scholarly journals Correlative 3D x-ray fluorescence and ptychographic tomography of frozen-hydrated green algae

2018 ◽  
Vol 4 (11) ◽  
pp. eaau4548 ◽  
Author(s):  
Junjing Deng ◽  
Yuan Hung Lo ◽  
Marcus Gallagher-Jones ◽  
Si Chen ◽  
Alan Pryor ◽  
...  
Keyword(s):  
Mammalian Cells ◽  
Tomographic Reconstruction ◽  
Reconstruction Algorithm ◽  
Three Dimensions ◽  
Light Sources ◽  
X Ray ◽  
Reconstruction Quality ◽  
Wide Range ◽  
Conventional Tomography ◽  
Efficient Data

Accurate knowledge of elemental distributions within biological organisms is critical for understanding their cellular roles. The ability to couple this knowledge with overall cellular architecture in three dimensions (3D) deepens our understanding of cellular chemistry. Using a whole, frozen-hydrated Chlamydomonas reinhardtii cell as an example, we report the development of 3D correlative microscopy through a combination of simultaneous cryogenic x-ray ptychography and x-ray fluorescence microscopy. By taking advantage of a recently developed tomographic reconstruction algorithm, termed GENeralized Fourier Iterative REconstruction (GENFIRE), we produce high-quality 3D maps of the unlabeled alga’s cellular ultrastructure and elemental distributions within the cell. We demonstrate GENFIRE’s ability to outperform conventional tomography algorithms and to further improve the reconstruction quality by refining the experimentally intended tomographic angles. As this method continues to advance with brighter coherent light sources and more efficient data handling, we expect correlative 3D x-ray fluorescence and ptychographic tomography to be a powerful tool for probing a wide range of frozen-hydrated biological specimens, ranging from small prokaryotes such as bacteria, algae, and parasites to large eukaryotes such as mammalian cells, with applications that include understanding cellular responses to environmental stimuli and cell-to-cell interactions.

scholarly journals Three-dimensional propagation in near-field tomographic X-ray phase retrieval

2016 ◽  
Vol 72 (2) ◽  
pp. 215-221 ◽  
Author(s):  
Aike Ruhlandt ◽  
Tim Salditt
Keyword(s):  
Phase Retrieval ◽  
Near Field ◽  
Three Dimensional ◽  
Three Dimensions ◽  
Current Phase ◽  
Computationally Efficient ◽  
X Ray ◽  
Reconstruction Quality ◽  
Consistency Constraints

This paper presents an extension of phase retrieval algorithms for near-field X-ray (propagation) imaging to three dimensions, enhancing the quality of the reconstruction by exploiting previously unused three-dimensional consistency constraints. The approach is based on a novel three-dimensional propagator and is derived for the case of optically weak objects. It can be easily implemented in current phase retrieval architectures, is computationally efficient and reduces the need for restrictive prior assumptions, resulting in superior reconstruction quality.

A hybrid tomographic reconstruction algorithm for high speed X-ray tomography

2015 ◽  
Vol 196 ◽  
pp. 27-35 ◽  
Author(s):  
Xiaogang Yang ◽  
J. Ruud van Ommen ◽  
Jasper Schoormans ◽  
Robert F. Mudde
Keyword(s):  
High Speed ◽  
Tomographic Reconstruction ◽  
Reconstruction Algorithm ◽  
X Ray

scholarly journals X-ray detectors at the Linac Coherent Light Source

2015 ◽  
Vol 22 (3) ◽  
pp. 577-583 ◽  
Author(s):  
Gabriel Blaj ◽  
Pietro Caragiulo ◽  
Gabriella Carini ◽  
Sebastian Carron ◽  
Angelo Dragone ◽  
...  
Keyword(s):  
Light Source ◽  
Light Sources ◽  
Coherent Light ◽  
X Ray ◽  
Wide Range ◽  
Linac Coherent Light Source ◽  
Design Requirements ◽  
New Generation ◽  
Coherent Light Source ◽  
Detector Design

