tomography – Lightsources.org

It sucked to be the prey of ancient cephalopods

2022/06/232022/06/30

The Jurassic cephalopod Vampyronassa rhodanica, thought to be the oldest known ancestor of the modern-day vampire squid (Vampyroteuthis infernalis), was likely an active hunter – a mode of life that is in contrast with its opportunistic descendant. Scientists led by Sorbonne University came to this conclusion after analysing microtomographic data of this rare fossil, acquired at the ESRF and the Muséum national d’Histoire naturelle in Paris. The results are published today in Scientific Reports.

Vampyronassa rhodanica is thought to be one of the oldest relatives of the modern-day vampire squid (Vampyroteuthis infernalis), which is the only remaining living species of its family. This modern form lives in extreme deep ocean environments, often with little oxygen, and feeds on drifting organic matter. Like V. infernalis, the body of V. rhodanica was mostly made of soft tissue. As this rarely fossilises, little is known about the physical characteristics and evolutionary history of this family.

Despite the scarcity of fossil material from this family, Alison Rowe, from Sorbonne University and colleagues were able to study 3 well-preserved V. rhodanica specimens from La Voulte-sur-Rhône (Ardèche, France), dating to more than 164 million years ago. The eight-armed specimens were small, measuring around 10 cm in length, and had elongated oval-shaped bodies with two small fins.

They took them to the ESRF for non-destructive 3-D imaging: “We used synchrotron tomography at the ESRF in order to better identify the outlines of the various anatomical features”, says Rowe. However, the task was challenging, as Vincent Fernández, scientist at the ESRF, explains: “The fossils are on small slabs, which are very difficult to scan. On top of that, soft tissues are preserved but we needed phase contrast imaging to visualise the faint density variation in the data. The coherence of beamline ID19 was therefore very important to perform propagation phase-contrast computed-tomography and track all the minute details, such as the suckers and small fleshy extensions, called cirri”.

Read more on the ESRF website

Image: Hypothesised reconstruction of Vampyronassa rhodanica

Credit: A. Lethiers, CR2P-SU

Kuda’s #LightSourceSelfie

2021/11/112021/11/11

Kudakwashe Jakata is a Post-Doc in Materials Science at the European Synchrotron Radiation Facility (ESRF) in Grenoble, France. He first experienced the ESRF as a user and reflects on the challenges of his early tomography experiments, what gets him up every day and a future where African scientists can conduct experiments at a light source based in Africa.

EBS X-rays show lung vessels altered by COVID-19

2021/11/042021/12/16

The damage caused by Covid-19 to the lungs’ smallest blood vessels has been intricately captured using high-energy X-rays emitted by a special type of particle accelerator.

Scientists from UCL and the European Synchrotron Research Facility (ESRF) used a new revolutionary imaging technology called Hierarchical Phase-Contrast Tomography (HiP-CT), to scan donated human organs, including lungs from a Covid-19 donor.

Using HiP-CT, the research team, which includes clinicians in Germany and France, have seen how severe Covid-19 infection ‘shunts’ blood between the two separate systems – the capillaries which oxygenate the blood and those which feed the lung tissue itself. Such cross-linking stops the patient’s blood from being properly oxygenated, which was previously hypothesised but not proven.

HiP-CT enables 3D mapping across a range of scales, allowing clinicians to view the whole organ as never before by imaging it as a whole and then zooming down to cellular level

How catalysts age

2021/06/092021/06/11

PSI researchers have developed a new tomography method with which they can measure chemical properties inside catalyst materials in 3-D extremely precisely and faster than before. The application is equally important for science and industry. The researchers published their results today in the journal Science Advances.

The material group of vanadium phosphorus oxides (VPOs) is widely used as a catalyst in the chemical industry. VPOs have been used in the production of maleic anhydride since the 1970s. Maleic anhydride in turn is the starting material for the production of various plastics, increasingly including biodegradable ones. In industry, the catalytic materials are typically used for several years, because they play an important role in the chemical reactions but are not consumed in the process. Nevertheless, a VPO catalyst changes over time as a result of this use.

