Three-Dimensional Correlative Imaging of a Malaria-Infected Cell with a Hard X-ray Nanoprobe.

Benefiting from the recent advances of synchrotron X-ray nanoprobes, we demonstrate three-dimensional (3D) correlative nanoimaging on malaria-infected human red blood cells. By combining X-ray fluorescence tomography and phase contrast nanotomography on the same cell with sub-100 nm pixel size, we establish a routine workflow from the data acquisition, data processing, to tomographic reconstruction. We quantitatively compare the elemental volumes obtained with different reconstruction methods, with the total variation minimization giving the most satisfactory results. We reveal elemental correlations in different cell compartments more reliably on reconstructions as opposed to 2D projections. Finally, we determine for the first time the 3D mass fraction maps of multiple elements at the subcellular level. The estimated total number of Fe atoms and the total mass of red blood cells show very good agreement with previously reported values.

3D high resolution imaging for microelectronics: A multi-technique survey on copper pillars.

In microelectronics, recently developed 3D integration offers the possibility to stack the dice or wafers vertically instead of putting their different parts next to one another, in order to save space. As this method becomes of greater interest, the need for 3D imaging techniques becomes higher. We here report a study about different 3D characterization techniques applied to copper pillars, which are used to stack different dice together. Destructive techniques such as FIB/SEM, FIB/FIB, and PFIB/PFIB slice and view protocols have been assessed, as well as non-destructive ones, such as laboratory-based and synchrotron-based computed tomographies. A comparison of those techniques in the specific case of copper pillars is given, taking into account the constraints linked to the microelectronics industry, mainly concerning resolution and sample throughput. Laboratory-based imaging techniques are shown to be relevant in the case of punctual analyses, while synchrotron based tomographies offer highly resolved volumes for larger batches of samples.

Registration of phase-contrast images in propagation-based X-ray phase tomography.

X-ray phase tomography aims at reconstructing the 3D electron density distribution of an object. It offers enhanced sensitivity compared to attenuation-based X-ray absorption tomography. In propagation-based methods, phase contrast is achieved by letting the beam propagate after interaction with the object. The phase shift is then retrieved at each projection angle, and subsequently used in tomographic reconstruction to obtain the refractive index decrement distribution, which is proportional to the electron density. Accurate phase retrieval is achieved by combining images at different propagation distances. For reconstructions of good quality, the phase-contrast images recorded at different distances need to be accurately aligned. In this work, we characterise the artefacts related to misalignment of the phase-contrast images, and investigate the use of different registration algorithms for aligning in-line phase-contrast images. The characterisation of artefacts is done by a simulation study and comparison with experimental data. Loss in resolution due to vibrations is found to be comparable to attenuation-based computed tomography. Further, it is shown that registration of phase-contrast images is nontrivial due to the difference in contrast between the different images, and the often periodical artefacts present in the phase-contrast images if multilayer X-ray optics are used. To address this, we compared two registration algorithms for aligning phase-contrast images acquired by magnified X-ray nanotomography: one based on cross-correlation and one based on mutual information. We found that the mutual information-based registration algorithm was more robust than a correlation-based method.

Thermally reversible nanoparticle gels with tuneable porosity showing structural colour.

We present colloidal gels formed from dispersions of PEG- and PEG+DNA-coated silica nanoparticles showing structural colour. The PEG- and PEG+DNA-coated silica colloids are functionalized using exclusively covalent bonds in aqueous conditions. Both sets of colloids self-assemble into thermally-reversible colloidal gels with porosity that can be tuned by changing the colloid volume fraction, although the interaction potentials of the colloids in the two systems are different. Confocal microscopy and image analysis tools are used to characteraize the gels' microstructures. Optical reflection spectroscopy is employed to study the underlying gel nanostructure and to characterize the optical response of the gels. X-ray nanotomography is used to visualize the nanoscale phase separation between the colloid-rich gel branches and the colloid-free gel pores. These nanoparticle gels open new routes for creating structural colour where the gel structure is decoupled from the form factor of the individual colloids. This approach can be extended to create unexplored three dimensional macroscale materials with length scales spanning hundreds of nanometers, which has been difficult to achieve using other methods.

X-Ray Phase Contrast Tomography Reveals Early Vascular Alterations and Neuronal Loss in a Multiple Sclerosis Model.

