http://research.engr.oregonstate.edu/immiscibles/sites/research.engr.oregonstate.edu.immiscibles/files/Papers/Wildenschild_Sheppard_AWR_2012.pdf

X-ray imaging and analysis techniques for quantifying pore-scale structure and processes in subsurface porous medium systems

The DIALS project is a collaboration between Diamond Light Source, Lawrence Berkeley National Laboratory and CCP4 to develop a new software suite for the analysis of crystallographic X-ray diffraction data, initially encompassing spot finding, indexing, refinement and integration. The design, core algorithms and structure of the software are introduced, alongside results from the analysis of data from biological and chemical crystallography experiments.

/pdf/dials-implementation-and-evaluation-of-a-new-integration-4cyo1zqxbp.pdf

DIALS: implementation and evaluation of a new integration package

Progress in imaging and metrology depends on exquisite control over and comprehensive characterization of wave fields. As reflected in its name, coherent diffractive imaging relies on high coherence when reconstructing highly resolved images from diffraction intensities alone without the need for image-forming lenses. Fully coherent light can be described adequately by a single pure state. Yet partial coherence and imperfect detection often need to be accounted for, requiring statistical optics or the superposition of states. Furthermore, the dynamics of samples are increasingly the very objectives of experiments. Here we provide a general analytic approach to the characterization of diffractive imaging systems that can be described as low-rank mixed states. We use experimental data and simulations to show how the reconstruction technique compensates for and characterizes various sources of decoherence quantitatively. Based on ptychography, the procedure is closely related to quantum state tomography and is equally applicable to high-resolution microscopy, wave sensing and fluctuation measurements. As a result, some of the most stringent experimental conditions in ptychography can be relaxed, and susceptibility to imaging artefacts is reduced. Furthermore, the method yields high-resolution images of mixed states within the sample, which may include quantum mixtures or fast stationary stochastic processes such as vibrations, switching or steady flows.

Reconstructing state mixtures from diffraction measurements

A high-brilliance synchrotron P12 beamline of the EMBL located at the PETRA III storage ring (DESY, Hamburg) is dedicated to biological small-angle X-ray scattering (SAXS) and has been designed and optimized for scattering experiments on macromolecular solutions. Scatterless slits reduce the parasitic scattering, a custom-designed miniature active beamstop ensures accurate data normalization and the photon-counting PILATUS 2M detector enables the background-free detection of weak scattering signals. The high flux and small beam size allow for rapid experiments with exposure time down to 30–50 ms covering the resolution range from about 300 to 0.5 nm. P12 possesses a versatile and flexible sample environment system that caters for the diverse experimental needs required to study macromolecular solutions. These include an in-vacuum capillary mode for standard batch sample analyses with robotic sample delivery and for continuous-flow in-line sample purification and characterization, as well as an in-air capillary time-resolved stopped-flow setup. A novel microfluidic centrifugal mixing device (SAXS disc) is developed for a high-throughput screening mode using sub-microlitre sample volumes. Automation is a key feature of P12; it is controlled by a beamline meta server, which coordinates and schedules experiments from either standard or nonstandard operational setups. The integrated SASFLOW pipeline automatically checks for consistency, and processes and analyses the data, providing near real-time assessments of overall parameters and the generation of low-resolution models within minutes of data collection. These advances, combined with a remote access option, allow for rapid high-throughput analysis, as well as time-resolved and screening experiments for novice and expert biological SAXS users.

/pdf/versatile-sample-environments-and-automation-for-biological-2blmf63qvj.pdf

Versatile sample environments and automation for biological solution X‐ray scattering experiments at the P12 beamline (PETRA III, DESY)

A recently developed computational imaging technique, X-ray ptychographic tomography, is used to study integrated circuits, and a 3D image of a processor chip with a resolution of 14.6 nm is obtained. As computer chips have become increasingly crammed with nanometre-scale devices and circuitry, new microscopy techniques that can resolve the smallest features are required to enable chip design and inspection. X-ray imaging is uniquely suited for non-destructive, high-resolution imaging and Mirko Holler et al. make use of a recently developed computational imaging technique, X-ray ptychography, to generate high-resolution three-dimensional images of integrated circuits. They test X-ray ptychography on a circuit with known features, and then apply it to an Intel processor chip manufactured in the 22-nanometre technology, obtaining detailed three-dimensional maps of the devices with a resolution down to 14.6 nanometres. This technique could be used to assist quality control during chip production. Modern nanoelectronics1,2 has advanced to a point at which it is impossible to image entire devices and their interconnections non-destructively because of their small feature sizes and the complex three-dimensional structures resulting from their integration on a chip. This metrology gap implies a lack of direct feedback between design and manufacturing processes, and hampers quality control during production, shipment and use. Here we demonstrate that X-ray ptychography3,4—a high-resolution coherent diffractive imaging technique—can create three-dimensional images of integrated circuits of known and unknown designs with a lateral resolution in all directions down to 14.6 nanometres. We obtained detailed device geometries and corresponding elemental maps, and show how the devices are integrated with each other to form the chip. Our experiments represent a major advance in chip inspection and reverse engineering over the traditional destructive electron microscopy and ion milling techniques5,6,7. Foreseeable developments in X-ray sources8, optics9 and detectors10, as well as adoption of an instrument geometry11 optimized for planar rather than cylindrical samples, could lead to a thousand-fold increase in efficiency, with concomitant reductions in scan times and voxel sizes.

