scholarly journals High-throughput microCT scanning of small specimens: preparation, packing, parameters and post-processing

2020 ◽  
Vol 10 (1) ◽  
Author(s):  
Christy A. Hipsley ◽  
Rocio Aguilar ◽  
Jay R. Black ◽  
Scott A. Hocknull
Keyword(s):  
High Throughput ◽  
Large Scale ◽  
Three Dimensions ◽  
Museum Collections ◽  
Evolutionary Time ◽  
Phenotypic Data ◽  
Queensland Museum ◽  
X Ray ◽  
Degrade Image Quality ◽  
Spatio Temporal

Abstract High-resolution X-ray microcomputed tomography, or microCT (μCT), enables the digital imaging of whole objects in three dimensions. The power of μCT to visualize internal features without disarticulation makes it particularly valuable for the study of museum collections, which house millions of physical specimens documenting the spatio-temporal patterns of life. Despite the potential for comparative analyses, most μCT studies include limited numbers of museum specimens, due to the challenges of digitizing numerous individuals within a project scope. Here we describe a method for high-throughput μCT scanning of hundreds of small (< 2 cm) specimens in a single container, followed by individual labelling and archival storage. We also explore the effects of various packing materials and multiple specimens per capsule to minimize sample movement that can degrade image quality, and hence μCT investment. We demonstrate this protocol on vertebrate fossils from Queensland Museum, Australia, as part of an effort to track community responses to climate change over evolutionary time. This system can be easily modified for other types of wet and dry material amenable to X-ray attenuation, including geological, botanical and zoological samples, providing greater access to large-scale phenotypic data and adding value to global collections.

scholarly journals High-throughput microCT scanning of small specimens: preparation, packing, parameters and post-processing

2020 ◽  
Author(s):  
Christy A. Hipsley ◽  
Rocio Aguilar ◽  
Jay R. Black ◽  
Scott A. Hocknull
Keyword(s):  
High Throughput ◽  
Large Scale ◽  
Three Dimensions ◽  
Museum Collections ◽  
Evolutionary Time ◽  
Phenotypic Data ◽  
Queensland Museum ◽  
X Ray ◽  
Degrade Image Quality ◽  
Spatio Temporal

AbstractHigh-resolution X-ray microcomputed tomography, or microCT (μCT), enables the digital imaging of whole objects in three dimensions. The power of μCT to visualise internal features without disarticulation makes it particularly valuable for the study of museum collections, which house millions of physical specimens documenting the spatio-temporal patterns of life. Despite its potential for comparative analyses, most μCT studies include limited numbers of museum specimens, due to the challenges of digitising numerous individuals within a project scope. Here we describe a method for high-throughput μCT scanning of hundreds of small (< 2 cm) specimens in a single container, followed by individual labelling and archival storage. We also explore the effects of various packing materials and multiple specimens per capsule to minimize sample movement that can degrade image quality, and hence μCT investment. We demonstrate this protocol on vertebrate fossils from Queensland Museum, Australia, as part of an effort to track community responses to climate change over evolutionary time. This system can be easily modified for other types of wet and dry material amenable to X-ray attenuation, including geological, botanical and zoological samples, providing greater access to large-scale phenotypic data and adding value to global collections.

scholarly journals High-Throughput Phenotyping Methods for Breeding Drought-Tolerant Crops

2021 ◽  
Vol 22 (15) ◽  
pp. 8266
Author(s):  
Minsu Kim ◽  
Chaewon Lee ◽  
Subin Hong ◽  
Song Lim Kim ◽  
Jeong-Ho Baek ◽  
...  
Keyword(s):  
Drought Stress ◽  
High Throughput ◽  
Large Scale ◽  
Crop Yields ◽  
Plant Traits ◽  
Rapid Development ◽  
Plant Responses ◽  
Phenotypic Data ◽  
Agricultural Technologies ◽  
High Throughput Phenotyping

