Table of contents

Preface

On behalf of the Program Committee I would like to thank all the participants of the 13th International X-ray Microscopy Conference, XRM2016, for their contributions. The conference was hosted by the Diamond Light Source and took place in the nearby historic city of Oxford, United Kingdom from the 15th to the19th August, 2016. The goal of this biennial conference is to address the most recent advances in X-ray microscopy by bringing together experts in the development and the application of X-ray microscopes. The conference also explored the position of X-ray microscopy alongside related techniques and disciplines.

The present proceedings contain over 60 contributions, providing a representative selection of the conference content. Overall there were more than 380 participants in this conference, with a total of 72 oral presentations and 250 posters contributed. In addition we had three sessions of early career flash talks, which were well received. The manuscripts submitted for these proceedings were reviewed by a large team of referees. I thank them for their rapid and thorough work on the manuscripts as well as the authors for their contributions.

The conference contained ten different topics. They are categorized into four groups here for a better overview:

- Bio-imaging, Multi-modal imaging, Environmental and geosciences

- Elemental contrast and chemistry, Energy and materials

- Diffraction imaging

- New sources and facilities, Novel techniques & applications, Optics, detectors and instrumentation, Data processing.

Following the tradition of the XRM conference series, the Werner Meyer-Ilse Memorial Award (WIMA) rewards young scientists for exceptional contributions to the advancement of X-ray microscopy. The WIMA committee awarded the prize to Junjing Deng (Northwestern University, USA) and Matias Kagias (ETH Zurich / PSI, Switzerland). The winners for the poster prizes, who presented their work during the early career flash talk sessions, were Burcu Kepsutlu (Helmholtz Zentrum Berlin, Germany) Simone Sala (UCL London, UK) and Ottó Márkus (KIT Karlsruhe, Germany).

One highlight of the conference was the honoring of Janos Kirz and Günther Schmahl for their outstanding contributions and leadership over the years and especially for the conference series. We all remember the song composed by Chris Jacobsen that we sang together during the Wednesday special event presentation.

Multiple sponsors had kindly contributed to the conference. I would like to acknowledge the following sponsors: Zeiss (conference dinner and conference AV); Silson (delegate giveaway); Bruker micro CT (literature package); Dectris Ltd (lanyards); and in alphabetic order: Applied Nanotools; Axilion; Axo Dresden/Huber Diffraction; Excillum AB; Hamamatsu Photonics; Lyncean Technologies Inc.; Norcada Inc; NTT Advanced Technology Corporation; PI miCos; Quantum Detectors; Queensgate; Rigaku; SGX Sensortech; Suna-Precision GmbH; Toyama Co. Ltd; XIA. Many of these sponsors provided exhibits during the conference offering the latest X-ray microscopy related products.

Finally I would like to express my gratitude to all those who have contributed to XRM2016: the International Advisory Committee and the local Scientific Programme Committee for their support and advice, all the speakers for preparing and presenting inspiring talks and, last but by no means least, the Local Organising Committee for its enthusiastic efforts that have turned this conference into reality.

I acknowledge my co-chairs, Liz Duke and Burkhard Kaulich, and our former Physical Sciences Director, Trevor Rayment, for the numerous and helpful discussions regarding the content and details of the conference. My special thanks go to Emma Clarke for her relentless work and effort. The support of the Diamond helpers and the communications team are also acknowledged.

It has been a great honour to host the XRM2016 conference and we hope that all the participants have found the conference to be enjoyable and rewarding. We look forward to seeing you all at XRM2018 in Saskatoon, Canada.

Christoph Rau

Editor XRM2016 proceedings

Chair XRM2016 conference

All papers published in this volume of Journal of Physics: Conference Series have been peer reviewed through processes administered by the proceedings Editors. Reviews were conducted by expert referees to the professional and scientific standards expected of a proceedings journal published by IOP Publishing.

We present propagation-based phase-contrast tomography of mouse sciatic nerves stained with osmium, leading to an enhanced contrast in the myelin sheath around the axons, in order to visualize the threedimensional (3D) structure of the nerve. We compare different experimental parameters and show that contrast and resolution are high enough to identify single axons in the nerve, including characteristic functional structures such as Schmidt-Lanterman incisures.

Atherosclerosis refers to narrowing or blocking of blood vessels that can lead to a heart attack, chest pain or stroke. Constricted segments of diseased arteries exhibit considerably increased wall shear stress, compared to the healthy ones. One of the possibilities to improve patient's treatment is the application of nano-therapeutic approaches, based on shear stress sensitive nano-containers. In order to tailor the chemical composition and subsequent physical properties of such liposomes, one has to know precisely the morphology of critically stenosed arteries at micrometre resolution. It is often obtained by means of histology, which has the drawback of offering only two-dimensional information. Additionally, it requires the artery to be decalcified before sectioning, which might lead to deformations within the tissue. Micro computed tomography (μCT) enables the three-dimensional (3D) visualization of soft and hard tissues at micrometre level. μCT allows lumen segmentation that is crucial for subsequent flow simulation analysis. In this communication, tomographic images of a human coronary artery before and after decalcification are qualitatively and quantitatively compared. We analyse the cross section of the diseased human coronary artery before and after decalcification, and calculate the lumen area of both samples.

