Reduced volume of diabetic pancreatic islets in rodents detected by synchrotron X-ray phase-contrast microtomography and deep learning network

The pancreatic islet is a highly structured micro-organ that produces insulin in response to rising blood glucose. Here we develop a label-free and automatic imaging approach to visualize the islets in situ in diabetic rodents by the synchrotron radiation X-ray phase-contrast microtomography (SRμCT) at the ID17 station of the European Synchrotron Radiation Facility. The large-size images (3.2 mm × 15.97 mm) were acquired in the pancreas in STZ-treated mice and diabetic GK rats. Each pancreas was dissected by 3000 reconstructed images. The image datasets were further analysed by a self-developed deep learning method, AA-Net. All islets in the pancreas were segmented and visualized by the three-dimension (3D) reconstruction. After quantifying the volumes of the islets, we found that the number of larger islets (=>1500 μm³) was reduced by 2-fold (wt 1004 ± 94 vs GK 419 ± 122, P < 0.001) in chronically developed diabetic GK rat, while in STZ-treated diabetic mouse the large islets were decreased by half (189 ± 33 vs 90 ± 29, P < 0.001) compared to the untreated mice. Our study provides a label-free tool for detecting and quantifying pancreatic islets in situ. It implies the possibility of monitoring the state of pancreatic islets in vivo diabetes without labelling.

Lesion extension and neuronal loss following spinal cord injury using X-ray phase-contrast tomography in mice

Following a spinal cord injury (SCI) the degree of functional (motor, autonomous or sensory) correlates with the severity of nervous tissue disruption. An imaging technique able to capture non-invasively and simultaneously the complex mechanisms of neuronal loss, vascular damages and perilesional tissue reorganization is currently lacking in experimental SCI studies. Synchrotron X-ray phase-contrast Tomography (SXPCT) has emerged as a non-destructive 3D neuroimaging technique with high contrast and spatial resolution. In this framework, we developed a multimodal approach combining SXPCT, histology and correlative methods to study neuro-vascular architecture in normal and C4-contused mouse spinal cords (C57BL/6J mice, age 2-3 months). The evolution of SCI lesion was imaged at the cell resolution level during the acute (30 minutes) and subacute (7 days) phases. Spared motor neurons were segmented and quantified in different volumes localized at and away from the epicenter. SXPCT was able to capture neuronal loss and blood-brain barrier breakdown following SCI. 3D quantification based on SXPCT acquisitions showed no additional motor neuron loss between 30 minutes and 7 days post-SCI. In addition, the analysis of hemorrhagic (at 30 minutes) and lesion (at 7 days) volumes revealed a high similarity in size, suggesting no extension of tissue degeneration between early and later time points. Moreover, glial scar borders were unevenly distributed, with rostral edges being the most extended. In conclusion, SXPCT capability to image at high-resolution cellular changes in 3D enables understanding the relationship between hemorrhagic events and nervous structure damages in SCI.

X-ray multiscale 3D neuroimaging to quantify cellular aging and neurodegeneration postmortem in a model of Alzheimer’s disease

Purpose

Modern neuroimaging lacks the tools necessary for whole-brain, anatomically dense neuronal damage screening. An ideal approach would include unbiased histopathologic identification of aging and neurodegenerative disease.

Methods

We report the postmortem application of multiscale X-ray phase-contrast computed tomography (X-PCI-CT) for the label-free and dissection-free organ-level to intracellular-level 3D visualization of distinct single neurons and glia. In deep neuronal populations in the brain of aged wild-type and of 3xTgAD mice (a triply-transgenic model of Alzheimer’s disease), we quantified intracellular hyperdensity, a manifestation of aging or neurodegeneration.