In a collaborative effort, scientists from two research divisions at the Paul Scherrer Institute PSI – the Photon Science Division and the Energy and Environment Division – together with researchers at ETH Zurich and the Swiss company Clariant AG, have now investigated in detail the ageing process of VPO catalysts. In the course of their research, they also developed a new experimental method.

Read more in the PSI website

Image: Zirui Gao, a researcher at PSI, has developed a new algorithm for experimental studies that significantly shortens the duration of certain imaging measurements that would otherwise take too long. The researchers used it to investigate ageing processes in a much-used catalyst material on the nanoscale.

Credit: Paul Scherrer Institute/Markus Fischer

ESRF and UCL scientists awarded Chan Zuckerberg Initiative grant for human organ imaging project

2020/12/022020/12/03

The project, named “Anatomical to cellular synchrotron imaging of the whole human body”, promises to develop a transformational X-ray tomography technology that will enable the scanning of a whole human body with resolution of 25 microns, thinner than a human hair – tens of times the resolution of a CT scanner. Further, it can then zoom into local areas with cellular-level imaging, or one micron – over 100x better resolution than a CT scanner. This imaging project is based on the recent Extremely Brilliant Source (EBS) upgrade to the ESRF that has created the world’s first high-energy fourth-generation synchrotron, which is currently the brightest X-ray source in the world. Feasibility studies have already demonstrated it can resolve unprecedented detail revealing the damage caused by COVID-19 on human lungs, linking from the major airways all the way down to the finest micro-vasculature in an intact lung.

The project is led by an international multidisciplinary team of synchrotron imaging scientists (at UCL and ESRF), mathematicians and computer scientists (at UCL) and medics (at Hannover-biobank, Mainz and Heidelberg), brought together to image deep-tissue in COVID-19-injured organs.

Read more on the ESRF website

Image: Paul Tafforeau, ESRF scientist imaging the complete brain and lung of a COVID-19 victim using HiP-CT at the ESRF-EBS, the world’s brightest X-ray source. By resolving cellular features (ca. one-micron resolution) in local areas we hope to help determine if COVID-19 affects the vasculature in the organs.
Credit: ESRF

Uncovering the secrets of a fish with a super strong jaw

2020/11/182020/11/26

Black drum is a fish from the United States with one of the strongest bite force in the fish world. It can easily crunch through shells, its main source of food. Weight for weight, it has a bite that is as strong as the bite of a crocodile.

The jaw of this fish has scientists fascinated: it is not made of cortical bone, like most jaws, and it has a 3D arrangement of beams. “This is something never seen before in any other animal. It looks like a sponge… how can such a structure, which seems weak, carry all this load?” queries project leader Ron Shahar, veterinarian and engineer at The Hebrew University of Jerusalem in Israel.

In the quest to find how this structure is built and how it operates, Shahar is joined by Paul Zaslansky, a dentist at the Charité Hospital in Berlin (Germany), as well as physicists Alexander Rack and Marta Majkut at the ESRF.

Read more on the ESRF website

Image: A detailed view of the set-up with the jaw and all the teeth

Credit: A. Rack

Imaging how anticancer compounds move inside the cells

2020/02/262020/03/05

Chemotherapeutics are key players in the clinical setting to fight most types of cancer, and novel chemicals hold the promise to facilitate new and unique intracellular interactions that modulate the cell machinery and destroy the tumour cells. Equally necessary are new tools that enable the unequivocal location and quantification of such molecules in the intracellular nano-space, so that their therapeutic action is fully understood.

Researchers from IMDEA Nanociencia, the ALBA Synchrotron, the European Synchrotron Radiation Facility (ESRF) and the National Centre for Biotechnology (CNB) have developed a new family of organo-iridium drug candidates about a hundred times more potent than the clinically used drug cisplatin.
In order to understand the therapeutic potential of the compound, it is mandatory to accurately localize its fate within the cell ultrastructure with minimal perturbation. To this aim researchers have correlated on the same cell, for the first time, two 3D X-ray imaging techniques with a resolution of tenths of nanometers: cryo soft X-ray tomography, at MISTRAL beamline at ALBA Synchrotron, and cryo X-ray fluorescence tomography, at ID16A beamline at ESRF. These techniques help elucidate the 3D architecture of the whole cell and to reveal the intracellular location of different atomic elements, respectively.

