Framework to optimize fixed-length micro-CT systems for propagation-based phase-contrast imaging.

A laboratory X-ray imaging system with a setup that closely resembles commercial micro-CT systems with a fixed source-to-detector distance of ∼90 cm is investigated for single distance propagation-based phase-contrast imaging and computed tomography (CT). The system had a constant source-to-detector distance, and the sample positions were optimized. Initially, a PTFE wire was imaged, both in 2D and 3D, to characterize fringe contrast and spatial resolution for different X-ray source settings and source-to-sample distances. The results were compared to calculated values based on theoretical models and to simulated (wave-optics based) results, with good agreement being found. The optimization of the imaging system is discussed. CT scans of two biological samples, a tissue-engineered esophageal scaffold and a rat heart, were then acquired at the optimum parameters, demonstrating that significant image quality improvements can be obtained with widely available components placed inside fixed-length cabinets through proper optimization of propagation-based phase-contrast.

On the equivalence of the X-ray scattering retrieval with beam tracking and analyser-based imaging using a synchrotron source.

X-ray phase contrast imaging (XPCI) methods give access to contrast mechanisms that are based on the refractive properties of matter on top of the absorption coefficient in conventional x-ray imaging. Ultra small angle x-ray scattering (USAXS) is a phase contrast mechanism that arises due to multiple refraction events caused by physical features of a scale below the physical resolution of the used imaging system. USAXS contrast can therefore give insight into subresolution structural information, which is an ongoing research topic in the vast field of different XPCI techniques. In this study, we quantitatively compare the USAXS signal retrieved by the beam tracking XPCI technique with the gold standard of the analyzer based imaging XPCI technique using a synchrotron x-ray source. We find that, provided certain conditions are met, the two methods measure the same quantity.

X-ray Phase-Contrast Radiography and Tomography with a Multiaperture Analyzer.

We present a multiaperture analyzer setup for performing x-ray phase contrast imaging in planar and three-dimensional modalities. The method is based on strongly structuring the x-ray beam with an amplitude modulator, before it reaches the sample, and on a multiaperture analyzing element before detection. A multislice representation of the sample is used to establish a quantitative relation between projection images and the corresponding three-dimensional distributions, leading to successful tomographic reconstruction. Sample absorption, phase, and scattering are retrieved from the measurement of five intensity projections. The method is tested on custom-built phantoms with synchrotron radiation: sample absorption and phase can be reliably retrieved also in combination with strong scatterers, simultaneously attaining high sensitivity and dynamic range.

The 6-hydroxydopamine model and parkinsonian pathophysiology: Novel findings in an older model. / El modelo de 6-hidroxidopamina y la fisiopatología parkinsoniana: nuevos hallazgos en un viejo modelo.

The neurotoxin 6-hydroxydopamine (6-OHDA) is widely used to induce models of Parkinson's disease (PD). We now know that the model induced by 6-OHDA does not include all PD symptoms, although it does reproduce the main cellular processes involved in PD, such as oxidative stress, neurodegeneration, neuroinflammation, and neuronal death by apoptosis. In this review we analyse the factors affecting the vulnerability of dopaminergic neurons as well as the close relationships between neuroinflammation, neurodegeneration, and apoptosis in the 6-OHDA model. Knowledge of the mechanisms involved in neurodegeneration and cell death in this model is the key to identifying potential therapeutic targets for PD.

Theory and preliminary experimental verification of quantitative edge illumination x-ray phase contrast tomography.

X-ray phase contrast imaging (XPCi) methods are sensitive to phase in addition to attenuation effects and, therefore, can achieve improved image contrast for weakly attenuating materials, such as often encountered in biomedical applications. Several XPCi methods exist, most of which have already been implemented in computed tomographic (CT) modality, thus allowing volumetric imaging. The Edge Illumination (EI) XPCi method had, until now, not been implemented as a CT modality. This article provides indications that quantitative 3D maps of an object's phase and attenuation can be reconstructed from EI XPCi measurements. Moreover, a theory for the reconstruction of combined phase and attenuation maps is presented. Both reconstruction strategies find applications in tissue characterisation and the identification of faint, weakly attenuating details. Experimental results for wires of known materials and for a biological object validate the theory and confirm the superiority of the phase over conventional, attenuation-based image contrast.

T staging esophageal tumors with x rays.

