Advanced phase‐contrast imaging using a grating interferometer

Phase‐sensitive X‐ray imaging methods can provide substantially increased contrast over conventional absorption‐based imaging, and therefore new and otherwise inaccessible information. Differential phase‐contrast (DPC) imaging, which uses a grating interferometer and a phase‐stepping technique, has been integrated into TOMCAT, a beamline dedicated to tomographic microscopy and coherent radiology experiments at the Swiss Light Source. Developments have been made focusing on the fast acquisition and post‐processing of data to enable a high‐throughput of samples, with obvious advantages, also through increasing the efficiency of the detecting system, of helping to reduce radiation dose imparted to the sample. A novel aquarium design allows a vertical rotation axis below the sample with measurements performed in aqueous environment. Optimization of the data acquisition procedure enables a full phase volume (1024 × 1024 pixels × 1000 projections × 9 phase steps, i.e. 9000 projections in total) to be acquired in 20 min (with a pixel size of 7.4 µm), and the subsequent post‐processing has been integrated into the beamline pipeline for sinogram generation. Local DPC tomography allows one to focus with higher magnification on a particular region of interest of a sample without the presence of local tomography reconstruction artifacts. Furthermore, `widefield' imaging is shown for DPC scans for the first time, enabling the field of view of the imaging system to be doubled for samples that are larger than the magnification allows. A case study is illustrated focusing on the visualization of soft tissue features, and particularly the substantia nigra of a rat brain. Darkfield images, based on local X‐ray scattering, can also be extracted from a grating‐based DPC scan: an example of the advantages of darkfield contrast is shown and the potential of darkfield X‐ray tomography is discussed.     

The first microbeam synchrotron X‐ray fluorescence beamline at the Siam Photon Laboratory

The first microbeam synchrotron X‐ray fluorescence (µ‐SXRF) beamline using continuous synchrotron radiation from Siam Photon Source has been constructed and commissioned as of August 2011. Utilizing an X‐ray capillary half‐lens allows synchrotron radiation from a 1.4 T bending magnet of the 1.2 GeV electron storage ring to be focused from a few millimeters‐sized beam to a micrometer‐sized beam. This beamline was originally designed for deep X‐ray lithography (DXL) and was one of the first two operational beamlines at this facility. A modification has been carried out to the beamline in order to additionally enable µ‐SXRF and synchrotron X‐ray powder diffraction (SXPD). Modifications included the installation of a new chamber housing a Si(111) crystal to extract 8 keV synchrotron radiation from the white X‐ray beam (for SXPD), a fixed aperture and three gate valves. Two end‐stations incorporating optics and detectors for µ‐SXRF and SXPD have then been installed immediately upstream of the DXL station, with the three techniques sharing available beam time. The µ‐SXRF station utilizes a polycapillary half‐lens for X‐ray focusing. This optic focuses X‐ray white beam from 5 mm × 2 mm (H × V) at the entrance of the lens down to a diameter of 100 µm FWHM measured at a sample position 22 mm (lens focal point) downstream of the lens exit. The end‐station also incorporates an XYZ motorized sample holder with 25 mm travel per axis, a 5× ZEISS microscope objective with 5 mm × 5 mm field of view coupled to a CCD camera looking to the sample, and an AMPTEK single‐element Si (PIN) solid‐state detector for fluorescence detection. A graphic user interface data acquisition program using the LabVIEW platform has also been developed in‐house to generate a series of single‐column data which are compatible with available XRF data‐processing software. Finally, to test the performance of the µ‐SXRF beamline, an elemental surface profile has been obtained for a piece of ancient pottery from the Ban Chiang archaeological site, a UNESCO heritage site. It was found that the newly constructed µ‐SXRF technique was able to clearly distinguish the distribution of different elements on the specimen.     

Improved tomographic reconstructions using adaptive time‐dependent intensity normalization

The first processing step in synchrotron‐based micro‐tomography is the normalization of the projection images against the background, also referred to as a white field. Owing to time‐dependent variations in illumination and defects in detection sensitivity, the white field is different from the projection background. In this case standard normalization methods introduce ring and wave artefacts into the resulting three‐dimensional reconstruction. In this paper the authors propose a new adaptive technique accounting for these variations and allowing one to obtain cleaner normalized data and to suppress ring and wave artefacts. The background is modelled by the product of two time‐dependent terms representing the illumination and detection stages. These terms are written as unknown functions, one scaled and shifted along a fixed direction (describing the illumination term) and one translated by an unknown two‐dimensional vector (describing the detection term). The proposed method is applied to two sets (a stem Salix variegata and a zebrafish Danio rerio) acquired at the parallel beam of the micro‐tomography station 2‐BM at the Advanced Photon Source showing significant reductions in both ring and wave artefacts. In principle the method could be used to correct for time‐dependent phenomena that affect other tomographic imaging geometries such as cone beam laboratory X‐ray computed tomography.     

