In situ observation of the percolation threshold in multiphase magma analogues.

Magmas vesiculate during ascent, producing complex interconnected pore networks, which can act as outgassing pathways and then deflate or compact to volcanic plugs. Similarly, in-conduit fragmentation events during dome-forming eruptions create open systems transiently, before welding causes pore sealing. The percolation threshold is the first-order transition between closed- and open-system degassing dynamics. Here, we use time-resolved, synchrotron-source X-ray tomography to image synthetic magmas that go through cycles of opening and closing, to constrain the percolation threshold Φ C at a range of melt crystallinity, viscosity and overpressure pertinent to shallow magma ascent. During vesiculation, we observed different percolative regimes for the same initial bulk crystallinity depending on melt viscosity and gas overpressure. At high viscosity (> 106 Pa s) and high overpressure (~ 1-4 MPa), we found that a brittle-viscous regime dominates in which brittle rupture allows system-spanning coalescence at a low percolation threshold (Φ C ~0.17) via the formation of fracture-like bubble chains. Percolation was followed by outgassing and bubble collapse causing densification and isolation of the bubble network, resulting in a hysteresis in the evolution of connectivity with porosity. At low melt viscosity and overpressure, we observed a viscous regime with much higher percolation threshold (Φ C > 0.37) due to spherical bubble growth and lower degree of crystal connection. Finally, our results also show that sintering of crystal-free and crystal-bearing magma analogues is characterised by low percolation thresholds (Φ C = 0.04 - 0.10). We conclude that the presence of crystals lowers the percolation threshold during vesiculation and may promote outgassing in shallow, crystal-rich magma at initial stages of Vulcanian and Strombolian eruptions.

In situ investigation of phase transformations in Ti-6Al-4V under additive manufacturing conditions combining laser melting and high-speed micro-X-ray diffraction.

We present combined in situ X-ray diffraction and high-speed imaging to monitor the phase evolution upon cyclic rapid laser heating and cooling mimicking the direct energy deposition of Ti-6Al-4V in real time. Additive manufacturing of the industrially relevant alloy Ti-6Al-4V is known to create a multitude of phases and microstructures depending on processing technology and parameters. Current setups are limited by an averaged measurement through the solid and liquid parts. In this work the combination of a micro-focused intense X-ray beam, a fast detector and unidirectional cooling provide the spatial and temporal resolution to separate contributions from solid and liquid phases in limited volumes. Upon rapid heating and cooling, the ß â†” α' phase transformation is observed repeatedly. At room temperature, single phase α' is observed. Secondary ß-formation upon formation of α' is attributed to V partitioning to the ß-phase leading to temporary stabilization. Lattice strains in the α'-phase are found to be sensitive to the α' → ß phase transformation. Based on lattice strain of the ß-phase, the martensite start temperature is estimated at 923 K in these experiments. Off-axis high speed imaging confirms a technically relevant solidification front velocity and cooling rate of 10.3 mm/s and 4500 K/s, respectively.

Fast iterative reconstruction of data in full interior tomography.

This paper introduces two novel strategies for iterative reconstruction of full interior tomography (FINT) data, i.e. when the field of view is entirely inside the object support and knowledge of the object support itself or the attenuation coefficients inside specific regions of interest are not available. The first approach is based on data edge-padding. The second technique creates an intermediate virtual sinogram, which is, then, reconstructed by a standard iterative algorithm. Both strategies are validated in the framework of the alternate direction method of multipliers plug-and-play with gridding projectors that provide a speed-up of three orders of magnitude with respect to standard operators implemented in real space. The proposed methods are benchmarked on synchrotron-based X-ray tomographic microscopy datasets of mouse lung alveoli. Compared with analytical techniques, the proposed methods substantially improve the reconstruction quality for FINT underconstrained datasets, facilitating subsequent post-processing steps.

Synchrotron-based X-ray tomographic microscopy for visualization of three-dimensional collagen matrices.