The degenerative effects of multiple sclerosis at the level of the vascular and neuronal networks in the central nervous system are currently the object of intensive investigation. Preclinical studies have demonstrated the efficacy of mesenchymal stem cell (MSC) therapy in experimental autoimmune encephalomyelitis (EAE), the animal model for multiple sclerosis, but the neuropathology of specific lesions in EAE and the effects of MSC treatment are under debate. Because conventional imaging techniques entail protocols that alter the tissues, limiting the reliability of the results, we have used non-invasive X-ray phase-contrast tomography to obtain an unprecedented direct 3D characterization of EAE lesions at micro-to-nano scales, with simultaneous imaging of the vascular and neuronal networks. We reveal EAE-mediated alterations down to the capillary network. Our findings shed light on how the disease and MSC treatment affect the tissues, and promote X-ray phase-contrast tomography as a powerful tool for studying neurovascular diseases and monitoring advanced therapies.

Biochemistry of malaria parasite infected red blood cells by X-ray microscopy.

Red blood cells infected by the malaria parasite Plasmodium falciparum are correlatively imaged by tomography using soft X-rays as well as by scanning hard nano-X-ray beam to obtain fluorescence maps of various elements such as S and Fe. In this way one can deduce the amount of Fe bound either in hemoglobin or in hemozoin crystals in the digestive vacuole of the malaria parasite as well as determine the hemoglobin concentrations in the cytosols of the red blood cell and of the parasite. Fluorescence map of K shows that in the parasite's schizont stage the K concentration in the red blood cell cytosol is diminished by a factor of seven relative to a pristine red blood cell but the total amount of K in the infected red blood cell is the same as in the pristine red blood cell.

Holographic imaging with a hard x-ray nanoprobe: ptychographic versus conventional phase retrieval.

We have performed near-field x-ray imaging with simultaneous object and probe reconstruction. By an advanced ptychographic algorithm based on longitudinal and lateral translations, full-field images of nanoscale objects are reconstructed with quantitative contrast values, along with the extended wavefronts used to illuminate the objects. The imaging scheme makes idealizing assumptions on the probe obsolete, and efficiently disentangles phase shifts related to the object from the imperfections in the illumination. We validate this approach by comparison to the conventional reconstruction scheme without simultaneous probe retrieval, based on the contrast transfer function algorithm. To this end, a set of semiconductor nanowires with controlled chemical composition (InP core, insulating SiO2 layer, and indium tin oxide cover) is imaged using the quasi-point source illumination realized by the hard x-ray nanofocus (26 nm×39 nm spot size) of the ID16A Nano-Imaging beamline at the European Synchrotron Radiation Facility.

Myelinated mouse nerves studied by X-ray phase contrast zoom tomography.

We have used X-ray phase contrast tomography to resolve the structure of uncut, entire myelinated optic, saphenous and sciatic mouse nerves. Intrinsic electron density contrast suffices to identify axonal structures. Specific myelin labeling by an osmium tetroxide stain enables distinction between axon and surrounding myelin sheath. Utilization of spherical wave illumination enables zooming capabilities which enable imaging of entire sciatic internodes as well as identification of sub-structures such as nodes of Ranvier and Schmidt-Lanterman incisures.

Trace element landscape of resting and activated human neutrophils on the sub-micrometer level.

Every infection is a battle for trace elements. Neutrophils migrate first to the infection site and accumulate quickly to high numbers. They fight pathogens by phagocytosis and intracellular toxication. Additionally, neutrophils form neutrophil extracellular traps (NETs) to inhibit extracellular microbes. Yet, neutrophil trace element characteristics are largely unexplored. We investigated unstimulated and phorbol myristate acetate-stimulated neutrophils using synchrotron radiation X-ray fluorescence (SR-XRF) on the sub-micron spatial resolution level. PMA activates pinocytosis, cytoskeletal rearrangements and the release of NETs, all mechanisms deployed by neutrophils to combat infection. By analyzing Zn, Fe, Cu, Mn, P, S, and Ca, not only the nucleus but also vesicular granules were identifiable in the elemental maps. Inductively Coupled Plasma Mass Spectrometry (ICP-MS) revealed a neutrophil-specific composition of Zn, Fe, Cu, and Mn in comparison with J774 and HeLa cells, indicating a neutrophil-specific metallome complying with their designated functions. When investigating PMA-activated neutrophils, the SR-XRF analysis depicted typical subcellular morphological changes: the transformation of nucleus and granules and the emergence of void vacuoles. Mature NETs were evenly composed of Fe, P, S, and Ca with occasional hot spots containing Zn, Fe, and Ca. An ICP-MS-based quantification of NET supernatants revealed a NETosis-induced decrease of soluble Zn, whereas Fe, Cu, and Mn concentrations were only slightly affected. In summary, we present a combination of SR-XRF and ICP-MS as a powerful tool to analyze trace elements in human neutrophils. The approach will be applicable and valuable to numerous aspects of nutritional immunity.

