X-ray tomography – Lightsources.org

Novel AI Method Sharpens 3D X-ray Vision

2026/01/122026/01/29

NSLS-II scientists see around hidden corners of tiny objects, even when significant portions of data are missing

X-ray tomography is a powerful tool that enables scientists and engineers to peer inside of objects in 3D, including computer chips and advanced battery materials, without performing anything invasive. It’s the same basic method behind medical CT scans. Scientists or technicians capture X-ray images as an object is rotated, and then advanced software mathematically reconstructs the object’s 3D internal structure. But imaging fine details on the nanoscale, like features on a microchip, requires a much higher spatial resolution than a typical medical CT scan — about 10,000 times higher.

The Hard X-ray Nanoprobe (HXN) beamline at the National Synchrotron Light Source II (NSLS-II), a U.S. Department of Energy (DOE) Office of Science user facility at DOE’s Brookhaven National Laboratory, is able to achieve that kind of resolution with X-rays that are more than a billion times brighter than traditional CT scans.

Tomography only works well when these projection images can be taken from all angles. In many real-world cases, however, that’s impossible. For example, scientists can’t spin a flat computer chip around 180 degrees without blocking some of the X-rays. When parallel to the surface at high angles, fewer X-rays can penetrate the chip, limiting the viewing angles of the measurement. The missing data from this angular range produces a “blind spot,” leading the reconstruction software to produce blurry, distorted images.

“We call this the ‘missing wedge’ problem,” said Hanfei Yan, lead beamline scientist at the HXN beamline and corresponding author of this work. “For decades, this problem has limited the applications of X-ray and electron tomography in many areas of science and technology.”

Read more on the BNL website

Image: This 3D image of an integrated circuit showing slices through its thickness was reconstructed with a new technique that incorporates artificial intelligence called the “perception fused iterative tomography reconstruction engine.”

Credit: Brookhaven National Laboratory

X-rays reveal fossil stealth technology

2025/08/122025/08/28

Using state-of-the-art X-ray microtomography at the Swiss Light Source SLS, operated by the Paul Scherrer Institute PSI, researchers have gained insights into the silent hunting techniques of a giant ichthyosaur – a marine predator that roamed the dimly lit oceans 183 million years ago.

In the twilight of the Jurassic period, a giant ruled the seas: Temnodontosaurus, an ichthyosaur that was more than ten metres long, with eyes the size of footballs. It glided virtually noiselessly through the dark waters – always on the lookout for prey. This marine predator relied on specialised stealth strategies: no eddies, no noise – advancing silently before making a lightning attack.

What may sound like a scene from a wildlife documentary is actually based on the latest scientific findings. An international research team led by Johan Lindgren from Lund University has managed, for the first time, to analyse the soft tissue structures of an exceptionally well-preserved forefin of one of these marine giants. The structure of the forefin suggests an evolutionary adaptation to suppress noise when swimming – comparable to the serrated flight feathers of an owl, which glides through the night almost without a sound. In order to determine the detailed structure of the soft tissue, the Temnodontosaurus’s forefin was sent on a journey – to undergo X-ray tomography at the Swiss Light Source SLS in Villigen.

From land animal to silent leviathan

Ichthyosaurs lived on Earth between 250 and 90 million years ago, making them one of the most successful groups of marine tetrapods – four-limbed vertebrates – that we know of. Like modern whales, these ancient aquatic reptiles descended from land-dwelling animals that gradually adapted fully to life in the ocean by developing fins and streamlined, almost dolphin-like bodies.

The new study, published in the journal Nature, describes an almost complete forefin of the largest ocean megapredator during the Early Jurassic. “The wing-like shape of the flippers, the absence of bones at the distal end – the part furthest from the body – the longitudinal skin structures and the distinctly jagged trailing edge indicate that this massive animal had developed means of minimising noise when swimming,” explains Johan Lindgren, the study’s lead author, who specialises in the analysis of fossilised soft tissues in marine reptiles. This means that the ichthyosaur must have moved through the water almost noiselessly. “We have never before seen such sophisticated evolutionary adaptations in a marine animal.”

Although many unusual ichthyosaurs have been found in which the soft tissue has been preserved, even including some with complete body outlines, the known soft parts have so far been restricted to a small group of dolphin-sized species. The new discovery is remarkable in that it represents the first soft tissue of a large ichthyosaur. Also, the structure of the flipper is unlike that of any other known aquatic animal, living or extinct. Its jagged rear edge is reinforced by novel rod-like mineralised structures, which the team refers to as “chondroderms”. The fossilised fin was discovered by chance at a road construction site near Dotternhausen in southern Germany – by fossil collector Georg Göltz, a co-author of the study, who was looking out for other fossils there.