A new stand‐alone QEXAFS data acquisition system for in situ studies

To meet the demands of the QEXAFS (quick‐scanning extended X‐ray absorption fine structure) technique for a fast, user‐friendly and flexible data acquisition a new stand‐alone system with new software exploiting a multi‐functional USB board was designed. The chosen approach allows the scanning of several analogue and digital data sources with up to 500000 samples each second over hours storable in binary or ASCII format without any dead‐time. At the same time it is possible to visualize the acquired data instantaneously which provides a maximum of interactivity during the running experiment and also optimal conditions to select the best suited beamline and detector settings prior to each measurement. Furthermore, the QEXAFS monochromator and typically three current amplifiers are entirely controlled by the new software so that all monochromator settings can be synchronized with the data acquisition enabling programmed scans with alternating parameter sets. This versatile concept also enables the user to react immediately to changes in the sample during in situ studies. An interface to a three‐axis stepper motor control unit is additionally included to control a sample stage which can again be synchronized with the data acquisition. Thus, spatially resolved scans and the usage of scan tools for sample alignment are feasible with the new system. Typical examples to demonstrate the features of the new data acquisition system are presented, the designed graphical user interface is described in detail and, furthermore, the crucial design parameters of a typical QEXAFS set‐up are discussed.     

syris: a flexible and efficient framework for X‐ray imaging experiments simulation

An open‐source framework for conducting a broad range of virtual X‐ray imaging experiments, syris, is presented. The simulated wavefield created by a source propagates through an arbitrary number of objects until it reaches a detector. The objects in the light path and the source are time‐dependent, which enables simulations of dynamic experiments, e.g. four‐dimensional time‐resolved tomography and laminography. The high‐level interface of syris is written in Python and its modularity makes the framework very flexible. The computationally demanding parts behind this interface are implemented in OpenCL, which enables fast calculations on modern graphics processing units. The combination of flexibility and speed opens new possibilities for studying novel imaging methods and systematic search of optimal combinations of measurement conditions and data processing parameters. This can help to increase the success rates and efficiency of valuable synchrotron beam time. To demonstrate the capabilities of the framework, various experiments have been simulated and compared with real data. To show the use case of measurement and data processing parameter optimization based on simulation, a virtual counterpart of a high‐speed radiography experiment was created and the simulated data were used to select a suitable motion estimation algorithm; one of its parameters was optimized in order to achieve the best motion estimation accuracy when applied on the real data. syris was also used to simulate tomographic data sets under various imaging conditions which impact the tomographic reconstruction accuracy, and it is shown how the accuracy may guide the selection of imaging conditions for particular use cases.     

Polycapillary‐optics‐based micro‐XANES and micro‐EXAFS at a third‐generation bending‐magnet beamline

A focusing system based on a polycapillary half‐lens optic has been successfully tested for transmission and fluorescence µ‐X‐ray absorption spectroscopy at a third‐generation bending‐magnet beamline equipped with a non‐fixed‐exit Si(111) monochromator. The vertical positional variations of the X‐ray beam owing to the use of a non‐fixed‐exit monochromator were shown to pose only a limited problem by using the polycapillary optic. The expected height variation for an EXAFS scan around the Fe K‐edge is approximately 200 µm on the lens input side and this was reduced to ～1 µm for the focused beam. Beam sizes (FWHM) of 12–16 µm, transmission efficiencies of 25–45% and intensity gain factors, compared with the non‐focused beam, of about 2000 were obtained in the 7–14 keV energy range for an incoming beam of 0.5 × 2 mm (vertical × horizontal). As a practical application, an As K‐edge µ‐XANES study of cucumber root and hypocotyl was performed to determine the As oxidation state in the different plant parts and to identify a possible metabolic conversion by the plant.     