With histopathology results typically taking several days, the ability to stage tumors during interventions could provide a step change in various cancer interventions. X-ray technology has advanced significantly in recent years with the introduction of phase-based imaging methods. These have been adapted for use in standard labs rather than specialized facilities such as synchrotrons, and approaches that enable fast 3D scans with conventional x-ray sources have been developed. This opens the possibility to produce 3D images with enhanced soft tissue contrast at a level of detail comparable to histopathology, in times sufficiently short to be compatible with use during surgical interventions. In this paper we discuss the application of one such approach to human esophagi obtained from esophagectomy interventions. We demonstrate that the image quality is sufficiently high to enable tumor T staging based on the x-ray datasets alone. Alongside detection of involved margins with potentially life-saving implications, staging tumors intra-operatively has the potential to change patient pathways, facilitating optimization of therapeutic interventions during the procedure itself. Besides a prospective intra-operative use, the availability of high-quality 3D images of entire esophageal tumors can support histopathological characterization, from enabling "right slice first time" approaches to understanding the histopathology in the full 3D context of the surrounding tumor environment.

X-ray phase-contrast imaging with nanoradian angular resolution.

We present a new quantitative x-ray phase-contrast imaging method based on the edge illumination principle, which allows achieving unprecedented nanoradian sensitivity. The extremely high angular resolution is demonstrated theoretically and through experimental images obtained at two different synchrotron radiation facilities. The results, achieved at both very high and very low x-ray energies, show that this highly sensitive technique can be efficiently exploited over a very broad range of experimental conditions. This method can open the way to new, previously inaccessible scientific applications in various fields including biology, medicine and materials science.

A laboratory-based beam tracking x-ray imaging method achieving two-dimensional phase sensitivity and isotropic resolution with unidirectional undersampling.

Beam tracking X-ray Phase Contrast Imaging is a "Shack-Hartmann" type approach which uses a pre-sample mask to split the x-rays into "beamlets" which are interrogated by a detector with sufficient resolution. The ultimate spatial resolution is determined by the size of the mask apertures, however achieving this resolution level requires "stepping" the sample or the mask in increments equal to the aperture size ("dithering"). If an array of circular apertures is used (which also provides two-dimensional phase sensitivity) instead of long parallel slits, this stepping needs to be carried out in two directions, which lengthens scan times significantly. We present a mask design obtained by offsetting rows of circular apertures, allowing for two-dimensional sensitivity and isotropic resolution while requiring sample or mask stepping in one direction only. We present images of custom-built phantoms and biological specimens, demonstrating that quantitative phase retrieval and near aperture-limited spatial resolutions are obtained in two orthogonal directions.

Post-acquisition mask misalignment correction for edge illumination x-ray phase contrast imaging.

Edge illumination x-ray phase contrast imaging uses a set of apertured masks to translate phase effects into variation of detected intensity. While the system is relatively robust against misalignment, mask movement during acquisition can lead to gradient artifacts. A method has been developed to correct the images by quantifying the misalignment post-acquisition and implementing correction maps to remove the gradient artifact. Images of a woven carbon fiber composite plate containing porosity were used as examples to demonstrate the image correction process. The gradient formed during image acquisition was removed without affecting the image quality, and results were subsequently used for quantification of porosity, indicating that the gradient correction did not affect the quantitative content of the images.

The effect of a variable focal spot size on the contrast channels retrieved in edge-illumination X-ray phase contrast imaging.

Multi-modal X-ray imaging allows the extraction of phase and dark-field (or "Ultra-small Angle Scatter") images alongside conventional attenuation ones. Recently, scan-based systems using conventional sources that can simultaneously output the above three images on relatively large-size objects have been developed by various groups. One limitation is the need for some degree of spatial coherence, achieved either through the use of microfocal sources, or by placing an absorption grating in front of an extended source. Both these solutions limit the amount of flux available for imaging, with the latter also leading to a more complex setup with additional alignment requirements. Edge-illumination partly overcomes this as it was proven to work with focal spots of up to 100 micron. While high-flux, 100 micron focal spot sources do exist, their comparatively large footprint and high cost can be obstacles to widespread translation. A simple solution consists in placing a single slit in front of a large focal spot source. We used a tunable slit to study the system performance at various effective focal spot sizes, by extracting transmission, phase and dark-field images of the same specimens for a range of slit widths. We show that consistent, repeatable results are obtained for varying X-ray statistics and effective focal spot sizes. As the slit width is increased, the expected reduction in the raw differential phase peaks is observed, compensated for in the retrieval process by a broadened sensitivity function. This leads to the same values being correctly retrieved, but with a slightly larger error bar i.e. a reduction in phase sensitivity. Concurrently, a slight increase in the dark-field signal is also observed.

Cycloidal-spiral sampling for three-modal x-ray CT flyscans with two-dimensional phase sensitivity.