High-tech methods reveal prehistoric stealth technology

To better understand the structures preserved in the fossil, the fin underwent a series of highly sensitive procedures. Synchrotron-based X-ray microtomography at the TOMCAT beamline of the SLS at PSI played a key role. “The high resolution and high contrast of our tomography procedure meant that we were able to visualise the fine internal structure of the chondroderms in three dimensions,” says Federica Marone, a beamline scientist at PSI’s Center for Photon Science. “This imaging technique was crucial to helping us understand the mechanical function of the rod-like reinforcements –particularly their role in minimising noise while swimming.”

Read more on SLS website

Image: This is what the silent Jurassic hunter might have looked like: Temnodontosaurus in action.

Credit: Adobe Stock

New bizarre Triassic reptile with a feather-like crest discovered

2025/07/232025/07/24

A new species of early reptile from the Triassic period has been discovered, with unique structures growing from its skin that formed an alternative to feathers. This ‘wonder‘ fossil changes our understanding of reptile evolution. The team of scientists, led by the State Museum of Natural History Stuttgart, published the description of the new species in the journal Nature. The skull of the reptile was scanned at the new beamline BM18.

The 247-million-year-old reptile is called Mirasaura grauvogeli, which means ‘Grauvogel’s Wonder Reptile’, in honour of the fossil collector who found it, Louis Grauvogel. The fossil was found in the 1930s in Alsace (France) and transferred to the State Museum of Natural History in Stuttgart in 2019. The bizarre creature shows characteristics from reptiles but presents a dorsal crest with previously unknown, structurally complex appendages growing from its skin, with some similarities to feathers.

The crest was probably used for display to other members of the same species. The finding shows that complex skin structures are not only found in birds and their closest relatives but may predate modern reptiles. This discovery changes our understanding of reptile evolution. “At first scientists were puzzled about the crest, but after preparation, a reptile skull was revealed. We can now safely say that is a new species from a very strange group reptiles called drepanosaurs”, explains palaeontologist Stephan Spiekman, first author of the study, from the State Museum of Natural History Stuttgart, Germany.

In order to analyse the specimen, which was a few centimetres in length and less than 0.5 millimetres in width, the team came to the ESRF’s new experimental station BM18. There, they scanned the skull using X-ray tomography, which revealed a bird-like shape with a narrow, mostly toothless snout, large forward-facing eye sockets and a large, domed skull. Kathleen Dollman, scientist at the ESRF and co-author of the publication, says: “The fossil is incredible and showed these feather-like structures beautifully. I knew that imaging such fine details was going to be challenging, but when we started to see the first images on BM18 I knew that we had found something special”.

Spiekman adds: “Without the ESRF we could not have been able to do the reconstruction of the skull, because the fossil is so small that it is incredibly difficult to scan – it took me four months of working on the data to get the full reconstruction!”. This is the first Nature publication stemming from research carried out at the new BM18 beamline.

With the findings, the team hypothesized that the snout was probably used to extract insects from narrow tree holes, the big forward-facing eyes are typical of animal living in trees and the domed skull shows a fontanelle, which indicates that the specimen was very young when it died. It also had teeth in the roof of the mouth, as many different groups of extinct reptiles do.

Not hairs, not feathers, but something similar

Body coverings such as hair and feathers have played a central role in evolution. They enabled warm- bloodedness by insulating the body, and were used for courtship, display, deterrence of enemies and, in the case of feathers, flight. Their structure in mammals and birds is characterised by longer and more complex skin outgrowths that differ significantly from the simple and flat scales of reptiles.

The crest of Mirasaura consists of individual, densely overlapping appendages that each possess a feather-like contour with a narrow central ridge. While real feathers consist of many delicate branched structures called barbs, there is no evidence of such branching in the appendages of Mirasaura. Because of this, the team believes that the structure of the complex, unique skin appendages of Mirasaura evolved largely independently of those of birds.

Read more on ESRF website

Ptychographic computed X-ray tomography reveals structure of porous membranes on the nano scale

2023/11/162023/11/21

Article published in Communications Materials presents significant findings and discusses the possibilities offered by this technique combined with synchrotron light sources

Porous materials play key roles in a variety of contexts, from transporting water and nutrients in biological systems to storing oil and water in reservoirs of rock. And synthetic polymer membranes are essential to separation processes, as in the case of chromatography. They have well-established applications in water desalination, hemodialysis, and gas separation, and these uses are expanding into processes that filter out pollutants from contaminated water. Their benefits include energy efficiency, smaller carbon footprint, and compact design that provides a large area of membrane in a small volume.

