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Flexible workflows for on-the-fly electron-microscopy single-particle image processing using Scipion

Electron microscopy of macromolecular structures is an approach that is in increasing demand in the field of structural biology. The automation of image acquisition has greatly increased the potential throughput of electron microscopy. Here, the focus is on the possibilities in Scipion to implement flexible and robust image-processing workflows that allow the electron-microscope operator and the user to monitor the quality of image acquisition, assessing very simple acquisition measures or obtaining a first estimate of the initial volume, or the data resolution and heterogeneity, without any need for programming skills. These workflows can implement intelligent automatic decisions and they can warn the user of possible acquisition failures. These concepts are illustrated by analysis of the well known 2.2 Å resolution β-galactosidase data set.




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Solution scattering at the Life Science X-ray Scattering (LiX) beamline

This work reports the instrumentation and software implementation at the Life Science X-ray Scattering (LiX) beamline at NSLS-II in support of biomolecular solution scattering. For automated static measurements, samples are stored in PCR tubes and grouped in 18-position sample holders. Unattended operations are enabled using a six-axis robot that exchanges sample holders between a storage box and a sample handler, transporting samples from the PCR tubes to the X-ray beam for scattering measurements. The storage box has a capacity of 20 sample holders. At full capacity, the measurements on all samples last for ∼9 h. For in-line size-exclusion chromatography, the beamline-control software coordinates with a commercial high-performance liquid chromatography (HPLC) system to measure multiple samples in batch mode. The beamline can switch between static and HPLC measurements instantaneously. In all measurements, the scattering data span a wide q-range of typically 0.006–3.2 Å−1. Functionalities in the Python package py4xs have been developed to support automated data processing, including azimuthal averaging, merging data from multiple detectors, buffer scattering subtraction, data storage in HDF5 format and exporting the final data in a three-column text format that is acceptable by most data analysis tools. These functionalities have been integrated into graphical user interfaces that run in Jupyter notebooks, with hooks for external data analysis software.




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Bias in Science and Communication. A Field Guide. By Matthew Welsh. IOP Publishing, 2018. Pp. 177. ISBN 978-0-7503-1312-4.

Book review




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The Philosophy of Science – A Companion. Edited by Anouk Baberousse, Denis Bonnay and Mikael Cozic. Oxford University Press, 2018. Pp. 768. Price GBP 64.00. ISBN-13 9780190690649.

Book review




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Pattern matching indexing of Laue and monochromatic serial crystallography data for applications in Materials Science

An algorithm, based on the matching of q-vectors pairs, is combined with three-dimensional pattern matching using a nearest-neighbors approach to index Laue and monochromatic serial crystallography data recorded on small unit cell samples.




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Forthcoming article in Acta Crystallographica Section B Structural Science, Crystal Engineering and Materials




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how good is data science for today's world?




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Scientists Determine Geese Involved in Hudson River Plane Crash Were Migratory

Scientists at the Smithsonian Institution examined the feather remains from the Jan. 15, 2009, US Airways Flight 1549 bird strike to determine not only the species, but also that the Canada geese involved were from a migratory, rather than resident, population. This knowledge is essential for wildlife professionals to develop policies and techniques that will reduce the risk of future collisions. The team’s findings were published in the journal “Frontiers in Ecology and the Environment” in June.

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Astrophysical Observatory scientists are monitoring the mysterious movements of glaciers

In southeastern Greenland, two rivers of ice named Helheim and Kangerdlugssuaq flow in spurts and starts toward the coast. They are much like any other […]

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Smithsonian Scientist Discovers Two New Bat Species Hiding in Museum Collections for More Than 150 Years

While studying bats recently at the Academy of Natural Sciences in Philadelphia, Smithsonian mammalogist Kristofer Helgen discovered a new species of flying fox bat from […]

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Smithsonian Names Eva Pell as Under Secretary for Science

Today the Smithsonian Institution announced Eva J. Pell, Senior Vice President for Research and Dean of the Graduate School at Pennsylvania State University, will be the new Under Secretary for Science at the Institution.

