Probe retrieval in ptychographic coherent diffractive imaging.

Ptychography is a coherent diffractive imaging method that uses multiple diffraction patterns obtained through the scan of a localized illumination on the specimen. Until recently, reconstruction algorithms for ptychographic datasets needed the a priori knowledge of the incident illumination. A new reconstruction procedure that retrieves both the specimen's image and the illumination profile was recently demonstrated with hard X-ray data.

A Geiger-mode avalanche photodiode array for X-ray photon correlation spectroscopy.

X-ray photon correlation spectroscopy (XPCS) provides an opportunity to study the dynamics of systems by measuring the temporal fluctuations in a far-field diffraction pattern. A two-dimensional detector system has been developed to investigate fluctuations in the frequency range of several Hz to kHz. The X-ray detector system consists of a thin 100 microm scintillation crystal coupled to a Geiger-mode avalanche photodiode array.

Hard X-ray phase-contrast imaging with the Compact Light Source based on inverse Compton X-rays.

The first imaging results obtained from a small-size synchrotron are reported. The newly developed Compact Light Source produces inverse Compton X-rays at the intersection point of the counter propagating laser and electron beam. The small size of the intersection point gives a highly coherent cone beam with a few milliradian angular divergence and a few percent energy spread.

Structure of confined fluids by x-ray interferometry using diffraction gratings.

We develop a novel method for structure determination of confined fluids using diffraction-grating-based x-ray interferometry.Within this approach, diffraction from a microfluidic array, which acts both as confinement and transmission diffraction grating, provides the reference wave, whereas the density modulations of the confined fluid, acting as a weak phase object, generate the object wave. The ensemble-averaged density profile of the fluid perpendicular to the confining channel is then unambiguously obtained from the interference between the reference and object waves by direct Fourier inversion.

The fractional Talbot effect in differential x-ray phase-contrast imaging for extended and polychromatic x-ray sources.

The influence of different physical parameters, such as the source size and the energy spectrum, on the functional capability of a grating interferometer applied for phase-contrast imaging is discussed using numerical simulations based on Fresnel diffraction theory. The presented simulation results explain why the interferometer could be well combined with polychromatic laboratory x-ray sources in recent experiments. Furthermore, it is shown that the distance between the two gratings of the interferometer is not in general limited by the width of the photon energy spectrum.

Region-of-interest tomography for grating-based X-ray differential phase-contrast imaging.

We report numerical and experimental results demonstrating accurate region-of-interest computed tomography (CT) reconstruction based on differential phase-contrast projection (DPC) images. The approach removes the constraint of covering the entire sample within the field of view of the image detector. Particularly for biomedical applications, the presented DPC-CT region-of-interest approach will allow for the visualization of previously inaccessible details deep inside an entire animal or organ.

Colloidal monolayer trapped near a charged wall: a synchrotron x-ray diffraction study.

Using x-ray diffraction from microfluidic channel arrays, we have determined concentration profiles of charge-stabilized silica colloids (radius 60+/-2 nm) confined between two like-charged dielectric walls at a few hundred nanometer distance. In solutions of very low ionic strength, strongly repulsive Coulomb interactions drive the colloids toward the central region between the walls. The addition of a small quantity of salt ions (0.

Neutron dark-field tomography.

We report how a grating interferometer yields neutron dark-field scatter images for tomographic investigations. The image contrast is based on ultrasmall-angle scattering. It provides otherwise inaccessible spatially resolved information about the distribution of micrometer and submicrometer sized structural formations.

Neutron decoherence imaging for visualizing bulk magnetic domain structures.

Here we introduce a novel neutron imaging method, which is based on the effect that the spatial coherence of the neutron wave front can be changed through small-angle scattering of neutrons at magnetic domain walls in the specimen. We show that the technique can be used to visualize internal bulk magnetic domain structures that are difficult to access by other techniques. The method is transferable to a wide variety of specimens, extendable to three dimensions, and well suited for investigating materials under the influence of external parameters, as, e.

High-resolution scanning x-ray diffraction microscopy.

Coherent diffractive imaging (CDI) and scanning transmission x-ray microscopy (STXM) are two popular microscopy techniques that have evolved quite independently. CDI promises to reach resolutions below 10 nanometers, but the reconstruction procedures put stringent requirements on data quality and sample preparation. In contrast, STXM features straightforward data analysis, but its resolution is limited by the spot size on the specimen.

Genome information management and integrated data analysis with HaloLex.

HaloLex is a software system for the central management, integration, curation, and web-based visualization of genomic and other -omics data for any given microorganism. The system has been employed for the manual curation of three haloarchaeal genomes, namely Halobacterium salinarum (strain R1), Natronomonas pharaonis, and Haloquadratum walsbyi. HaloLex, in particular, enables the integrated analysis of genome-wide proteomic results with the underlying genomic data.

X-ray phase radiography and tomography of soft tissue using grating interferometry.

X-ray phase and absorption radiographs and tomograms of the heart of a rat were taken with an X-ray grating interferometer with monochromatic synchrotron radiation at a photon energy of 17.5 keV. The phase images show largely superior quality with respect to the absorption images taken with the same dose, particularly much better contrast and contrast-to-noise ratio.