Free-electron lasers (FELs) present new challenges for camera development compared with conventional light sources. At SLAC a variety of technologies are being used to match the demands of the Linac Coherent Light Source (LCLS) and to support a wide range of scientific applications. In this paper an overview of X-ray detector design requirements at FELs is presented and the various cameras in use at SLAC are described for the benefit of users planning experiments or analysts looking at data. Features and operation of the CSPAD camera, which is currently deployed at LCLS, are discussed, and the ePix family, a new generation of cameras under development at SLAC, is introduced.

scholarly journals Evaluating scintillator performance in time-resolved hard X-ray studies at synchrotron light sources

2016 ◽  
Vol 23 (3) ◽  
pp. 685-693 ◽  
Author(s):  
Michael E. Rutherford ◽  
David J. Chapman ◽  
Thomas G. White ◽  
Michael Drakopoulos ◽  
Alexander Rack ◽  
...  
Keyword(s):  
Synchrotron Radiation ◽  
Dynamic Range ◽  
Short Pulse ◽  
European Synchrotron Radiation Facility ◽  
Light Sources ◽  
Time Resolved ◽  
X Ray ◽  
Short Pulse Duration ◽  
Wide Range ◽  
Synchrotron Light Sources

The short pulse duration, small effective source size and high flux of synchrotron radiation is ideally suited for probing a wide range of transient deformation processes in materials under extreme conditions. In this paper, the challenges of high-resolution time-resolved indirect X-ray detection are reviewed in the context of dynamic synchrotron experiments. In particular, the discussion is targeted at two-dimensional integrating detector methods, such as those focused on dynamic radiography and diffraction experiments. The response of a scintillator to periodic synchrotron X-ray excitation is modelled and validated against experimental data collected at the Diamond Light Source (DLS) and European Synchrotron Radiation Facility (ESRF). An upper bound on the dynamic range accessible in a time-resolved experiment for a given bunch separation is calculated for a range of scintillators. New bunch structures are suggested for DLS and ESRF using the highest-performing commercially available crystal LYSO:Ce, allowing time-resolved experiments with an interframe time of 189 ns and a maximum dynamic range of 98 (6.6 bits).

scholarly journals Transforming X-ray detection with hybrid photon counting detectors

2019 ◽  
Vol 377 (2147) ◽  
pp. 20180241 ◽  
Author(s):  
Andreas Förster ◽  
Stefan Brandstetter ◽  
Clemens Schulze-Briese
Keyword(s):  
Dynamic Range ◽  
Direct Detection ◽  
Accurate Determination ◽  
Photon Counting ◽  
Coherent Scattering ◽  
High Energy ◽  
Light Sources ◽  
X Ray Diffraction ◽  
X Ray ◽  
Wide Range

Hybrid photon counting (HPC) detectors have radically transformed basic research at synchrotron light sources since 2006. They excel at X-ray diffraction applications in the energy range from 2 to 100 keV. The main reasons for their superiority are the direct detection of individual photons and the accurate determination of scattering and diffraction intensities over an extremely high dynamic range. The detectors were first adopted in macromolecular crystallography where they revolutionized data collection. They were soon also used for small-angle scattering, coherent scattering, powder X-ray diffraction, spectroscopy and increasingly high-energy applications. Here, we will briefly survey the history of HPC detectors, explain their technology and then show in detail how improved detection has transformed a wide range of experimental techniques. We will end with an outlook to the future, which will probably see HPC technology find even broader use, for example, in electron microscopy and medical applications. This article is part of the theme issue ‘Fifty years of synchrotron science: achievements and opportunities’.

Three-Dimensional Tomographic Reconstruction for Microscale Object Modeling

2015 ◽  
Author(s):  
Kyung-Chan Jin ◽  
Sung-Ho Lee ◽  
Geon-Hee Kim
Keyword(s):  
Rotation Axis ◽  
Tomographic Reconstruction ◽  
Three Dimensional ◽  
Circular Trajectory ◽  
Total Variation Minimization ◽  
X Ray ◽  
Iterative Processing ◽  
Conventional Tomography ◽  
Ct System ◽  
Homogeneous Regions