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Salad science: Coaxing caterpillars to reveal the secrets of their leafy desires

Testing caterpillars’ taste buds is no simple task. Just like your local salad bar, plants in the wild come in different shapes, textures and flavors. Herbivores rely on each of these cues to tell them what to eat. Deciphering this code is Lind’s task. He’s examining 40 different plant species – half invasive, half native.

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Video: Common birds in Washington, D.C. are helping Smithsonian scientists track intensity of the West Nile Virus

Scientists from the Smithsonian Migratory Bird Center at the National Zoo have taken blood samples from thousands of birds and mosquitoes in an effort to track the progress of the West Nile Virus in the eastern United States. Come along in this video as Smithsonian scientists net birds living in downtown Washington, D.C., extract small amounts of blood, and then release them back into the "wild."

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Climate change may drastically alter Chesapeake Bay, scientists say

It is one of the largest and most productive estuaries in the world, yet dramatic changes are in store for the Chesapeake Bay in coming […]

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For first time, scientists prove locusts use vision to place their legs when walking

In their laboratory, scientists from the University of Cambridge, the University of Southampton and the Smithsonian Tropical Research Institute in Panama, observed as a number of adult locusts walked along a horizontal ladder. After covering the right or left eye of an insect, the scientists observed a significant increase in the error rate of rungs missed by the front leg on the side of the covered eye.

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Smithsonian scientists give giant pandas a helping hand at reproduction

Timing was critical because female giant pandas ovulate only once a year. A short period of two to three days around ovulation is the only time she is able to conceive. Gestation typically lasts from 90 to 185 days.

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Meteorite that fell in Lorton, Va., identified by Smithsonian scientists

A meteorite that crashed through the roof of a Lorton, Va., doctors’ office on Monday, Jan. 18, 2010 was recently identified by scientists in the […]

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Net survey: For quarter century, scientists have been counting creatures traveling Chesapeake Bay tributary

More than 25 years ago, researchers at the Smithsonian Environmental Research Center's Fish and Invertebrate Ecology Lab began taking weekley surveys of the species that make their way in and out of Muddy Creek.

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Scientists find ultrasonic calls of bats also serve a social function

The new study suggests that echolocation calls also serve a social function--bats listen to the ultrasonic calls of other bats to identify roost mates, bats of the same species, members of the opposite sex and intruders to their territory.

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New Zealand Embassy donates kiwi pair to National Zoo Breeding Science Center

Kiwis come to National Zoo. The Smithsonian’s National Zoo will be using a new kiwi pair donated by the New Zealand Embassy to establish a breeding science center. […]

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Scientists establish first frozen repository of Hawaiian coral

Unless action is taken now, coral reefs and many of the animals that depend on them may cease to exist within the next 40 years, causing the first global extinction of a worldwide ecosystem during current history.

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Maryland Blue Crab Science at the Smithsonian

Take to the water with this behind-the-scenes video about Maryland blue crab research at the Smithsonian's Environmental Research Center. Fisheries Ecologist Eric Johnson takes viewers on a journey along the Rhode River to show how scientists tag and monitor Maryland blue crabs in the Chesapeake Bay watershed.

The post Maryland Blue Crab Science at the Smithsonian appeared first on Smithsonian Insider.





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National Zoo scientists successfully grow two species of anemones in aquarium tanks

The anemones—both of which are commonly called Tealia red anemones under the species of Urticina—spawned in late April and early May, just days apart. Henley collected the eggs and sperm from the more than 2,000-gallon tank and put them together in smaller tanks to increase the chances of fertilization. After fertilization, the larvae settled and metamorphosed into a polyp.

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Scientists issue call to action for archaeological sites threatened by rising seas, urban development

Should global warming cause sea levels to rise as predicted in coming decades, thousands of archaeological sites in coastal areas around the world will be lost to erosion. With no hope of saving all of these sites, three archaeologists—Leslie Reeder of Southern Methodist University, Jon Erlandson of the University of Oregon and Torben Rick from the Smithsonian's National Museum of Natural History—have issued a call to action for scientists to assess the sites most at risk around the world.