Reconstruction of wave front and object for inline holography from a set of detection planes.

We illustrate the errors inherent in the conventional empty beam correction of full field X-ray propagation imaging, i.e. the division of intensities in the detection plane measured with an object in the beam by the intensity pattern measured without the object, i.e. the empty beam intensity pattern. The error of this conventional approximation is controlled by the ratio of the source size to the smallest feature in the object, as is shown by numerical simulation. In a second step, we investigate how to overcome the flawed empty beam division by simultaneous reconstruction of the probing wavefront (probe) and of the object, based on measurements in several detection planes (multi-projection approach). The algorithmic scheme is demonstrated numerically and experimentally, using the defocus wavefront of the hard X-ray nanoprobe setup at the European Synchrotron Radiation Facility (ESRF).

Determination of elemental distribution in green micro-algae using synchrotron radiation nano X-ray fluorescence (SR-nXRF) and electron microscopy techniques--subcellular localization and quantitative imaging of silver and cobalt uptake by Coccomyxa actinabiotis.

The newly discovered unicellular micro-alga Coccomyxa actinabiotis proves to be highly radio-tolerant and strongly concentrates radionuclides, as well as large amounts of toxic metals. This study helps in the understanding of the mechanisms involved in the accumulation and detoxification of silver and cobalt. Elemental distribution inside Coccomyxa actinabiotis cells was determined using synchrotron nano X-ray fluorescence spectroscopy at the ID22 nano fluorescence imaging beamline of the European Synchrotron Radiation Facility. The high resolution and high sensitivity of this technique enabled the assessment of elemental associations and exclusions in subcellular micro-algae compartments. A quantitative treatment of the scans was implemented to yield absolute concentrations of each endogenous and exogenous element with a spatial resolution of 100 nm and compared to the macroscopic content in cobalt and silver determined using inductively coupled plasma-mass spectrometry. The nano X-ray fluorescence imaging was complemented by transmission electron microscopy coupled to X-ray microanalysis (TEM-EDS), yielding differential silver distribution in the cell wall, cytosol, nucleus, chloroplast and mitochondria with unique resolution. The analysis of endogenous elements in control cells revealed that iron had a unique distribution; zinc, potassium, manganese, molybdenum, and phosphate had their maxima co-localized in the same area; and sulfur, copper and chlorine were almost homogeneously distributed among the whole cell. The subcellular distribution and quantification of cobalt and silver in micro-alga, assessed after controlled exposure to various concentrations, revealed that exogenous metals were mainly sequestered inside the cell rather than on mucilage or the cell wall, with preferential compartmentalization. Cobalt was homogeneously distributed outside of the chloroplast. Silver was localized in the cytosol at low concentration and in the whole cell excluding the nucleus at high concentration. Exposure to low concentrations of cobalt or silver did not alter the localization nor the concentration of endogenous elements within the cells. To our knowledge, this is the first report on element co-localization and segregation at the sub-cellular level in micro-algae by means of synchrotron nano X-ray fluorescence spectroscopy.

Effect of solution heat treatment on the internal architecture and compressive strength of an AlMg4.7Si8 alloy.

The evolution of the microstructure of an AlMg4.7Si8 alloy is investigated by scanning electron microscopy and ex situ synchrotron tomography in as-cast condition and subsequent solution treatments for 1 h and 25 h at 540 °C, respectively. The eutectic Mg2Si phase, which presents a highly interconnected structure in the as-cast condition, undergoes significant morphological changes during the solution heat treatment. Statistical analyses of the particle distribution, the sphericity, the mean curvatures and Gaussian curvatures describe the disintegration of the interconnected seaweed-like structure followed by the rounding of the disintegrated fractions of the eutectic branches quantitatively. The ternary eutectic Si resulting from the Si-surplus to the stoichiometric Mg2Si ratio of the alloy undergoes similar changes. The morphological evolution during solution heat treatment is correlated with results of elevated temperature compression tests at 300 °C. The elevated temperature compressive strength is more sensitive to the degree of interconnectivity of the three dimensional Mg2Si network than to the shape of the individual particles.