Drought is a main factor limiting crop yields. Modern agricultural technologies such as irrigation systems, ground mulching, and rainwater storage can prevent drought, but these are only temporary solutions. Understanding the physiological, biochemical, and molecular reactions of plants to drought stress is therefore urgent. The recent rapid development of genomics tools has led to an increasing interest in phenomics, i.e., the study of phenotypic plant traits. Among phenomic strategies, high-throughput phenotyping (HTP) is attracting increasing attention as a way to address the bottlenecks of genomic and phenomic studies. HTP provides researchers a non-destructive and non-invasive method yet accurate in analyzing large-scale phenotypic data. This review describes plant responses to drought stress and introduces HTP methods that can detect changes in plant phenotypes in response to drought.

scholarly journals Large-scale, high-throughput screening for coagulation and hematologic phenotypes in mice*

2002 ◽  
Vol 11 (3) ◽  
pp. 185-193 ◽  
Author(s):  
Luanne L. Peters ◽  
Eleanor M. Cheever ◽  
Heather R. Ellis ◽  
Phyllis A. Magnani ◽  
Karen L. Svenson ◽  
...  
Keyword(s):  
High Throughput ◽  
High Throughput Screening ◽  
Large Scale ◽  
Inbred Mouse ◽  
Inbred Strains ◽  
Sample Volume ◽  
Small Sample ◽  
Mouse Strains ◽  
Phenotypic Data ◽  
Multiple Tests

The Mouse Phenome Project is an international effort to systematically gather phenotypic data for a defined set of inbred mouse strains. For such large-scale projects the development of high-throughput screening protocols that allow multiple tests to be performed on a single mouse is essential. Here we report hematologic and coagulation data for more than 30 inbred strains. Complete blood counts were performed using an Advia 120 analyzer. For coagulation testing, we successfully adapted the Dade Behring BCS automated coagulation analyzer for use in mice by lowering sample and reagent volume requirements. Seven automated assay procedures were developed. Small sample volume requirements make it possible to perform multiple tests on a single animal without euthanasia, while reductions in reagent volume requirements reduce costs. The data show that considerable variation in many basic hematological and coagulation parameters exists among the inbred strains. These data, freely available on the World Wide Web, allow investigators to knowledgeably select the most appropriate strain(s) to meet their individual study designs and goals.

scholarly journals High-Throughput Plant Phenotyping Platform (HT3P) as a Novel Tool for Estimating Agronomic Traits From the Lab to the Field

2021 ◽  
Vol 8 ◽  
Author(s):  
Daoliang Li ◽  
Chaoqun Quan ◽  
Zhaoyang Song ◽  
Xiang Li ◽  
Guanghui Yu ◽  
...  
Keyword(s):  
High Throughput ◽  
Large Scale ◽  
Agronomic Traits ◽  
Global Climate ◽  
Plant Phenotyping ◽  
Phenotypic Data ◽  
Operating Modes ◽  
Sensing Platform ◽  
Exploitation And Utilization ◽  
High Throughput Phenotyping

Food scarcity, population growth, and global climate change have propelled crop yield growth driven by high-throughput phenotyping into the era of big data. However, access to large-scale phenotypic data has now become a critical barrier that phenomics urgently must overcome. Fortunately, the high-throughput plant phenotyping platform (HT3P), employing advanced sensors and data collection systems, can take full advantage of non-destructive and high-throughput methods to monitor, quantify, and evaluate specific phenotypes for large-scale agricultural experiments, and it can effectively perform phenotypic tasks that traditional phenotyping could not do. In this way, HT3Ps are novel and powerful tools, for which various commercial, customized, and even self-developed ones have been recently introduced in rising numbers. Here, we review these HT3Ps in nearly 7 years from greenhouses and growth chambers to the field, and from ground-based proximal phenotyping to aerial large-scale remote sensing. Platform configurations, novelties, operating modes, current developments, as well the strengths and weaknesses of diverse types of HT3Ps are thoroughly and clearly described. Then, miscellaneous combinations of HT3Ps for comparative validation and comprehensive analysis are systematically present, for the first time. Finally, we consider current phenotypic challenges and provide fresh perspectives on future development trends of HT3Ps. This review aims to provide ideas, thoughts, and insights for the optimal selection, exploitation, and utilization of HT3Ps, and thereby pave the way to break through current phenotyping bottlenecks in botany.

scholarly journals Calcium [Ca] tracers using X-Ray fluorescence (XRF) as a potential high throughput measurement technique in ringless highly diverse tropical ecosystems.