Results

In 3xTgAD mice, the observed hyperdensity was identified as amyloid-β and hyper-phosphorylated tau protein deposits with calcium and iron involvement, by correlating the X-PCI-CT data to immunohistochemistry, X-ray fluorescence microscopy, high-field MRI, and TEM. As a proof-of-concept, X-PCI-CT was used to analyze hippocampal and cortical brain regions of 3xTgAD mice treated with LY379268, selective agonist of group II metabotropic glutamate receptors (mGlu2/3 receptors). Chronic pharmacologic activation of mGlu2/3 receptors significantly reduced the hyperdensity particle load in the ventral cortical regions of 3xTgAD mice, suggesting a neuroprotective effect with locoregional efficacy.

Conclusions

This multiscale micro-to-nano 3D imaging method based on X-PCI-CT enabled identification and quantification of cellular and sub-cellular aging and neurodegeneration in deep neuronal and glial cell populations in a transgenic model of Alzheimer’s disease. This approach quantified the localized and intracellular neuroprotective effects of pharmacological activation of mGlu2/3 receptors.

A Multi-Scale and Multi-Technique Approach for the Characterization of the Effects of Spatially Fractionated X-ray Radiation Therapies in a Preclinical Model

The purpose of this study is to use a multi-technique approach to detect the effects of spatially fractionated X-ray Microbeam (MRT) and Minibeam Radiation Therapy (MB) and to compare them to seamless Broad Beam (BB) irradiation. Healthy- and Glioblastoma (GBM)-bearing male Fischer rats were irradiated in-vivo on the right brain hemisphere with MRT, MB and BB delivering three different doses for each irradiation geometry. Brains were analyzed post mortem by multi-scale X-ray Phase Contrast Imaging-Computed Tomography (XPCI-CT), histology, immunohistochemistry, X-ray Fluorescence (XRF), Small- and Wide-Angle X-ray Scattering (SAXS/WAXS). XPCI-CT discriminates with high sensitivity the effects of MRT, MB and BB irradiations on both healthy and GBM-bearing brains producing a first-time 3D visualization and morphological analysis of the radio-induced lesions, MRT and MB induced tissue ablations, the presence of hyperdense deposits within specific areas of the brain and tumor evolution or regression with respect to the evaluation made few days post-irradiation with an in-vivo magnetic resonance imaging session. Histology, immunohistochemistry, SAXS/WAXS and XRF allowed identification and classification of these deposits as hydroxyapatite crystals with the coexistence of Ca, P and Fe mineralization, and the multi-technique approach enabled the realization, for the first time, of the map of the differential radiosensitivity of the different brain areas treated with MRT and MB. 3D XPCI-CT datasets enabled also the quantification of tumor volumes and Ca/Fe deposits and their full-organ visualization. The multi-scale and multi-technique approach enabled a detailed visualization and classification in 3D of the radio-induced effects on brain tissues bringing new essential information towards the clinical implementation of the MRT and MB radiation therapy techniques.

Multiscale X-ray phase contrast imaging of human cartilage for investigating osteoarthritis formation

Background

The evolution of cartilage degeneration is still not fully understood, partly due to its thinness, low radio-opacity and therefore lack of adequately resolving imaging techniques. X-ray phase-contrast imaging (X-PCI) offers increased sensitivity with respect to standard radiography and CT allowing an enhanced visibility of adjoining, low density structures with an almost histological image resolution. This study examined the feasibility of X-PCI for high-resolution (sub-) micrometer analysis of different stages in tissue degeneration of human cartilage samples and compare it to histology and transmission electron microscopy.

Methods

Ten 10%-formalin preserved healthy and moderately degenerated osteochondral samples, post-mortem extracted from human knee joints, were examined using four different X-PCI tomographic set-ups using synchrotron radiation the European Synchrotron Radiation Facility (France) and the Swiss Light Source (Switzerland). Volumetric datasets were acquired with voxel sizes between 0.7 × 0.7 × 0.7 and 0.1 × 0.1 × 0.1 µm³. Data were reconstructed by a filtered back-projection algorithm, post-processed by ImageJ, the WEKA machine learning pixel classification tool and VGStudio max. For correlation, osteochondral samples were processed for histology and transmission electron microscopy.