INTRODUCTION: Three-dimensional collagen matrices (3D-CMs) may be visualized by cumbersome reconstructions of serial sections. We report here on the method of synchrotron-based X-ray tomographic microscopy (SRXTM) to image 3D-CMs in native tissue probes. MATERIAL AND METHODS: SRXTM of 3D-CMs (mucoderm®, mucograft®) was performed at the TOMCAT beamline of the Swiss Light Source (SLS) at the Paul Scherrer Institute (Villigen, Switzerland). RESULTS: SRXTM combines the advantages of high-resolution scanning electron microscopy (SEM) imaging with the low-resolution reconstructions of micro-CT (µCT) imaging. It may be used to non-destructively visualize and analyze structures within the 3D-CMs without the need of serial sectioning and reconstruction. CONCLUSION: High-resolution SRXTM is a useful tool in analyzing the topology and morphometry of structures in 3D-CMs. The outcome justifies the efforts in sophisticated data processing. CLINICAL RELEVANCE: SRXTM may help to understand the clinical characteristics of 3D-CMs in more detail.

Simple merging technique for improving resolution in qualitative single image phase contrast tomography.

For dynamic samples and/or for simple ease-of-use experiments, single-image phase contrast tomography is a very effective method for the 3D visualization of materials which would otherwise be indiscernible in attenuation based x-ray imaging. With binary samples (e.g. air-material) and monochromatic wavefields a transport-of-intensity (TIE)-based phase retrieval algorithm is known to retrieve accurate quantitative maps of the phase distribution. For mixed material samples and/or white beam radiation the algorithm can still produce useful qualitative tomographic reconstructions with significantly improved area contrast. The stability of the algorithm comes with a recognized associated loss of spatial resolution due to its essential behaviour as a low-pass filter. One possible answer to this is an image fusion technique that merges the slices reconstructed from raw phase contrast images and those after phase retrieval, where the improved contrast may be acquired without the associated loss of high-frequency information. We present this technique as a simple few-parameter Fourier method, which is easily tunable and highly compatible with current reconstruction steps.

Quantifying phosphoric acid in high-temperature polymer electrolyte fuel cell components by X-ray tomographic microscopy.

Synchrotron-based X-ray tomographic microscopy is investigated for imaging the local distribution and concentration of phosphoric acid in high-temperature polymer electrolyte fuel cells. Phosphoric acid fills the pores of the macro- and microporous fuel cell components. Its concentration in the fuel cell varies over a wide range (40-100 wt% H3PO4). This renders the quantification and concentration determination challenging. The problem is solved by using propagation-based phase contrast imaging and a referencing method. Fuel cell components with known acid concentrations were used to correlate greyscale values and acid concentrations. Thus calibration curves were established for the gas diffusion layer, catalyst layer and membrane in a non-operating fuel cell. The non-destructive imaging methodology was verified by comparing image-based values for acid content and concentration in the gas diffusion layer with those from chemical analysis.

Deep-biosphere consortium of fungi and prokaryotes in Eocene subseafloor basalts.

The deep biosphere of the subseafloor crust is believed to contain a significant part of Earth's biomass, but because of the difficulties of directly observing the living organisms, its composition and ecology are poorly known. We report here a consortium of fossilized prokaryotic and eukaryotic micro-organisms, occupying cavities in deep-drilled vesicular basalt from the Emperor Seamounts, Pacific Ocean, 67.5 m below seafloor (mbsf). Fungal hyphae provide the framework on which prokaryote-like organisms are suspended like cobwebs and iron-oxidizing bacteria form microstromatolites (Frutexites). The spatial inter-relationships show that the organisms were living at the same time in an integrated fashion, suggesting symbiotic interdependence. The community is contemporaneous with secondary mineralizations of calcite partly filling the cavities. The fungal hyphae frequently extend into the calcite, indicating that they were able to bore into the substrate through mineral dissolution. A symbiotic relationship with chemoautotrophs, as inferred for the observed consortium, may be a pre-requisite for the eukaryotic colonization of crustal rocks. Fossils thus open a window to the extant as well as the ancient deep biosphere.

Regridding reconstruction algorithm for real-time tomographic imaging.

Sub-second temporal-resolution tomographic microscopy is becoming a reality at third-generation synchrotron sources. Efficient data handling and post-processing is, however, difficult when the data rates are close to 10 GB s(-1). This bottleneck still hinders exploitation of the full potential inherent in the ultrafast acquisition speed. In this paper the fast reconstruction algorithm gridrec, highly optimized for conventional CPU technology, is presented. It is shown that gridrec is a valuable alternative to standard filtered back-projection routines, despite being based on the Fourier transform method. In fact, the regridding procedure used for resampling the Fourier space from polar to Cartesian coordinates couples excellent performance with negligible accuracy degradation. The stronger dependence of the observed signal-to-noise ratio for gridrec reconstructions on the number of angular views makes the presented algorithm even superior to filtered back-projection when the tomographic problem is well sampled. Gridrec not only guarantees high-quality results but it provides up to 20-fold performance increase, making real-time monitoring of the sub-second acquisition process a reality.

