Soft X-ray Imaging Research Articles

Multi-energy SXR cameras for magnetically confined fusion plasmas (invited).

A compact multi-energy soft x-ray camera has been developed for time, energy and space-resolved measurements of the soft-x-ray emissivity in magnetically confined fusion plasmas. Multi-energy soft x-ray imaging provides a unique opportunity for measuring, simultaneously, a variety of important plasma properties (Te, nZ, ΔZeff, and ne,fast). The electron temperature can be obtained by modeling the slope of the continuum radiation from ratios of the available brightness and inverted radial emissivity profiles over multiple energy ranges. Impurity density measurements are also possible using the line-emission from medium- to high-Z impurities to separate the background as well as transient levels of metal contributions. This technique should be explored also as a burning plasma diagnostic in-view of its simplicity and robustness.

Report on recent results of the PERCIVAL soft X-ray imager

The PERCIVAL (Pixelated Energy Resolving CMOS Imager, Versatile And Large) soft X-ray 2D imaging detector is based on stitched, wafer-scale sensors possessing a thick epi-layer, which together with back-thinning and back-side illumination yields elevated quantum efficiency in the photon energy range of 125–1000 eV. Main application fields of PERCIVAL are foreseen in photon science with FELs and synchrotron radiation. This requires high dynamic range up to 105 ph @ 250 eV paired with single photon sensitivity with high confidence at moderate frame rates in the range of 10–120 Hz. These figures imply the availability of dynamic gain switching on a pixel-by-pixel basis and a highly parallel, low noise analog and digital readout, which has been realized in the PERCIVAL sensor layout. Different aspects of the detector performance have been assessed using prototype sensors with different pixel and ADC types. This work will report on the recent test results performed on the newest chip prototypes with the improved pixel and ADC architecture. For the target frame rates in the 10–120 Hz range an average noise floor of 14e− has been determined, indicating the ability of detecting single photons with energies above 250 eV. Owing to the successfully implemented adaptive 3-stage multiple-gain switching, the integrated charge level exceeds 4 · 106 e− or 57000 X-ray photons at 250 eV per frame at 120 Hz. For all gains the noise level remains below the Poisson limit also in high-flux conditions. Additionally, a short overview over the updates on an oncoming 2 Mpixel (P2M) detector system (expected at the end of 2016) will be reported.

Relative intersection of confidence intervals rule for sharper restoration of soft x-ray images.

We present a novel method for restoration of images of nanostructures obtained with a soft-ray microscope that uses a 46.9 nm soft x-ray laser microscope for illumination. To suppress the noise and to preserve the image sharpness, we develop a method based on pixel adaptive zero-order modeling of the observed object. Neighboring areas of each pixel are selected using the relative intersection of confidence intervals rule and used for restoration. Due to the non-uniform distribution of noise in the images, we use robust spatial noise modeling. The method provides sharp restored images-sharper than competitive approaches. The sharpness is measured using local phase coherence in the complex wavelet transform domain and shows visible improvement of the novel method.

Phenomic Approaches and Tools for Phytopathologists

Plant phenomics approaches aim to measure traits such as growth, performance, and composition of plants using a suite of noninvasive technologies. The goal is to link phenotypic traits to the genetic information for particular genotypes, thus creating the bridge between the phenome and genome. Application of sensing technologies for detecting specific phenotypic reactions occurring during plant-pathogen interaction offers new opportunities for elucidating the physiological mechanisms that link pathogen infection and disease symptoms in the host, and also provides a faster approach in the selection of genetic material that is resistant to specific pathogens or strains. Appropriate phenomics methods and tools may also allow presymptomatic detection of disease-related changes in plants or to identify changes that are not visually apparent. This review focuses on the use of sensor-based phenomics tools in plant pathology such as those related to digital imaging, chlorophyll fluorescence imaging, spectral imaging, and thermal imaging. A brief introduction is provided for less used approaches like magnetic resonance, soft x-ray imaging, ultrasound, and detection of volatile compounds. We hope that this concise review will stimulate further development and use of tools for automatic, nondestructive, and high-throughput phenotyping of plant-pathogen interaction.

