A virtual world of paleontology

Computer-aided visualization and analysis of fossils has revolutionized the study of extinct organisms. Novel techniques allow fossils to be characterized in three dimensions and in unprecedented detail. This has enabled paleontologists to gain important insights into their anatomy, development, and preservation. New protocols allow more objective reconstructions of fossil organisms, including soft tissues, from incomplete remains. The resulting digital reconstructions can be used in functional analyses, rigorously testing long-standing hypotheses regarding the paleobiology of extinct organisms. These approaches are transforming our understanding of long-studied fossil groups, and of the narratives of organismal and ecological evolution that have been built upon them

Research Status and Prospect for CT Imaging

Computed tomography (CT) is a very valuable imaging method and plays an important role in clinical diagnosis. As people pay more and more attention to radiation doses these years, decreasing CT radiation dose without affecting image quality is a hot direction for research of medical imaging in recent years. This chapter introduces the research status of low-dose technology from following aspects: low-dose scan implementation, reconstruction methods and image processing methods. Furthermore, other technologies related to the development tendency of CT, such as automatic tube current modulation technology, rapid peak kilovoltage (kVp) switching technology, dual-source CT technology and Nano-CT, are also summarized. Finally, the future research prospect are discussed and analyzed

Strukturelle Charakterisierung der Wechselwirkungszone zwischen Glasionomer Zement und Schmelz und Dentin in menschlichen Zähnen