Molecular distribution in mammalian cells was studied by soft X-ray scanning transmission microscopy with respect to the quantitative aspect of analysis. NEXAFS profiles at the C, N and O K-absorption edges were combined and used for the analysis. For the estimation of quantity for nucleic acids and proteins, NEXAFS profiles of DNA and bovine serum albumin (BSA) at the N K-absorption edge were applied assuming that those were their representatives. The method has a potential to explore the other molecular components than nucleic acids and proteins.

Volumetric datasets with micrometer spatial and sub-second temporal resolutions are nowadays routinely acquired using synchrotron X-ray tomographic microscopy (SRXTM). Although SRXTM technology allows the examination of multiple samples with short scan times, many specimens are larger than the field-of-view (FOV) provided by the detector. The extension of the FOV in the direction perpendicular to the rotation axis remains non-trivial. We present a method that can efficiently increase the FOV merging volumetric datasets obtained by region-of-interest tomographies in different 3D positions of the sample with a minimal amount of artefacts and with the ability to handle large amounts of data. The method has been successfully applied for the three-dimensional imaging of a small number of mouse lung acini of intact animals, where pixel sizes down to the micrometer range and short exposure times are required.

Vegetative cells and heterocysts in the filamentous cyanobacterium Anabaena sp. PCC 7120 were observed by soft X-ray microscopy. Carbon-to-nitrogen (C/N) ratio of each cell was estimated by the difference of the absorbance of the images below and above the nitrogen K-edge absorption. It was revealed that the C/N ratios in vegetative cells and heterocysts are 4.54 and 2.46, respectively.

The acinus represents the functional unit of the mammalian lung. It is defined as the small tree of gas-exchanging airways, which is fed by the most distal purely conducting airway. Different hypotheses exist on how the fine structure of the acinus changes during ventilation and development. Since in classical 2-dimensional (2D) sections of the lung the borders of the acini are not detectable, every study of acini requires 3-dimensional (3D) datasets. As a basis for further studies of pulmonary acini we imaged rodent lungs as close to life as possible using phase contrast synchrotron radiation-based X-ray tomographic microscopy (SRXTM), and developed a protocol for the segmentation of the alveolar septa. The method is based on a combined multilevel filtering approach. Seeds are automatically defined for separate regions of tissue and airspace during each 2D filtering level and then given as input to a 3D random walk segmentation. Thus, the different types of artifacts present in the images are treated separately, taking into account the sample's structural complexity. The proposed procedure yields high-quality 3D segmentations of acinar microstructure that can be used for a reliable morphological analysis.

The presented scanning transmission x-ray microscope (STXM), build on top of our existing modular platform (FlexIX) for high resolution imaging experiments, allows versatile investigations of different samples. The FlexIX endstation allows to switch between a Full Field and a STXM mode. For the STXM mode we use a spatialy resolved detector together with an energy dispersive detector, this allows to investigate the morphology and the chemical or elemental distribution of the sample simultaneous. The combination of the nanoscopy endstation and the XUV beamline P04 results in a powerful tool for investigations of life science samples.

X-ray fluorescence microscopy (XRFM) is a powerful technique to detect and localize elements in cells. To derive information useful for biology and medicine, it is essential not only to localize, but also to map quantitatively the element concentration. Here we applied quantitative XRFM to iron in phagocytic cells. Iron, a primary component of living cells, can become toxic when present in excess. In human fluids, free iron is maintained at 10^-18 M concentration thanks to iron binding proteins as lactoferrin (Lf). The iron homeostasis, involving the physiological ratio of iron between tissues/secretions and blood, is strictly regulated by ferroportin, the sole protein able to export iron from cells to blood. Inflammatory processes induced by lipopolysaccharide (LPS) or bacterial pathoge inhibit ferroportin synthesis in epithelial and phagocytic cells thus hindering iron export, increasing intracellular iron and bacterial multiplication. In this respect, Lf is emerging as an important regulator of both iron and inflammatory homeostasis. Here we studied phagocytic cells inflamed by bacterial LPS and untreated or treated with milk derived bovine Lf. Quantitative mapping of iron concentration and mass fraction at high spatial resolution is obtained combining X-ray fluorescence microscopy, atomic force microscopy and synchrotron phase contrast imaging.

Fine structures of bio-specimens obtained by soft X-ray (SX) imaging are clearer compared with those obtained by visible imaging owing to the difference in extinction coefficients between the two wavelength regions. However, it is difficult to identify the fine structure imaged in the 2.3 – 4.5 nm wavelength region by appearance alone. Here, we obtain and compare SX and fluorescence images of Leydig cells of a mouse testis loaded with fluorophores. Identification of the fine structures in the SX image is carried out by comparison with the fluorescence images with the use of principal component analysis (PCA). The result shows that the common structures between the SX- and the fluorescence- images.

Microstructures of unprocessed filamentous cyanobacterium, Pseudanabaena foetida sp., producing a musty smell were observed using soft X-ray microscopy. Carbon-enriched structures and granules as well as oxygen-enriched granules which have been already reported were observed. Except for early log growth phase, the oxygen-enriched granules were observed. However, the carbon-enriched structures were observed throughout log growth phase. The result suggests there is a relationship between the oxygen-enriched granules and 2-methylisoborneol (2-MIB) productivity, since the 2-MIB productivity of each cell is increased depending on the culture period in log growth phase.