Coherent diffractive imaging using phase front modifications.

We introduce a coherent diffractive imaging technique that utilizes multiple exposures with modifications to the phase profile of the transmitted wave front to compensate for the missing phase information. This is a single spot technique sensitive to both the transmission and phase shift through the sample. Along with the details of the method, we present results from the first proof of principle experiment.

Design, fabrication, and characterization of diffraction gratings for neutron phase contrast imaging.

We have developed a neutron phase contrast imaging method based on a grating interferometer setup. The principal constituents are two absorption gratings made of gadolinium and a phase modulating grating made of silicon. The design parameters of the setup, such as periodicity, structure heights of the gratings, and the distances between the gratings, are calculated.

Evolution in the laboratory: the genome of Halobacterium salinarum strain R1 compared to that of strain NRC-1.

We report the sequence of the Halobacterium salinarum strain R1 chromosome and its four megaplasmids. Our set of protein-coding genes is supported by extensive proteomic and sequence homology data. The structures of the plasmids, which show three large-scale duplications (adding up to 100 kb), were unequivocally confirmed by cosmid analysis.

Towards environmentally friendly, dry deposited, water developable molecular glass photoresists.

Photoresists based on molecular glasses are gaining more and more importance as resist material to replace polymer based photoresist. In addition environmental issues have to be considered in the long-term. Therefore the paper describes novel negative photoresists containing a ternary mixture of a glassy low molecular functional polyphenol where the film preparation is possible by solvent-free physical vapor deposition.

Metabolism of halophilic archaea.

In spite of their common hypersaline environment, halophilic archaea are surprisingly different in their nutritional demands and metabolic pathways. The metabolic diversity of halophilic archaea was investigated at the genomic level through systematic metabolic reconstruction and comparative analysis of four completely sequenced species: Halobacterium salinarum, Haloarcula marismortui, Haloquadratum walsbyi, and the haloalkaliphile Natronomonas pharaonis. The comparative study reveals different sets of enzyme genes amongst halophilic archaea, e.

Reconstruction, modeling & analysis of Halobacterium salinarum R-1 metabolism.

We present a genome-scale metabolic reconstruction for the extreme halophile Halobacterium salinarum. The reconstruction represents a summary of the knowledge regarding the organism's metabolism, and has already led to new research directions and improved the existing annotation. We used the network for computational analysis and studied the aerobic growth of the organism using dynamic simulations in media with 15 available carbon and energy sources.

Hard-X-ray dark-field imaging using a grating interferometer.

Imaging with visible light today uses numerous contrast mechanisms, including bright- and dark-field contrast, phase-contrast schemes and confocal and fluorescence-based methods. X-ray imaging, on the other hand, has only recently seen the development of an analogous variety of contrast modalities. Although X-ray phase-contrast imaging could successfully be implemented at a relatively early stage with several techniques, dark-field imaging, or more generally scattering-based imaging, with hard X-rays and good signal-to-noise ratio, in practice still remains a challenging task even at highly brilliant synchrotron sources.

A small protein from the bop-brp intergenic region of Halobacterium salinarum contains a zinc finger motif and regulates bop and crtB1 transcription.

Bacteriorhodopsin, the photosynthetic protein of Halobacterium salinarum, is optimally expressed under anaerobic growth conditions. We identified Brz (OE3104F, bacteriorhodopsin-regulating zinc finger protein), a new regulator of the bop gene. It is a small protein with a zinc finger motif, encoded directly upstream of the bop gene in the same orientation.

X-ray imaging with the PILATUS 100k detector.

We report on the application of the PILATUS 100K pixel detector for medical imaging. Experimental results are presented in the form of X-ray radiographs using standard X-ray absorption contrast and a recently developed phase contrast imaging method. The results obtained with the PILATUS detector are compared to results obtained with a conventional X-ray imaging system consisting of an X-ray scintillation screen, lens optics, and a charge coupled device.

High-resolution brain tumor visualization using three-dimensional x-ray phase contrast tomography.

We report on significant advances and new results concerning a recently developed method for grating-based hard x-ray phase tomography. We demonstrate how the soft tissue sensitivity of the technique is increased and show in vitro tomographic images of a tumor bearing rat brain sample, without use of contrast agents. In particular, we observe that the brain tumor and the white and gray brain matter structure in a rat's cerebellum are clearly resolved.

Microarray analysis in the archaeon Halobacterium salinarum strain R1.

Background: Phototrophy of the extremely halophilic archaeon Halobacterium salinarum was explored for decades. The research was mainly focused on the expression of bacteriorhodopsin and its functional properties. In contrast, less is known about genome wide transcriptional changes and their impact on the physiological adaptation to phototrophy.

Inspection of refractive X-ray lenses using high-resolution differential phase contrast imaging with a microfocus X-ray source.

A refractive x-ray lens was characterized using a magnifying cone beam setup for differential phase contrast imaging in combination with a microfocus x-ray tube. Thereby, the differential and the total phase shift of x rays transmitted through the lens were determined. Lens aberrations have been characterized based on these refractive properties.