Objectives: Glass ionomer cements (GIC) are biomaterials with one particular advantage for dentistry: their self-adherence to both dentine and enamel in teeth. Although brittle, GICs have multiple merits that entail remarkable endurance on the tooth substrates through long-term chemical interactions. To quantify these effects, this in vitro study characterizes the structure of the interaction zone between a conventional restorative GIC and tooth tissues using 2D and 3D techniques, with increasing water storage times. Methods: caries free human molars were restored with a conventional GIC (Ketac Fil Plus, 3M, Neuss, Germany) in class I cavities without cavity conditioning. Thereafter, each sample was sliced to expose internal surfaces, followed by storage at room temperature in water containing 0.5% chloramine-T for 1 week, 3 months, 6 months, 9 months and 18 months. Samples were imaged down to the micrometer length scale using different techniques: light/optical microscopy, scanning electron microscopy (SEM) with energy dispersive X-ray chemical mapping (EDX) in two dimensions (2D) and by confocal laser scanning microscopy (CLSM), X-ray computed microtomography (µCT), and phase-contrast-enhanced µCT (PCE-CT) in a synchrotron radiation facility in three dimensions (3D). Additional replicas were prepared and compared to direct sample imaging by SEM, to reveal the GIC-tooth substrate interfaces. Results: All 2D and 3D techniques revealed increasing chemical and density changes in both GIC and dentine with increasing time, quantified both at the base and at the outer surface of the cavity. In many regions, both mixed and cohesive cracks were observed in GIC. In dentine, the greatest changes over time were observed at the interface closer to the pulp. Little change was observed in enamel over time. Many samples exhibited an interaction interphase layer (IIL) at the interface between GIC and both dentine and enamel. The IIL was more acid resistant than both GIC and the tooth hard tissue near it, appearing speckled. Various ions diffuse across the IIL region: Ca and P from tooth tissues impregnate the GIC, whereas F, Sr, Al and La from the GIC were identified in the tooth substrates. Pores in GIC, particularly near the GIC-dentine interface, often contain spherical bodies consisting mainly of Si. Conclusions: between GIC and the dental hard tissues, a good attachment was almost always observed. An IIL that formed at the interface was resistant to acid etching. Through complementary 2D and 3D materials characterization techniques, attributes of the IIL were quantified. Water storage of up to 18 months revealed both an active IIL and maturation of spherical bodies, suggestive of a long-term, chemically reactive GIC.Einleitung: Glasionomerzemente (GIZ) sind Biomaterialien mit einem besonderen Vorteil für die Zahnmedizin: Sie haften sowohl am Dentin als auch am Zahnschmelz in den Zähnen. Obwohl sie relativ spröde Materialien sind, haben GIZ mehrere Vorteile, die eine außergewöhnliche Langlebigkeit der Restaurationen durch langfristige chemische Wechselwirkungen mit den Zahnhartsubstraten mit sich bringen. Um diese Effekte zu quantifizieren, wurde in dieser in-vitro-Studie die Struktur der Wechselwirkungszone zwischen einem konventionellen restaurativen GIZ und dem Zahngewebe in Abhängigkeit von unterschiedlichen Aufbewahrungszeiten in Wasser durch 2D- und 3D-Techniken charakterisiert. Methoden: Kariesfreie menschliche Molaren wurden mit einem konventionellen GIZ (Ketac Fil Plus 3M) in der Klasse I Kavitäten behandelt. Danach wurde jede Probe in Scheiben geschnitten, um innere Oberflächen freizulegen, und anschließend 1 Woche, 3, 6, 9 und 18 Monate bei Raumtemperatur in Wasser mit 0,5% Chloramin-T gelagert. Die Proben wurden unter Verwendung verschiedener Methoden hochaufgelöst im Mikrometerbereich abgebildet. Dazu zählen: Lichtmikroscopie, Rasterelektronenmikroskopie mit energiedispersiver Röntgenspektroskopie und konfokale Laser-Scanning-Mikroskopie, Röntgen-Mikro-Computertomography und Röntgen-Phasenkontrast verstärkte. Zusätzlich wurden vergleichbare Proben und Replikate hergestellt, um GIZ-Zahn-Substrat-Grenzflächen zu vergleichen. Ergebnisse: Alle 2D- und 3D-Techniken ergaben, mit zunehmender Zeit chemische und Dichteänderungen in beiden GIZ und Dentin zu erhöhen, quantifizierten sowohl an der Basis als auch an der äußeren Oberfläche der Kavität. In vielen Regionen wurden bei GIZ sowohl gemischte als auch kohäsive Risse beobachtet. Im Dentin wurden die größten zeitlichen Veränderungen an der Grenzfläche näher an der Pulpa beobachtet. Im Laufe der Zeit wurde nur eine geringe Veränderung des Zahnschmelzes beobachtet. Viele Proben zeigten eine Interaktions-Interphasenschicht (IIS) an der Grenzfläche zwischen GIZ und sowohl Dentin als auch Schmelz. Die IIS war säurebeständiger als das GIZ und das Zahnhartgewebe in der Nähe und schien gesprenkelt zu sein. Verschiedene Ionen diffundieren über die IIS-Region: Ca und P aus Zahngeweben imprägnieren den GIZ, während F, Sr, Al und La aus GIZ in den Zahnsubstraten identifiziert wurden. Poren im GIZ, insbesondere in der Nähe der GIZ-Dentin-Grenzfläche, enthalten häufig kugelförmige Körper, die hauptsächlich aus Si bestehen. Schlussfolgerung: Zwischen GIZ und den zahnärztlichen Hartgeweben wurde fast immer eine gute Anhaftung beobachtet. Eine IIS, die sich an der Grenzfläche bildete, war resistent gegen Säureätzung. Durch komplementäre 2D- und 3D-Materialcharakterisierungstechniken wurden Attribute der IIS quantifiziert. Wasserlagerung bis zu 18 Monate ergaben sowohl eine aktive IIS als auch die Reifung von kugelförmigen Körpern suggerieren eine langfristige, chemische Reaktion von GIZ mit den Zahnhartsubstanzen

Crystallization of hydrated and anhydrous salts in porous limestone resolved by synchrotron X-ray microtomography

ACLInternational audienceThe crystallization processes of two anhydrous salts (NaCl and Na 2SO4) and one hydrated (sodium sulfate) salt in the pore space of a natural building stone, Savonnières limestone, are studied. We imaged the salt solution distribution before and after crystallization and the solid crystal distribution in between repeated crystallization cycles using synchrotron X-ray microtomography. This technique proves to be very useful to study salt crystallization processes at the pore scale. The use of simultaneous phase-and-amplitude retrieval during X-ray tomographic reconstruction allows a clear segmentation of sodium sulfate solution and hydrated sodium sulfate crystals without the need for a dopant. Salt crystals can precipitate under unconfined as well as confined conditions in the multiple pore systems of Savonnières limestone, depending on their interconnection. Salt solution and salt crystals are located in mechanically weak zones of the limestone, which can be linked to damage patterns observed in this stone after repeated salt weathering cycles. The distribution and the process of pore filling by salt crystals that are revealed here advance the understanding of salt damage in porous media and may open ways to perform remediation. © 2014 Elsevier B.V. All rights reserved