2021 ◽  
Author(s):  
Koen Hufkens ◽  
Solenn Regeur ◽  
Camille Rivard ◽  
Jan Van den Bulcke ◽  
Hans Beeckman ◽  
...  
Keyword(s):  
Stable Isotope ◽  
High Throughput ◽  
Large Scale ◽  
Isotope Composition ◽  
Tropical Tree ◽  
Congo Basin ◽  
Plant Responses ◽  
Ancillary Data ◽  
Local Climate ◽  
X Ray

&lt;p&gt;Our understanding of plant responses to climate change, and their feedbacks to the climate system, rely heavily on consistent long-term observations. Yet, measuring tropical plant species is particularly demanding and results in a lack of spatial and temporal coverage to build relationships between forest dynamics and climatology in the central Congo Basin. Here dendrochronology and wood chemical analyses might provide important ecophysiological information addressing this knowledge gap, especially in tropical forests where the lack of a pronounced seasonality often makes it difficult to discern variability in xylem cell size and density. Conventional optical dendrochronology measurements therefore have strong limitations within these ecosystems, however chemical and elemental analysis can provide additional information. For example, seasonal fluctuations in the carbon (&amp;#948;13C) and oxygen (&amp;#948;18O) stable isotope composition of cellulose is linked to variations in local climate and changes in physiological function. A fewstudies have shown that intra-annual and inter-annual variations in the content of calcium [Ca] in tropical tree rings can be used to age tropical trees without rings, constraining estimates of biomass accumulation. Other studies have linked calcium accumulation in different plant organs to the rate of transpiration in trees making it a powerful predictor of inter-annual variability in rainfall for monsoon regions and a strong novel proxy for drought stress.&lt;/p&gt;&lt;p&gt;Here we present the first results of X-ray Fluorescence (XRF) measurements conducted at the SOLEIL synchrotron and analysis of [Ca] and [Sr], combined with ancillary data such as anatomical, stable isotope and climatological measurements for three tropical tree species. Most species show variability in calcium corresponding to previous proxy measurements, corroborating previous results and showing the potential of non-destructive XRF measurements of wood samples in support of ecophysiological research. The potential of high throughput scanning, in contrast to stable isotope measurements, opens possibilities to gather data on the large scale required to understand diverse tropical forest ecosystems and their responses to (drought) disturbances.&lt;/p&gt;

scholarly journals High-throughput three-dimensional visualization of root system architecture of rice using X-ray computed tomography

2019 ◽  
Author(s):  
Shota Teramoto ◽  
Satoko Takayasu ◽  
Yuka Kitomi ◽  
Yumiko Arai-Sanoh ◽  
Takanari Tanabata ◽  
...  
Keyword(s):  
Image Processing ◽  
High Throughput ◽  
Large Scale ◽  
Three Dimensional ◽  
Ct Scanning ◽  
Root System Architecture ◽  
Ct Images ◽  
X Ray ◽  
X Ray Computed ◽  
Crown Roots

Abstract Background: Plants adjust their root system architecture (RSA) against changing environments to optimize their growth. Nondestructive phenotyping of roots beneath the soil not only reveal the response of RSA against environmental stimuli but also allow for designing an ideal RSA for crop cultivation. Generally, roots beneath the soil surface are three-dimensionally visualized using X-ray computed tomography (CT). However, root isolation from X-ray CT images involves a longer time; in addition, CT scanning and reconstruction processes require longer periods. For large-scale root phenotyping, a shorter image acquisition time is required. Thus, the objective of this study is to develop a high-throughput pipeline to visualize rice RSA consisting of radicle and crown roots in the soil, from X-ray CT images.Results: We performed the following three processes to develop the pipeline. First, we used calcined clay with uniform soil particle size as the soil substrate. The size of voids between the soil particles was less than the scanning resolution, resulting in a clear root shape in the CT images. Second, we optimized the parameters for rapid X-ray CT scanning. Higher tube voltage and current produced the highest root-to-soil contrast images. Third, we used a 3-D median filter to reduce noise, and an edge detection alogism to isolate the root segments. The detection limits of the root diameters of the pots of diameters 16 cm and 20 cm were 0.2 mm and 0.3 mm, respectively. Because the crown root diameter of rice is generally higher than 0.2 mm, almost all crown roots could be visualized. Our condition allows for simultaneously performing CT scanning and reconstruction by a high-performance computing technology. Consequently, our pipeline visualizes rice RSA in the soil, requiring less than 10 min (33 s, if a rough image is acceptable) for CT scanning and reconstruction, and 2 min for image processing to visualize rice RSA. We scanned the roots of the upland rice (considered in this study) daily, and our pipeline successfully visualized the root development dynamics over three weeks. Conclusions: We developed a rapid three-dimensional visualization method to visualize rice RSA in the soil using X-ray CT and a fully automated-image processing method known as RSAvis3D. Our methodology allows for high-throughput measuring and requires no manual operators in image processing, thereby providing a potentially efficient large-scale root phenotyping.