High‐energy X‐ray diffraction using the Pixium 4700 flat‐panel detector

The Pixium 4700 detector represents a significant step forward in detector technology for high‐energy X‐ray diffraction. The detector design is based on digital flat‐panel technology, combining an amorphous Si panel with a CsI scintillator. The detector has a useful pixel array of 1910 × 2480 pixels with a pixel size of 154 µm × 154 µm, and thus it covers an effective area of 294 mm × 379 mm. Designed for medical imaging, the detector has good efficiency at high X‐ray energies. Furthermore, it is capable of acquiring sequences of images at 7.5 frames per second in full image mode, and up to 60 frames per second in binned region of interest modes. Here, the basic properties of this detector applied to high‐energy X‐ray diffraction are presented. Quantitative comparisons with a widespread high‐energy detector, the MAR345 image plate scanner, are shown. Other properties of the Pixium 4700 detector, including a narrow point‐spread function and distortion‐free image, allows for the acquisition of high‐quality diffraction data at high X‐ray energies. In addition, high frame rates and shutterless operation open new experimental possibilities. Also provided are the necessary data for the correction of images collected using the Pixium 4700 for diffraction purposes.     

Evaluation of the improved three‐dimensional resolution of a synchrotron radiation computed tomograph using a micro‐fabricated test pattern

A micro test pattern prepared by focused ion beam milling was used to evaluate the three‐dimensional resolution of a microtomograph at the BL20B2 beamline of SPring‐8. The resolutions along the direction within the tomographic slice plane and perpendicular to it were determined from the modulation transfer functions. The through‐plane resolution perpendicular to the tomographic slice was evaluated to be 8 µm, which corresponds to the spatial resolution of two‐dimensional radiographs. In contrast, the in‐plane resolution within the slice was evaluated to be 12 µm. Real‐space interpolation was performed prior to the tomographic reconstruction, giving an improved in‐plane resolution of 8.5 µm. However, the 8 µm pitch pattern was resolved in the interpolated slice image. To reflect this result, another resolution measure from the peak‐to‐valley difference plot was introduced. This resolution measure gave resolution limits of 7.4 µm for the in‐plane direction and 6.1 µm for the through‐plane direction. The three‐dimensional test pattern along with the interpolated reconstruction enables the quantitative evaluation of the spatial resolution of microtomographs.     

Design of an ultrahigh‐energy‐resolution and wide‐energy‐range soft X‐ray beamline

A new ultrahigh‐energy‐resolution and wide‐energy‐range soft X‐ray beamline has been designed and is under construction at the Shanghai Synchrotron Radiation Facility. The beamline has two branches: one dedicated to angle‐resolved photoemission spectroscopy (ARPES) and the other to photoelectron emission microscopy (PEEM). The two branches share the same plane‐grating monochromator, which is equipped with four variable‐line‐spacing gratings and covers the 20–2000 eV energy range. Two elliptically polarized undulators are employed to provide photons with variable polarization, linear in every inclination and circular. The expected energy resolution is approximately 10 meV at 1000 eV with a flux of more than 3 × 10¹⁰ photons s^?1 at the ARPES sample positions. The refocusing of both branches is based on Kirkpatrick–Baez pairs. The expected spot sizes when using a 10 µm exit slit are 15 µm × 5 µm (horizontal × vertical FWHM) at the ARPES station and 10 µm × 5 µm (horizontal × vertical FWHM) at the PEEM station. The use of plane optical elements upstream of the exit slit, a variable‐line‐spacing grating and a pre‐mirror in the monochromator that allows the influence of the thermal deformation to be eliminated are essential for achieving the ultrahigh‐energy resolution.     

Reconstruction of spatial distributions of sound velocity and absorption in soft biological tissues using model ultrasonic tomographic data

A two-step algorithm is used to reconstruct the spatial distributions of the acoustic characteristics of soft biological tissues-the sound velocity and absorption coefficient. Knowing these distributions is urgent for early detection of benign and malignant neoplasms in biological tissues, primarily in the breast. At the first stage, large-scale distributions are estimated; at the second step, they are refined with a high resolution. Results of reconstruction on the base of model initial data are presented. The principal necessity of preliminary reconstruction of large-scale distributions followed by their being taken into account at the second step is illustrated. The use of CUDA technology for processing makes it possible to obtain final images of 1024 × 1024 samples in only a few minutes.     

Real‐time image‐content‐based beamline control for smart 4D X‐ray imaging

Real‐time processing of X‐ray image data acquired at synchrotron radiation facilities allows for smart high‐speed experiments. This includes workflows covering parameterized and image‐based feedback‐driven control up to the final storage of raw and processed data. Nevertheless, there is presently no system that supports an efficient construction of such experiment workflows in a scalable way. Thus, here an architecture based on a high‐level control system that manages low‐level data acquisition, data processing and device changes is described. This system is suitable for routine as well as prototypical experiments, and provides specialized building blocks to conduct four‐dimensional in situ, in vivo and operando tomography and laminography.     