We have used STXM and PEEM to reveal the underpinning chemistry and nanoscale structure behind palaeo-climate geochemical signatures, such as trace Mg in shells- proposed proxies for palaeo-ocean temperature. This has allowed us to test the chemical assumptions and mechanisms underpinning the use of such empirical proxies. We have determined the control on driving chemical variations in biogenic carbonates using STXM at the absorption edge of Mg, B, and Na in the shells of modern plankton. The power of these observations lies in their ability to link changes in chemistry, microstructure, and growth process in biogenic carbonate to environmental influences. We have seen that such changes occur at length scales of tens of nanometres and demonstrated that STXM provides an invaluable route to understanding chemical environment and key heterogeneity at the appropriate length scale. This new understanding provides new routes for future measurements of past climate variation in the sea floor fossil record.

We present a series of soft sediment geological phantoms constructed to simulate volcanic ash deposits preserved within sediment cores. This study aimed to systematically discern which sediment components are most effectively detected and therefore characterised by X-ray microCT (μCT). Samples with low or overlapping attenuation contrast but distinct morphologies such as coarse grained (>125 μm) ash within fine mud (<4 μm) can be manually separated using analysis software, while samples with high attenuation contrast display distinct horizons that are easily segmented using attenuation thresholds. We anticipate that this work will have broader applications within Earth Science to optimise the exploration of sediment with μCT analysis.

Using a microfocus X-ray tube and pixelated energy-resolving detector it is possible to measure the X-ray absorption spectrum of a material with high spatial resolution. Given sufficient energy resolution in the detector it is possible to detect and identify absorption edges which are characteristic to individual chemical elements. Using computed tomography the three dimensional (3D) internal elemental chemistry of an object can be reconstructed. The application of spectroscopic X-ray tomography is demonstrated by mapping distribution of heavy elements inside a mineralised ore sample. We correlate and validate this data with high resolution X-ray tomography and energy-dispersive X-ray spectroscopy data.

Magnetic iron oxide nanoparticle clusters (mnpc) coated with organic stabilizers were investigated using scanning transmission x-ray microscopy (STXM). Simultaneous surface and bulk sensitive Fe L₃ edge absorption spectra, obtained using a photomultiplier tube and a channeltron, were used to detect subtle changes in the oxidation state in the surface and bulk of Iron Oxide mnpc. The effectiveness of this mode of STXM operation is demonstrated for these nanoparticle clusters.

Iron ore sinter constitutes the major component of the iron-bearing burden in blast furnaces, and its reduction mechanism is one of the keys to improving the productivity of ironmaking. Iron ore sinter is composed of multiple iron oxide phases and calcium ferrites (CFs), and their heterogeneous reduction was investigated in terms of changes in iron chemical state: Fe^III, Fe^II, and Fe⁰ were examined macroscopically by 2D X-ray absorption and microscopically by 3D transmission X-ray microscopy (TXM). It was shown that the reduction starts at iron oxide grains rather than at calcium ferrite (CF) grains, especially those located near micropores. The heterogeneous reduction causes crack formation and deteriorates the mechanical strength of the sinter. These results help us to understand the fundamental aspects of heterogeneous reduction schemes in iron ore sinter.

We characterize individual Ag-TCNQ nanocrystals during switching their resistivity state in operando. Raman and soft X-ray absorption microspectroscopy are employed to disclose the electronic state of the organic component in dependency of applied voltage. Whereas Raman microspectroscopy offers qualitative insight into the conversion of negatively charged TCNQ molecules to their neutral counterpart, quantification of the neutral fraction can be achieved using X-ray absorption spectroscopy. These results allow a detailed investigation of resistivity switching in electrically bistable Ag-TCNQ nanocrystals.

X-ray nano CT has been vastly applied to study the microstructure of solid oxide fuel cell (SOFC) electrodes. One widely accepted indicator of electrochemical performance is the triple phase boundary (TPB): a location where the three materials responsible for ionic, electronic and gas-phase reactant transport are in contact. X-ray absorption tomography has been used extensively in the characterisation of these TPBs, utilising the different attenuation properties of the constituent materials. Here we present a quantitative comparison of the attenuation properties for elements commonly employed in solid oxide fuel cell materials.

Porous support layers in electrochemical devices ensure mechanical stability of membrane assemblies such as solid oxide fuel cells and oxygen transport membranes (OTMs). At the same time, porous layers affect diffusive mass transport of gaseous reactants and contribute to performance losses at high fuel utilisation and conversion ratios. Microstructural characteristics are vital to calculate mass transport phenomena, where tortuosity remains notoriously difficult to determine. Here, the tortuosity of tubular porous support layers of OTMs is evaluated via high resolution X-ray nano computed tomography. The high resolution reveals the complex microstructure of the samples to then execute a selection of image-based tortuosity calculation algorithms. Visible differences between geometric and flux-based algorithms are observed and have thus to be applied with caution.

