GIDVis is a software package based on MATLAB specialized for, but not limited to, the visualization and analysis of grazing-incidence thin-film X-ray diffraction data obtained during sample rotation around the surface normal. GIDVis allows the user to perform detector calibration, data stitching, intensity corrections, standard data evaluation (e.g. cuts and integrations along specific reciprocal-space directions), crystal phase analysis etc. To take full advantage of the measured data in the case of sample rotation, pole figures can easily be calculated from the experimental data for any value of the scattering angle covered. As an example, GIDVis is applied to phase analysis and the evaluation of the epitaxial alignment of pentacene­quinone crystallites on a single-crystalline Au(111) surface.

DatView is a new graphical user interface (GUI) for plotting parameters to explore correlations, identify outliers and export subsets of data. It was designed to simplify and expedite analysis of very large unmerged serial femtosecond crystallography (SFX) data sets composed of indexing results from hundreds of thousands of microcrystal diffraction patterns. However, DatView works with any tabulated data, offering its functionality to many applications outside serial crystallography. In DatView's user-friendly GUI, selections are drawn onto plots and synchronized across all other plots, so correlations between multiple parameters in large multi-parameter data sets can be rapidly identified. It also includes an item viewer for displaying images in the current selection alongside the associated metadata. For serial crystallography data processed by indexamajig from CrystFEL [White, Kirian, Martin, Aquila, Nass, Barty & Chapman (2012). J. Appl. Cryst. 45, 335–341], DatView generates a table of parameters and metadata from stream files and, optionally, the associated HDF5 files. By combining the functionality of several commonly needed tools for SFX in a single GUI that operates on tabulated data, the time needed to load and calculate statistics from large data sets is reduced. This paper describes how DatView facilitates (i) efficient feedback during data collection by examining trends in time, sample position or any parameter, (ii) determination of optimal indexing and integration parameters via the comparison mode, (iii) identification of systematic errors in unmerged SFX data sets, and (iv) sorting and highly flexible data filtering (plot selections, Boolean filters and more), including direct export of subset CrystFEL stream files for further processing.

Grazing-incidence small-angle X-ray scattering (GISAXS) coupled with computed tomography (CT) has enabled the visualization of the spatial distribution of nanostructures in thin films. 2D GISAXS images are obtained by scanning along the direction perpendicular to the X-ray beam at each rotation angle. Because the intensities at the q positions contain nanostructural information, the reconstructed CT images individually represent the spatial distributions of this information (e.g. size, shape, surface, characteristic length). These images are reconstructed from the intensities acquired at angular intervals over 180°, but the total measurement time is prolonged. This increase in the radiation dosage can cause damage to the sample. One way to reduce the overall measurement time is to perform a scanning GISAXS measurement along the direction perpendicular to the X-ray beam with a limited interval angle. Using filtered back-projection (FBP), CT images are reconstructed from sinograms with limited interval angles from 3 to 48° (FBP-CT images). However, these images are blurred and have a low image quality. In this study, to optimize the CT image quality, total variation (TV) regularization is introduced to minimize sinogram image noise and artifacts. It is proposed that the TV method can be applied to downsampling of sinograms in order to improve the CT images in comparison with the FBP-CT images.

BornAgain is a free and open-source multi-platform software framework for simulating and fitting X-ray and neutron reflectometry, off-specular scattering, and grazing-incidence small-angle scattering (GISAS). This paper concentrates on GISAS. Support for reflectometry and off-specular scattering has been added more recently, is still under intense development and will be described in a later publication. BornAgain supports neutron polarization and magnetic scattering. Users can define sample and instrument models through Python scripting. A large subset of the functionality is also available through a graphical user interface. This paper describes the software in terms of the realized non-functional and functional requirements. The web site https://www.bornagainproject.org/ provides further documentation.

A software package for Grazing Incident Wide Angle X-ray Scattering (GIWAXS) geared toward weakly ordered materials, including: scattering intensity normalization/uncertainty, scattering pattern indexing, and refractive shift correction.

A new genetic study by a team of Cuban and American researchers confirms that American crocodiles are hybridizing with wild populations of critically endangered Cuban crocodiles, which may cause a population decline of this species found only in the Cuban Archipelago.