PITRE: software for phase‐sensitive X‐ray image processing and tomography reconstruction

Synchrotron‐radiation computed tomography has been applied in many research fields. Here, PITRE (Phase‐sensitive X‐ray Image processing and Tomography REconstruction) and PITRE_BM (PITRE Batch Manager) are presented. PITRE supports phase retrieval for propagation‐based phase‐contrast imaging/tomography (PPCI/PPCT), extracts apparent absorption, refractive and scattering information of diffraction enhanced imaging (DEI), and allows parallel‐beam tomography reconstruction for conventional absorption CT data and for PPCT phase retrieved and DEI‐CT extracted information. PITRE_BM is a batch processing manager for PITRE: it executes a series of tasks, created viaPITRE, without manual intervention. Both PITRE and PITRE_BM are coded in Interactive Data Language (IDL), and have a user‐friendly graphical user interface. They are freeware and can run on Microsoft Windows systems via IDL Virtual Machine, which can be downloaded for free and does not require a license. The data‐processing principle and some examples of application will be presented.     

Combination of HAADF‐STEM and ADF‐STEM Tomography for Core–Shell Hybrid Materials

Characterization of core–shell type nanoparticles in 3D by transmission electron microscopy (TEM) can be very challenging. Especially when both heavy and light elements coexist within the same nanostructure, artifacts in the 3D reconstruction are often present. A representative example would be a particle comprising an anisotropic metallic (Au) nanoparticle coated with a (mesoporous) silica shell. To obtain a reliable 3D characterization of such an object, a dose‐efficient strategy is proposed to simultaneously acquire high‐angle annular dark‐field scanning TEM and annular dark‐field tilt series for tomography. The 3D reconstruction is further improved by applying an advanced masking and interpolation approach to the acquired data. This new methodology enables us to obtain high‐quality reconstructions from which also quantitative information can be extracted. This approach is broadly applicable to investigate hybrid core–shell materials.     

Joint B0 and image estimation integrated with model based reconstruction for field map update and distortion correction in prostate diffusion MRI

In prostate Diffusion Weighted MRI, differences in susceptibility values exist at the interface between the prostate and rectal-air. This can result in off-resonance magnetic field leading to geometric distortions including signal stretching and signal pile-up in the reconstructed images. Using a set of EPI data acquired with blip-up and blip-down phase encoding gradient directions, model based reconstruction has recently been proposed that can correct these distortions by using a B₀ field estimated from a separate B₀ scan. However, change in the size of the rectal air region across time can occur that can result in a mismatch of the B₀ field to the EPI scan. Also, the measured B₀ field itself can be erroneous in regions of low Signal to Noise ratio around the prostate rectal air interface. In this work, using a set of single shot EPI data acquired with blip-up and blip-down phase encoding gradient directions, a novel joint model based reconstruction is proposed that can account for changes in the off resonance effects between the B₀ and EPI scans. For ten prostate patients, using a measured B₀ field as an initial B₀ estimate, on a 5-point scale (1–5) image quality scores evaluated by an experienced radiologist, the proposed framework achieved scores of 3.50 ± 0.85 and 3.40 ± 0.51 for b-values of 0 and 500 s/mm², respectively compared to 3.40 ± 0.70 and 3.30 ± 0.67 for model based reconstruction. The proposed framework is also capable of estimating a distortion corrected EPI image even without an initial B₀ field estimate in situations where a separate B₀ scan cannot be obtained due to time constraint.     

Single‐cell resolution in high‐resolution synchrotron X‐ray CT imaging with gold nanoparticles

Gold nanoparticles are excellent intracellular markers in X‐ray imaging. Having shown previously the suitability of gold nanoparticles to detect small groups of cells with the synchrotron‐based computed tomography (CT) technique both ex vivo and in vivo, it is now demonstrated that even single‐cell resolution can be obtained in the brain at least ex vivo. Working in a small animal model of malignant brain tumour, the image quality obtained with different imaging modalities was compared. To generate the brain tumour, 1 × 10⁵ C6 glioma cells were loaded with gold nanoparticles and implanted in the right cerebral hemisphere of an adult rat. Raw data were acquired with absorption X‐ray CT followed by a local tomography technique based on synchrotron X‐ray absorption yielding single‐cell resolution. The reconstructed synchrotron X‐ray images were compared with images obtained by small animal magnetic resonance imaging. The presence of gold nanoparticles in the tumour tissue was verified in histological sections.     