Membranes that can fulfill technological objectives have complex porous structures that ensure the required selectivity, mechanical stability, and characteristics for rapid transport; the effectiveness and performance of these membranes is defined by characteristics such as porosity and interconnectivity, which can be particularly difficult to measure when they are brought down to the nano scale.

The limitations of electron microscopy and advantages of ptychographic X-ray computed tomography

Techniques such as scanning electron microscopy (SEM), atomic force microscopy (AFM), and transmission electron microscopy (TEM) have helped scientists better understand the transport mechanisms in these applications and develop membranes for different purposes. But even though they are powerful, these techniques also have significant limitations: the samples must be dehydrated and covered with a metallic layer, and must also remain in a vacuum during analysis, which can affect the structure of these membranes and hinder analysis under near-real conditions.

Furthermore, when the pores of the material reach the nano scale, the total sample volume must be significantly reduced in order to attain the resolution necessary for analysis. Within this context, X-ray tomography has emerged as a good alternative. This method not only offers non-destructive visualization, but samples can be analyzed in ambient conditions with significantly larger total sample volumes.

Conventional X-ray tomography, which analyzes different absorption in different parts of a sample, faces challenges related to resolution limits when analyzing less dense materials (such as membranes). But as new fourth-generation synchrotron light sources have recently come online and ptychographic X-ray tomography has been developed, images of these materials can be obtained with nanometric resolution.

Ptychographic X-ray computed tomography (PXCT) is a powerful phase-contrast imaging technique that uses a series of two-dimensional projections of the object from different angles to reconstruct its three-dimensional structure in high resolution, revealing information about porosities and interconnectivity.

Read more on CNPEM website

The shape of snow: New insights could help climate models

2023/07/172023/08/31

Scientists from the Institut des Géosciences de l’Environnement of Grenoble, the Centre d’Etudes de la Neige and the Groupe de Météorologie Expérimentale et Instrumentale have developed a new approach for measuring the interaction between snow and sunlight. This methodology is important to improve the accuracy of climate models. They did X-ray tomography experiments at ESRF ID19 beamline. The results are published in Nature Communications.

Once deposited on the ground, snow is a material composed of air and ice crystals, whose shape and arrangement vary greatly at the micrometre scale. This is known as the microstructure of snow. This “skeleton” of ice and air governs the propagation of light within the snowpack through optical phenomena such as refraction and internal reflections in the ice phase.

However, despite its extreme complexity and irregularity, natural snow is still represented in a simplistic manner in almost all optical models, including those implemented in climate models. These models typically depict snow as a collection of ice particles with perfect geometric shapes, mainly spheres. Among the many implications for the energy balance of snow, this simplification leads to significant uncertainties in climate modelling, with potential impacts of up to 1.2°C on global air temperature.

In this new study, the authors from the Institut des Géosciences de l’Environnement of Grenoble (IGE / CNRS – INRAE – IRD – UGA – Grenoble INP-UGA), the Centre d’Etudes de la Neige (CEN / CNRM / Météo-France – CNRS) and the Groupe de Météorologie Expérimentale et Instrumentale (GMEI / CNRM / Météo-France – CNRS) have accurately simulated the light propagation in a collection of 3D images of snow microstructure obtained by X-ray tomography, using a ray-tracing model. Very different snow types were investigated, from fresh snow (PP) to refrozen melt-freeze forms (MF). Some images were obtained at the 3SR-Lab. Several snow microstructures required higher resolution and were acquired at ESRF beamline ID19.

Read more on the ESRF website

Image: Snow microstructure: This is what fresh snow looks like at the micrometre scale

Seeing more deeply into nanomaterials

2022/04/132022/04/21

New 3D imaging tool reveals engineered and self-assembled nanoparticle lattices with highest resolution yet—7nm—about 1/100,000 of the width of a human hair

From designing new biomaterials to novel photonic devices, new materials built through a process called bottom-up nanofabrication, or self-assembly, are opening up pathways to new technologies with properties tuned at the nanoscale. However, to fully unlock the potential of these new materials, researchers need to “see” into their tiny creations so that they can control the design and fabrication in order to enable the material’s desired properties.

