Journal of Physics: Conference Series 849 (2017)

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.

Journal of Physics: Conference Series 849 (2017)

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.

Nano Letters 17 (2017)

We have investigated strained GaAs–GaInP core–shell nanowires using transmission electron microscopy and nanofocused scanning X-ray diffraction. Nominally identical growth conditions for each sample were achieved by using nanoimprint lithography to create wafer-scale arrays of Au seed particles. However, we observe large individual differences, with neighboring nanowires showing either straight, bent, or twisted morphology. Using scanning X-ray diffraction, we reconstructed and quantified the bending and twisting of the nanowires in three dimensions. In one nanowire, we find that the shell lattice is tilted with respect to the core lattice, with an angle that increases from 2° at the base to 5° at the top. Furthermore, the azimuthal orientation of the tilt changes by 30° along the nanowire axis. Our results demonstrate how strained core–shell nanowire growth can lead to a rich interplay of composition, lattice mismatch, bending and lattice tilt, with additional degrees of complexity compared with thin films.

Talanta 161 (2016)

Human dopaminergic system in general, and substantia nigra (SN) neurons, in particular, are implicated in the pathologies underlying the human brain aging. The interplay between aberrations in the structural organization and elemental composition of SN neuron bodies has recently gained in importance as selected metals: Fe, Cu, Zn, Ca were found to trigger oxidative-stress-mediated aberration in their molecular assembly due to concomitant protein (alpha-synuclein, tau-protein) aggregation, gliosis and finally oxidative stress. In the present study, we demonstrate an integrated approach to the analysis of the structural organization, assembly, and metals’ accumulation in two distinct areas of SN: in the neuromelanin neurons and neuropil. By using the highly brilliant source of PETRA III and the Kirkpatrick-Baez nano-focus, large area histological brain slices are scanned at the sub-neuronal resolution, taking advantage of continuous motor movement and reduced acquisition time. Elemental analysis with synchrotron radiation based X-ray Fluorescence (SRXRF) is combined with X-ray Phase Contrast Imaging (XPCI) to correct for inherent aberrations in the samples’ density and thickness, often referred to as the mass thickness effect. Based on the raw SRXRF spectra, we observed the accumulation of P, S, Cl, K, Ca, Fe, Cu and Zn predominantly in the SN neurons. However, upon the mass thickness correction, the distributions of Cl became significantly more uniform. Simultaneously with the fluorescence signal, the Small Angle X-ray Scattering (SAXS) is recorded by a pixel detector positioned in the far-field, enabling fast online computation of the darkfield and differential phase contrast (DPC). The data has demonstrated the SN neurons and neuropil produces excellent contrast which is due to their different mass density and scattering strength, indicative of differences in local structure and assembly therein. In all, the results show that combined SRXRF-XPCI-SAXS experiments can robustly serve as a unique tool for understanding the interplay between the chemical composition and structural organization that may drive the biochemical age-related processes occurring in the human dopaminergic system.

Biophysical Journal 110 (2016)

Adult human mesenchymal stem cells show structural rearrangements of their cytoskeletal network during mechanically induced differentiation toward various cell types. In particular, the alignment of acto-myosin fibers is cell fate-dependent and can serve as an early morphological marker of differentiation. Quantification of such nanostructures on a mesoscopic scale requires high-resolution imaging techniques. Here, we use small- angle x-ray scattering with a spot size in the micro- and submicrometer range as a high-resolution and label-free imaging technique to reveal structural details of stem cells and differentiated cell types. We include principal component analysis into an automated empirical analysis scheme that allows the local characterization of oriented structures. Results on freeze-dried samples lead to quantitative structural information for all cell lines tested: differentiated cells reveal pronounced structural orientation and a relatively intense overall diffraction signal, whereas naive human mesenchymal stem cells lack these features. Our data support the hypothesis of stem cells establishing ordered structures along their differentiation process.

Nature Materials 15 (2015)

In situ X-ray diffraction (XRD) and transmission electron microscopy (TEM) have been used to investigate many physical science phenomena, ranging from phase transitions, chemical reactions and crystal growth to grain boundary dynamics. A major limitation of in situ XRD and TEM is a compromise that has to be made between spatial and temporal resolution. Here, we report the development of in situ X-ray nanodiffraction to measure high-resolution diffraction patterns from single grains with up to 5 ms temporal resolution. We observed, for the first time, grain rotation and lattice deformation in chemical reactions induced by X-ray photons: Br⁻ + hν → Br + e⁻ and e⁻ + Ag⁺ → Ag⁰. The grain rotation and lattice deformation associated with the chemical reactions were quantified to be as fast as 3.25 rad s⁻¹ and as large as 0.5 Å, respectively. The ability to measure high-resolution diffraction patterns from individual grains with a temporal resolution of several milliseconds is expected to find broad applications in materials science, physics, chemistry and nanoscience.