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Lemelson Center receives $2.6 million grant for informal science education

“Places of Invention,” a planned 3,500-square-foot exhibition at the National Museum of American History scheduled to open in 2014, will feature a selection of “hot spots” of invention and innovation—places where a critical mass of inventive people, networks, institutions, funding and other resources come together and creativity flourishes.

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Invasive oriental shrimp found in Chesapeake Bay by Smithsonian scientists

Twenty years ago scientists at the Marine Invasions Lab of the Smithsonian Environmental Research Center in Edgewater, Md., began studying the interactions between native grass […]

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New online video series to feature Tropical Research Institute scientists

Smithsonian Tropical Research Institute community ecologist Sunshine Van Bael primarily examines the relationship between leaf cutter ants–the world’s first farmers–and the fungi that they cultivate.

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New online video series to feature Tropical Research Institute scientists

Office of Public Affairs videographers Johnny Gibbons and Brian Ireley recently headed down to the Punta Culebra Nature Center on the edge of Panama City […]

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Smithsonian scientists discover seven new species of blenny fish

Using modern genetic analysis, combined with traditional morphology, scientists from the Smithsonian’s National Museum of Natural History and the Ocean Science Foundation have discovered seven […]

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Facebook friends help scientists quickly identify nearly 5,000 fish specimens collected in Guyana

Faced with insufficient time and inadequate library resources to tackle the problem on their own, they instead posted a catalog of specimen images to Facebook and turned to their network of colleagues for help.

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Oysters on floating plates help scientists study acidification and shell growth

A team of scientists from the Smithsonian Environmental Research Center in Edgewater, Md., is taking a closer look at how rising acidification of ocean water may be impacting estuaries and near shore environments on the Chesapeake Bay

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Smithsonian scientists find declining rainfall is a major influence for migrating birds

“Our results support the idea that environmental conditions on tropical non-breeding areas can influence the departure time for spring migration,” said Colin Studds, a postdoctoral fellow at the Smithsonian Conservation Biology Institute's Migratory Bird Center and lead author of the study.

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Scientists discover new species of dinosaur bridging a gap in the dinosaur family tree

A team of scientists led by the Smithsonian Institution has discovered a fossilized dinosaur skull and neck vertebrae that not only reveal a new species, but also an evolutionary link between two groups of dinosaurs.

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Changes in vegetation determine how animals migrate, scientists find in new National Zoo study

The predictability and scale of seasonal changes in a habitat help determine the distance migratory species move and whether the animals always travel together to the same place or independently to different locations.

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Methods for calculating species extinction rates overestimate extinction, says Smithsonian scientist

The most widely used methods for calculating species extinction rates are "fundamentally flawed" and overestimate extinction rates by as much as 160 percent, life scientists report May 19 in the journal Nature.

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Scientists discover the largest assembly of whale sharks ever recorded

This new research, which involved both surface and aerial surveys, has revealed an enormous aggregation of whale sharks—the largest ever reported—with up to 420 individuals off the coast of the Yucatán Peninsula in Mexico.

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Scientists turn to social networking and citizen scientists to help keep track of amphibians

Any adventurer, hiker or backyard naturalist with a camera can help scientists survey and hopefully save the world’s amphibians thanks to a new social networking site that links “citizen scientists” with researchers tracking the decline of amphibians around the globe.

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Bone fragment is only Ice Age artwork from America to show a “proboscidean”

Researchers from the Smithsonian Institution and the University of Florida have announced the discovery of a bone fragment, approximately 13,000 years old, in Florida with an incised image of a mammoth or mastodon.

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Scientists show that modern humans never co-existed with Homo erectus

New excavations in Indonesia and dating analyses by scientists at the Smithsonian and their colleagues show that modern humans never co-existed with Homo erectus.

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