This has been a complex challenge that researchers from the U.S. Department of Energy’s (DOE) Brookhaven National Laboratory and Columbia University have overcome for the first time, imaging the inside of a novel material self-assembled from nanoparticles with seven nanometer resolution, about 1/100,000 of the width of a human hair. In a new paper published on April 7, 2022 in Science, the researchers showcase the power of their new high-resolution x-ray imaging technique to reveal the inner structure of the nanomaterial.

The team designed the new nanomaterial using DNA as a programmable construction material, which enables them to create novel engineered materials for catalysis, optics, and extreme environments. During the creation process of these materials, the different building blocks made of DNA and nanoparticles shift into place on their own based on a defined “blueprint”—called a template—designed by the researchers. However, to image and exploit these tiny structures with x-rays, they needed to convert them into inorganic materials that could withstand x-rays while providing useful functionality. For the first time, the researchers could see the details, including the imperfections within their newly arranged nanomaterials.

Read more on the BNL website

Image: An artist’s impression of how the researchers used x-ray tomography as a magnifying lens to see into the inner structure of nanomaterials

The reign of the dinosaurs ended in spring

2022/02/232022/02/24

The asteroid that killed nearly all dinosaurs struck Earth during springtime. An international team of scientists from the Vrije Universiteit (VU) Amsterdam (The Netherlands), Uppsala University (Sweden), Vrije Universiteit Brussel (Belgium) and the ESRF, the European Synchrotron (France), have determined when the meteorite crashed onto the Earth, after analysing the remains of fish that died just after the impact. Their results are published in the journal Nature today.

Around 66 million years ago, the Chicxulub meteorite crashed into the Earth, in what today is the Yucatán peninsula in Mexico, marking the demise of dinosaurs and end of the Cretaceous period. This mass extinction still puzzles scientists today, as it was one of the most selective in the history of life: all non-avian dinosaurs, pterosaurs, ammonites, and most marine reptiles disappeared, whilst mammals, birds, crocodiles, and turtles survived.

A team of scientists from the Vrije Universiteit, Uppsala University, and the ESRF have now shed light on the circumstances surrounding the diverse extinction across the different groups. The answers came from the bones of fish that died moments after the meteorite struck.

Read more on the ESRF website

Image: Melanie During points to a section of a Paddlefish dentary showing high bone cell density (i.e. summer)

Credit: Melanie During

Time to fly! One scientist’s story of being inspired and inspiring others

2022/01/262022/01/26

Shiva Shirani is from Iran and is currently completing a PhD at the University of Malaga. Shiva’s research area is Synchrotron X-ray imaging applied to cementitious material with the goal to decrease our CO2 footprint and protect the planet. Many participants in our #LightSourceSelfies campaign have talked about the need to overcome setbacks and failure. There will always be challenges but success will come. Shiva’s research ideas led to her being granted an OPEN SESAME Fellowship to become a young scientific visitor at ID19 tomography beamline at the ESRF. But prior to this, there were setbacks. Shiva’s story, which she tells with honestly and passion, charts these setbacks and how she eventually found people who believed in her ideas. People who helped Shiva find her “two wings to fly”.

One of these people was the late Claudio Ferrero, one of Shiva’s supervisors at the ESRF. Claudio recognised the unique way that Shiva shares her passion for science with the world via Twitter and Instagram and encouraged her to continue this inspirational science communication. In the early stages of planning the #LightSourceSelfies campaign, Lightsources.org and SESAME recognised this too! We were delighted when Shiva agreed to participate in our campaign and we are very grateful to the ESRF who subsequently helped Shiva with the filming.

Here we present Shiva Shirani’s #LightSourceSelfie!

SESAME’s #LightSourceSelfie featuring Shiva Shirani

How some plants evolved to depend on fire for survival

2021/10/282021/11/04

Researchers based at Monash University and the Swedish Museum of Natural History have pioneered the use of nuclear imaging techniques at ANSTO’s Australian Centre for Neutron Scattering to resolve long-standing gaps in knowledge of the evolution of plants, including Australian natives, that adapted to depend on fires.

Their work has highlighted the key role of wildfires* in the evolution of floral ecosystems.

Dr Chris Mays, a Postdoctoral Researcher at the Swedish Museum of Natural History and Research Affiliate at Monash University, has used fossils of plant reproductive structures, like pine cones, to show how they have adapted to fire.

Plants are known to have adapted during two pivotal intervals in their evolutionary history: a mass extinction event in the end Permian period (252 million years ago) and the rise of the flowering plants during the mid-Cretaceous hothouse period (120–95 million years ago).