The ability to explore electronic structure and their role in determining material's macroscopic behaviour is essential to explain and engineer functions of material and device. Since its debut in 2004, graphene has attracted global research interest due to its unique properties. Chemical vapor deposition (CVD) has emerged as an important method for the massive preparation and production of graphene for various applications. Here by employing angle-resolved photoemission spectroscopy with nanoscale spatial resolution ∼ 100 nm (Nano-ARPES), we describe the approach to measure the electronic structure of polycrystalline graphene on copper foils, demonstrating the power of Nano-ARPES to detect the electronic structure of microscopic single crystalline domains, being fully compatible with conventional ARPES. Similar analysis could be employed to other microscopic materials

Gas transport properties are closely related to the tortuosity of the pore network within porous materials. For the first time, this study explores a multi-scale imaging and modelling method to measure the tortuosity of an Solid Oxide Fuel Cell (SOFC) electrode material with pore sizes spanning over hundreds of orders of magnitude. This analysis is normally challenging using image-based techniques, as pores of different sizes may not be easily resolved at the same time using X-ray computed tomography (CT). In this study, a tubular SOFC anode, fabricated by a phase inversion technique, is used to illustrate this approach. A heat flux analogy is used to simulate mass transport and the results show that the embedded large-scale finger-like pores can significantly improve mass transport by providing less tortuous pathways.

Nuclear graphite is used as a neutron moderator in fission power stations. To investigate the microstructural changes that occur during such use, it has been studied for the first time by X-ray microtomography with in situ heating and compression. This experiment was the first to involve simultaneous heating and mechanical loading of radioactive samples at Diamond Light Source, and represented the first study of radioactive materials at the Diamond-Manchester Imaging Branchline I13-2. Engineering methods and safety protocols were developed to ensure the safe containment of irradiated graphite as it was simultaneously compressed to 450N in a Deben 10kN Open-Frame Rig and heated to 300°C with dual focused infrared lamps. Central to safe containment was a double containment vessel which prevented escape of airborne particulates while enabling compression via a moveable ram and the transmission of infrared light to the sample. Temperature measurements were made in situ via thermocouple readout. During heating and compression, samples were simultaneously rotated and imaged with polychromatic X-rays. The resulting microtomograms are being studied via digital volume correlation to provide insights into how thermal expansion coefficients and microstructure are affected by irradiation history, load and heat. Such information will be key to improving the accuracy of graphite degradation models which inform safety margins at power stations.

We developed two types of in-situ three-dimensional imaging systems on the basis of full-field transmission X-ray computed tomography (XCT) methods for polymer electrolyte fuel cells (PEFCs) under operating conditions at beamline BL36XU at SPring-8. One was for a wide field of view (more than 500 μm) to obtain the whole membrane electrode assembly (MEA) images, and the other was for nano spatial resolution (less than 100 nm) using a Fresnel zone plate as objective optics. We succeeded in in-situ three-dimensional visualization of an MEA in PEFC using both XCT measurement systems and show preliminary results.

The sub-micron spatial distribution of chemical states of carbon fiber (CF) and the interface between CF and resin must affect physical properties of carbon-fiber-reinforced plastic (CFRP). In order to evaluate scanning transmission X-ray microscopy (STXM) techniques for application to the chemical-state analysis of CFRP, we performed STXM measurements near C K-edge energies. The results of the spectral deconvolution analysis suggest the presence of another phase at the interface of CF and resin, which may be a coating layer. In addition, the preferred orientation of the stuck of graphene sheets to the fiber axis direction of CF was observed by using linear polarized X-ray beams.

We present a study on the influence of different scan and reconstruction parameters on the image quality of the differential phase signals obtained from speckle-based X-ray phase-contrast imaging measurements in single-shot as well as 2D and 1D speckle-stepping modes. In particular, the effects of the analysis window size and the number of diffuser steps on the spatial resolution and signal sensitivity of images of a phantom sample are investigated and discussed. It is shown that the trade-off between spatial resolution, scan time and simplicity of the setup has to carefully be addressed for each specific experiment.

We present diffraction imaging results obtained from multiple near-field diffraction constraints. An iterative phase retrieval algorithm was implemented that uses data redundancy achieved by measuring near-field diffraction intensities at various sample-detector distances. The procedure allows for reconstructing the exit surface wave of a sample within a multiple constraint satisfaction framework neither making use of a priori knowledge as enforced in coherent diffraction imaging (CDI) nor exact scanning grid knowledge as required in ptychography. We also investigate the potential of the presented technique to deal with polychromatic radiation as important for potential application in diffraction imaging by means of tabletop EUV and X-ray sources.

Computed tomography reaches the best spatial resolution for the three-dimensional visualization of human tissues among the available nondestructive clinical imaging techniques. Nowadays, sub-millimeter voxel sizes are regularly obtained. Regarding investigations on true micrometer level, lab-based micro-CT (μCT) has become gold standard. The aim of the present study is firstly the hierarchical investigation of a human knee post mortem using hard X-ray μCT and secondly a multimodal imaging using absorption and phase contrast modes in order to investigate hard (bone) and soft (cartilage) tissues on the cellular level. After the visualization of the entire knee using a clinical CT, a hierarchical imaging study was performed using the lab-system nanotom® m. First, the entire knee was measured with a pixel length of 65 μm. The highest resolution with a pixel length of 3 μm could be achieved after extracting cylindrically shaped plugs from the femoral bones. For the visualization of the cartilage, grating-based phase contrast μCT (I13-2, Diamond Light Source) was performed. With an effective voxel size of 2.3 μm it was possible to visualize individual chondrocytes within the cartilage.