Results

X-PCI provides a three-dimensional visualization of healthy and moderately degenerated cartilage samples down to a (sub-)cellular level with good correlation to histologic and transmission electron microscopy images. X-PCI is able to resolve the three layers and the architectural organization of cartilage including changes in chondrocyte cell morphology, chondrocyte subgroup distribution and (re-)organization as well as its subtle matrix structures.

Conclusions

X-PCI captures comprehensive cartilage tissue transformation in its environment and might serve as a tissue-preserving, staining-free and volumetric virtual histology tool for examining and chronicling cartilage behavior in basic research/laboratory experiments of cartilage disease evolution.

Imaging atelectrauma in Ventilator-Induced Lung Injury using 4D X-ray microscopy

Mechanical ventilation can damage the lungs, a condition called Ventilator-Induced Lung Injury (VILI). However, the mechanisms leading to VILI at the microscopic scale remain poorly understood. Here we investigated the within-tidal dynamics of cyclic recruitment/derecruitment (R/D) using synchrotron radiation phase-contrast imaging (PCI), and the relation between R/D and cell infiltration, in a model of Acute Respiratory Distress Syndrome in 6 anaesthetized and mechanically ventilated New-Zealand White rabbits. Dynamic PCI was performed at 22.6 µm voxel size, under protective mechanical ventilation [tidal volume: 6 ml/kg; positive end-expiratory pressure (PEEP): 5 cmH₂O]. Videos and quantitative maps of within-tidal R/D showed that injury propagated outwards from non-aerated regions towards adjacent regions where cyclic R/D was present. R/D of peripheral airspaces was both pressure and time-dependent, occurring throughout the respiratory cycle with significant scatter of opening/closing pressures. There was a significant association between R/D and regional lung cellular infiltration (p = 0.04) suggesting that tidal R/D of the lung parenchyma may contribute to regional lung inflammation or capillary-alveolar barrier dysfunction and to the progression of lung injury. PEEP may not fully mitigate this phenomenon even at high levels. Ventilation strategies utilizing the time-dependence of R/D may be helpful in reducing R/D and associated injury.

Multiscale pink-beam microCT imaging at the ESRF-ID17 biomedical beamline

Recent trends in hard X-ray micro-computed tomography (microCT) aim at increasing both spatial and temporal resolutions. These challenges require intense photon beams. Filtered synchrotron radiation beams, also referred to as `pink beams', which are emitted by wigglers or bending magnets, meet this need, owing to their broad energy range. In this work, the new microCT station installed at the biomedical beamline ID17 of the European Synchrotron is described and an overview of the preliminary results obtained for different biomedical-imaging applications is given. This new instrument expands the capabilities of the beamline towards sub-micrometre voxel size scale and simultaneous multi-resolution imaging. The current setup allows the acquisition of tomographic datasets more than one order of magnitude faster than with a monochromatic beam configuration.

X-ray phase contrast tomography for the investigation of amyotrophic lateral sclerosis

Amyotrophic lateral sclerosis (ALS) is a progressive neurodegenerative disorder affecting motor neurons. Pre-clinical studies drive the development of animal models that well mimic ALS disorder and enable both the dissection of disease processes and an early assessment of therapy efficacy. A comprehensive knowledge of neuronal and vascular lesions in the brain and spinal cord is an essential factor to understand the development of the disease. Spatial resolution and bidimensional imaging are important drawbacks limiting current neuroimaging tools, while neuropathology relies on protocols that may alter tissue chemistry and structure. In contrast, recent ex vivo studies in mice demonstrated that X-ray phase-contrast tomography enables study of the 3D distribution of both vasculature and neuronal networks, without sample sectioning or use of staining. Here we present our findings on ex vivo SOD1G93A ALS mice spinal cord at a micrometric scale. An unprecedented direct quantification of neuro-vascular alterations at different stages of the disease is shown.