Hard X-ray nanoprobe investigations of the subtissue metal distributions within Daphnia magna.

The unique potential of nanoscale elemental imaging of major/minor and trace-level elemental distributions within thin biological tissue sections of the ecotoxicological model organism Daphnia magna is demonstrated by synchrotron radiation nano-X-ray fluorescence (nano-XRF). The applied highly specialized sample preparation method, coupled with the high spatial resolution (∼180 nm) and high X-ray photon flux (6 × 10(11) photons/s) available at the European Synchrotron Radiation Facility (ESRF) ID22NI beamline proved to be critical for the high-quality visualization of (trace-)metal distributions on the submicron level within the target structures of interest. These include the branchial sacs on the thoracic appendages (epipodites) of D. magna, which are osmoregulatory regions where ion exchange occurs. For the main element of interest (Zn), detection limits of 0.7 ppm (3 ag) was reached in fast-scanning mode using an acquisition time of 0.3 s/pixel. As demonstrated, synchrotron radiation nano-XRF revealed the elemental distributions of Ca, Fe, and Zn within this osmoregulatory region on the submicron scale, aiding the exploration of possible detoxification mechanisms of Zn within D. magna at the subtissue level.

Sub-micrometre holotomographic characterisation of the effects of solution heat treatment on an AlMg7.3Si3.5 alloy.

A strip cast AlMg7.3Si3.5 alloy is investigated by sub-micrometre holotomographic analysis achieving a voxel size of (60 nm)3 by cone beam magnification of the focused synchrotron beam using Kirkpatrick-Baez mirrors. The three-dimensional microstructure of the same specimen volume in the as-cast state is compared with that after exposure to 540 °C for 30 min resolving microstructural features down to 180 nm. The three-dimensional analysis of the architecture of the eutectic Mg2Si and the Fe-aluminides reveals how the as-cast microstructure changes during the solution treatment. The alloy in the as-cast condition contains a highly interconnected seaweed-like Mg2Si eutectic. The level of three-dimensional interconnectivity of the Mg2Si eutectic phase decreases by only partial disintegration during the heat treatment correcting the two-dimensional metallographic impression of isolated round particles. Statistical analyses of the particle distribution, sphericity, mean curvatures and Gaussian curvatures describe quantitatively the architectural changes of the Mg2Si phase. This explains the decrease of the high temperature strength of the alloy by the solution treatment tested in hot compression.

Biomedical applications of the ESRF synchrotron-based microspectroscopy platform.

Very little is known about the sub-cellular distribution of metal ions in cells. Some metals such as zinc, copper and iron are essential and play an important role in the cell metabolism. Dysfunctions in this delicate housekeeping may be at the origin of major diseases. There is also a prevalent use of metals in a wide range of diagnostic agents and drugs for the diagnosis or treatment of a variety of disorders. This is becoming more and more of a concern in the field of nanomedicine with the increasing development and use of nanoparticles, which are suspected of causing adverse effects on cells and organ tissues. Synchrotron-based X-ray and Fourier-transformed infrared microspectroscopies are developing into well-suited sub-micrometer analytical tools for addressing new problems when studying the role of metals in biology. As a complementary tool to optical and electron microscopes, developments and studies have demonstrated the unique capabilities of multi-keV microscopy: namely, an ultra-low detection limit, large penetration depth, chemical sensitivity and three-dimensional imaging capabilities. More recently, the capabilities have been extended towards sub-100nm lateral resolutions, thus enabling sub-cellular chemical imaging. Possibilities offered by these techniques in the biomedical field are described through examples of applications performed at the ESRF synchrotron-based microspectroscopy platform (ID21 and ID22 beamlines).

Monoclinic phase transformations of zirconia-based dental prostheses, induced by clinically practised surface manipulations.

Full-ceramic zirconia crowns and bridges have become very popular with dentists and patients because of their excellent esthetics and mechanical properties. We studied phase transformations within the outermost surface layer of 3 mol.% yttria-stabilized zirconia (Y-TZP) samples of small, clinically relevant thicknesses, manipulated by polishing, grinding and fracture as might be encountered in everyday clinical practice. Stress-induced transformations of the tetragonal phase were studied in three dimensions in order to better understand the organization and extent of the monoclinically transformed phase. By means of laboratory- and synchrotron-based X-ray diffraction measurements, coupled with electron microscopy and multimodal tomography, it was possible for the first time to visualize and quantify the phase distributions non-destructively and in three dimensions. Highly variable degrees of local transformation result in ragged transformed zones of very inhomogeneous thickness. The overall thickness of the transformation layers strongly depends on the severity and rate of loading. Gentle diamond cutting resulted in surprisingly low transformation ratios of less than 0.1%. When Y-TZP constructions are manipulated before bonding, toughness of the outer layers is reduced and they may become brittle with important implications for the stability of the bond: dental practitioners thus need to be cautious when altering the surfaces of these materials after sintering.