>Read more on the ALBA website

First x-ray microtomography images obtained at Sirius

2019/12/192019/12/20

Two days after storing electrons in Sirius’ storage ring, the CNPEM´s team have performed the first x-ray microtomography analysis at the new Brazilian synchrotron light source. Through a simple proof of concept experiment, using less than ten thousandth of the expected power, it was possible to observe the arrival of synchrotron light for the first time in one of Sirius’ future experimental stations. This is a major milestone for the project, and a victory for Brazil’s science and technology.

“These early rock microtomography demonstrate the functionality of this great machine, designed and built by Brazilians to bring our science to a new level. Sirius is still in the early stages of commissioning, but these early tests that allowed X-ray images to be made ensure that the future will be very bright! We are very excited about the possibility to provide to the Brazilian scientific community a new level of experimental techniques as soon as possible”, said Antonio José Roque da Silva, Director General of CNPEM and the Sirius Project.
The first images were taken at one of the beamlines set up for testing, using X-ray tomography imaging techniques. These analyses mark another important milestone in the Sirius commissioning process. The team is now dedicated to achieving higher and higher currents needed to produce synchrotron light of enough intensity for the first scientific experiments.

>Read more on the LNLS website

Image: (screenshot) Projection of a carbonate rock sample, which has the same composition of the rocks from the Brazilian pre-salt reservoirs.

Direct evidence of small airway closure in acute respiratory distress syndrome

2019/09/162019/09/17

Airway closure is thought to play an important role in acute respiratory distress syndrome (ARDS).

Airway closure has been imaged for the first time in an ARDS model by synchrotron phase contrast imaging providing direct evidence of this phenomenon.

ARDS is an acute inflammatory lung condition associated with high permeability oedema, surfactant dysfunction and widespread collapse of pulmonary alveoli, called atelectasis, which leads to decreased lung compliance and volume [1]. Clinicians have long suspected that the collapsibility of small airways is increased in this clinical syndrome, causing atelectasis [2,3]. While patients invariably require mechanical ventilation to survive, this life support measure can worsen lung injury due to exaggerated stress and strain applied to the tissue, which is magnified by mechanical inhomogeneity of lung tissue and atelectasis. Efforts to develop ventilation strategies that protect the lung, critically depend on our understanding of the mechanical behaviour of lung tissue and airways at the microscale. However, traditional computed tomography studies have not been able to clearly identify airway closure as a cause of atelectasis, due to their limited spatial resolution. To better identify the mechanisms involved in airway closure, it is necessary to use approaches that allow the study of individual airways. Here, the same individual small airways in intact lungs of anesthetised and mechanically ventilated rabbits with ARDS was studied using high resolution synchrotron phase-contrast computed tomography at beamline ID17.

World record in tomography: watching how metal foam forms

2019/08/212019/08/22

An international research team at the Swiss Light Source (SLS) has set a new tomography world record using a rotary sample table developed at the HZB.

With 208 three-dimensional tomographic X-ray images per second, they were able to document the dynamic processes involved in the foaming of liquid aluminium. The method is presented in the journal Nature Communications.
The precision rotary sample table designed at the HZB rotates around its axis at several hundred revolutions per second with extreme precision. The HZB team headed Dr. Francisco García-Moreno combined the rotary sample table with high-resolution optics and achieved a world record of over 25 tomographic images per second using the BESSY II EDDI beamline in 2018.

Image: The precision rotary sample table designed at the HZB turns around its axis at several hundred revolutions per second with extreme precision.
Credit: © HZB

SESAME hosts BEATS kick-off meeting

2019/03/212019/03/25

The kick-off meeting of the BEAmline for Tomography at SESAME (BEATS) project, was held in Allan, Jordan and hosted by SESAME on the 12th and 13th March 2019. BEATS is an EU funded project with the objective to design, procure, construct and commission a facility for hard X-ray full-field tomography at the SESAME synchrotron. The European grant is worth 6 million euros and will span a four-year period from beginning 2019 to end 2022 and is funded by the European Union’s Horizon 2020 research and innovation programme under grant agreement n°822535.