scholarly journals SorGSD: updating and expanding the sorghum genome science database with new contents and tools

2021 ◽  
Vol 14 (1) ◽  
Author(s):  
Yuanming Liu ◽  
Zhonghuang Wang ◽  
Xiaoyuan Wu ◽  
Junwei Zhu ◽  
Hong Luo ◽  
...  
Keyword(s):  
High Throughput ◽  
Large Scale ◽  
Agronomic Traits ◽  
Genetic Research ◽  
General Information ◽  
Genomic Variation ◽  
Nucleotide Polymorphisms ◽  
Sorghum Genome ◽  
Online Data ◽  
Phenotypic Data

Abstract Background As the fifth major cereal crop originated from Africa, sorghum (Sorghum bicolor) has become a key C4 model organism for energy plant research. With the development of high-throughput detection technologies for various omics data, much multi-dimensional and multi-omics information has been accumulated for sorghum. Integrating this information may accelerate genetic research and improve molecular breeding for sorghum agronomic traits. Results We updated the Sorghum Genome SNP Database (SorGSD) by adding new data, new features and renamed it to Sorghum Genome Science Database (SorGSD). In comparison with the original version SorGSD, which contains SNPs from 48 sorghum accessions mapped to the reference genome BTx623 (v2.1), the new version was expanded to 289 sorghum lines with both single nucleotide polymorphisms (SNPs) and small insertions/deletions (INDELs), which were aligned to the newly assembled and annotated sorghum genome BTx623 (v3.1). Moreover, phenotypic data and panicle pictures of critical accessions were provided in the new version. We implemented new tools including ID Conversion, Homologue Search and Genome Browser for analysis and updated the general information related to sorghum research, such as online sorghum resources and literature references. In addition, we deployed a new database infrastructure and redesigned a new user interface as one of the Genome Variation Map databases. The new version SorGSD is freely accessible online at http://ngdc.cncb.ac.cn/sorgsd/. Conclusions SorGSD is a comprehensive integration with large-scale genomic variation, phenotypic information and incorporates online data analysis tools for data mining, genome navigation and analysis. We hope that SorGSD could provide a valuable resource for sorghum researchers to find variations they are interested in and generate customized high-throughput datasets for further analysis.

Comparing 3D vs 2D approach in vorticity estimates

2021 ◽  
Author(s):  
Chiara Montemagni ◽  
Stefano Zanchetta ◽  
Salvatore Iaccarino ◽  
Chiara Montomoli ◽  
Rodolfo Carosi ◽  
...  
Keyword(s):  
Large Scale ◽  
Regional Scale ◽  
Shear Zones ◽  
Three Dimensions ◽  
Two Dimensional ◽  
Micro Ct ◽  
Main Central Thrust ◽  
X Ray ◽  
Aspect Ratios ◽  
Scale Shear