Simplified retrieval method for Edge Illumination X-ray phase contrast imaging allowing multi-modal imaging with fewer input frames

We present data from an implementation of Edge Illumination (EI) that uses a detector aperture designed for increasing dynamic range, suitable for clinically relevant X-ray energies and demonstrated here using synchrotron radiation. By utilising a sufficiently large crosstalk between pixels, this implementation enables single-scan imaging for phase and absorption, and double-scan for phase, absorption and dark field imaging. The presence of the detector mask enables a direct comparison between conventional EI and beam tracking (BT), which we conduct through Monte Carlo and analytical modelling in the case of a single-scan being used for the retrieval of all three contrasts. In the present case, where the X-ray beam width is comparable to the pixel size, we provide an analysis on best-positioning of the beam on the detector for accurate signal retrieval. Further, we demonstrate an application of this method by distinguishing different concentrations of microbubbles via their dark field signals at high energy using an EI system.

High resolution 3D visualization of the spinal cord in a post-mortem murine model

A crucial issue in the development of therapies to treat pathologies of the central nervous system is represented by the availability of non-invasive methods to study the three-dimensional morphology of spinal cord, with a resolution able to characterize its complex vascular and neuronal organization. X-ray phase contrast micro-tomography enables a high-quality, 3D visualization of both the vascular and neuronal network simultaneously without the need of contrast agents, destructive sample preparations or sectioning. Until now, high resolution investigations of the post-mortem spinal cord in murine models have mostly been performed in spinal cords removed from the spinal canal. We present here post-mortem phase contrast micro-tomography images reconstructed using advanced computational tools to obtain high-resolution and high-contrast 3D images of the fixed spinal cord without removing the bones and preserving the richness of micro-details available when measuring exposed spinal cords. We believe that it represents a significant step toward the in-vivo application.

Single-shot K-edge subtraction x-ray discrete computed tomography with a polychromatic source and the Pixie-III detector

K-edge subtraction (KES) imaging is a technique able to map a specific element such as e.g. a contrast agent within the tissues, by exploiting the sharp rise of its absorption coefficient at the K-edge energy. Whereas mainly explored at synchrotron radiation sources, the energy discrimination properties of modern x-ray photon counting detectors (XPCDs) pave the way for an implementation of single-shot KES imaging with conventional polychromatic sources. In this work we present an x-ray CT imaging system based on the innovative Pixie-III detector and discrete reconstruction. The results reported here show that a reliable automatic localization of Barium (above a certain concentration) is possible with a few dozens of tomographic projections for a volume having an axial slice of 512 [Formula: see text] 512 pixels. The final application is a routine high-fidelity 3D mapping of a specific element ready for further morphological quantification by means of x-ray CT with potential promising applications in vivo.

Micro-imaging of Brain Cancer Radiation Therapy Using Phase-contrast Computed Tomography

PURPOSE

Experimental neuroimaging provides a wide range of methods for the visualization of brain anatomic morphology down to subcellular detail. Still, each technique-specific detection mechanism presents compromises among the achievable field-of-view size, spatial resolution, and nervous tissue sensitivity, leading to partial sample coverage, unresolved morphologic structures, or sparse labeling of neuronal populations and often also to obligatory sample dissection or other sample invasive manipulations. X-ray phase-contrast imaging computed tomography (PCI-CT) is an experimental imaging method that simultaneously provides micrometric spatial resolution, high soft-tissue sensitivity, and ex vivo full organ rodent brain coverage without any need for sample dissection, staining or labeling, or contrast agent injection. In the present study, we explored the benefits and limitations of PCI-CT use for in vitro imaging of normal and cancerous brain neuromorphology after in vivo treatment with synchrotron-generated x-ray microbeam radiation therapy (MRT), a spatially fractionated experimental high-dose radiosurgery. The goals were visualization of the MRT effects on nervous tissue and a qualitative comparison of the results to the histologic and high-field magnetic resonance imaging findings.

