Pump-probe X-ray holographic imaging of laser-induced cavitation bubbles with femtosecond FEL pulses.

Cavitation bubbles can be seeded from a plasma following optical breakdown, by focusing an intense laser in water. The fast dynamics are associated with extreme states of gas and liquid, especially in the nascent state. This offers a unique setting to probe water and water vapor far-from equilibrium. However, current optical techniques cannot quantify these early states due to contrast and resolution limitations. X-ray holography with single X-ray free-electron laser pulses has now enabled a quasi-instantaneous high resolution structural probe with contrast proportional to the electron density of the object. In this work, we demonstrate cone-beam holographic flash imaging of laser-induced cavitation bubbles in water with nanofocused X-ray free-electron laser pulses. We quantify the spatial and temporal pressure distribution of the shockwave surrounding the expanding cavitation bubble at time delays shortly after seeding and compare the results to numerical simulations.

Iterative micro-tomography of biopsy samples from truncated projections with quantitative gray values.

Three-dimensional reconstruction from truncated two-dimensional projections cannot be solved analytically without prior knowledge of the sample or access to the non-truncated projections. To suppress reconstruction artifacts in region of interest (ROI) or local tomography, an iterative algorithm has been devised based on back-projection and re-projection, assuming an approximately cylindrical shape of the entire sample of general homogeneity, which is especially applicable for micro-tomography of biopsy samples from biological tissue. Tomographic reconstruction is iteratively refined by minimizing the mismatch between an empty ROI and the reconstruction from the difference between measured sinogram and forward projected ROI reconstruction. By numerical simulation and experimental demonstration, it is shown that the algorithm is not only able to reconstruct quantitative gray values, but also to reduce artifacts of peripheral glow, and may lead to increased image sharpness. The method is particularly suitable for examination of biopsy/autopsy-samples of soft tissue by micro/nano-computed tomography.

Spectral µCT with an energy resolving and interpolating pixel detector.

A main challenge in x-ray µCT with laboratory radiation derives from the broad spectral content, which in contrast to monochromatic synchrotron radiation gives rise to reconstruction artifacts and impedes quantitative reconstruction. Due to the low spectral brightness of these sources, monochromatization is unfavorable and parallel recording of a broad bandpath is practically indispensable. While conventional CT sums up all spectral components into a single detector value, spectral CT discriminates the data in several spectral bins. Here we show that a new generation of charge integrating and interpolating pixel detectors is ideally suited to implement spectral CT with a resolution in the range of 10 µm. We find that the information contained in several photon energy bins largely facilitates automated classification of materials, as demonstrated for of a mouse cochlea. Bones, soft tissues, background and metal implant materials are discriminated automatically. Importantly, this includes taking a better account of phase contrast effects, based on tailoring reconstruction parameters to specific energy bins.

Correlative microscopy approach for biology using X-ray holography, X-ray scanning diffraction and STED microscopy.

We present a correlative microscopy approach for biology based on holographic X-ray imaging, X-ray scanning diffraction, and stimulated emission depletion (STED) microscopy. All modalities are combined into the same synchrotron endstation. In this way, labeled and unlabeled structures in cells are visualized in a complementary manner. We map out the fluorescently labeled actin cytoskeleton in heart tissue cells and superimpose the data with phase maps from X-ray holography. Furthermore, an array of local far-field diffraction patterns is recorded in the regime of small-angle X-ray scattering (scanning SAXS), which can be interpreted in terms of biomolecular shape and spatial correlations of all contributing scattering constituents. We find that principal directions of anisotropic diffraction patterns coincide to a certain degree with the actin fiber directions and that actin stands out in the phase maps from holographic recordings. In situ STED recordings are proposed to formulate models for diffraction data based on co-localization constraints.

Publisher Correction: Four dimensional material movies: High speed phase-contrast tomography by backprojection along dynamically curved paths.

A correction to this article has been published and is linked from the HTML and PDF versions of this paper. The error has been fixed in the paper.

Four dimensional material movies: High speed phase-contrast tomography by backprojection along dynamically curved paths.

We present an approach towards four dimensional (4d) movies of materials, showing dynamic processes within the entire 3d structure. The method is based on tomographic reconstruction on dynamically curved paths using a motion model estimated by optical flow techniques, considerably reducing the typical motion artefacts of dynamic tomography. At the same time we exploit x-ray phase contrast based on free propagation to enhance the signal from micron scale structure recorded with illumination times down to a millisecond (ms). The concept is demonstrated by observing the burning process of a match stick in 4d, using high speed synchrotron phase contrast x-ray tomography recordings. The resulting movies reveal the structural changes of the wood cells during the combustion.

Erratum: X-Ray Optics on a Chip: Guiding X Rays in Curved Channels [Phys. Rev. Lett. 115, 203902 (2015)].

This corrects the article DOI: 10.1103/PhysRevLett.115.203902.

How many photons are needed to reconstruct random objects in coherent X-ray diffractive imaging?

