly journals Micro-computed tomography: A novel diagnostic technique for the evaluation of gastrointestinal specimens

2021 ◽  
Vol 09 (12) ◽  
pp. E1886-E1889
Author(s):  
Noboru Kawata ◽  
Alexei Teplov ◽  
Peter Ntiamoah ◽  
Jinru Shia ◽  
Meera Hameed ◽  
...  
Keyword(s):  
Computed Tomography ◽  
Three Dimensional ◽  
Diagnostic Technique ◽  
Human Colon ◽  
Ffpe Tissue ◽  
Micro Ct ◽  
Micro Computed Tomography ◽  
Cross Sectional ◽  
Tissue Samples ◽  
Formalin Fixed Paraffin Embedded

AbstractMicro-computed tomography (micro-CT) is a non-destructive modality that can be used to obtain high-resolution three-dimensional (3 D) images of the whole sample tissue; the usefulness of micro-CT has been reported for evaluation of breast cancer and lung cancer. However, this novel diagnostic technique has never been used for evaluating endoscopically resected gastrointestinal specimens. In the present study, we scanned 13 formalin-fixed paraffin-embedded (FFPE) tissue blocks of a normal human colon and gastric tissue samples using micro-CT. The evaluation comprised a comparison of the acquired whole block images with the images of the corresponding cross-sectional slice of the hematoxylin and eosin-stained slide. Micro-CT was able to produce images of the whole sample and clearly depict tissues such as glandular structures, muscularis mucosae, and blood vessels in the FFPE tissue blocks of normal gastrointestinal samples. Furthermore, the 3 D reconstructed could be used to create a cross-sectional image and reflected the surface structure of samples obtained from any site. Micro-CT has the potential to become a highly promising pathological diagnostic assistance tool for endoscopically resected gastrointestinal specimens in combination with conventional microscopic examination.

scholarly journals Marginal and Internal Adaptation Evaluation of Dental Composites Using Micro-CT

2019 ◽  
Vol 2019 ◽  
pp. 1-6
Author(s):  
Adrian Tudor Stan ◽  
Laura Cîrligeriu ◽  
Laura Idorași ◽  
Meda Lavinia Negruțiu ◽  
Cosmin Sinescu ◽  
...  
Keyword(s):  
Composite Resin ◽  
Resin Composite ◽  
Three Dimensional ◽  
Ct Scanning ◽  
Dental Composite ◽  
Micro Ct ◽  
Gap Formation ◽  
Micro Computed Tomography ◽  
Vertical Slot ◽  
Internal Adaptation

The aim of the study was to determine the marginal and internal adaptation after curing of different composite resin restorations, using a nondestructive X-ray micro-computed tomography (micro-CT). Forty previously extracted human molars, kept in 10% formalin to preserve the bonding capabilities of the tooth structures, were divided into four groups based on the composite system used and different light-curing times. Class II (vertical slot) cavities were prepared on one proximal side and restored with dental composite using a Tofflemire matrix, with a bulk-fill composite resin (Venus Bulk Fill, Heraeus Kulzer) and a universal posterior composite (G-ænial Posterior, GC). A curing lamp (Kerr Demi Ultra) was used with different curing times. Micro-CT scanning was performed by using Nikon XTH 225ST to reveal any defects in adaptation or gaps at the tooth restoration interface. The 3D images of the adaptation around the restorations were reconstructed using VG Studio Max 2.2 and myVGL 2.2.6 64-bit software. All samples from the G-ænial group showed marginal and internal gaps, with G-ænial Posterior having higher polymerization shrinkage and marginal gap values. In the Venus Bulk Fill group, there were fewer restorations with internal and external gap formation. Micro-CT is a three-dimensional imaging technique that can nondestructively detect adaptation around the resin composite restorations at every level of the sample.

scholarly journals Critical Instrumentation Area: Influence of Root Canal Anatomy on the Endodontic Preparation

2014 ◽  
Vol 25 (3) ◽  
pp. 232-236 ◽  
Author(s):  
Maria Antonieta Veloso Carvalho de Oliveira ◽  
Jessyca Figueira Venâncio ◽  
Analice Giovani Pereira ◽  
Luís Henrique Araújo Raposo ◽  
João Carlos Gabrielli Biffi
Keyword(s):  
Root Canal ◽  
Three Dimensional ◽  
Micro Computed Tomography ◽  
Subsequent Increase ◽  
Cross Sectional ◽  
Radiographic Images ◽  
Canal Area ◽  
Root Canal Anatomy ◽  
Before And After ◽  
Canal Enlargement

