Virtual edge illumination and one dimensional beam tracking for absorption, refraction, and scattering retrieval

We propose two different approaches to retrieve x-ray absorption, refraction, and scattering signals using a one dimensional scan and a high resolution detector. The first method can be easily implemented in existing procedures developed for edge illumination to retrieve absorption and refraction signals, giving comparable image quality while reducing exposure time and delivered dose. The second method tracks the variations of the beam intensity profile on the detector through a multi-Gaussian interpolation, allowing the additional retrieval of the scattering signal

X–ray absorption, phase and dark–field tomography through a beam tracking approach

We present a development of the beam–tracking approach that allows its implementation in computed tomography. One absorbing mask placed before the sample and a high resolution detector are used to track variations in the beam intensity distribution caused by the sample. Absorption, refraction, and dark–field are retrieved through a multi–Gaussian interpolation of the beam. Standard filtered back projection is used to reconstruct three dimensional maps of the real and imaginary part of the refractive index, and of the dark–field signal. While the method is here demonstrated using synchrotron radiation, its low coherence requirements suggest a possible implementation with laboratory sources

Laboratory-based edge-illumination phase-contrast imaging: Dark-field retrieval and high-resolution implementations

Edge illumination is an X-ray phase-contrast imaging technique capable of quantitative retrieval of phase and amplitude images. The retrieval of the ultra-small-angle X-ray scattering was recently developed and implemented with the area-imaging counterpart of an edge-illumination system, sometimes referred to as coded-aperture setup. This is an incoherent and achromatic technique, well suited for translation of the potential of X-ray phase contrast imaging into efficient laboratory-scale setups. We report on recent advances of these developments along two main directions. One relates to the expansion of the technique with respect to the data analysis and corrections that are required when non-ideal optical elements are used and optimized sampling strategies. The second is directed towards high-resolution and high-energy implementations. A laboratory-based prototype for high-energy X-ray phase-contrast microscopy was built and its performance was modelled and experimentally characterized

Phase-contrast microscopy at high x-ray energy with a laboratory setup

We report on the design and realization of an x-ray imaging system for quantitative phase-contrast microscopy at high x-ray energy with laboratory-scale instrumentation. Phase and amplitudewere separated quantitatively at x-ray energies up to 80 keV with micrometric spatial resolution. The accuracy of the results was tested against numerical simulations, and the spatial resolution was experimentally quantified by measuring a Siemens star phase object. This simple setup should find broad application in those areas of x-ray imaging where high energy and spatial resolution are simultaneously required and in those difficult cases where the sample contains materials with similar x-ray absorption

A single-image retrieval method for edge illumination X-ray phase-contrast imaging: Application and noise analysis

Purpose: Edge illumination (EI) X-ray phase-contrast imaging (XPCI) has been under development at University College London in recent years, and has shown great potential for both laboratory and synchrotron applications. In this work, we propose a new acquisition and processing scheme. Contrary to existing retrieval methods for EI, which require as input two images acquired in different setup configurations, the proposed approach can retrieve an approximate map of the X-ray phase from a single image, thus significantly simplifying the acquisition procedure and reducing data collection times. Methods: The retrieval method is analytically derived, based on the assumption of a quasi-homogeneous object, i.e. an object featuring a constant ratio between refractive index and absorption coefficient. The noise properties of the input and retrieved images are also theoretically analyzed under the developed formalism. The method is applied to experimental synchrotron images of a biological object. Results: The experimental results show that the method can provide high-quality images, where the “edge” signal typical of XPCI images is transformed to an “area” contrast that enables an easier interpretation of the sample geometry. Moreover, the retrieved images confirm that the method is highly stable against noise. Conclusions: We anticipate that the developed approach will become the method of choice for a variety of applications of EI XPCI, thanks to its ability to simplify the acquisition procedure and reduce acquisitions time and dose to the sample. Future work will focus on the adaptation of the method to computed tomography and to polychromatic radiation from X-ray tubes

Simple and robust synchrotron and laboratory solutions for high-resolution multimodal X-ray phase-based imaging

Edge illumination X-ray phase contrast imaging techniques are capable of quantitative retrieval of differential phase, absorption and X-ray scattering. We have recently developed a series of approaches enabling high-resolution implementations, both using synchrotron radiation and laboratory-based set-ups. Three-dimensional reconstruction of absorption, phase and dark-field can be achieved with a simple rotation of the sample. All these approaches share a common trait which consists in the use of an absorber that shapes the radiation field, in order to make the phase modulations introduced by the sample detectable. This enables a well-defined and high-contrast structuring of the radiation field as well as an accurate modelling of the effects that are related to the simultaneous use of a wide range of energies. Moreover, it can also be adapted for use with detectors featuring large pixel sizes, which could be desirable when a high detection efficiency is important