>Read more on the SESAME website

Tomography beamline at SESAME is officially launched

2019/01/092019/01/17

On 1st January 2019, the European Horizon 2020 project BEAmline for Tomography at SESAME (BEATS) was launched with the objective to design, procure, construct and commission a beamline for hard X-ray full-field tomography at the SESAME synchrotron in Jordan.

The European grant is worth 6 million euros and will span a four-year period from beginning 2019 to end 2022.
Led by the ESRF, the European synchrotron (France), BEATS involves leading research facilities in the Middle East (SESAME and the Cyprus Institute), and European synchrotron radiation facilities ALBA-CELLS (Spain), DESY (Germany), the ESRF (France), Elettra (Italy), INFN (Italy), PSI (Switzerland), SESAME (Jordan) and SOLARIS (Poland). The initiative is funded by the European Union’s Horizon 2020 research and innovation programme.

Nine partner institutes will join forces to lay the groundwork for the efficient and sustainable operation of the SESAME research infrastructure. Through the development and consolidation of the scientific case for a beamline for tomography, and actions to fortify the scientific community, the partners will pay particular attention to the R&D and technology needs of the SESAME Members. Built upon the OPEN SESAME project, BEATS will address the issue of sustainability of operation by preparing medium- to long-term funding scenarios for the tomography beamline and the facility.

The quest for better medical imaging at MAX IV

2018/11/102018/11/13

Advances in the world of physics often quickly lead to advances in the world of medical diagnostics. From the moment Wilhelm Röntgen discovered X-rays he was using them to look through his wife’s hand.

A lot of the physics principles at the foundation of MAX IV are also at the foundation of medical imaging technologies such as nuclear magnetic resonance imaging, x-ray computed tomography and positron emission tomography.
Positron emission spectroscopy is more commonly known as PET imaging. It’s a method used to study metabolic processes in the body as a research tool but also to diagnose disease. An important use today is in the diagnosis of metastases in cancer patients, but it can also be used to diagnose certain types of dementia.

In PET, a positron-emitting radionuclide is injected into a patient and travels around the body until it accumulates somewhere, depending on the chemical composition. For example, the fluorine-18 radionuclide when bound to deoxyglucose accumulates in metabolically active cells which is useful for finding metastases. The radionuclide is unstable and emits positrons which is the antimatter equivalent of an electron. When a positron and an electron inevitably meet, they annihilate one another, producing two pulses of gamma radiation traveling in opposite directions. By placing a detector around a patient, it is possible to measure the gamma radiation and convert the signal into something that can be more easily measured. These detectors are made up of materials known as scintillators which take high energy radiation and emit lower energy radiation that can be detected using fast photodetectors – photomultiplier tubes.

A guide to central nervous system tomography

2018/10/122018/10/19

In-depth investigations on I13 to optimise soft tissue synchrotron X-ray microtomography

The Bradbury Lab at King’s College London, headed by Professor Elizabeth Bradbury, investigates damage to the central nervous system (CNS), and how the body responds to it. The traditional way of investigating soft tissue samples such as those of the central nervous system is 2D histology, in which slices are taken, stained and imaged. However, this process has limitations – slice thickness has a lower limit and measurements within cut slices are subject to inaccuracies arising from mechanical processing distortions. The group sent PhD student (now Dr) Merrick Strotton to the Diamond-Manchester Imaging Branchline I13-2 to investigate whether X-ray microtomography (a nominally non-destructive technique for taking a series of 2D images and turning them into a 3D volume) could avoid these issues. It wasn’t clear how to achieve the best possible results, and so alongside the biomedical studies, Dr Strotton worked with Diamond’s Dr Andrew Bodey on a series of methodological investigations on how to optimise imaging for soft tissue samples, the first results of which have recently been published in Scientific Reports.