The post Genetic study confirms American crocodiles and critically endangered Cuban crocodiles are hybridizing in the wild appeared first on Smithsonian Insider.

What do you want to be when you grow up? Would you want to explore the world searching for long lost creatures of our past? […]

The post Five amazing fossil finds that will make you want to be a fossil hunter appeared first on Smithsonian Insider.

From bizarre bugs to penis spines on bats, our world is infinitely expanded when we look down the microscope! Check out the stories behind these […]

The post What is that?! Five Amazing Microscopic Images appeared first on Smithsonian Insider.

“Early Women in Science” is an online exhibition of 16 women scientists who began their work before 1922. A Biodiversity Heritage Library exhibition, it profiles forward-thinking […]

The post “Early Women in Science” Profiles Trailblazing Women appeared first on Smithsonian Insider.

Have an upset stomach? Pop a chalky, chewable antacid. Maybe you’ve got a painful cut or burn. No problem; reach for a healing ointment or […]

The post Glittering, mesmerizing, lifesaving: Hospital exhibit showcases minerals used in medicine appeared first on Smithsonian Insider.

Crystal structure identification of thin organic films entails a number of technical and methodological challenges. In particular, if molecular crystals are epitaxially grown on single-crystalline substrates a complex scenario of multiple preferred orientations of the adsorbate, several symmetry-related in-plane alignments and the occurrence of unknown polymorphs is frequently observed. In theory, the parameters of the reduced unit cell and its orientation can simply be obtained from the matrix of three linearly independent reciprocal-space vectors. However, if the sample exhibits unit cells in various orientations and/or with different lattice parameters, it is necessary to assign all experimentally obtained reflections to their associated individual origin. In the present work, an effective algorithm is described to accomplish this task in order to determine the unit-cell parameters of complex systems comprising different orientations and polymorphs. This method is applied to a polycrystalline thin film of the conjugated organic material 6,13-pentacene­quinone (PQ) epitaxially grown on an Ag(111) surface. All reciprocal vectors can be allocated to unit cells of the same lattice constants but grown in various orientations [sixfold rotational symmetry for the contact planes (102) and (102)]. The as-determined unit cell is identical to that reported in a previous study determined for a fibre-textured PQ film. Preliminary results further indicate that the algorithm is especially effective in analysing epitaxially grown crystallites not only for various orientations, but also if different polymorphs are present in the film.

The post Museum Conservation Institute research scientist Ed Vicenzi discusses his work analyzing daguerreotypes appeared first on Smithsonian Insider.

The post The amazing story of adaptation and survival in our species, Homo sapiens. appeared first on Smithsonian Insider.

The Smithsonian Libraries offer a vast amount of resources to the general public. This video gives you a peek into the amazing world of discovery […]

The post Video: A peek into the amazing world offered by Smithsonian Libraries appeared first on Smithsonian Insider.

Learn how to use the Smithsonian Wild website to find amazing camera trap photos of mammals from around the world

The post Learn to use the Smithsonian Wild website of amazing animal photos! appeared first on Smithsonian Insider.

The moon passed between the Earth and the sun on Thursday, Oct. 23. While avid stargazers in North America looked up to watch the spectacle, the […]

The post Polar-orbiting satellite captures amazing X-ray footage of solar eclipse appeared first on Smithsonian Insider.

using Irfanview & UnFREEz

Studies at two remote Smithsonian Institution Global Earth Observatory sites in Panama and Thailand show the first evidence of long-term effects of nitrogen pollution in tropical trees.

The post Air pollution is fertilizing tropical forests appeared first on Smithsonian Insider.

Given its scale and diversity, the Smithsonian’s collection of 154 million items presents a unique digitization challenge. This video showcases a conveyor belt driven imaging […]

The post Digitizing the Smithsonian’s Botany Collection appeared first on Smithsonian Insider.

A method is described for indexing grazing-incidence X-ray diffraction data of epitaxially grown thin films comprising various crystal orientations and/or polymorphs by measuring reciprocal-lattice vectors.

Georgi Dimchev
Apr 9, 2020; 133:jcs239020-jcs239020
Articles

A preponderance of scientific evidence shows that even low doses of ionizing radiation, such as gamma rays and X-rays, are likely to pose some risk of adverse health effects, says a new report from the National Academies National Research Council.