Optimization of soft X-ray tomography on the COMPASS tokamak

Abstract The COMPASS tokamak is equipped with the soft X-ray (SXR) diagnostic system based on silicon photodiode arrays shielded by a thin beryllium foil. The diagnostic is composed of two pinhole cameras having 35 channels each and one vertical pinhole camera with 20 channels, which was installed recently to improve tomographic inversions. Lines of sight of the SXR detectors cover almost complete poloidal cross section of the COMPASS vessel with a spatial resolution of 1-2 cm and temporal resolution of about 3 μs. Local emissivity is reconstructed via Tikhonov regularization constrained by minimum Fisher information that provides reliable and robust solution despite limited number of projections and ill-conditionality of this task. Improved border conditions and numerical differentiation matrices suppressing artifacts in reconstructed radiation were implemented in the code. Furthermore, a fast algorithm eliminating iterative processes was developed, and it is foreseen to be tested in real-time plasma control.

Nanoimaging granule dynamics and subcellular structures in activated mast cells using soft X-ray tomography.

Mast cells play an important role in allergic responses. During activation, these cells undergo degranulation, a process by which various kinds of mediators stored in the granules are released. Granule homeostasis in mast cells has mainly been studied by electron microscopy (EM), where the fine structures of subcellular organelles are partially destroyed during sample preparation. Migration and fusion of granules have not been studied in detail in three dimensions (3D) in unmodified samples. Here, we utilized soft X-ray tomography (SXT) coupled with fluorescence microscopy to study the detailed structures of organelles during mast cell activation. We observed granule fission, granule fusion to plasma membranes, and small vesicles budding from granules. We also detected lipid droplets, which became larger and more numerous as mast cells were activated. We observed dramatic morphological changes of mitochondria in activated mast cells and 3D-reconstruction revealed the highly folded cristae inner membrane, features of functionally active mitochondria. We also observed giant vesicles containing granules, mitochondria, and lipid droplets, which we designated as granule-containing vesicles (GCVs) and verified their presence by EM in samples prepared by cryo-substitution, albeit with a less clear morphology. Thus, our studies using SXT provide significant insights into mast cell activation at the organelle level.

Micrometer-resolution imaging using MÖNCH: towards G2-less grating interferometry.

MÖNCH is a 25 µm-pitch charge-integrating detector aimed at exploring the limits of current hybrid silicon detector technology. The small pixel size makes it ideal for high-resolution imaging. With an electronic noise of about 110 eV r.m.s., it opens new perspectives for many synchrotron applications where currently the detector is the limiting factor, e.g. inelastic X-ray scattering, Laue diffraction and soft X-ray or high-resolution color imaging. Due to the small pixel pitch, the charge cloud generated by absorbed X-rays is shared between neighboring pixels for most of the photons. Therefore, at low photon fluxes, interpolation algorithms can be applied to determine the absorption position of each photon with a resolution of the order of 1 µm. In this work, the characterization results of one of the MÖNCH prototypes are presented under low-flux conditions. A custom interpolation algorithm is described and applied to the data to obtain high-resolution images. Images obtained in grating interferometry experiments without the use of the absorption grating G2 are shown and discussed. Perspectives for the future developments of the MÖNCH detector are also presented.

Soft X-ray tomography in support of impurity control in tokamaks

This contribution reviews an important example of current developments in diagnostic systems and data analysis tools aimed at improved understanding and control of transport processes in magnetically confined high temperature plasmas. The choice of tungsten for the plasma facing components of ITER and probably also DEMO means that impurity control in fusion plasmas is now a crucial challenge. Soft X-ray (SXR) diagnostic systems serve as a key sensor for experimental studies of plasma impurity transport with a clear prospective of its control via actuators based mainly on plasma heating systems. The SXR diagnostic systems typically feature high temporal resolution but limited spatial resolution due to access restrictions. In order to reconstruct the spatial distribution of the SXR radiation from line integrated measurements, appropriate tomographic methods have been developed and validated, while novel numerical methods relevant for real-time control have been proposed. Furthermore, in order to identify the main contributors to the SXR plasma radiation, at least partial control over the spectral sensitivity range of the detectors would be beneficial, which motivates for developments of novel SXR diagnostic methods. Last, but not least, semiconductor photosensitive elements cannot survive in harsh conditions of future fusion reactors due to radiation damage, which calls for development of radiation hard SXR detectors. Present research in this field is exemplified on recent results from tokamaks COMPASS, TORE SUPRA and the Joint European Torus JET. Further planning is outlined.