When scanning a relatively high resolution, thick object using conventional computed tomography (CT), the scanning axis of the X-ray gantry and detector is approximately perpendicular to the rotation axis of the sample. However, the inner interconnections in flat 3D devices are not reconstructed correctly in regular circular CT. In this paper, we focus on 3D tomographic reconstruction of inner interconnections by CT with particular attention to off-centered circular trajectory CT. However, in off-centered circular trajectory CT, the limited tilting angles of projections result in a missing wedge artifact because the object cannot usually be tilted beyond the limit and the data in the remaining projections are not obtained. Therefore, to alleviate missing wedge artifacts, we propose a reconstruction scheme of combining by filtered back projection (FBP) and constraint-based total variation minimization (c-TVM). In the c-TVM method, the artifact of missing wedge is minimized and the reconstructed region is suppressed with high frequency details while leaving the boundaries between homogeneous regions. In our experiments, the CT system obtained the projected images from a rotating sample using a fixed-mounted X-ray source and detector. We acquired 400 rotational projection images of a vertical connection in an off-centered circular trajectory with 30° tilting angles. We then reconstructed the aligned 3D views of the sample. Finally, we demonstrated that the proposed FBP and c-TVM combination with iterative processing yields a superior 3D reconstruction model to conventional tomography.

PETROPHYSICAL PROPERTIES DERIVED FROM X-RAY CT IMAGES

2003 ◽  
Vol 43 (1) ◽  
pp. 577 ◽  
Author(s):  
C.H. Arns ◽  
A. Sakellariou ◽  
T.J. Senden ◽  
A.P. Sheppard ◽  
R.M. Sok ◽  
...  
Keyword(s):  
Elastic Properties ◽  
Excellent Agreement ◽  
Ct Images ◽  
Three Dimensions ◽  
Rock Properties ◽  
Experimental Measurements ◽  
Petrophysical Properties ◽  
Tomographic Images ◽  
X Ray ◽  
Wide Range

A micro-CT facility for imaging, visualising and modelling sedimentary rock properties in three dimensions (3D) is described. The facility is capable of acquiring 3D X-ray CT images of full-diameter cores and core plugs at up to 2,0003 voxels with resolutions down to 2μm. This allows the 3D pore-space of a rock to be imaged and, with the aid of SEM, to identify regions of different mineralogy. Computational results are presented which demonstrate that accurate predictions of petrophysical properties can be made directly from the digitised tomographic images. Computations of both formation factor and permeability from micro-tomographic images of Fontainebleau sandstone are shown to be in excellent agreement with experimental measurements over a wide range of porosities. Computed elastic properties for dry and water-saturated conditions are shown to be consistent with the exact Gassmann’s equations and are in excellent agreement with experimental measurements. Experimental measurements of Vp/Vs ratio for cemented sandstone morphologies are very noisy and cannot be used to infer relationships between elastic properties, mineralogy and rock microstructure. Computations on tomographic images show that the Vp/Vs ratio exhibits predictable limiting behavior which holds for any number of solid phases and is insensitive to the manner in which the phases are distributed. This allows the development of more accurate empirical methods for deriving the full velocity-porosity relationship for cemented sands. The results demonstrate the feasibility of combining digitised images with numerical calculations to accurately predict petrophysical properties of individual rock morphologies.

X-ray crystallographic studies of protein–ligand interactions

2003 ◽  
Vol 31 (5) ◽  
pp. 973-979 ◽  
Author(s):  
R.A. Palmer ◽  
H. Niwa
Keyword(s):  
Binding Site ◽  
Protein Structures ◽  
Three Dimensions ◽  
Small Samples ◽  
Mistletoe Lectin ◽  
Surface Binding ◽  
X Ray ◽  
X Ray Crystallography ◽  
Sugar Binding ◽  
Wide Range