Ptychographic imaging with soft X-rays, especially in the water window energy range, suffers from limited detector dynamic range that directly influences the maximum spatial resolution achievable. High-dynamic-range data can be obtained by multiple exposures. By this approach we have increased the dynamic range of a ptychographic data set by a factor of 76 and obtained diffraction signal till the corners of the detector. The real space half period resolution was improved from 50 nm for the single exposure data to 18 nm for the high-dynamic-range data.

We present a new ptychographic x-ray microscope dedicated to soft x-ray tomography and spectromicroscopy of nano-materials at the Advanced Light Source. The microscope utilizes an ultra-stable, high performance scanning mechanism with laser interferometer feedback for sample positioning and a fast frame rate charge-coupled device detector for soft x-ray diffraction measurements. The microscope can achieve point scan rates of 120 Hz with 1 nm RMS positioning accuracy. A high performance data pipeline has been developed which enables real time ptychographic reconstructions and user-friendly operation. This instrument, called The Nanosurveyor, can achieve a spatial resolution at least 10 times finer than the x-ray spot size in both two and three dimensions with sensitivity to electronicand magnetic states of nano-materials. In this paper we demonstrate the tomographic and spectromicroscopic capability of the Nanosurveyor instrument. At high brightness x-ray sources this instrument will enable spectromicroscopy and tomography of materials with diffraction limited spatial resolution.

Perovskite materials that contain transition metal-oxides often exhibit multifunctional properties with considerable utility in a device setting. BiFeO₃ is a multiferroic perovskite material that exhibits room temperature anti-ferromagnetic and ferroelectric ordering. Optical excitation of BiFeO₃ crystals results in an elastic structural deformation of the lattice with a fast response on the pico-second time scale. Here we report on dynamic optical excitation coupled with Bragg coherent X-ray diffraction measurements to investigate the structural properties of BiFeO₃ nanoscale crystals. A continuous distortion of the diffraction speckle pattern was observed with increasing illumination. This was attributed to strain resulting from photo-induced lattice deformation.

There is a lack of the necessary methodology for three-dimensional (3D) investigation of soft tissues with cellular resolution without staining or tissue transformation. Synchrotron radiation based hard X-ray in-line phase contrast tomography using single-distance phase reconstruction (SDPR) provides high spatial resolution and density contrast for the visualization of individual cells using a standard specimen preparation and data reconstruction. In this study, we demonstrate the 3D characterization of a formalin-fixed paraffin-embedded (FFPE) human cerebellum specimen by SDPR at the Diamond-Manchester Imaging Branchline I13-2 (Diamond Light Source, UK) at pixel sizes down to 0.45 μm. The approach enables visualization of cerebellar layers (Stratum moleculare and Stratum granulosum), the 3D characterization of individual cells (Purkinje, stellate and granule cells) and can even resolve some subcellular structures (nucleus and nucleolus of Purkinje cells). The tomographic results are qualitatively compared to hematoxylin and eosin (H&E) stained histological sections. We demonstrate the potential benefits of hard X-ray microtomography for the investigations of biological tissues in comparison to conventional histology.

We describe the implementation and execution of ptychotomography at I13-1, the coherence branchline at Diamond Light Source. The data collection and image reconstruction protocol is demonstrated with the three dimensional reconstruction of a nanoporous gold sample.

We present some preliminary results from a study aimed at the characterization of the wavefront of X-ray free electron laser (XFEL) beams in the same operation conditions as for single particle imaging (or flash X-ray imaging) experiments. The varying illumination produced by wavefront fluctuations between several pulses leads to a partially coherent average beam which can be decomposed into several coherent modes using ptychographic reconstruction algorithms. Such a decomposition can give insight into pulse-to-pulse variations of the wavefront. We discuss data collected at the Linac Coherent Light Source (LCLS) and FERMI.

Ptychography is a diffraction-based X-ray microscopy method that can image extended samples quantitatively while remove the resolution limit imposed by image-forming optical elements. As a natural extension of scanning transmission X-ray microscopy (STXM) imaging method, we developed soft X-ray ptychographic coherent diffraction imaging (PCDI) method at the STXM endstation of BL08U beamline of Shanghai Synchrotron Radiation Facility. Compared to the traditional STXM imaging, the new PCDI method has resulted in significantly lower dose, higher resolution and higher efficiency imaging in our platform. In the demonstration experiments shown here, a spatial resolution of sub-10 nm was obtained for a gold nanowires sample, which is much better than the limit resolution 30 nm of the STXM method, while the radiation dose is only 1/12 of STXM.

Coherent diffractive imaging (CDI) has become a standard method on a variety of synchrotron beam lines. The high brilliance short wavelength radiation from these sources can be used to reconstruct attenuation and relative phase of a sample with nanometre resolution via CDI methods. However, the interaction between the sample and high energy ionising radiation can cause degradation to sample structure. We demonstrate, using a laboratory based high harmonic generation (HHG) based extreme ultraviolet (EUV) source, imaging a sample of hippocampal neurons using the ptychography method. The significant increase in contrast of the sample in the EUV light allows identification of damage induced from exposure to 7.3 keV photons, without causing any damage to the sample itself.

