Regridding reconstruction algorithm for real-time tomographic imaging

Marone, Federica; Stampanoni, Marco

doi:10.1107/s0909049512032864

Cited by 401 publications

(279 citation statements)

References 28 publications

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“…Thin sections were reduced in size and mounted on a 3-mm-wide brass peg and analysed on the TOMCAT beamline at the Swiss Light Source at the Paul Scherrer Institute 40 . The X-ray energy was optimized for maximum contrast at 13-20 keV.…”

Section: Methodsmentioning

confidence: 99%

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Fossilized iron bacteria reveal a pathway to the biological origin of banded iron formation

et al. 2013

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Debates on the formation of banded iron formations in ancient ferruginous oceans are dominated by a dichotomy between abiotic and biotic iron cycling. This is fuelled by difficulties in unravelling the exact processes involved in their formation. Here we provide fossil environmental evidence for anoxygenic photoferrotrophic deposition of analogue banded iron rocks in shallow marine waters associated with an Early Quaternary hydrothermal vent field on Milos Island, Greece. Trace metal, major and rare earth elemental compositions suggest that the deposited rocks closely resemble banded iron formations of Precambrian origin. Well-preserved microbial fossils in combination with chemical data imply that band formation was linked to periodic massive encrustation of anoxygenic phototrophic biofilms by iron oxyhydroxide alternating with abiotic silica precipitation. The data implicate cyclic anoxygenic photoferrotrophy and their fossilization mechanisms in the construction of microskeletal fabrics that result in the formation of characteristic banded iron formation bands of varying silica and iron oxide ratios.

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Section: Methodsmentioning

confidence: 99%

“…A total of 1501 projections were acquired equiangularly over 180°, post-processed online and rearranged into flat-and darkfield-corrected sinograms. Reconstruction was performed on a Linux PC farm using highly optimized routines based on the Fourier Transform method 40 . A Â 20 lens was used, resulting in stacks with a voxel size of 0.37 mm.…”

Section: Methodsmentioning

confidence: 99%

Fossilized iron bacteria reveal a pathway to the biological origin of banded iron formation

et al. 2013

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“…The projection images of the three different contrast modalities are then obtained from the intensity using a Fourier-based approach (Pfeiffer et al, 2006(Pfeiffer et al, , 2008. For tomography, these steps are repeated for different rotation angles of the sample and the resulting projection images are reconstructed using the reconstruction algorithm gridrec (Marone & Stampanoni, 2012).…”

Section: Grating Interferometry the Experimental Set-up Of A Gratingmentioning

confidence: 99%

Combining Monte Carlo methods with coherent wave optics for the simulation of phase-sensitive X-ray imaging

et al. 2014

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Phase-sensitive X-ray imaging shows a high sensitivity towards electron density variations, making it well suited for imaging of soft tissue matter. However, there are still open questions about the details of the image formation process. Here, a framework for numerical simulations of phase-sensitive X-ray imaging is presented, which takes both particle-and wave-like properties of X-rays into consideration. A split approach is presented where we combine a Monte Carlo method (MC) based sample part with a wave optics simulation based propagation part, leading to a framework that takes both particle-and wavelike properties into account. The framework can be adapted to different phasesensitive imaging methods and has been validated through comparisons with experiments for grating interferometry and propagation-based imaging. The validation of the framework shows that the combination of wave optics and MC has been successfully implemented and yields good agreement between measurements and simulations. This demonstrates that the physical processes relevant for developing a deeper understanding of scattering in the context of phase-sensitive imaging are modelled in a sufficiently accurate manner. The framework can be used for the simulation of phase-sensitive X-ray imaging, for instance for the simulation of grating interferometry or propagation-based imaging.

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“…Thousand five hundred and one equiangular projections were acquired over 180 for each dataset. Projections were postprocessed and rearranged into flat-and dark-field-corrected sinograms, and reconstruction was performed on a 60-core Linux PC farm, using a highly optimised routine based on the Fourier transform method and a regridding procedure (Marone and Stampanoni, 2012) resulting in volumetric data with voxel dimensions of 0.65 and 0.325 lm, respectively. These data were analysed, manipulated and segmented digitally using AVISO 8.0 standard edition software for computed tomography developed by Visualisation Sciences Group.…”

Section: Synchrotron Radiation X-ray Tomographic Microscopymentioning

confidence: 99%

Histology of the heterostracan dermal skeleton: Insight into the origin of the vertebrate mineralised skeleton

Keating

Marquart

Donoghue

2015

Journal of Morphology

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Living vertebrates are divided into those that possess a fully formed and fully mineralised skeleton (gnathostomes) versus those that possess only unmineralised cartilaginous rudiments (cyclostomes). As such, extinct phylogenetic intermediates of these living lineages afford unique insights into the evolutionary assembly of the vertebrate mineralised skeleton and its canonical tissue types. Extinct jawless and jawed fishes assigned to the gnathostome stem evidence the piecemeal assembly of skeletal systems, revealing that the dermal skeleton is the earliest manifestation of a homologous mineralised skeleton. Yet the nature of the primitive dermal skeleton, itself, is poorly understood. This is principally because previous histological studies of early vertebrates lacked a phylogenetic framework required to derive evolutionary hypotheses. Nowhere is this more apparent than within Heterostraci, a diverse clade of primitive jawless vertebrates. To this end, we surveyed the dermal skeletal histology of heterostracans, inferred the plesiomorphic heterostracan skeleton and, through histological comparison to other skeletonising vertebrate clades, deduced the ancestral nature of the vertebrate dermal skeleton. Heterostracans primitively possess a fourlayered skeleton, comprising a superficial layer of odontodes composed of dentine and enameloid; a compact layer of acellular parallel-fibred bone containing a network of vascular canals that supply the pulp canals (L1); a trabecular layer consisting of intersecting radial walls composed of acellular parallel-fibred bone, showing osteon-like development (L2); and a basal layer of isopedin (L3). A three layered skeleton, equivalent to the superficial layer L2 and L3 and composed of enameloid, dentine and acellular bone, is possessed by the ancestor of heterostracans 1 jawed vertebrates. We conclude that an osteogenic component is plesiomorphic with respect to the vertebrate dermal skeleton. Consequently, we interpret the dermal skeleton of denticles in chondrichthyans and jawless thelodonts as independently and secondarily simplified. J.

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Regridding reconstruction algorithm for real-time tomographic imaging

Cited by 401 publications

References 28 publications

Fossilized iron bacteria reveal a pathway to the biological origin of banded iron formation

Fossilized iron bacteria reveal a pathway to the biological origin of banded iron formation

Combining Monte Carlo methods with coherent wave optics for the simulation of phase-sensitive X-ray imaging

Histology of the heterostracan dermal skeleton: Insight into the origin of the vertebrate mineralised skeleton

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