Physical Review Letters 115 (2015)

We study the propagation of hard x rays in single curved x-ray waveguide channels and observe waveguide effects down to surprisingly small radii of curvature R≃10  mm and a large contour length s≃5  mm, deflecting beams up to 30°. At these high angles, about 2 orders of magnitude above the critical angle of total reflection θc, most radiation modes are lost by “leaking” into the cladding, while certain “survivor” modes persist. This may open up a new form of integrated x-ray optics “on a chip,” requiring curvatures mostly well below the extreme values studied here, e.g., to split and to delay x-ray pulses.

Journal of Applied Crystallography 48 (2015)

This article describes holographic imaging experiments using a hard X-ray multilayer zone plate (MZP) with an outermost zone width of 10 nm at a photon energy of 18 keV. An order-sorting aperture (OSA) is omitted and emulated during data analysis by a “software OSA”. Scanning transmission X-ray microscopy usually carried out in the focal plane is generalized to the holographic regime. The MZP focus is characterized by a three-plane phase-retrieval algorithm to an FWHM of 10 nm.

Journal of Synchrotron Radiation 22 (4) (2015)

A compound optical system for coherent focusing and imaging at the nanoscale is reported, realised by high-gain fixed-curvature elliptical mirrors in combination with X-ray waveguide optics or different cleaning apertures. The key optical concepts are illustrated, as implemented at the Göttingen Instrument for Nano-Imaging with X-rays (GINIX), installed at the P10 coherence beamline of the PETRA Ⅲ storage ring at DESY, Hamburg, and examples for typical applications in biological imaging are given. Characteristic beam configurations with the recently achieved values are also described, meeting the different requirements of the applications, such as spot size, coherence or bandwidth. The emphasis of this work is on the different beam shaping, filtering and characterization methods.

Journal of Applied Crystallography 48 (2015)

Simultaneous scanning Bragg contrast and small-angle ptychographic imaging of a single solar cell nanowire are demonstrated, using a nanofocused hard X-ray beam and two detectors. The 2.5 µm-long nanowire consists of a single-crystal InP core of 190 nm diameter, coated with amorphous SiO₂ and polycrystalline indium tin oxide. The nanowire was selected and aligned in real space using the small-angle scattering of the 140 × 210 nm X-ray beam. The orientation of the nanowire, as observed in small-angle scattering, was used to find the correct rotation for the Bragg condition. After alignment in real space and rotation, high-resolution (50 nm step) raster scans were performed to simultaneously measure the distribution of small-angle scattering and Bragg diffraction in the nanowire. Ptychographic reconstruction of the coherent small-angle scattering was used to achieve sub-beam spatial resolution. The small-angle scattering images, which are sensitive to the shape and the electron density of all parts of the nanowire, showed a homogeneous profile along the nanowire axis except at the thicker head region. In contrast, the scanning Bragg diffraction microscopy, which probes only the single-crystal InP core, revealed bending and crystalline inhomogeneity. Both systematic and non-systematic real-space movement of the nanowire were observed as it was rotated, which would have been difficult to reveal only from the Bragg scattering. These results demonstrate the advantages of simultaneously collecting and analyzing the small-angle scattering in Bragg diffraction experiments.

Advanced Materials 2015 (2015)

Hard X-ray diffraction (XRD) using a nanofocused beam is used to measure both lattice contraction and bending in a single nanowire device under electric bias. The shape of the nanowire is reconstructed in 3D with sub-nm precision. As the bias voltage is gradually increased, nonreversible structural changes in the contact regions are observed, correlated with degradation of the electrical conductance.

Nano Letters 14 (12) (2014)

Submicron sized sensors could allow higher resolution in X-ray imaging and diffraction measurements, which are ubiquitous for materials science and medicine. We present electrical measurements of a single 100 nm diameter InP nanowire transistor exposed to hard X-rays. The X-ray induced conductance is over 5 orders of magnitude larger than expected from reported data for X-ray absorption and carrier lifetimes. Time-resolved measurements show very long characteristic lifetimes on the order of seconds, tentatively attributed to long-lived traps, which give a strong amplification effect. As a proof of concept, we use the nanowire to directly image an X-ray nanofocus with submicron resolution.