An international, multidisciplinary organizing committee has been appointed to plan the Second International Summit on Human Genome Editing, which will take place Nov. 27-29 in Hong Kong.

On the eve of the Second International Summit on Human Genome Editing, we were informed of the birth of twins in China whose embryonic genomes had been edited.

In December 2015, the U.S. National Academy of Sciences and U.S. National Academy of Medicine, the Royal Society of the United Kingdom, and the Chinese Academy of Sciences hosted an international summit in Washington, D.C., to discuss scientific, ethical, and governance issues associated with human genome editing.

At colleges and universities around the nation, scientists and graduate students are seeking out ways to bring their knowledge, skills, and resources to bear in the struggle against COVID-19.

When "Offramp" host John Rabe's father, Bill, created the list at Lake Superior State University in Michigan he likely didn't know it would thrive nearly 40 years later.  As language evolves there should never be a shortage of words and phrases we want to "kick to the curb."

This morning on "AirTalk," I asked listeners to pick the ones they "hate on."  We got some good ones, including my overused "unpack," as in "let's unpack that idea."  Falling into word patterns can happen so subtly that we don't even know it until someone points it out.

My nomination for the list -- "it is what it is."   What are yours?

This content is from Southern California Public Radio. View the original story at SCPR.org.

Restoration of upland bog habitats by blocking drainage channels has caused concern among some sheep farmers that this will reduce the quality of grazing areas. However, UK researchers have shown that drainage does not encourage growth of plants favoured by sheep, nor do sheep use drained areas more. Therefore they conclude such restoration measures are unlikely to detrimentally affect sheep grazing.

With the emerging synergy between hybrid cloud and AI, we will witness tremendous innovation and business value in the enterprise IT world.

Scientists recommend policies that alternate between mowing and grazing to manage Europe’s high-nature-value grasslands. This comes after a new seven-year study found that a high plant-species diversity helps grasslands to maintain productivity and to resist depletion of phosphorus caused by livestock grazing and depletion of potassium caused by mowing.

The preferred habitats of wetland bird species - including 12 that are endangered - have been identified by a new study. From conducting counts at 137 sites across Sweden, it was found that total species richness was highest in sites that had a tendency to flood; wet grassland areas that were grazed as opposed to mowed; and sites that were far from areas of woodland. The authors suggest this research could help determine the most suitable locations for future wetland conservation projects.

As the threat of novel corona virus COVID-19 spreads through the world, we live in an increasingly anxious time. While healthcare workers fight the virus in the front line, we do our part by practicing social distancing to slow the pandemic. Today's guest blogger, Toshi Takeuchi, would like to share how he spends his time by analyzing data in MATLAB.... read more >>

Soil is an overlooked source of persistent organic pollutants (POPs) for grazing cows, finds a new study of contaminated farms in Switzerland. The researchers tested a new modelling tool to track two specific environmental POPs — known as polychlorinated biphenyls (PCBs) and dioxins (PCDD/Fs) — as they moved from the farm environment into a cow’s body over time. The tool could be used to assess measures designed to decontaminate animals or to prevent contamination, such as grazing regimes that aim to reduce the risk of cows eating soil accidentally.

Myke fixes problems, Grey automates his to-do list, and they both discuss hiring people.

Would someone get this man a superhero costume already?

This company takes its treats to the next (green) level.

Researchers have created a laser powerful enough to detect minute concentrations of gases in the atmosphere or in your mouth.

Michael Pollan explains how having such a centralized food system can be dangerous to the country.

Botanophobics may want to avert their eyes.

Outside of the kitchen, garlic has many potential health, beauty and agricultural benefits.

The 150-foot-wide asteroid 2012 DA14 may harbor $65 billion of recoverable water and $130 billion in metals.

Space shuttle Endeavour, you're a star. A captivating new time-lapse movie has condensed Endeavour's recent three-day road trip to a Los Angeles museum into mer

This NASA image highlights wildfires, hurricanes and dust storms to show off the Earth's air quality.

There are many reasons to cast your eyes skyward this month.

This April and May, see Mars shine, look out for meteor showers, marvel at Saturn's rings and keep your eyes peeled for a total lunar eclipse.

Dogs have incredible senses and are like superheroes on four legs. Take this quiz to test your canine know-how.