X-ray crystallography enables details of covalent and non-covalent interactions to be analysed quantitatively in three dimensions, thus providing the basis for the understanding of binding of ligands to proteins as well as modes of action such as cell-surface binding. This article is concerned with current methods employed for the X-ray analysis of protein structures complexed with ligands. It deals mainly with ‘what can be done’ in current research, rather than providing details of ‘how to do it’. In recent years significant advances have been made in a variety of techniques: growing protein crystals from very small samples by scanning a wide range of conditions; X-ray intensity data collection and measurement through the use of charge-coupled devices and high-intensity, versatile synchrotron sources; cryo-crystallography which both stabilizes the crystals and provides improved data; methods for analysing and interpreting the structures, dependent, at least in part, on both structural and sequence databases; and improvements in hardware and software. To illustrate the type of results achievable two examples involving protein–sugar interactions are discussed: (i) SNAII (the lectin Sambucus nigra agglutinin-II from elder) N-terminal sugar-binding site where terminal sugar units in a glycosylation chain from a symmetry-related molecule bind and (ii) MLI (mistletoe lectin I) C-terminal sugar-binding site with lactose.

scholarly journals In-situ nanoscale imaging of charge transfer of BiNiO3 under high pressure

2014 ◽  
Vol 70 (a1) ◽  
pp. C403-C403
Author(s):  
Wenge Yang ◽  
Yijin Liu ◽  
Junyue Wang ◽  
Wendy Mao ◽  
Ho-kwang Mao
Keyword(s):  
High Pressure ◽  
Thermal Expansion ◽  
Charge Transfer ◽  
Negative Thermal Expansion ◽  
High Energy ◽  
Three Dimensions ◽  
High Energy Resolution ◽  
X Ray ◽  
Wide Range ◽  
Nanoscale Imaging

Over last decades, both synchrotron radiation techniques and high pressure research have made great progress. Advanced synchrotron capabilities with high spatial resolution, high flux, and high energy resolution provides us many new avenues to conduct advanced high pressure researches. In this talk, we will focus on the new developments of the nanoscale imaging techniques on the pressure induced phase separation in three dimensions. BiNiO3 under goes a charge transfer induced phase transition under high pressure or temperature, which shows excellent colossal negative thermal expansion effect [1]. Co-exist of both high density and low density phases over a wide range pressure or temperature plays the key roles on the negative thermal expansion behavior. We utilized a newly developed X-ray absorption near edge spectroscopy tomography method, and successfully resolved the mixture of high/low pressure phases as a function of pressure at tens of nanometer resolution. By choosing incident x-ray energy near Ni absorption edge, the pressure induced valence transition can be mapped at tens of nanometer scale in 3d, which provides crucial information on the HP-LP phase boundary [2]. As temperature driven grain growth upon heating, we can draw fundamental information on the pressure-induced phase growth mechanism.

Nondestructive Inspection of Thin, Low-Z Samples using Multiplexed Compton Scatter Tomography

1997 ◽  
Vol 503 ◽  
Author(s):  
B. L. Evans ◽  
J. B. Martin ◽  
L. W. Burggraf
Keyword(s):  
Signal To Noise Ratio ◽  
Reconstruction Algorithm ◽  
Filtered Backprojection ◽  
Line Broadening ◽  
Compton Scatter ◽  
X Ray ◽  
Tomography System ◽  
Transmission Computed Tomography ◽  
High Purity Germanium ◽  
Scattered Energy

ABSTRACTThe viability of a Compton scattering tomography system for nondestructively inspecting thin, low Z samples for corrosion is examined. This technique differs from conventional x-ray backscatter NDI because it does not rely on narrow collimation of source and detectors to examine small volumes in the sample. Instead, photons of a single energy are backscattered from the sample and their scattered energy spectra are measured at multiple detector locations, and these spectra are then used to reconstruct an image of the object. This multiplexed Compton scatter tomography technique interrogates multiple volume elements simultaneously. Thin samples less than 1 cm thick and made of low Z materials are best imaged with gamma rays at or below 100 keV energy. At this energy, Compton line broadening becomes an important resolution limitation. An analytical model has been developed to simulate the signals collected in a demonstration system consisting of an array of planar high-purity germanium detectors. A technique for deconvolving the effects of Compton broadening and detector energy resolution from signals with additive noise is also presented. A filtered backprojection image reconstruction algorithm with similarities to that used in conventional transmission computed tomography is developed. A simulation of a 360–degree inspection gives distortion-free results. In a simulation of a single-sided inspection, a 5 mm × 5 mm corrosion flaw with 50% density is readily identified in 1-cm thick aluminum phantom when the signal to noise ratio in the data exceeds 28.

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