First order algorithms in variational image processing

Variational methods in imaging are nowadays developing towards a quite universal and flexible tool, allowing for highly successful approaches on tasks like denoising, deblurring, inpainting, segmentation, super-resolution, disparity, and optical flow estimation. The overall structure of such approaches is of the form ${\cal D}(Ku) + \alpha {\cal R} (u) \rightarrow \min_u$ ; where the functional ${\cal D}$ is a data fidelity term also depending on some input data $f$ and measuring the deviation of $Ku$ from such and ${\cal R}$ is a regularization functional. Moreover $K$ is a (often linear) forward operator modeling the dependence of data on an underlying image, and $\alpha$ is a positive regularization parameter. While ${\cal D}$ is often smooth and (strictly) convex, the current practice almost exclusively uses nonsmooth regularization functionals. The majority of successful techniques is using nonsmooth and convex functionals like the total variation and generalizations thereof or $\ell_1$-norms of coefficients arising from scalar products with some frame system. The efficient solution of such variational problems in imaging demands for appropriate algorithms. Taking into account the specific structure as a sum of two very different terms to be minimized, splitting algorithms are a quite canonical choice. Consequently this field has revived the interest in techniques like operator splittings or augmented Lagrangians. Here we shall provide an overview of methods currently developed and recent results as well as some computational studies providing a comparison of different methods and also illustrating their success in applications.Comment: 60 pages, 33 figure

Stepped vitrification technique for human ovarian tissue cryopreservation

The advantage of stepped vitrification (SV) is avoiding ice crystal nucleation, while decreasing the toxic effects of high cryoprotectant concentrations. We aimed to test this method for human ovarian tissue cryopreservation. Ovarian cortex was taken from 7 fertile adult women. Samples were subjected to an SV protocol performed in an automatic freezer, which allowed sample transfer to ever higher concentrations of dimethyl sulfoxide (DMSO) as the temperature was reduced. Histological evaluation of the vitrified-warmed tissue showed large numbers of degenerated follicles after 24 hours of in vitro culture. We therefore evaluated DMSO perfusion rates by X-ray computed tomography, ice crystal formation by freeze-substitution, and cell toxicity by transmission electron microscopy, seeking possible reasons why follicles degenerated. Although cryoprotectant perfusion was considered normal and no ice crystals were formed in the tissue, ultrastructural analysis detected typical signs of DMSO toxicity, such as mitochondria degeneration, alterations in chromatin condensation, cell vacuolization and extracellular matrix swelling in both stromal and follicular cells. The findings indicated that the method failed to preserve follicles due to the high concentrations of DMSO used. However, adaptations can be made to avoid toxicity to follicles caused by elevated levels of cryoprotectants.Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP) 2016/22947-

GENFIRE: A generalized Fourier iterative reconstruction algorithm for high-resolution 3D imaging

Tomography has made a radical impact on diverse fields ranging from the study of 3D atomic arrangements in matter to the study of human health in medicine. Despite its very diverse applications, the core of tomography remains the same, that is, a mathematical method must be implemented to reconstruct the 3D structure of an object from a number of 2D projections. In many scientific applications, however, the number of projections that can be measured is limited due to geometric constraints, tolerable radiation dose and/or acquisition speed. Thus it becomes an important problem to obtain the best-possible reconstruction from a limited number of projections. Here, we present the mathematical implementation of a tomographic algorithm, termed GENeralized Fourier Iterative REconstruction (GENFIRE). By iterating between real and reciprocal space, GENFIRE searches for a global solution that is concurrently consistent with the measured data and general physical constraints. The algorithm requires minimal human intervention and also incorporates angular refinement to reduce the tilt angle error. We demonstrate that GENFIRE can produce superior results relative to several other popular tomographic reconstruction techniques by numerical simulations, and by experimentally by reconstructing the 3D structure of a porous material and a frozen-hydrated marine cyanobacterium. Equipped with a graphical user interface, GENFIRE is freely available from our website and is expected to find broad applications across different disciplines.Comment: 18 pages, 6 figure