This paper presents an investigation of the reconstructibility of coherent X-ray diffractive imaging diffraction patterns for a class of binary random `bitmap' objects. Combining analytical results and numerical simulations, the critical fluence per bitmap pixel is determined, for arbitrary contrast values (absorption level and phase shift), both for the optical near- and far-field. This work extends previous investigations based on information theory, enabling a comparison of the amount of information carried by single photons in different diffraction regimes. The experimental results show an order-of-magnitude agreement.

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

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

Combined in-situ imaging of structural organization and elemental composition of substantia nigra neurons in the elderly.

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.

Using sparsity information for iterative phase retrieval in x-ray propagation imaging.

For iterative phase retrieval algorithms in near field x-ray propagation imaging experiments with a single distance measurement, it is indispensable to have a strong constraint based on a priori information about the specimen; for example, information about the specimen's support. Recently, Loock and Plonka proposed to use the a priori information that the exit wave is sparsely represented in a certain directional representation system, a so-called shearlet system. In this work, we extend this approach to complex-valued signals by applying the new shearlet constraint to amplitude and phase separately. Further, we demonstrate its applicability to experimental data.

New X-Ray Tomography Method Based on the 3D Radon Transform Compatible with Anisotropic Sources.

In this work, we propose a novel computed tomography (CT) approach for three-dimensional (3D) object reconstruction, based on a generalized tomographic geometry with two-dimensional angular sampling (two angular degrees of freedom). The reconstruction is based on the 3D Radon transform and is compatible with anisotropic beam conditions. This allows isotropic 3D imaging with a source, which can be extended along one direction for increased flux, while high resolution is achieved by a small source size only in the orthogonal direction. This novel scheme for analytical CT is demonstrated by numerical simulations and proof-of-concept experiments. In this way high resolution and coherence along a single direction determines the reconstruction quality of the entire 3D data set, opening up, for example, new opportunities to achieve nanoscale resolution and/or phase contrast with low brilliance sources such as laboratory x-ray or neutron sources.

Actin bundles cross-linked with α-actinin studied by nanobeam X-ray diffraction.

We have performed scanning nano-beam small-angle X-ray scattering (nano-SAXS) experiments on in vitro-formed actin filaments cross-linked with [Formula: see text]-actinin. The experimental method combines a high resolution in reciprocal space with a real space resolution as given by the spot-size of the nano-focused X-ray beam, and opens up new opportunities to study local super-molecular structures of actin filaments. In this first proof-of-concept, we show that the local orientation of actin bundles formed by the cross-linking can be visualized by the X-ray darkfield maps. The filament bundles give rise to highly anisotropic diffraction patterns showing distinct streaks perpendicular to the bundle axes. Interestingly, some diffraction patterns exhibit a fine structure in the form of intensity modulations allowing for a more detailed analysis of the order within the bundles. A first empirical quantification of these modulations is included in the present work.

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

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

X-Ray Optics on a Chip: Guiding X Rays in Curved Channels.

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 θ(c), 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.

Quantitative X-ray phase contrast waveguide imaging of bacterial endospores.

Quantitative waveguide-based X-ray phase contrast imaging has been carried out on the level of single, unstained, unsliced and freeze-dried bacterial cells of Bacillus thuringiensis and Bacillus subtilis using hard X-rays of 7.9 keV photon energy. The cells have been prepared in the metabolically dormant state of an endospore. The quantitative phase maps obtained by iterative phase retrieval using a modified hybrid input-output algorithm allow for mass and mass density determinations on the level of single individual endospores but include also large field of view investigations. Additionally, a direct reconstruction based on the contrast transfer function is investigated, and the two approaches are compared. Depending on the field of view and method, a resolution down to 65 nm was achieved at a maximum applied dose of below 5 × 105 Gy. Masses in the range of about ∼110-190 (20) fg for isolated endospores have been obtained.

X-ray holographic imaging of hydrated biological cells in solution.

We demonstrate nanoscale x-ray holographic imaging using optimized illumination wave fronts emitted by x-ray waveguide channels. Mode filtering minimizes wave-front distortions and artifacts encountered in most hard x-ray focusing schemes, enabling quantitative reconstruction of the projected density, as evidenced by a test pattern imaged with a field of view of about 20×40 µm and at 22 nm resolution. The dose efficiency and contrast sensitivity make the optical scheme compatible with samples of intrinsically low contrast, typical for hydrated soft matter. This is demonstrated by imaging bacteria in the hydrated and living state, with quantitative phase contrast revealing dense structures of the bacterial nucleoids associated with compactified DNA. In response to continued irradiation, characteristic changes in these dense structures are observed.

Collective lipid bilayer dynamics excited by surface acoustic waves.

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.

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

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

Phase retrieval for object and probe using a series of defocus near-field images.

Full field x-ray propagation imaging can be severely deteriorated by wave front aberrations. Here we present an extension of ptychographic phase retrieval with simultaneous probe and object reconstruction suitable for the near-field diffractive imaging setting. Update equations used to iteratively solve the phase problem from a set of near-field images in view of reconstruction both object and probe are derived. The algorithm is tested based on numerical simulations including photon shot noise. The results indicate that the approach provides an efficient way to overcome restrictive idealizations of the illumination wave in the near-field (propagation) imaging.