X-ray mosaic nanotomography of large microorganisms.

Full-field X-ray microscopy is a valuable tool for 3D observation of biological systems. In the soft X-ray domain organelles can be visualized in individual cells while hard X-ray microscopes excel in imaging of larger complex biological tissue. The field of view of these instruments is typically 10(3) times the spatial resolution. We exploit the assets of the hard X-ray sub-micrometer imaging and extend the standard approach by widening the effective field of view to match the size of the sample. We show that global tomography of biological systems exceeding several times the field of view is feasible also at the nanoscale with moderate radiation dose. We address the performance issues and limitations of the TOMCAT full-field microscope and more generally for Zernike phase contrast imaging. Two biologically relevant systems were investigated. The first being the largest known bacteria (Thiomargarita namibiensis), the second is a small myriapod species (Pauropoda sp.). Both examples illustrate the capacity of the unique, structured condenser based broad-band full-field microscope to access the 3D structural details of biological systems at the nanoscale while avoiding complicated sample preparation, or even keeping the sample environment close to the natural state.

Experimental taphonomy of giant sulphur bacteria: implications for the interpretation of the embryo-like Ediacaran Doushantuo fossils.

The Ediacaran Doushantuo biota has yielded fossils interpreted as eukaryotic organisms, either animal embryos or eukaryotes basal or distantly related to Metazoa. However, the fossils have been interpreted alternatively as giant sulphur bacteria similar to the extant Thiomargarita. To test this hypothesis, living and decayed Thiomargarita were compared with Doushantuo fossils and experimental taphonomic pathways were compared with modern embryos. In the fossils, as in eukaryotic cells, subcellular structures are distributed throughout cell volume; in Thiomargarita, a central vacuole encompasses approximately 98 per cent cell volume. Key features of the fossils, including putative lipid vesicles and nuclei, complex envelope ornament, and ornate outer vesicles are incompatible with living and decay morphologies observed in Thiomargarita. Microbial taphonomy of Thiomargarita also differed from that of embryos. Embryo tissues can be consumed and replaced by bacteria, forming a replica composed of a three-dimensional biofilm, a stable fabric for potential fossilization. Vacuolated Thiomargarita cells collapse easily and do not provide an internal substrate for bacteria. The findings do not support the hypothesis that giant sulphur bacteria are an appropriate interpretative model for the embryo-like Doushantuo fossils. However, sulphur bacteria may have mediated fossil mineralization and may provide a potential bacterial analogue for other macroscopic Precambrian remains.

Image processing pipeline for synchrotron-radiation-based tomographic microscopy.

With synchrotron-radiation-based tomographic microscopy, three-dimensional structures down to the micrometer level can be visualized. Tomographic data sets typically consist of 1000 to 1500 projections of 1024 x 1024 to 2048 x 2048 pixels and are acquired in 5-15 min. A processing pipeline has been developed to handle this large amount of data efficiently and to reconstruct the tomographic volume within a few minutes after the end of a scan. Just a few seconds after the raw data have been acquired, a selection of reconstructed slices is accessible through a web interface for preview and to fine tune the reconstruction parameters. The same interface allows initiation and control of the reconstruction process on the computer cluster. By integrating all programs and tools, required for tomographic reconstruction into the pipeline, the necessary user interaction is reduced to a minimum. The modularity of the pipeline allows functionality for new scan protocols to be added, such as an extended field of view, or new physical signals such as phase-contrast or dark-field imaging etc.

Brachiopod punctae: a complexity in shell biomineralisation.

Perforations ("punctae") are one of the most characteristic morphological shell features in calcite brachiopods. The significance of punctae is that they represent discontinuities in shell biomineralisation and thus add a level of complexity that must be accounted for in any model of brachiopod shell formation. A significant hindrance to understanding punctae growth and formation is the absence of sufficient information on volume, size and density. Here, we use synchrotron-radiation X-ray tomographic microscopy (SRXTM) to obtain three-dimensional information about punctae of five species of calcite brachiopods. X-ray tomography shows that punctae morphology is species-specific and reveals previously unknown levels of complexity for each species. This information is combined with previous data on morphology to discuss the function and growth of punctae. Overall the present study demonstrates the need to increase our understanding of discontinuities and the role of cell biology in the context of biomineralisation.