Effects of Laser Source Parameters on the Generation of Narrow Band and Directed Laser Ultrasound

The successful application of laser techniques for ultrasonic testing depends on the efficient coupling of optical energy into elastic energy so that laser probe detection sensitivity may be maximized. Through optimization of the laser source which is used to generate ultrasonic waves, the overall performance of laser ultrasonic systems may be enhanced by improving the efficiency with which optical energy is converted to elastic energy. This optimization depends primarily on the source laser wavelength which governs the physical interaction of the optical energy with the material of interest. For a given laser source wavelength, several techniques have been demonstrated which modify the laser source to enhance the detectability of laser ultrasonic waves and include the repetitively pulsed laser source [1,2], or temporal array, and the phased array laser source [3],or phased array. These techniques directly address the wave detectability issue by controlling the amplitude and/or the frequency content of the laser ultrasonic wave. Even though the overall conversion efficiency of optical energy to elastic energy is not improved primarily by repetitive pulsing or phasing laser arrays, the detectability of a given laser ultrasonic wave may be enhanced beyond that obtained using a single laser source

Diversity of Zoanthids (Anthozoa: Hexacorallia) on Hawaiian Seamounts: Description of the Hawaiian Gold Coral and Additional Zoanthids

The Hawaiian gold coral has a history of exploitation from the deep slopes and seamounts of the Hawaiian Islands as one of the precious corals commercialised in the jewellery industry. Due to its peculiar characteristic of building a scleroproteic skeleton, this zoanthid has been referred as Gerardia sp. (a junior synonym of Savalia Nardo, 1844) but never formally described or examined by taxonomists despite its commercial interest. While collection of Hawaiian gold coral is now regulated, globally seamounts habitats are increasingly threatened by a variety of anthropogenic impacts. However, impact assessment studies and conservation measures cannot be taken without consistent knowledge of the biodiversity of such environments. Recently, multiple samples of octocoral-associated zoanthids were collected from the deep slopes of the islands and seamounts of the Hawaiian Archipelago. The molecular and morphological examination of these zoanthids revealed the presence of at least five different species including the gold coral. Among these only the gold coral appeared to create its own skeleton, two other species are simply using the octocoral as substrate, and the situation is not clear for the final two species. Phylogenetically, all these species appear related to zoanthids of the genus Savalia as well as to the octocoral-associated zoanthid Corallizoanthus tsukaharai, suggesting a common ancestor to all octocoral-associated zoanthids. The diversity of zoanthids described or observed during this study is comparable to levels of diversity found in shallow water tropical coral reefs. Such unexpected species diversity is symptomatic of the lack of biological exploration and taxonomic studies of the diversity of seamount hexacorals

Deep generative modeling for single-cell transcriptomics.

Single-cell transcriptome measurements can reveal unexplored biological diversity, but they suffer from technical noise and bias that must be modeled to account for the resulting uncertainty in downstream analyses. Here we introduce single-cell variational inference (scVI), a ready-to-use scalable framework for the probabilistic representation and analysis of gene expression in single cells ( https://github.com/YosefLab/scVI ). scVI uses stochastic optimization and deep neural networks to aggregate information across similar cells and genes and to approximate the distributions that underlie observed expression values, while accounting for batch effects and limited sensitivity. We used scVI for a range of fundamental analysis tasks including batch correction, visualization, clustering, and differential expression, and achieved high accuracy for each task

Imaging-guided chest biopsies: techniques and clinical results

Background This article aims to comprehensively describe indications, contraindications, technical aspects, diagnostic accuracy and complications of percutaneous lung biopsy. Methods Imaging-guided biopsy currently represents one of the predominant methods for obtaining tissue specimens in patients with lung nodules; in many cases treatment protocols are based on histological information; thus, biopsy is frequently performed, when technically feasible, or in case other techniques (such as bronchoscopy with lavage) are inconclusive. Results Although a coaxial system is suitable in any case, two categories of needles can be used: fine-needle aspiration biopsy (FNAB) and core-needle biopsy (CNB), with the latter demonstrated to have a slightly higher overall sensitivity, specificity and accuracy. Conclusion Percutaneous lung biopsy is a safe procedure even though a few complications are possible: pneumothorax, pulmonary haemorrhage and haemoptysis are common complications, while air embolism and seeding are rare, but potentially fatal complications