METHODS AND MATERIALS

MRT was administered in vivo to the brain of both healthy and cancer-bearing rats. At 45 days after treatment, the brain was dissected out and imaged ex vivo using propagation-based PCI-CT.

RESULTS

PCI-CT visualizes the brain anatomy and microvasculature in 3 dimensions and distinguishes cancerous tissue morphology, necrosis, and intratumor accumulation of iron and calcium deposits. Moreover, PCI-CT detects the effects of MRT throughout the treatment target areas (eg, the formation of micrometer-thick radiation-induced tissue ablation). The observed neurostructures were confirmed by histologic and immunohistochemistry examination and related to the micro-magnetic resonance imaging data.

CONCLUSIONS

PCI-CT enabled a unique 3D neuroimaging approach for ex vivo studies on small animal models in that it concurrently delivers high-resolution insight of local brain tissue morphology in both normal and cancerous micro-milieu, localizes radiosurgical damage, and highlights the deep microvasculature. This method could assist experimental small animal neurology studies in the postmortem evaluation of neuropathology or treatment effects.

In-situ visualization of sound-induced otolith motion using hard X-ray phase contrast imaging

Regarding the basics of ear structure-function relationships in fish, the actual motion of the solid otolith relative to the underlying sensory epithelium has rarely been investigated. Otolith motion has been characterized based on a few experimental studies and on approaches using mathematical modeling, which have yielded partially conflicting results. Those studies either predicted a simple back-and-forth motion of the otolith or a shape-dependent, more complex motion. Our study was designed to develop and test a new set-up to generate experimental data on fish otolith motion in-situ. Investigating the basic parameters of otolith motion requires an approach with high spatial and temporal resolution. We therefore used hard X-ray phase contrast imaging (XPCI). We compared two anatomically well-studied cichlid species, Steatocranus tinanti and Etroplus maculatus, which, among other features, differ in the 3D shape of their otoliths. In a water-filled tank, we presented a pure tone of 200 Hz to 1) isolated otoliths embedded in agarose serving as a simple model or 2) to a fish (otoliths in-situ). Our new set-up successfully visualized the motion of otoliths in-situ and therefore paves the way for future studies evaluating the principles of otolith motion.

Characterization of a sCMOS-based high-resolution imaging system

The detection system is a key part of any imaging station. Here the performance of the novel sCMOS-based detection system installed at the ID17 biomedical beamline of the European Synchrotron Radiation Facility and dedicated to high-resolution computed-tomography imaging is analysed. The system consists of an X-ray-visible-light converter, a visible-light optics and a PCO.Edge5.5 sCMOS detector. Measurements of the optical characteristics, the linearity of the system, the detection lag, the modulation transfer function, the normalized power spectrum, the detective quantum efficiency and the photon transfer curve are presented and discussed. The study was carried out at two different X-ray energies (35 and 50 keV) using both 2× and 1× optical magnification systems. The final pixel size resulted in 3.1 and 6.2 µm, respectively. The measured characteristic parameters of the PCO.Edge5.5 are in good agreement with the manufacturer specifications. Fast imaging can be achieved using this detection system, but at the price of unavoidable losses in terms of image quality. The way in which the X-ray beam inhomogeneity limited some of the performances of the system is also discussed.

Feasibility Study of the 3D Visualization at High Resolution of Intra-Cranial Rabbit Eyes With X-Ray CT Phase-Contrast Imaging

Purpose

The intracranial three-dimensional (3D) visualization of the whole volume of the eyeball at micrometric resolution has not been achieved yet either in clinical nor in preclinical diagnostic research. Overcoming this limitation may provide a new tool for clinical and preclinical studies of different pathologies of the various sections of the eye. The aim of this work is to give the first insight of a volumetric visualization at the high resolution of the entire enucleated and intracranial postmortem rabbit eyeballs.

Methods

X-ray computed tomography phase-contrast imaging was used to obtain 3D models of enucleated and intracranial rabbit eyes. Images were compared with the ones measured by using optical coherence tomography (OCT) images. The experiment was carried out at the European Synchrotron Radiation Facility.