Phase-contrast imaging with x-rays is a developing field for imaging weakly absorbing materials. In this work, two phase-contrast imaging methods, grating- and speckle-based imaging, that measure the derivative of the phase shift, have been implemented with a laboratory source and compared experimentally. It was found that for the same dose conditions, the speckle-tracking differential phase-contrast images have considerably higher contrast-to-noise ratio than the grating-based images, but at the cost of lower resolution. Grating-based imaging performs better in terms of resolution, but would require longer exposure times, mainly due to absorption in the grating interferometer.

In recent years, efforts have been made on the information extraction method in x-ray grating-based phase contrast imaging. Among them, the reverse projection method proposed by P.P. Zhu in 2010 features as a fast, low-dose method to extract information without stepping the gratings. It enables to extend the phase contrast imaging system to the vivo studies. However, it has strict requirement on the system stability and the source stability. In this manuscript, an improved acquisition scheme has been proposed using a staggered grating making the reverse projection method more efficient with a lower requirement of the system and source stability.

ANATOMIX is a 200-m-long undulator beamline for full-field tomography techniques at photon energies from 5 to 25 keV. It is currently under construction at Synchrotron SOLEIL, the French national light source near Paris. ANATOMIX will feature experimental stations both for parallel-beam microtomography (with a beam of up to 40 mm width) and for zone-plate transmission X-ray microscopy (down to pixel sizes of 30 nm) in absorption and phase contrast. The location of ANATOMIX on a canted straight section of the SOLEIL storage ring implies specific challenges for the design and operation conditions of the beamline. In this paper we present general design aspects and the status of construction.

Users of the Diamond-Manchester Imaging Branchline I13-2 commonly spend many months analysing the large volumes of tomographic data generated in a single beamtime. This is due to the difficulties inherent in performing complicated, computationally-expensive analyses on large datasets with workstations of limited computing power. To improve productivity, a 'data beamline' was launched in January 2016. Users are scheduled for visits to the data beamline in the same way as for regular beamlines, with bookings made via the User Administration System and provision of financial support for travel and subsistence. Two high-performance graphics workstations were acquired, with sufficient RAM to enable simultaneous analysis of several tomographic volumes. Users are given high priority on Diamond's central computing cluster for the duration of their visit, and if necessary, archived data are restored to a high-performance disk array. Within the first six months of operation, thirteen user visits were made, lasting an average of 4.5 days each. The I13-2 data beamline was the first to be launched at Diamond Light Source and, to the authors' knowledge, the first to be formalised in this way at any synchrotron.

ANTARES beamline (BL), operating at very low photon energies, is a new soft X-ray scanning microscope recently built at SOLEIL Synchrotron, that offers a spectroscopic non-destructive nano-probe to study advanced materials. It combines a set of Fresnel Zone Plates (FZP) able to focalize the beam spot up to a few tenths of nanometres with a stable and precise sample nanopositioning (<1 nm). High energy-, angular- and spatial- resolution allow accurate electronic and chemical imaging combining angle-resolved photoelectron spectroscopy (NanoARPES or k-nanoscope) and core level detection by using both photoemission and X-ray absorption. Here, we report our latest results related to the optimization of the post-focusing mirrors system as well as its impact on the ultimate spatial resolution of the whole microscope.

Edge illumination X-ray phase contrast imaging techniques are capable of quantitative retrieval of differential phase, absorption and X-ray scattering. We have recently developed a series of approaches enabling high-resolution implementations, both using synchrotron radiation and laboratory-based set-ups. Three-dimensional reconstruction of absorption, phase and dark-field can be achieved with a simple rotation of the sample. All these approaches share a common trait which consists in the use of an absorber that shapes the radiation field, in order to make the phase modulations introduced by the sample detectable. This enables a well-defined and high-contrast structuring of the radiation field as well as an accurate modelling of the effects that are related to the simultaneous use of a wide range of energies. Moreover, it can also be adapted for use with detectors featuring large pixel sizes, which could be desirable when a high detection efficiency is important.

A super-resolution method in projection-type x-ray imaging is proposed. In this method, interference fringes generated with a two-beam interferometer are used for detecting the fine periodic structure of the object. When the sample has a fine periodic structure, the structure can be detected as interaction between the periodic structure of object and the standing wave formed by the two-beam interferometer. Feasibility studies have been carried out using wavefront-division interferometer with total-reflection-mirror optics and a resolution test chart as a model sample. The fine structures with a period up to 100 nm were detected as modulation of transmitting x-ray intensity at 11.5 keV.

Image resolvability is the primary concern in imaging. This paper reports an estimation of the full width at half maximum of the point spread function from a Fourier domain plot of real sample images by neither using test objects, nor defining a threshold criterion. We suggest that this method can be applied to any type of image, independently of the imaging modality.

At the Advanced Light Source (ALS), Beamline 8.3.2 performs hard X-ray micro-tomography under conditions of high temperature, pressure, mechanical loading, and other realistic conditions using environmental test cells. With scan times of 10s–100s of seconds, the microstructural evolution of materials can be directly observed over multiple time steps spanning prescribed changes in the sample environment. This capability enables in-situ quasi-static mechanical testing of materials. We present an overview of our in-situ mechanical testing capabilities and recent hardware developments that enable flexural testing at high temperature and in combination with acoustic emission analysis.