High-resolution non-destructive three-dimensional imaging of integrated circuits

The hybrid pixel technology combines silicon sensors with CMOS-processing chips by a 2D micro bump-bonding interconnection technology developed at Paul Scherrer Institute [C. Broennimann, E.F. Eikenberry, B. Henrich, R. Horisberger, G. Huelsen, E. Pohl, B. Schmitt, C. Schulze-Briese, M. Suzuki, T. Tomizaki, H. Toyokawa, A. Wagner. J. Synchrotron Rad. 13 (2005) 120 [1] ; T. Rohe, C. Broennimann, F. Glaus, J. Gobrecht, S. Heising, M. Horisberger, R. Horisberger, H.C. Kaestl, J. Lehmann, S. Streuli, Nucl. Instr. and Meth. Phys. Res. A 565 (2006) 303 [2] ]. PILATUS hybrid pixel detectors like other instruments [X. Llopart, M. Campell, R. Dinapoli, D. San Segundo, E. Pernigotti. IEEE Trans. Nucl. Sci. 49 (2002) 2279 [3] ; N. Boudet, J.-F. Berar, L. Blanquart, P. Breugon, B. Caillot, J.-C. Clemens, I. Koudobine, P. Delpierre, C. Mouget, R. Potheau, I. Valin, Nucl. Instr. and Meth. Phys. Res. A 510 (2003) 41 [4] ] are operating in the so-called “single photon counting mode”: Every X-ray quantum is directly converted into an electrical signal and counted by the detector system. Several prototype detectors in various geometries were produced, tested and established at different synchrotron beamlines worldwide. We explain the technology and present some recent highlights from various fields of applications.

PILATUS: A single photon counting pixel detector for X-ray applications

The MYTHEN detector is a one-dimensional microstrip detector with single photon counting readout optimized for time resolved powder diffraction experiments at the Swiss Light Source (SLS). The system has been successfully tested for many different synchrotron radiation applications including phase contrast and tomographic imaging, small angle scattering, diffraction and time resolved pump and probe experiments for X-ray energies down to 5 keV and counting rate up to 3 MHz. The frontend electronics is designed in order to be coupled to 50 μm pitch microstrip sensors but some interest in enhancing the spatial resolution is arising for imaging and powder diffraction experiments. A test structure with strip pitches in the range 10–50 μm has been tested and the gain and noise on the readout electronics have been measured for the different strip pitches, observing no large difference down to 25 μm. Moreover, the effect of the charge sharing between neighboring strips on the spatial resolution has been quantified by measuring the Point Spread Function (PSF) of the system for the different pitches.

Performance of a single photon counting microstrip detector for strip pitches down to 10 μm

At the Paul Scherrer Institute PSI an X-ray single photon counting pixel detector (PILATUS) based on the hybrid-pixel detector technology was developed in collaboration with SPring-8. The detection element is a 320 or 450 μm thick silicon sensor forming pixelated pn-diodes with a pitch of 172 μm×172 μm. An array of 2×8 custom CMOS readout chips are indium bump-bonded to the sensor, which leads to 33.5 mm×83.8 mm detective area. Each pixel contains a charge-sensitive amplifier, a single level discriminator and a 20 bit counter. This design realizes a high dynamic range, short readout time of less than 3 ms, a high framing rate of over 200 images per second and an excellent point-spread function. The maximum counting rate achieves more than 2×106 X-rays/s/pixel.

Single photon counting pixel detectors for synchrotron radiation experiments

/pdf/protein-crystallography-with-the-pilatus-6m-pixel-detector-218lfw7o0g.pdf

Protein crystallography with the PILATUS 6M pixel detector

Pilatus is a silicon hybrid pixel detector system for detecting X-rays in single photon counting mode. The PILATUS II chip, fabricated in a radiation tolerant design with a standard 0.25 mum CMOS process, was used to construct multichip modules with a size of 84 times 34 mm2 comprising 94'965 pixels. All calibrations and characterizations were carried out with monochromatic X-rays from a synchrotron source. In order to set any required threshold above the noise level between 2.14 keV and 22 keV the detector was calibrated with X-rays. An algorithm to adjust thresholds pixel-by-pixel and create trim files based on X-ray flat-field images was developed. The threshold dispersion was reduced from 343 eV to 36 eV by the means of trim files. An electronic noise of 447 eV has been measured. The PILATUS modules are suitable for various X-ray applications such as diffraction and imaging techniques.

/pdf/characterization-and-calibration-of-pilatus-detectors-avj7kmgnus.pdf

Characterization and Calibration of PILATUS Detectors

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