Impact of Catalyst Ink Stirring Condition on Oxygen Transport within PEFC

Polymer electrolyte fuel cells (PEFCs) are regarded as a promising alternative power source for automobiles (fuel cell electric vehicle; FCEV). Cost reduction and increasing power density of PEFCs are the key challenges for commercialization of FCEVs, and reduction of Platinum amount in the catalyst layer (CL) is essential to achieve cost reduction of FCEVs. In order to accomplish the reduction of Platinum loading without sacrificing PEFC performance under high current density operation, it is important to make more effective use of Pt used in the CL of the membrane electrode assembly (MEA), and the mass transport of reactants within the CL should be enhanced significantly. From this background, fabrication process of the CL should be investigated in more detail. The fabrication process of the CL includes an ink preparation process and a coating and dry process. In the former process, the materials composing the CL are mixed and dispersed in the solvent. A blend of water and alcohol is typically used as a dispersion medium for Pt-supported carbon and ionomer. The composition of the dispersion medium, the choice of alcohol, solid contents, and mixing conditions are major controlling parameters. The catalyst ink is deposited on a substrate or directly onto a PEM. The screen printing, die coating, or spray-coating is a major choice for the deposition method. The CL structure is finally formed after drying the deposited CL ink under elevated temperature. Extensive number of studies have been conducted to understand the impact of each parameters on PEFC performance, but the mechanism of structural formation of the CL has not been fully understood. In this study, Impact of stirring condition of the catalyst ink on the CL structure, cell performance and oxygen transport phenomena was investigated by using cyclic voltammetry (CV) measurement, limiting current density measurement, and soft X-ray imaging. To investigate the impact of stirring condition, we prepared two catalyst ink with the same composition but the different stirring condition; stirred with Zr ball (ink A) and without Zr ball (ink B). Figure 1 shows the result of CV measurement, and it showed that the CL prepared from the ink A have larger electrochemical surface area. Because the amount of Pt-supported carbon contained within the MEA should be the same, this result clearly suggested that the stirring condition of the catalyst ink affect the CL structure and its Pt utilization ratio. In addition, the i-V characteristics of these CLs (Figure 2) clearly showed that the CL prepared from the ink A have better performance than the CL prepared from the ink B, and the performance drop of the CL prepared from ink B was serious under the cell temperature of 30 deg.C. To understand this performance drop in more detail, the soft X-ray imaging technique and the oxygen transport resistance measurement were carried out. Results of the soft X-ray imaging (Figure 3) showed that more liquid water was accumulated within the MEA prepared from ink B. In addition, the oxygen transport resistance suggested that the oxygen transport resistance within the MEA prepared by using the ink A is smaller than the MEA prepared by using the ink B. These results clearly showed that the stirring condition of the catalyst ink strongly affect the structure of the CL and the transport phenomena within the MEA. The stirring condition might affect not only the aggregation of the Pt-supported carbon but also the ionomer coverage on it, and their impact on the PEFC performance is still not clear. It is highly important to understand the CL fabrication process more scientifically, and it helps to develop high-performance CL. Acknowledgement: This work was supported by the New Energy and Industrial Technology Development Organization (NEDO), Japan. Figure 1

Contributed Review: The novel gas puff targets for laser-matter interaction experiments.

Various types of targetry are used nowadays in laser matter interaction experiments. Such targets are characterized using different methods capable of acquiring information about the targets such as density, spatial distribution, and temporal behavior. In this mini-review paper, a particular type of target will be presented. The targets under consideration are gas puff targets of various and novel geometries. Those targets were investigated using extreme ultraviolet (EUV) and soft X-ray (SXR) imaging techniques, such as shadowgraphy, tomography, and pinhole camera imaging. Details about characterization of those targets in the EUV and SXR spectral regions will be presented.

Calibration of a two-color soft x-ray diagnostic for electron temperature measurement.

The two-color soft x-ray (SXR) tomography diagnostic on the Madison Symmetric Torus is capable of making electron temperature measurements via the double-filter technique; however, there has been a 15% systematic discrepancy between the SXR double-filter (SXRDF) temperature and Thomson scattering (TS) temperature. Here we discuss calibration of the Be filters used in the SXRDF measurement using empirical measurements of the transmission function versus energy at the BESSY II electron storage ring, electron microprobe analysis of filter contaminants, and measurement of the effective density. The calibration does not account for the TS and SXRDF discrepancy, and evidence from experiments indicates that this discrepancy is due to physics missing from the SXRDF analysis rather than instrumentation effects.