Physical Review Letters 113 (2014)

We use standing surface acoustic waves to induce coherent phonons in model lipid multilayers deposited on a piezoelectric surface. Probing the structure by phase-controlled stroboscopic x-ray pulses we find that the internal lipid bilayer electron density profile oscillates in response to the externally driven motion of the lipid film. The structural response to the well-controlled motion is a strong indication that bilayer structure and membrane fluctuations are intrinsically coupled, even though these structural changes are averaged out in equilibrium and time integrating measurements. Here the effects are revealed by a timing scheme with temporal resolution on the picosecond scale in combination with the sub-nm spatial resolution, enabled by high brilliance synchrotron x-ray reflectivity.

Applied Surface Science 307 (2014)

Recently, we demonstrated unprecedented sub-5 nm point focusing of hard X-rays (at 7.9 keV) based on the combination of a high gain Kirkpatrick–Baez (KB) mirror system and a high resolution W/Si multilayer zone plate (MZP). This MZP was prepared by the combination of pulsed laser deposition (PLD) and focused ion beam (FIB). Despite the small focus size, the MZP's quality suffered from sufficient but comparatively low efficiency (2%). In this paper we discuss how to overcome limitations of MZP fabrication by PLD by investigating the material systems W/Si, W/ZrO₂, and Ta₂O₅/ZrO₂. We give a detailed description on the optimization processes for the deposition of smooth multilayers with highly precise layer thicknesses on a rotating wire. Furthermore, we present our latest results regarding a Ta₂O₅/ZrO₂ MZP, which has been proven already to be a system of high potential in the very first experiments as the efficiency reached 6.9% (at 18 keV).

Journal of Synchrotron Radiation 21 (2014)

Coherent (X-ray) diffractive imaging (CDI) is an increasingly popular form of X-ray microscopy, mainly due to its potential to produce high-resolution images and the lack of an objective lens between the sample and its corresponding imaging detector. One challenge, however, is that very high dynamic range diffraction data must be collected to produce both quantitative and high-resolution images. In this work, hard X-ray ptychographic coherent diffractive imaging has been performed at the P10 beamline of the PETRA III synchrotron to demonstrate the potential of a very wide dynamic range imaging X-ray detector (the Mixed-Mode Pixel Array Detector, or MM-PAD). The detector is capable of single photon detection, detecting fluxes exceeding 1×10⁸ 8 keV photons pixel⁻¹ s⁻¹, and framing at 1 kHz. A ptychographic reconstruction was performed using a peak focal intensity on the order of 1×10¹⁰ photons µm⁻² s⁻¹ within an area of approximately 325 nm × 603 nm. This was done without need of a beam stop and with a very modest attenuation, while “still” images of the empty beam far-field intensity were recorded without any attenuation. The treatment of the detector frames and CDI methodology for reconstruction of non-sensitive detector regions, partially also extending the active detector area, are described.

Acta Crystallographica A 70 (2014)

Suitable detection systems that are capable of recording high photon count rates with single-photon detection are instrumental for coherent X-ray imaging. The new single-photon-counting pixel detector “Lambda” has been tested in a ptychographic imaging experiment on solar-cell nanowires using Kirkpatrick-Baez-focused 13.8 keV X-rays. Taking advantage of the high count rate of the Lambda and dynamic range expansion by the semi-transparent central stop, a high-dynamic-range diffraction signal covering more than seven orders of magnitude has been recorded, which corresponds to a photon flux density of about 10⁵ photons nm⁻² s⁻¹ or a flux of ~10¹⁰ photons s⁻¹ on the sample. By comparison with data taken without the semi-transparent central stop, an increase in resolution by a factor of 3–4 is determined: from about 125 nm to about 38 nm for the nanowire and from about 83 nm to about 21 nm for the illuminating wavefield.

Journal of Applied Crystallography 47 (2014)

Time-resolved coherent X-ray diffraction experiments of standing surface acoustic waves, illuminated under grazing incidence by a nanofocused synchrotron beam, are reported. The data have been recorded in stroboscopic mode at controlled and varied phase between the acoustic frequency generator and the synchrotron bunch train. At each time delay (phase angle), the coherent far-field diffraction pattern in the small-angle regime is inverted by an iterative algorithm to yield the local instantaneous surface height profile along the optical axis. The results show that periodic nanoscale dynamics can be imaged at high temporal resolution in the range of 50 ps (pulse length).