Regularized phase tomography enables study of mineralized and unmineralized tissue in porous bone scaffold.

Regularized phase tomography was used to image non-calcified fibrous matrix in in vitro cell-cultivated porous bone scaffold samples. 3D micro-architecture of bone and bone scaffold has previously been studied by micro-computed tomography, synchrotron radiation (SR) micro-computed tomography and microdiffraction. However, neither of these techniques can resolve the low-calcified immature pre-bone fibrous structures. Skelite porous scaffold discs were seeded with osteoblasts, a combination of osteoblast and pre-osteoclasts and, as controls, with pre-osteoclasts only, and then cultivated for 8 weeks. They were subsequently imaged using SR propagation-based phase contrast imaging. Reconstructions using a regularized holographic phase tomography approach were compared to standard (absorption) SR micro-computed tomography, which show that quantitative analysis, such as volume and thickness measurements, of both the calcified fraction and the immature bone matrix in the reconstructed volumes is enabled. Indications of the effect of this type of culture on Skelite, such as change in mineralization and deposit of mature bone on the walls of the scaffold, are found. The results are verified with a histological study.

Comparative study of multilayers used in monochromators for synchrotron-based coherent hard X-ray imaging.

A systematic study is presented in which multilayers of different composition (W/Si, Mo/Si, Pd/B(4)C), periodicity (from 2.5 to 5.5 nm) and number of layers have been characterized. In particular, the intrinsic quality (roughness and reflectivity) as well as the performance (homogeneity and coherence of the outgoing beam) as a monochromator for synchrotron radiation hard X-ray micro-imaging are investigated. The results indicate that the material composition is the dominating factor for the performance. By helping scientists and engineers specify the design parameters of multilayer monochromators, these results can contribute to a better exploitation of the advantages of multilayer monochromators over crystal-based devices; i.e. larger spectral bandwidth and high photon flux density, which are particularly useful for synchrotron-based micro-radiography and -tomography.

Study on the impregnation of archaeological waterlogged wood with consolidation treatments using synchrotron radiation microtomography.

In favourable conditions of low temperature and low oxygen concentration, archaeological waterlogged wooden artefacts, such as shipwrecks, can survive with a good state of preservation. Nevertheless, anaerobic bacteria can considerably degrade waterlogged wooden objects with a significant loss in polysaccharidic components. Due to these decay processes, wood porosity and water content increase under ageing. In such conditions, the conservation treatments of archaeological wooden artefacts often involve the replacement of water with substances which fill the cavities and help to prevent collapse and stress during drying. The treatments are very often expensive and technically difficult, and their effectiveness very much depends on the chemical and physical characteristics of the substances used for impregnation. Also important are the degree of cavity-filling, penetration depth and distribution in the structure of the wood. In this study, the distribution in wood cavities of some mixtures based on polyethylene glycols and colophony, used for the conservation of waterlogged archaeological wood, was investigated using synchrotron radiation X-ray computed microtomography (SR-microCT). This non-destructive imaging technique was useful for the study of the degraded waterlogged wood and enabled us to visualise the morphology of the wood and the distribution of the materials used in the wood treatments. The study has shown how deposition is strictly related to the dimension of the wooden cavities. The work is currently proceeding with the comparison of synchrotron observations with the data of the solutions viscosity and with those of the properties imparted to the wood by the treatments.

Region-of-interest tomography for grating-based X-ray differential phase-contrast imaging.

We report numerical and experimental results demonstrating accurate region-of-interest computed tomography (CT) reconstruction based on differential phase-contrast projection (DPC) images. The approach removes the constraint of covering the entire sample within the field of view of the image detector. Particularly for biomedical applications, the presented DPC-CT region-of-interest approach will allow for the visualization of previously inaccessible details deep inside an entire animal or organ. We envisage that this development will also be of interest for potential future clinical applications, because grating-based DPC-CT can be implemented with standard x-ray tube sources.