Results

Combining the unique possibilities offered by phase-contrast imaging, microtomography, and the properties of synchrotron radiation, the 3D visualization of the whole eyeball, at an isotropic voxel size of 3.1 μm3, is reported here for the first time.

Conclusions

High image contrast is achieved without the necessity of injection of contrast agents, thanks to the superior performances, achieved by x-ray phase-contrast imaging with respect to the conventional radiographic imaging. The measurement protocol developed within this work opens the way for in vivo high-resolution visualization of the entire organ.

Refraction and ultra-small-angle scattering of X-rays in a single-crystal diamond compound refractive lens

In this work a double-crystal setup is employed to study compound refractive lenses made of single-crystal diamond. The point spread function of the lens is calculated taking into account the lens transmission, the wavefront aberrations, and the ultra-small-angle broadening of the X-ray beam. It is shown that, similarly to the wavefront aberrations, the ultra-small-angle scattering effects can significantly reduce the intensity gain and increase the focal spot size. The suggested approach can be particularly useful for the characterization of refractive X-ray lenses composed of many tens of unit lenses.

Generalized pupil function of a compound X-ray refractive lens

Quality of a refractive compound X-ray lens can be limited by imperfections in surfaces of unit lenses and stacking precision. In general case both the lens transmission and optical aberrations define properties of a beam in the lens exit plane; together they can be expressed in terms of the generalized pupil function. In this work we measure this function for a diamond single crystal compound refractive lens. Consequently, we apply the pupil function to evaluate the performance of the examined compound refractive X-ray lens. A number of practically important conclusions can be drawn from such analysis.

A method for high-energy, low-dose mammography using edge illumination x-ray phase-contrast imaging

Since the breast is one of the most radiosensitive organs, mammography is arguably the area where lowering radiation dose is of the uttermost importance. Phase-based x-ray imaging methods can provide opportunities in this sense, since they do not require x-rays to be stopped in tissue for image contrast to be generated. Therefore, x-ray energy can be considerably increased compared to those usually exploited by conventional mammography. In this article we show how a novel, optimized approach can lead to considerable dose reductions. This was achieved by matching the edge-illumination phase method, which reaches very high angular sensitivity also at high x-ray energies, to an appropriate image processing algorithm and to a virtually noise-free detection technology capable of reaching almost 100% efficiency at the same energies. Importantly, while proof-of-concept was obtained at a synchrotron, the method has potential for a translation to conventional sources.

Hard X-ray index of refraction tomography of a whole rabbit knee joint: A feasibility study

We report results of the computed tomography reconstruction of the index of refraction in a whole rabbit knee joint examined at the photon energy of 51keV. Refraction based images make it possible to delineate the bone, cartilage, and soft tissues without adjusting the contrast window width and level. Density variations, which are related to tissue composition and are not visible in absorption X-ray images, are detected in the obtained refraction based images. We discuss why refraction-based images provide better detectability of low contrast features than absorption images.

Characterization of mouse spinal cord vascular network by means of synchrotron radiation X-ray phase contrast tomography

High resolution Synchrotron-based X-ray Phase Contrast Tomography (XPCT) allows the simultaneous detection of three dimensional neuronal and vascular networks without using contrast agents or invasive casting preparation. We show and discuss the different features observed in reconstructed XPCT volumes of the ex vivo mouse spinal cord in the lumbo-sacral region, including motor neurons and blood vessels. We report the application of an intensity-based segmentation method to detect and quantitatively characterize the modification in the vascular networks in terms of reduction in experimental visibility. In particular, we apply our approach to the case of the experimental autoimmune encephalomyelitis (EAE), i.e. human multiple sclerosis animal model.