The aim of this study was to evaluate the root canal anatomy of mandibular incisors before and after endodontic instrumentation, identifying regions inaccessible to the action of files (Critical instrumentation Area - CA) in a three-dimensional perspective. Thirty human mandibular central incisors were selected, assigned to two groups (n=15) and instrumented using ProTaper Universal rotary files. In the RX group, longitudinal digital radiographic images were obtained in the buccolingual (BL) and mesiodistal (MD) views. In the CT group, cross-sectional micro-computed tomography (µCT) images were obtained at 3, 9 and 15 mm from the apex. The canal area of the specimens was evaluated before and after instrumentation using digital images from each group. Data were analyzed using t-test, one-way ANOVA with subdivided parcels and Tukey's test (α=0.05). The canal area found in the MD radiographs was larger than in the BL radiographs, which was also confirmed in the transversal images (p<0.01). The CA was only detected in the MD radiographs and µCT scans. On the root canal configuration, a continuous reduction in the canal conicity was observed in BL radiographs, while in MD view there was a constriction at the cervical third and subsequent increase at the middle third (p<0.01). The conical shape of the root canal was observed only in the BL view. The canal enlargement in BL radiographs was not indicative of homogeneous instrumentation, since unprepared areas (CA) were also verified on the buccal and lingual walls in different images

Spatial Distribution of Dialysate in Patients and its Implications to Intradialysate Diffusion

2002 ◽  
Vol 22 (6) ◽  
pp. 698-704 ◽  
Author(s):  
Brian A. Hills ◽  
Seamus Birch ◽  
John R. Burke ◽  
Anthony C. LaMont
Keyword(s):  
Spatial Distribution ◽  
Peritoneal Dialysis ◽  
Spatial Information ◽  
Three Dimensional ◽  
Bulk Diffusion ◽  
Ct Scanning ◽  
Effective Area ◽  
Pelvic Cavity ◽  
Ct Scanner ◽  
Computed Tomographic

Objective To visualize and quantify the spatial distribution of dialysate in patients on continuous ambulatory peritoneal dialysis (CAPD) and, hence, estimate diffusion times for fluid “pockets” wherever intradialysate concentration gradients may not be dissipated by convective currents. Design Contrast medium was added to the dialysate of three supine CAPD patients before an exchange prior to computed tomographic (CT) scanning. Spatial information in the CT scanner was then downloaded to other computers and processed to produce impressive three-dimensional models of dialysate distribution using “wire frame technology.” Results Models differed between patients but all demonstrated pooling of dialysate in the paracolic gutters, subphrenic space, and, especially, in the pelvic cavity. Some pockets of fluid were almost isolated. Quantitatively, the models can account for over 80% of the volume of the exchange (2.5 L), displaying an effective area of contact of 913 – 1450 cm2 between parietal peritoneum and dialysate. This amounts to only 11% – 21% of the anatomic area, again emphasizing the uneven distribution of dialysate. Ignoring very thin (< 0.1 mm) films of dialysate, the bulk (80%) had mean thicknesses ranging from 1.6 to 1.9 cm. Transcendental equations for bulk diffusion were then applied to these findings to determine a theoretical time for urea of about 2 – 3 hours to half-saturation, or 5 – 7 hours to 80% saturation, in the absence of convective currents. Conclusions The distribution of dialysate within the peritoneal cavity is very uneven, resulting in long diffusion times in fluid pockets wherever convective currents may be minimal. Hence, intradialysate diffusion should not be ignored when modeling peritoneal dialysis.

Reconstruction of 3D images of internal log characteristics by means of successive 2D log computed tomography images

Holzforschung ◽  
2009 ◽  
Vol 63 (5) ◽  
Author(s):  
Qiang Wei ◽  
Shu Yin Zhang ◽  
Ying Hei Chui ◽  
Brigitte Leblon
Keyword(s):  
Computed Tomography ◽  
Sugar Maple ◽  
Black Spruce ◽  
Three Dimensional ◽  
Ct Scanning ◽  
Cross Sectional ◽  
3D Images ◽  
Computed Tomography Images ◽  
Future Work ◽  
Huge Challenge

Abstract Although three-dimensional (3D) internal log images are useful to wood scientists for assessing internal log features, little work has been carried out on this subject. The aim of this paper was to demonstrate how two-dimensional (2D) log images may be combined to create 3D images of internal log features. The selected log features include heartwood, sapwood, bark, and knots in a sugar maple log and a black spruce log. The 2D cross-sectional images of the logs were acquired through computed tomography (CT) scanning. For each log, 72 successive 2D cross-sectional CT images of the log were employed to create the corresponding 3D internal log images based on the marching cubes algorithm. The results suggest that the proposed method can produce clear 3D images for each selected internal log features in sugar maple and black spruce. The accuracy analysis of the 3D reconstruction is still a huge challenge and should be fully investigated in future work.