A three‐crystal spectrometer for high‐energy resolution fluorescence‐detected X‐ray absorption spectroscopy and X‐ray emission spectroscopy at SSRF

A Johann‐type spectrometer for the study of high‐energy resolution fluorescence‐detected X‐ray absorption spectroscopy, X‐ray emission spectroscopy and resonant inelastic X‐ray scattering has been developed at BL14W1 X‐ray absorption fine structure spectroscopy beamline of Shanghai Synchrotron Radiation Facility. The spectrometer consists of three crystal analyzers mounted on a vertical motion stage. The instrument is scanned vertically and covers the Bragg angle range of 71.5–88°. The energy resolution of the spectrometer ranges from sub‐eV to a few eV. The spectrometer has a solid angle of about 1.87 × 0^?3 of 4π sr, and the overall photons acquired by the detector could be 10⁵ counts per second for the standard sample. The performances of the spectrometer are illustrated by the three experiments that are difficult to perform with the conventional absorption or emission spectroscopy. Copyright © 2016 John Wiley & Sons, Ltd.     

Enhancements in full‐field PIXE imaging—Large area elemental mapping with increased lateral resolution devoid of optics artefacts

The combination of a pn‐junction charge‐coupled device‐based pixel detector with a poly‐capillary X‐ray optics was installed and examined at the Helmholtz‐Zentrum Dresden‐Rossendorf. The set‐up is intended for particle‐induced X‐ray emission imaging to survey the trace elemental composition of flat/polished geological samples. In the standard configuration, a straight X‐ray optics (20 μm capillary diameter) is used to guide the emitted photons from the sample towards the detector with nearly 70 000 pixels. Their dimensions of 48 × 48 μm² are the main limitation of the lateral resolution. This limitation can be bypassed by applying a dedicated subpixel algorithm to recalculate the footprint of the photon's electron cloud in the detector. The lateral resolution is then mainly determined by the capillary's diameter. Nevertheless, images are still superimposed by the X‐ray optics pattern. The optics' capillaries are grouped in hexagonal bundles resulting in a reduced transmission of X‐rays in the boundary regions. This influence can be largely suppressed by combining a series of short measurements at slightly shifted positions using a precision stage and correcting the image data for this shifting. The use of a subpixel grid for the image reconstruction allows a further increase of the spatial resolution. This approach of image‐stacking and multiframe super‐resolution in combination with the subpixel correction algorithm is presented and illustrated with experimental data. Additionally, a flat‐field correction is shown to remove the remaining imaging inhomogeneity caused by non‐uniform X‐ray transmission. The described techniques can be used for all X‐ray spectrometry methods using an X‐ray camera to obtain high‐quality elemental images.     

miXAFS: a program for X‐ray absorption fine‐structure data analysis

A new program called miXAFS for the analysis of X‐ray absorption fine‐structure (XAFS) data is presented. miXAFS can analyze the XAFS functions simultaneously for all measured X‐ray absorption edges of the constituent elements in a sample under the constraints for the structural parameters over the edges. The program provides a surface plot of the R‐factor as a function of two structural parameters, which is useful to validate the optimized structural parameters. The structural parameters can be obtained from the XAFS data in a few steps using the setting file and batch process. The program, which is coded in MATLAB and freely available, runs on Macintosh and Windows operating systems. It has a graphical user interface and loads experimental data and XAFS functions in a variety of ASCII data formats.     

An iterative image reconstruction algorithm combined with forward and backward diffusion filtering for in‐line X‐ray phase‐contrast computed tomography

In‐line X‐ray phase‐contrast computed tomography (IL‐PCCT) can reveal fine inner structures for low‐Z materials (e.g. biological soft tissues), and shows high potential to become clinically applicable. Typically, IL‐PCCT utilizes filtered back‐projection (FBP) as the standard reconstruction algorithm. However, the FBP algorithm requires a large amount of projection data, and subsequently a large radiation dose is needed to reconstruct a high‐quality image, which hampers its clinical application in IL‐PCCT. In this study, an iterative reconstruction algorithm for IL‐PCCT was proposed by combining the simultaneous algebraic reconstruction technique (SART) with eight‐neighbour forward and backward (FAB8) diffusion filtering, and the reconstruction was performed using the Shepp–Logan phantom simulation and a real synchrotron IL‐PCCT experiment. The results showed that the proposed algorithm was able to produce high‐quality computed tomography images from few‐view projections while improving the convergence rate of the computed tomography reconstruction, indicating that the proposed algorithm is an effective method of dose reduction for IL‐PCCT.