A sample cell for performing computed tomography (CT) was developed. The 3-dimensional (3D) structure of polystyrene spheres was observed and the fluctuation of reconstructed linear absorption coefficients (LAC) was 9.3%. To improve the quality of data in 3D spectro-microscopy, required measurement condition is discussed.

A new soft X-ray scanning transmission X-ray microscope (STXM) optimized for cryo spectro-tomography was designed and commissioned at the Canadian Light Source (CLS). The instrument was required to achieve ultra high vacuum and be compatible with in-situ plasma cleaning. It also required a scintillator detector, and the design of this detector had to evolve to meet these environmental requirements. The scintillator deposition technique, and the suppression of background by introduction of an edge filter are also presented.

Contamination of soft X-rays beamline optics due to carbon cracking and deposition under X- ray irradiation is especially critical for spectromicroscopy operations near the carbon K-absorption edge from organic materials, polymers and nanoparticles. In this paper we present the strategy and procedure followed on the HERMES beamline (Synchrotron SOLEIL) to minimize carbon contamination of the beamline optics. Measurements on a complex organic test sample are reported to demonstrate the performance of the beamline at the carbon K-edge in imaging, spectroscopy and spectromicroscopy modes.

The Advanced Light Source has developed a compact tomographic microscope based on soft x-ray ptychography for the study of nanoscale materials [1,2]. The microscope utilizes the sample manipulator mechanism from a commercial TEM coupled with laser interferometric feedback for zone plate positioning and a fast frame rate charge-coupled device detector for soft x-ray diffraction measurements. The microscope has achieved point to point (25 nm steps) scan rates of greater than 120 Hz with a positioning accuracy of better than 1 nm RMS. The instrument will enable the use of commercially available sample holders compatible with FEI transmission electron microscopes thus also allowing in-situ measurement of samples using both soft x-rays and electrons. This instrument is a refinement of a currently commissioned instrument called The Nanosurveyor, which has demonstrated resolution of better than 10 nm in two dimensions using 750 eV x-rays. Once moved to the new Coherent Scattering and Microscopy beamline it will enable spectromicroscopy and tomography of nano-materials with wavelength limited spatial resolution.

I13 is a 250 m long hard x-ray beamline for imaging and coherent diffraction at the Diamond Light Source. The beamline (6 keV to 35 keV) comprises two independent experimental endstations: one for imaging in direct space using x-ray microscopy and one for imaging in reciprocal space using coherent diffraction based imaging techniques [1]. In particular the coherence experiments pose very high demands on the performance on the beamline instrumentation, requiring extensive testing and optimisation of each component, even during the assembly phase. Various aspects like the quality of optical components, the mechanical design concept, vibrations, drifts, thermal influences and the performance of motion systems are of particular importance. In this paper we study the impact of the front-end slit size (FE slit size), which determines the horizontal source size, onto the coherence length and the detrimental impact of monochromator vibrations using in-situ x-ray metrology in conjunction with fringe visibility measurements and vibration measurements, based on centroid tracking of an x-ray pencil beam with a photon-counting detector.

With Pulsed Laser Deposition, Multilayer Zone Plates can be fabricated to focus hard x-ray beams into 2D spots smaller than 10 nm. To put these optics into use for imaging applications, we have commissioned a new dedicated sample tower as a high-resolution module for the GINIX instrument, stationed at the P10 beamline at PETRA III. Here we summarise the motorisation and show first imaging benchmark results obtained with a "traditional" Fresnel Zone Plate. The first 2D continuous STXM scan using the new EigerX 4M detector at full 750 Hz speed is shown: a field of view of roughly about 1 μm squared has been recorded with 255 × 255 images within 96 seconds.

A compact microscope based on nitrogen double stream gas puff target soft X-ray source, which emits radiation in the water-window spectral range, at the wavelength of λ = 2.88 nm, is presented. The microscope, employing ellipsoidal grazing incidence condenser and a Fresnel zone plate objective, is capable of capturing images with a 60 nm spatial resolution and exposure time as low as a few seconds. Examples of different applications of the SXR microscopy, and its applicability for various fields of science, are presented and discussed.

A high efficiency X-ray image detector was introduced in an x-ray imaging micro-tomography system. The detector is a visible light conversion type which consists of phosphor screen, straight-fiber (1:1) optics and scientific CMOS device. The obtained CT images show high reproducibility of X-ray linear absorption coefficient of test material (Cu/Al concentric pattern). The x-ray intensity could be reduced about 10 % of previous system with lens-coupled image detector system.

We have improved the performance of a previously reported multilayer zone plate by reducing its outermost zone width, using the same multilayer materials (MoSi₂ and Si) and fabrication technique. The focusing performance was evaluated at the BL24XU of SPring-8 using 20-keV X-rays. The line spread function (LSF) in the focal plane was measured using a dark-field knife-edge scan method, and the point spread function was obtained from the LSF through a tomographic reconstruction principle. The spatial resolution was estimated to be 30 nm, which is in relatively good agreement with the calculated diffraction-limited value of 25 nm, while the measured diffraction efficiency of the +1st order was 24%.