“These extreme warming periods were evolutionary ‘bottlenecks’, through which only fire-adapted plants survived. The evolutionary legacy is all around us in Australia, where a huge proportion of the plants today have fire-adaptive traits,” said Mays.

Using neutron tomography on Dingo, the researchers were able to virtually extract images of amber from within fossils and differentiate plant tissues.

“Neutron tomography is an ideal method for non-destructive, three-dimensional imaging of organically preserved, or ‘coalified’, fossil plants. These are the most common types of plant fossils in the rock record,” said Mays.

Because neutrons can easily penetrate through dense sediments, they can be used to see details of extremely fragile fossils, like those of coalified plants, without the need for meticulous extraction. This minimalist approach to fossil preparation ensures that such delicate fossils remain well-preserved in their protective sediments.

The plant fossils are hydrogen-rich, which means they stand out in contrast to the surrounding rock matrix when imaged with high-resolution neutron tomography.

“Neutrons can successfully differentiate fossil plant tissue that is compositionally similar, where other techniques routinely fail,” said Mays.

X-ray tomography on the Imaging and Medical beamline at the Australian Synchrotron was also undertaken to supplement the neutron investigations.

Read more on the ANSTO website

Image: Dr Maggie-Anne Harvey (left) and Dr Andrew Langendam preparing fossil plant specimens on Dingo

Credit: ANSTO

X-ray tomography as a new tool to analyse the voids in RRP Nb3Sn wires

2021/05/192021/06/09

Scientists have developed a new tool to investigate the internal features of Nb3Sn superconducting wires, combining X-ray tomographic data acquired at beamline ID19 with an unsupervised machine-learning algorithm. The method provides new insights for enhancing wire performance.

Interest in niobium-tin (Nb₃Sn) as a material for superconducting wires has recently been renewed because this material has been selected to replace niobium-titanium as the next step in accelerator magnet technology [1]. The design of these magnets relies on the availability of advanced Nb₃Sn wires capable of withstanding extreme mechanical and thermal loads. The Restacked Rod Process (RRP) is considered the most promising technology to produce Nb₃Sn wires at industrial scale for future accelerator magnets.

Nb₃Sn is a brittle superconducting compound that cannot be drawn directly in the form of a wire. Instead, ductile precursor components are embedded in a copper matrix, drawn, brought to the final shape and then heat-treated, so that Nb₃Sn forms in a reactive diffusion process. The result is a composite wire with several Nb₃Sn sub-elements surrounded by copper. However, the diffusion process can lead to voids, which can play a role in the electro-mechanical and thermal behaviour of the wire. A team of scientists have developed a novel, non-destructive and non-invasive method to investigate the voids in high-performance RRP Nb₃Sn superconducting wires, combining X-ray microtomography data at beamline ID19 with an unsupervised machine-learning algorithm, with a view to providing new insights into the development of these wires.

First glimpse of intricate details of Little Foot’s life

2021/03/022021/03/04

In June 2019, an international team brought the complete skull of the 3.67-million-year-old ‘Little Foot’ Australopithecus skeleton, from South Africa to the UK and achieved unprecedented imaging resolution of its bony structures and dentition in an X-ray synchrotron-based investigation at Diamond. The X-ray work is highlighted in a new paper in e-Life, published today focusing on the inner craniodental features of ‘Little Foot’. The remarkable completeness and great age of the ‘Little Foot’ skeleton makes it a crucially important specimen in human origins research and a prime candidate for exploring human evolution through high-resolution virtual analysis.

To recover the smallest possible details from a fairly large and very fragile fossil, the team decided to image the skull using synchrotron X-ray micro computed tomography at the I12 beamline at Diamond, revealing new information about human evolution and origins. This paper outlines preliminary results of the X-ray synchrotron-based investigation of the dentition and bones of the skull (i.e., cranial vault and mandible).

Read more on the Diamond website

Image: Fossil skull in Diamond’s beamline I12

Credit: Diamond Light Source

Graphite electrodes for rechargeable batteries investigated

2020/11/202020/11/26

Rechargeable graphite dual ion batteries are inexpensive and powerful.

A team of the Technical University of Berlin has investigated at the EDDI Beamline of BESSY II how the morphology of the graphite electrodes changes reversibly during cycling (operando).

The 3D X-ray tomography images combined with simultaneous diffraction now allow a precise evaluation of the processes, especially of changes in the volume of the electrodes. This can help to further optimise graphite electrodes.

Read more on the HZB website

Image: The tomogram during the charging process shows the spatially resolved changes in the graphite electrode thickness of a rechargeable aluminium ion battery in a discharged and charged state.