Journal of Synchrotron Radiation 21 (2014)

The technical realisation and the commissioning experiments of a high-speed X-ray detector based on a quadrant avalanche silicon photodiode and high-speed digitizers are described. The development is driven by the need for X-ray detectors dedicated to time-resolved diffraction and imaging experiments, ideally requiring pulse-resolved data processing at the synchrotron bunch repetition rate. By a novel multi-photon detection scheme, the exact number of X-ray photons within each X-ray pulse can be recorded. Commissioning experiments at beamlines P08 and P10 of the storage ring PETRA Ⅲ, at DESY, Hamburg, Germany, have been used to validate the pulse-wise multi-photon counting scheme at bunch frequencies ≥31 MHz, enabling pulse-by-pulse readout during the PETRA Ⅲ 240-bunch mode with single-photon detection capability. An X-ray flux of ≥3.7×10⁹ photons s⁻¹ can be detected while still resolving individual photons at low count rates.

Physical Review Letters 111 (2013)

We study the nonequilibrium shape fluctuations in fluorescence labeled phospholipid multibilayers composed of the model lipid DOPC and the well-known lipid dye Texas red, driven out of equilibrium by short laser pulses. The temporal evolution of the lipid bilayer undulations after excitation was recorded by time resolved x-ray diffraction. Already at moderate peak intensities (P_p≤10⁵ W/cm²), pulsed laser illumination leads to significant changes of the undulation modes in a well-defined lateral wavelength band. The observed phenomena evolve on nano- to microsecond time scales after optical excitation, and can be described in terms of a modulation instability in the lipid multilamellar stack.

Optics Express 21 (2013)

Compound optics such as lens systems can overcome the limitations concerning resolution, efficiency, or aberrations which fabrication constraints would impose on any single optical element. In this work we demonstrate unprecedented sub-5 nm point focusing of hard x-rays, based on the combination of a high gain Kirkpatrick-Baez (KB) mirror system and a high resolution W/Si multilayer zone plate (MZP) for ultra-short focal length f. The pre-focusing allows limiting the MZP radius to below 2 μm, compatible with the required 5 nm structure width and essentially unlimited aspect ratios, provided by enabling fabrication technology based on pulsed laser deposition (PLD) and focused ion beam (FIB).

Optics Letters 38 (23) (2013)

We present numerical simulations optimizing the layer shapes of curved focusing x-ray multilayer mirrors deployed at synchrotron radiation facilities using a wave-optical model. The confocal elliptical shapes of the inner layers are corrected for refraction based on the modified Bragg law. Simulated wave amplitudes are further propagated to the focal region, promising nanometer focusing.

Journal of Synchrotron Radiation 20 (2013)

In the past decade Kirkpatrick-Baez (KB) mirrors have been established as powerful focusing systems in hard X-ray microscopy applications. Here a ptychographic characterization of the KB focus in the dedicated nano-imaging setup GINIX (Göttingen Instrument for Nano-Imaging with X-rays) at the P10 coherence beamline of the PETRA Ⅲ synchrotron at HASLYLAB/DESY, Germany, is reported. More specifically, it is shown how aberrations in the KB beam, caused by imperfections in the height profile of the focusing mirrors, can be eliminated using a pinhole as a spatial filter near the focal plane. A combination of different pinhole sizes and illumination conditions of the KB setup makes the prepared optical setup well suited not only for high-resolution ptychographic coherent X-ray diffractive imaging but also for moderate-resolution/large-field-of-view propagation imaging in the divergent KB beam.

Optics Express 21 (2013)

The spatial coherence of free-electron laser radiation in the water window spectral range was studied, using the third harmonic (λ₃=2.66 nm) of DESY's Free-electron LASer in Hamburg (FLASH). Coherent single pulse diffraction patterns of 1,2-Dioleoyl-sn-glycero-3-phosphocholine (DOPC) multilamellar lipid stacks have been recorded. The intensity histogram of the speckle pattern around the first lamellar Bragg peak, corresponding to the d=5 nm periodicity of the stack, reveals an average number of transverse modes of M̄=3.0 of the 3rd harmonic. Using the lipid stack as a “monochromator”, pulse-to-pulse fluctuations in the third harmonic λ₃ have been determined to be 0.033 nm.

AIP Advances 3 (2013)

We have carried out time resolved stroboscopic diffraction experiments on standing surface acoustic waves (SAWs) of Rayleigh type on a LiNbO₃ substrate. A novel timing system has been developed and commissioned at the storage ring Petra Ⅲ of DESY, allowing for phase locked stroboscopic diffraction experiments applicable to a broad range of timescales and experimental conditions. The combination of atomic structural resolution with temporal resolution on the picosecond time scale allows for the observation of the atomistic displacements for each time (or phase) point within the SAW period. A seamless transition between dynamical and kinematic scattering regimes as a function of the instantaneous surface amplitude induced by the standing SAW is observed. The interpretation and control of the experiment, in particular disentangling the diffraction effects (kinematic to dynamical diffraction regime) from possible non-linear surface effects is unambiguously enabled by the precise control of phase between the standing SAW and the synchrotron bunches. The example illustrates the great flexibility and universality of the presented timing system, opening up new opportunities for a broad range of time resolved experiments.