&lt;p&gt;Kinematic analysis of flow is becoming a well-established methodology, increasingly applied for its capability to contribute to the solution of complex topics in structural geology and tectonics, such as shear zones deforming by general shear.&lt;/p&gt;&lt;p&gt;Vorticity evaluations based on stable porphyroclasts method have been used for many years to deduce large-scale tectonics of shear zones with different kinematics (Fossen &amp; Cavalcante, 2017). However, limitations occur because a complex three dimensional problem, the motion of rigid clasts in a flowing matrix, is reduced to its two-dimensional analysis on the XZ plane of the finite strain ellipsoid (Iacopini et al., 2011; Mancktelow, 2013). Therefore vorticity estimates are limited by the extrapolation to three dimensions of two-dimensional data.&lt;/p&gt;&lt;p&gt;We propose a totally new 3D approach based on the use of X-ray micro-computed tomography (X-ray micro-CT) that reflects the real 3D geometry and orientation of the porphyroclasts population. X-ray micro-CT allows to face the loss of dimensionality information imaging the rock sample in three dimensions and produces stacks of 2D grey-scale value images, called &amp;#8220;slices&amp;#8221;, that combined in 3D allow observing the internal structure of the scanned sample.&lt;/p&gt;&lt;p&gt;We tested this approach chiefly on mylonitic orthogneiss from an intensively studied crustal scale shear zone: the Main Central Thrust zone (MCTz) of the Himalaya orogenic belt. Mylonites samples from other regional-scale shear zones in the Alps have been also used for comparison.&lt;/p&gt;&lt;p&gt;The first and foremost consideration is that the use of micro-CT certainly increases the number of investigated clasts because hand samples are scanned: all clasts are evaluated. Micro-CT minimizes the problems due to the isolation factor, as it becomes possible to only select the clasts that do not interact with each other. Moreover, observation in three dimensions allows a more realistic evaluation of the aspect ratios and radii of clasts, avoiding erroneous measurements that generate systematic errors in the vorticity evaluation.&lt;/p&gt;&lt;p&gt;We would like to stress that using the microCT we are able to evaluate all the clasts in the sample, avoiding those which do not meet the prerequisites of the method, otherwise not possible using classical 2D thin section based analysis.&lt;/p&gt;&lt;p&gt;&amp;#160;&lt;/p&gt;&lt;p&gt;Fossen H. &amp; Cavalcante G.C.G., 2017. Earth-Sci. Rev., &lt;strong&gt;171&lt;/strong&gt;, 434&amp;#8211;455.&lt;/p&gt;&lt;p&gt;Iacopini D. et alii, 2011. GSL Spec. Publ., &lt;strong&gt;360&lt;/strong&gt;, 301&amp;#8211;318.&lt;/p&gt;&lt;p&gt;Mancktelow N.S., 2013. J. Struct. Geol.,&amp;#160;&lt;strong&gt;46&lt;/strong&gt;, 235-254.&lt;/p&gt;&lt;p&gt;Montemagni C. et alii, 2020. Terra Nova, &lt;strong&gt;32&lt;/strong&gt;, 215-224.&lt;/p&gt;

Accelerated Discovery of High-Refractive-Index Polyimides via First-Principles Molecular Modeling, Virtual High-Throughput Screening, and Data Mining

2019 ◽  
Author(s):  
Mohammad Atif Faiz Afzal ◽  
Mojtaba Haghighatlari ◽  
Sai Prasad Ganesh ◽  
Chong Cheng ◽  
Johannes Hachmann
Keyword(s):  
Data Mining ◽  
Refractive Index ◽  
High Throughput ◽  
First Principles ◽  
High Throughput Screening ◽  
Large Scale ◽  
Computational Study ◽  
High Refractive Index ◽  
Structural Features ◽  
Learning Program

<div>We present a high-throughput computational study to identify novel polyimides (PIs) with exceptional refractive index (RI) values for use as optic or optoelectronic materials. Our study utilizes an RI prediction protocol based on a combination of first-principles and data modeling developed in previous work, which we employ on a large-scale PI candidate library generated with the ChemLG code. We deploy the virtual screening software ChemHTPS to automate the assessment of this extensive pool of PI structures in order to determine the performance potential of each candidate. This rapid and efficient approach yields a number of highly promising leads compounds. Using the data mining and machine learning program package ChemML, we analyze the top candidates with respect to prevalent structural features and feature combinations that distinguish them from less promising ones. In particular, we explore the utility of various strategies that introduce highly polarizable moieties into the PI backbone to increase its RI yield. The derived insights provide a foundation for rational and targeted design that goes beyond traditional trial-and-error searches.</div>

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