We present a flyscan compatible acquisition scheme for three-modal X-Ray Computed Tomography (CT) with two-dimensional phase sensitivity. Our approach is demonstrated using a "beam tracking" setup, through which a sample's attenuation, phase (refraction) and scattering properties can be measured from a single frame, providing three complementary contrast channels. Up to now, such setups required the sample to be stepped at each rotation angle to sample signals at an adequate rate, to prevent resolution losses, anisotropic resolution, and under-sampling artefacts. However, the need for stepping necessitated a step-and-shoot implementation, which is affected by motors' overheads and increases the total scan time. By contrast, our proposed scheme, by which continuous horizontal and vertical translations of the sample are integrated with its rotation (leading to a "cycloidal-spiral" trajectory), is fully compatible with continuous scanning (flyscans). This leads to greatly reduced scan times while largely preserving image quality and isotropic resolution.

Enhanced detection of threat materials by dark-field x-ray imaging combined with deep neural networks.

X-ray imaging has been boosted by the introduction of phase-based methods. Detail visibility is enhanced in phase contrast images, and dark-field images are sensitive to inhomogeneities on a length scale below the system's spatial resolution. Here we show that dark-field creates a texture which is characteristic of the imaged material, and that its combination with conventional attenuation leads to an improved discrimination of threat materials. We show that remaining ambiguities can be resolved by exploiting the different energy dependence of the dark-field and attenuation signals. Furthermore, we demonstrate that the dark-field texture is well-suited for identification through machine learning approaches through two proof-of-concept studies. In both cases, application of the same approaches to datasets from which the dark-field images were removed led to a clear degradation in performance. While the small scale of these studies means further research is required, results indicate potential for a combined use of dark-field and deep neural networks in security applications and beyond.

Targeting and retention of HPV16 E7 to the endoplasmic reticulum enhances immune tumour protection.

The endoplasmic reticulum (ER) is where the major histocompatibility complex (MHC) class I molecules are loaded with epitopes to cause an immune cellular response. Most of the protein antigens are degraded in the cytoplasm to amino acids and few epitopes reach the ER. Antigen targeting of this organelle by Calreticulin (CRT) fusion avoids this degradation and enhances the immune response. We constructed a recombinant adenovirus to express the E7 antigen with an ER-targeting signal peptide (SP) plus an ER retention signal (KDEL sequence). In cell-culture experiments we demonstrated that this new E7 antigen, SP-E7-KDEL, targeted the ER. Infection of mice with this recombinant adenovirus that expresses SP-E7-KDEL showed interferon induction and tumour-protection response, similar to that provided by an adenovirus expressing the E7 antigen fused to CRT. This work demonstrated that just by adding a SP and the KDEL sequence, antigens can be targeted and retained in the ER with a consequent enhancement of immune response and tumour protection. These results will have significant clinical applications.

Signal and noise transfer properties of CMOS based active pixel flat panel imager coupled to structured CsI:Tl.

Complementary metal-oxide-semiconductors (CMOS) active pixel sensors can be optically coupled to CsI:Tl phosphors forming a indirect active pixel flat panel imager (APFPI) for high performance medical imaging. The aim of this work is to determine the x-ray imaging capabilities of CMOS-based APFPI and study the signal and noise transfer properties of CsI:Tl phosphors. Three different CsI:Tl phosphors from two different vendors have been used to produce three system configurations. The performance of each system configuration has been studied in terms of the modulation transfer function (MTF), noise power spectra, and detective quantum efficiency (DQE) in the mammographic energy range. A simple method to determine quantum limited systems in this energy range is also presented. In addition, with aid of monochromatic synchrotron radiation, the effect of iodine characteristic x-rays of the CsI:Tl on the MTF has been determined. A Monte Carlo simulation of the signal transfer properties of the imager is also presented in order to study the stages that degrade the spatial resolution of our current system. The effect of using substrate patterning during the growth of CsI:Tl columnar structure was also studied, along with the effect of CsI:Tl fixed pattern noise due to local variations in the scintillation light. CsI:Tl fixed pattern noise appears to limit the performance of our current system configurations. All the system configurations are quantum limited at 0.23 microC/kg with two of them having DQE (0) equal to 0.57. Active pixel flat panel imagers are shown to be digital x-ray imagers with almost constant DQE throughout a significant part of their dynamic range and in particular at very low exposures.

Deconvolution of x-ray phase contrast images as a way to retrieve phase information lost due to insufficient resolution.

When free-space propagation x-ray phase contrast imaging is implemented outside synchrotron radiation facilities, the combined effect of detector resolution and source size swamps the fine phase contrast fringes, often making them almost undetectable. In an attempt to mitigate this effect, a simple deconvolution procedure based on division in the Fourier space plus multiplication by an appropriate filter was applied to experimental x-ray phase contrast images of a simple geometric phantom. The filter parameter was varied in order to assess its impact on the level of retrieved phase signal. The deconvolved images were compared to simulated ones obtained under different resolution conditions, showing that this simple procedure provided signals equivalent to those that would be obtained with a detector with three times better resolution. By accepting an increase in the overall image noise, the method also appears to bring up secondary phase contrast fringes, which are not visible in the unprocessed signal.