A comparison between soft x-ray and magnetic phase data on the Madison symmetric torus.

The Soft X-Ray (SXR) tomography system on the Madison Symmetric Torus uses four cameras to determine the emissivity structure of the plasma. This structure should directly correspond to the structure of the magnetic field; however, there is an apparent phase difference between the emissivity reconstructions and magnetic field reconstructions when using a cylindrical approximation. The difference between the phase of the dominant rotating helical mode of the magnetic field and the motion of the brightest line of sight for each SXR camera is dependent on both the camera viewing angle and the plasma conditions. Holding these parameters fixed, this phase difference is shown to be consistent over multiple measurements when only toroidal or poloidal magnetic field components are considered. These differences emerge from physical effects of the toroidal geometry which are not captured in the cylindrical approximation.

Two-color spatial and temporal temperature measurements using a streaked soft x-ray imager.

A dual-channel streaked soft x-ray imager has been designed and used on high energy-density physics experiments at the National Ignition Facility. This streaked imager creates two images of the same x-ray source using two slit apertures and a single shallow angle reflection from a nickel mirror. Thin filters are used to create narrow band pass images at 510 eV and 360 eV. When measuring a Planckian spectrum, the brightness ratio of the two images can be translated into a color-temperature, provided that the spectral sensitivity of the two images is well known. To reduce uncertainty and remove spectral features in the streak camera photocathode from this photon energy range, a thin 100 nm CsI on 50 nm Al streak camera photocathode was implemented. Provided that the spectral shape is well-known, then uncertainties on the spectral sensitivity limits the accuracy of the temperature measurement to approximately 4.5% at 100 eV.

Non-monotonic growth rates of sawtooth precursors evidenced with a new method on ASDEX Upgrade

This paper describes a new method to derive, from soft x-ray (SXR) tomography, robust estimates of the core displacement, growth rate and frequency of a 1/1 sawtooth crash precursor. The method is valid for very peaked SXR profiles and is robust against both the inversion algorithm and the presence of tungsten in a rotating plasma. Three typical ASDEX Upgrade crashes are then analysed. In all cases a postcursor is observed, suggesting incomplete reconnection. Despite different dynamics, in all three cases the growth rate of the core displacement shows similar features. First, it is not constant, supporting the idea of non-linear growth. Second, it can be divided into clearly identified phases with quasi-constant growth rates, suggesting sudden change of growth regime rather than smooth transitions. Third, its evolution is non-monotonic, with phases of accelerated growth followed by damped phases. This damping is interpreted for two cases respectively as an effect of fast ions and of mode coupling, based on the result of a MHD simulation. The mode frequency is observed in all cases to be closely related to the plasma bulk rotation profile, with little or no visible effect of the electron diamagnetic drift frequency. The onset criterion could not be clearly identified and it is shown that the role of the pressure gradient is not as expected from a naive extrapolation of the linear stability theory.

Cryo-scanning transmission electron tomography of biological cells

Abstract

Table-top water-window soft X-ray microscope using a Z-pinching capillary discharge source

The development and demonstration of a table-top transmission soft X-ray (SXR) microscope, using a laboratory incoherent capillary discharge source has been carried out. This Z-pinching capillary discharge water-window SXR source, is a first of its kind to be used for high spatial resolution microscopy at λ = 2.88 nm (430 eV) . A grazing incidence ellipsoidal condenser mirror is used for focusing of the SXR radiation at the sample plane. The Fresnel zone plate objective lens is used for imaging of the sample onto a back-illuminated (BI) CCD camera. The achieved half-pitch spatial resolution of the microscope approaches 100 nm, as demonstrated by the knife-edge test. Details about the source, and the construction of the microscope are presented and discussed. Additionally, the SXR images of various samples, proving applicability of such microscope for observation of objects in the nanoscale, are shown.

Structural Changes In Cells Imaged by Soft X-ray Cryo-Tomography During Hepatitis C Virus Infection.