Dark-field imaging has been demonstrated to provide complementary information about the unresolved microstructure of the investigated sample. The usual implementation of a grating interferometer, which can provide access to the dark-field signal, consists of linear gratings limiting the sensitivity to only one direction (perpendicular to the grating lines). Recently, a novel grating design, composed of circular unit cells, was proposed allowing 2D-omnidirectional dark-field sensitivity in a single shot. In this work we present a further optimisation of the proposed grating by changing the arrangement of the unit cells from a Cartesian to a hexagonal grid. We experimentally compare the two designs and demonstrate that the latter has an improved performance.

Measurement conditions in X-ray phase tomography using a grating interferometer were evaluated to achieve fast measurements toward 4D X-ray phase tomography for biological samples. X-ray phase tomographic images obtained from different exposure time and the number of projections were examined to determine required statistics for high density resolution while keeping a fast measurement. Application of a high-efficiency fiber-coupled X-ray imaging detector to X-ray phase tomography was also discussed from a comparison between the fiber-coupled and lens-coupled detectors.

A Fresnel zone plate (FZP) with a gradually-decreasing zone thickness from the centre to the outer region, called as an Apodization FZP (A-FZP) has been developed for the purpose of the improvements of imaging properties of imaging (full-field) x-ray microscope. Diffraction efficiency distribution of a A-FZP has a sloped-shouldered shape like a Gaussian, resulting a Gaussian-like pupil and Gaussian-like point spread function without any side peaks. Using this A-FZP, imaging properties at the peripheral region of the field of view was remarkably improved by decreasing edge-enhancement contrast and ringing which have been serious problem on the imaging properties with the conventional FZP objective optics.

The Imaging Beamline IBL/P05 at the DESY storage ring PETRA III, operated by the Helmholtz-Zentrum Geesthacht, has two dedicated endstations optimized for micro- and nanotomography experiments [1-3]. Here we present the status of the nanotomography endstation, highlight the latest instrumentation upgrades and present first experimental results. In particular in materials science, where structures with ceramics or metallic materials are of interest, X-ray energies of 15 keV and above are required even for sample sizes of several 10 μm in diameter. The P05 imaging beamline is dedicated to materials science and is designed to allow for imaging applications with X-ray energies of 10 to 50 keV. In addition to the full field X-ray microscopy setup, the layout of the nanotomography endstation allows switching to cone-beam configuration. Kinematics for X-ray optics like compound refractive lenses (CRLs), Fresnel zone plates (FZP) or beam-shaping optics are implemented and the installation of a Kirkpatrick Baez-mirror (KB mirror) system is foreseen at a later stage of the beamline development. Altogether this leads to a high flexibility of the nanotomography setup such that the instrument can be tailored to the specific experimental requirements of a range of sample systems.

The CARNAÚBA beamline is the tender-to-hard X-ray (2 – 15 keV) scanning nanoprobe planned for the 4^th generation storage ring SIRIUS at the LNLS. CARNAÚBA uses an undulator source with vertical linear polarization in a low-beta straight section and grazing incidence-focusing mirrors to create a nanoprobe at 143 m from the source. The beamline optic is based on KB mirrors and provides high brilliance at an achromatic focal spot down to the diffraction limit diameter of ∼30 nm with a working distance of ∼6 cm. These characteristics are crucial for studying nanometric samples in experiments involving complex stages and environments. The CARNAÚBA beamline aims to perform raster scans using x-ray fluorescence, x-ray absorption spectroscopy, x-ray diffraction and coherent x-ray imaging techniques. Computed tomography will extend these methods to three dimensions.

A Wolter-type 4-mirror system was designed and evaluated by ray-trace calculation. The design and fabrication process were developed. The master mandrel of oxygen-free copper was shaped by diamond turning. The Pyrex glass replica was made by a vacuum replication technique. A visible light image of a metal mesh could be obtained using this replica mirror.

The data daemon, dada, is a server backend for unified access to 2D pixel detector image data stored with different detectors, file formats and saved with varying naming conventions and folder structures across instruments. Furthermore, dada implements basic pre-processing and analysis routines from pixel binning over azimuthal integration to raster scan processing. Common user interactions with dada are by a web frontend, but all parameters for an analysis are encoded into a Uniform Resource Identifier (URI) which can also be written by hand or scripts for batch processing.

Scanning hard X-ray imaging allows simultaneous acquisition of multimodal information, including X-ray fluorescence, absorption, phase and dark-field contrasts, providing structural and chemical details of the samples. Combining these scanning techniques with the infrastructure developed for fast data acquisition at Synchrotron Soleil permits to perform multimodal imaging and tomography during routine user experiments at the Nanoscopium beamline. A main challenge of such imaging techniques is the online processing and analysis of the generated very large volume (several hundreds of Giga Bytes) multimodal data-sets. This is especially important for the wide user community foreseen at the user oriented Nanoscopium beamline (e.g. from the fields of Biology, Life Sciences, Geology, Geobiology), having no experience in such data-handling. MMX-I is a new multi-platform open-source freeware for the processing and reconstruction of scanning multi-technique X-ray imaging and tomographic datasets. The MMX-I project aims to offer, both expert users and beginners, the possibility of processing and analysing raw data, either on-site or off-site. Therefore we have developed a multi-platform (Mac, Windows and Linux 64bit) data processing tool, which is easy to install, comprehensive, intuitive, extendable and user-friendly. MMX-I is now routinely used by the Nanoscopium user community and has demonstrated its performance in treating big data.