Optics Letters 37 (17) (2012)

We have derived a wave-optical model of curved nanofocusing x-ray multilayer mirrors used at synchrotron radiation sources, using a Takagi–Taupin-like approach. In a first approximation, the individual layers are assumed to be confocal elliptical. This assumption leads to a convenient spatial description in elliptical coordinates. As a first optimization, we study a rotation-like modification and compare numerical simulations to established results for planar multilayers.

AIP Advances 2 (2012)

We have used a combined optical system of a high gain elliptic Kirkpatrick-Baez mirror system (KB) and a multilayer Laue lens (MLL) positioned in the focal plane of the KB for hard x-rays nano-focusing. The two-step focusing scheme is based on a high acceptance and high gain elliptical mirror with moderate focal length and a MLL with ultra-short focal length. Importantly, fabrication constraints, i.e. in mirror polishing and bending, as well as MLL deposition can be significantly relaxed, since (a) the mirror focus in the range of 200–500 nm is sufficient, and (b) the number of layers of the MLL can be correspondingly small. First demonstrations of this setup at the coherence beamline of the PETRA Ⅲ storage ring yield a highly divergent far-field diffraction pattern, from which the autocorrelation function of the near-field intensity distribution was obtained. The results show that the approach is well suited to reach smallest spot sizes in the sub-10 nm range at high flux.

New Journal of Physics 13 (2011)

We model and describe the spatial coherence and mutual intensity of focused synchrotron radiation x-ray beams, based on ensemble averages of stochastic superpositions. Within this framework, we present numerical calculations for typical synchrotron sources with focusing mirrors, and simulate the evolution of coherence inside x-ray waveguides used for filtering by analytical and numerical methods. Simulated focus fields are compared with an experimental setup, including figure errors and vibrations.

Optics Express 19 (2011)

We have studied the spatial coherence properties of a nano-focused x-ray beam by grating (Talbot) interferometry in projection geometry. The beam is focused by a fixed curvature mirror system optimized for high flux density under conditions of partial coherence. The spatial coherence of the divergent exit wave emitted from the mirror focus is measured by Talbot interferometry The results are compared to numerical calculations of coherence propagation. In view of imaging applications, the magnified in-line image of a test pattern formed under conditions of partial coherence is analyzed quantitatively. Finally, additional coherence filtering by use of x-ray waveguides is demonstrated. By insertion of x-ray waveguides, the beam diameter can be reduced from typical values of 200 nm to values below 15 nm. In proportion to the reduction in the focal spot size, the numerical aperture (NA) of the projection imaging system is increased, as well as the coherence length, as quantified by grating interferometry.

AIP Conference Proceedings 1365 (2011)

We report the commissioning of the novel holography endstation for the P10 coherence beamline at PETRA III at DESY. The experimental imaging scheme is based on a highly coherent and divergent (cone) beam illumination, achieved by fixed‐curvature focusing mirrors with additional spatial and coherence filtering by x‐ray waveguides. The optical elements along the beam path and the instrument in commissioning are described. First experimental results are shown.

AIP Conference Proceedings 1234 (2010)

We present the design and instrumentation of a novel holography endstation for the P10 coherence beamline at PETRA Ⅲ at DESY. The experimental imaging scheme is based on a highly coherent and divergent (cone) beam illumination, achieved by fixed curvature focusing mirrors with additional spatial and coherence filtering by x‐ray waveguides. The optical elements along the beam path and the instrument under construction are described. Preliminary results obtained in a similar setting under comparable parameters are given as a benchmark, and first simulations of one of the two mirrors are presented to study the effect of imperfections on the field distribution in the focal plane.

Optics Communications 282 (2009)

We generalize the optical treatment of X-ray waveguides to index profiles of arbitrary shape. The modes of the waveguides are computed numerically by Numerov’s method. The method is first validated by considering profiles for which analytical solutions exist. Next, the effects of different shape functions and of interfacial roughness on the near and far-field intensity distributions are studied. The results are helpful to judge the real structure effects, e.g. resulting from fabrication imperfections, on the optical performance, as well as to optimize optical properties by designing generalized index profiles.