A braided stent becomes flattened inside a curved catheter tube: A micro-CT imaging study

2020 ◽  
Vol 31 (6) ◽  
pp. 373-380
Author(s):  
Taiki Shigematsu ◽  
Tomohiro Otani ◽  
Shotaro Tomotake ◽  
Shunya Shiozaki ◽  
Shigeo Wada
Keyword(s):  
Computational Study ◽  
Three Dimensional ◽  
Imaging Study ◽  
Outer Side ◽  
Micro Ct ◽  
Mechanical State ◽  
Micro Computed Tomography ◽  
Cross Sectional ◽  
Catheter Tube ◽  
Braided Stent

BACKGROUND: The braided stent is a widely accepted endovascular treatment device consisting of woven metal wires. One of the unsolved issues for the braided stent is the stent flattening phenomena when deployed into highly curved arteries. Although a recent computational study highlighted that the mechanical state of the stent inside the catheter before the deployment plays an essential role in causing stent flattening, there is no experimental observation for the stent inside the curved catheter. OBJECTIVE: We investigated braided stent shapes in curved catheter tubes with various curvatures by micro-computed tomography (CT). METHODS: A braided stent was deployed into catheter tubes and set in rectangular cases with constant curvature. The three-dimensional shape of the stent was imaged by micro-CT, and its cross-sectional flatness was quantitatively assessed. RESULTS: Stent flattening occurred in cases of high curvatures of the outer side of the tube curvature, and the degree of flatness increased with increasing tube curvature. This demonstrates that stent flattening can be caused inside the highly curved catheter before deployment. CONCLUSIONS: This preliminary and first observational report provides new insight into the mechanism of stent flattening and emphasizes the importance of the geometrical and mechanical state of the stent inside the catheter.

scholarly journals Phenotyping analysis of maize stem using micro-computed tomography at the elongation and tasseling stages

Plant Methods ◽  
2020 ◽  
Vol 16 (1) ◽  
Author(s):  
Ying Zhang ◽  
Liming Ma ◽  
Jinglu Wang ◽  
Xiaodong Wang ◽  
Xinyu Guo ◽  
...  
Keyword(s):  
Computed Tomography ◽  
Coefficient Of Determination ◽  
Phenotypic Traits ◽  
Growth Stages ◽  
Vascular Bundles ◽  
Micro Computed Tomography ◽  
Maize Cultivars ◽  
Structure Changes ◽  
Detection And Identification ◽  
Two Stages

Abstract Background Micro-computed tomography (μCT) bring a new opportunity to accurately quantify micro phenotypic traits of maize stem, also provide comparable benchmark to evaluate its dynamic development at the different growth stages. The progressive accumulation of stem biomass brings manifest structure changes of maize stem and vascular bundles, which are closely related with maize varietal characteristics and growth stages. Thus, micro-phenotyping (μPhenotyping) of maize stems is not only valuable to evaluate bio-mechanics and water-transport performance of maize, but also yield growth-based traits for quantitative traits loci (QTL) and functional genes location in molecular breeding. Result In this study, maize stems of 20 maize cultivars and two growth stages were imaged using μCT scanning technology. According to the observable differences of maize stems from the elongation and tasseling stages, function zones of maize stem were firstly defined to describe the substance accumulation of maize stems. And then a set of image-based μPhenotyping pipelines were implemented to quantify maize stem and vascular bundles at the two stages. The coefficient of determination (R2) of counting vascular bundles was higher than 0.95. Based on the uniform contour representation, intensity-related, geometry-related and distribution-related traits of vascular bundles were respectively evaluated in function zones and structure layers. And growth-related traits of the slice, epidermis, periphery and inner zones were also used to describe the dynamic growth of maize stem. Statistical analysis demonstrated the presented method was suitable to the phenotyping analysis of maize stem for multiple growth stages. Conclusions The novel descriptors of function zones provide effective phenotypic references to quantify the differences between growth stages; and the detection and identification of vascular bundles based on function zones are more robust to determine the adaptive image analysis pipeline. Developing robust and effective image-based phenotyping method to assess the traits of stem and vascular bundles, is highly relevant for understanding the relationship between maize phenomics and genomics.

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