Chronic hepatitis C virus (HCV) infection causes severe liver disease in millions of humans worldwide. Pathogenesis of HCV infection is strongly driven by a deficient immune response of the host, although intersection of different aspects of the virus life cycle with cellular homeostasis is emerging as an important player in the pathogenesis and progression of the disease. Cryo soft X-ray tomography (cryo-SXT) was performed to investigate the ultrastructural alterations induced by the interference of HCV replication with cellular homeostasis. Native, whole cell, three-dimensional (3D) maps were obtained in HCV replicon-harboring cells and in a surrogate model of HCV infection. Tomograms from HCV-replicating cells show blind-ended endoplasmic reticulum tubules with pseudospherical extrusions and marked alterations of mitochondrial morphology that correlated spatially with the presence of endoplasmic reticulum alterations, suggesting a short-range influence of the viral machinery on mitochondrial homeostasis. Both mitochondrial and endoplasmic reticulum alterations could be reverted by a combination of sofosbuvir/daclatasvir, which are clinically approved direct-acting antivirals for the treatment of chronic HCV infection. In addition to providing structural insight into cellular aspects of HCV pathogenesis, our study illustrates how cryo-SXT is a powerful 3D wide-field imaging tool for the assessment and understanding of complex cellular processes in a setting of near-native whole hydrated cells. Our results also constitute a proof of concept for the use of cryo-SXT as a platform that enables determining the potential impact of candidate compounds on the ultrastructure of the cell that may assist drug development at a preclinical level.

2-D soft x-ray arrays in the EAST.

A high spatial and temporal resolution soft x-ray (SXR) imaging diagnostic has been installed in EAST for the study of magnetohydrodynamics activities and core high-Z impurity transport. Up to 122 lines of sight view the poloidal plasma from three directions (two up-down symmetrical horizontal arrays and one vertical array), which renders the diagnostic able to provide detailed tomographic reconstructions under various conditions. Fourier-Bessel method based on flux coordinates was employed for 2-D SXR tomographic reconstruction. Examples of several events measured by SXR diagnostic in EAST are shown, namely the crash patterns of sawtooth, periodical burst of edge localized modes, and the transport of high-Z intrinsic impurities.

Herpes simplex virus 1 induces egress channels through marginalized host chromatin.

Lytic infection with herpes simplex virus type 1 (HSV-1) induces profound modification of the cell nucleus including formation of a viral replication compartment and chromatin marginalization into the nuclear periphery. We used three-dimensional soft X-ray tomography, combined with cryogenic fluorescence, confocal and electron microscopy, to analyse the transformation of peripheral chromatin during HSV-1 infection. Our data showed an increased presence of low-density gaps in the marginalized chromatin at late infection. Advanced data analysis indicated the formation of virus-nucleocapsid-sized (or wider) channels extending through the compacted chromatin of the host. Importantly, confocal and electron microscopy analysis showed that these gaps frequently contained viral nucleocapsids. These results demonstrated that HSV-1 infection induces the formation of channels penetrating the compacted layer of cellular chromatin and allowing for the passage of progeny viruses to the nuclear envelope, their site of nuclear egress.

Measurements of fast electron beams and soft X-ray emission from plasma-focus experiments

Abstract The paper reports results of the recent experimental studies of pulsed electron beams and soft X-rays in plasma-focus (PF) experiments carried out within a modified PF-360U facility at the NCBJ, Poland. Particular attention was focused on time-resolved measurements of the fast electron beams by means of two different magnetic analyzers, which could record electrons of energy ranging from about 41 keV to about 715 keV in several (6 or 8) measuring channels. For discharges performed with the pure deuterium filling, many strong electron signals were recorded in all the measuring channels. Those signals were well correlated with the first hard X-ray pulse detected by an external scintillation neutron-counter. In some of the analyzer channels, electron spikes (lasting about dozens of nanoseconds) and appearing in different instants after the current peculiarity (so-called current dip) were also recorded. For several discharges, fast ion beams, which were emitted along the z-axis and recorded with nuclear track detectors, were also investigated. Those measurements confirmed a multibeam character of the ion emission. The time-integrated soft X-ray images, which were taken side-on by means of a pinhole camera and sensitive X-ray films, showed the appearance of some filamentary structures and so-called hot spots. The application of small amounts of admixtures of different heavy noble gases, i.e. of argon (4.8% volumetric), krypton (1.6% volumetric), or xenon (0.8% volumetric), decreased intensity of the recorded electron beams, but increased intensity of the soft X-ray emission and showed more distinct and numerous hot spots. The recorded electron spikes have been explained as signals produced by quasi-mono-energetic microbeams emitted from tiny sources (probably plasma diodes), which can be formed near the observed hot spots.