Image formation principles in coded-aperture based x-ray phase contrast imaging.

A novel x-ray phase contrast imaging technique based on coded apertures was recently developed at University College London. This technique removes most limitations of previous phase contrast methods and provides image improvements comparable to those obtained with synchrotron radiation with conventional x-ray sources. Unlike other phase contrast approaches, the technique does not impose restrictive wavelength and/or angular filtering on the beam emitted by the source, meaning that the beam can be exploited in full thus minimizing exposure times. As a consequence, the method provides, for the first time, a concrete opportunity to transfer x-ray phase contrast imaging into real medical applications. This paper discusses the image formation principles, analyses the shape and nature of the phase contrast profiles obtained and draws a significant conclusion on the role of convolution integrals in the acquisition of phase contrast patterns, applicable also to other phase contrast imaging approaches.

Modelling of a novel x-ray phase contrast imaging technique based on coded apertures.

X-ray phase contrast imaging is probably the most relevant among emerging x-ray imaging techniques, and it has the proven potential of revolutionizing the field of diagnostic radiology. Impressive images of a wide range of samples have been obtained, mostly at synchrotron radiation facilities. The necessity of relying on synchrotron radiation has prevented to a large extent a widespread diffusion of phase contrast imaging, thus precluding its transfer to clinical practice. A new technique, based on the use of coded apertures, was recently developed at UCL. This technique was demonstrated to provide intense phase contrast signals with conventional x-ray sources and detectors. Unlike other attempts at making phase contrast imaging feasible with conventional sources, the coded-aperture approach does not impose substantial limitations and/or filtering of the radiation beam, and it therefore allows, for the first time, exposures compatible with clinical practice. The technique has been thoroughly modelled, and this paper describes the technique in detail by going through the different steps of the modelling. All the main factors influencing image quality are discussed, alongside the viability of realizing a prototype suitable for clinical use. The model has been experimentally validated and a section of the paper shows the comparison between simulated and experimental results.

Mexican Fruit Fly Populations in the Semi-Arid Highlands of the Sierra Madre Oriental in Northeastern Mexico.

The Mexican fruit fly, Anastrepha ludens Loew (Diptera: Tephritidae), is one of the most important pests of citrus in Mexico. We report the results of an analysis of A. ludens populations that inhabit the semi-arid highlands of the Sierra Madre Oriental in northeastern Mexico. This study aimed to provide information on population fluctuation of A. ludens and how it relates to climate variables, as well as insights into habitat and native parasitoids. Population peaked in the period July-November when ripe fruits of the wild host, Casimiroa pubescens Ramírez, were available. No adults were captured the rest of the year, suggesting that high populations depend on the availability of wild host fruit. No significant relationships between population fluctuation and climatic variables were observed, except for minimum temperature. Fruit samples of citron (Citrus medica L.), pomegranate (Punica granatum L.), and C. pubescens were collected to determine degree of infestation. Infestation levels (pupae/g) ranged between 0.0006 for citron, 0.0047 for pomegranate, and 0.0240 for C. pubescens. A native parasitoid of Tephritidae, Doryctobracon crawfordii (Viereck) (Braconidae), was identified. Parasitism percentage was calculated at 12.5% on C. pubescens fruits. No parasitoids were observed on citron or pomegranate fruit samples. These results contribute to knowledge on behavior of A. ludens native to temperate environments where no commercial hosts are available. Further research on host expansion of this pest in light of scenarios of global climate change is suggested.

Experimental validation of a simple model capable of predicting the phase contrast imaging capabilities of any x-ray imaging system.

Phase contrast (PC) imaging is one of the most exciting emerging x-ray imaging techniques, with the potential of removing some of the main limitations of conventional radiology. After extensive experimentation carried out particularly at synchrotron radiation (SR) facilities, the scientific community agrees that it is now time to translate these ideas towards the first clinical implementations. In this framework, a complete model, based on Fresnel/Kirchoff diffraction integrals, was devised. This model accounts for source dimensions, beam spectrum and divergence and detector point spread function (PSF), and can thus be applied to any x-ray imaging system. In particular, by accepting in input the above parameters along with the ones describing the sample, the model can be used to optimize the geometry of the set-up, i.e. to assess the source-to-sample and sample-to-detector distances which maximize feature detection. The model was evaluated by acquiring a range of images of different samples with a laboratory source, and a good agreement was found between simulated and experimental data in all cases. In order to maximize the generality of the results, all acquisitions were carried out using a polychromatic source and an energy-resolving detector; in this way, a range of monochromatic images could be obtained as well as polychromatic images, which can be created by integrating different parts of the acquired spectra. One of the most notable results obtained is that in many practical cases polychromatic PC imaging can provide the same image quality as its monochromatic counterpart. This is an important step in the wider application of PC using conventional sources.