Image: Segmentation of the low thoracic-high lumbar (T13-L1) level spinal cord sample from background, white & grey matter from spinal cord and vasculature from spinal cord with SuRVoS.
Credit: https://www.nature.com/articles/s41598-018-30520-8#Sec10

Research on ancient teeth reveals complexity of human evolution

2018/10/092018/10/10

Fossil records enable a detailed reconstruction of our planet’s history and of the evolution of our species. In particular, teeth are a sort of biological archive that record in their structures (enamel, dentine and pulp chamber) the different phases of the human evolution. An international team of researchers led by Clément Zanolli from the Université Toulouse III Paul Sabatier (France) has characterized human dental remains from Fontana Ranuccio (Latium) and Visogliano (Friuli-Venezia Giulia), Italy through a comparative high-resolution endostructural analysis based on microfocus X-ray microtomography (mCT) scanning and detailed morphological analyses. We examined the shape and arrangement of tooth tissues (see Fig. 1) and compared them with teeth of other human species (see Fig. 2).

With an age of around 450,000 years before present, the analysed dental remains from the sites of Fontana Ranuccio, located 50 km south-east of Rome, and Visogliano, located 18 km north-west of Trieste, are part of a very short list of fossil human remains from Middle Pleistocene Europe and are among the oldest human remains on the Italian Peninsula.
From the data obtained through X-ray μ-CT measurements performed at the TomoLab station of Elettra and at the Multidisciplinary Laboratory of the ‘Abdus Salam’ International Centre for Theoretical Physics in Trieste (Italy), we found that the teeth of both sites share similarities with Neanderthals but they are distinct from modern humans. This study adds to an emerging picture of complex human evolution in Middle Pleistocene Eurasia. The investigated fossil teeth show that Neanderthal dental features had evolved by around 450,000 years ago.

Image: Volume rendering of the Fontana Ranuccio (FR1R and FR2) and Visogliano (Vis. 1-Vis. 6) tooth specimens. The enamel is represented in blue while the dentine in yellow. All specimens were imaged by X-ray μCT at the Tomolab station of Elettra and at the Multidisciplinary Laboratory of the ICTP.
Credit: doi: 10.1371/journal.pone.0189773

World record: Fastest 3D tomographic images at BESSY II

2018/08/082018/08/09

An HZB team has developed an ingenious precision rotary table at the EDDI beamline at BESSY II and combined it with particularly fast optics.

This enabled them to document the formation of pores in grains of metal during foaming processes at 25 tomographic images per second – a world record.

The quality of materials often depends on the manufacturing process. In casting and welding, for example, the rate at which melts solidify and the resulting microstructure of the alloy is important. With metallic foams as well, it depends on exactly how the foaming process takes place. To understand these processes fully requires fast sensing capability. The fastest 3D tomographic images to date have now been achieved at the BESSY II X-ray source operated by the Helmholtz-Zentrum Berlin.

Dr. Francisco Garcia-Moreno and his team have designed a turntable that rotates ultra-stably about its axis at a constant rotational speed. This really depends on the highest precision: Any tumbling around the rotation axis or even minimal deviations in the rotation speed would prevent the reliable calculation of the 3D tomography. While commercially available solutions costing several hundred thousand euros allow up to 20 tomographic images per second, the Berlin physicists were able to develop a significantly cheaper solution that is even faster. ”My two doctoral students at the Technische Universität Berlin produced the specimen holders themselves on the lathe”, says Garcia-Moreno, who not only enjoys working out solutions to tricky technical problems, but possesses a lot of craftsman skill himself as well. Additional components were produced in the HZB workshop. In addition, Garcia-Moreno and his colleague Dr. Catalina Jimenez had already developed specialized optics for the fast CMOS camera during the preliminary stages of this work that allows even for simultaneous diffraction. This makes it possible to record approximately 2000 projections per second, from which a total of 25 three-dimensional tomographic images can be created.

Image: Experimental setup is composed of a fast-rotation stage, an IR heating lamp (temperature up to 800 °C), a BN crucible transparent to X-rays, a 200-μm thick LuAG:Ce scintillator, a white-beam optical system, and a PCO Dimax CMOS camera. The incident (red) and transmitted (green) X-ray beams as well as the light path from the scintillator to the camera (blue) are shown.
Credit: HZB