Virtual unrolling and deciphering of Herculaneum papyri by X-ray phase-contrast tomography

A collection of more than 1800 carbonized papyri, discovered in the Roman ‘Villa dei Papiri’ at Herculaneum is the unique classical library survived from antiquity. These papyri were charred during 79 A.D. Vesuvius eruption, a circumstance which providentially preserved them until now. This magnificent collection contains an impressive amount of treatises by Greek philosophers and, especially, Philodemus of Gadara, an Epicurean thinker of 1st century BC. We read many portions of text hidden inside carbonized Herculaneum papyri using enhanced X-ray phase-contrast tomography non-destructive technique and a new set of numerical algorithms for ‘virtual-unrolling’. Our success lies in revealing the largest portion of Greek text ever detected so far inside unopened scrolls, with unprecedented spatial resolution and contrast, all without damaging these precious historical manuscripts. Parts of text have been decoded and the ‘voice’ of the Epicurean philosopher Philodemus is brought back again after 2000 years from Herculaneum papyri.

Boundary value problem for phase retrieval from unidirectional X-ray differential phase images

The phase retrieval problem can be reduced to the second order partial differential equation. In order to retrieve the absolute values of the X-ray phase and to minimize the reconstruction artifacts we defined the mixed inhomogeneous boundary condition using available a priori information about the sample. Finite element technique was used to solve the boundary value problem. The approach is validated on numerical and experimental phantoms. In order to demonstrate a possible application of the method, we have processed an entire tomographic set of differential phase images and estimated the magnitude of the refractive index decrement for some tissues inside complex biomedical samples.

A single-image method for x-ray refractive index CT

X-ray refraction-based computer tomography imaging is a well-established method for nondestructive investigations of various objects. In order to perform the 3D reconstruction of the index of refraction, two or more raw computed tomography phase-contrast images are usually acquired and combined to retrieve the refraction map (i.e. differential phase) signal within the sample. We suggest an approximate method to extract the refraction signal, which uses a single raw phase-contrast image. This method, here applied to analyzer-based phase-contrast imaging, is employed to retrieve the index of refraction map of a biological sample. The achieved accuracy in distinguishing the different tissues is comparable with the non-approximated approach. The suggested procedure can be used for precise refraction computer tomography with the advantage of a reduction of at least a factor of two of both the acquisition time and the dose delivered to the sample with respect to any of the other algorithms in the literature.

Tomographic reconstruction of the refractive index with hard X-rays: an efficient method based on the gradient vector-field approach

The refractive-index gradient vector field approach establishes a connection between a tomographic data set of differential phase contrast images and the distribution of the partial spatial derivatives of the refractive index in an object. The reconstruction of the refractive index in a plane requires the integration of its gradient field. This work shows how this integration can be efficiently performed by converting the problem to the Poisson equation, which can be accurately solved even in the case of noisy and large datasets. The performance of the suggested method is discussed and demonstrated experimentally by computing the refractive index distribution in both a simple plastic phantom and a complex biological sample. The quality of the reconstruction is evaluated through the direct comparison with other commonly used methods. To this end, the refractive index is retrieved from the same data set using also (1) the filtered backprojection algorithm for gradient projections, and (2) the regularized phase-retrieval procedure. Results show that the gradient vector field approach combined with the developed integration technique provides a very accurate depiction of the sample internal structure. Contrary to the two other techniques, the considered method does not require a preliminary phase-retrieval and can be implemented with any advanced computer tomography algorithm. In this work, analyzer-based phase contrast images are used for demonstration. Results, however, are generally valid and can be applied for processing differential phase-contrast tomographic data sets obtained with other phase-contrast imaging techniques.

An efficient numerical tool for dose deposition prediction applied to synchrotron medical imaging and radiation therapy

Medical imaging and radiation therapy are widely used synchrotron-based techniques which have one thing in common: a significant dose delivery to typically biological samples. Among the ways to provide the experimenters with image guidance techniques indicating optimization strategies, Monte Carlo simulation has become the gold standard for accurately predicting radiation dose levels under specific irradiation conditions. A highly important hampering factor of this method is, however, its slow statistical convergence. A track length estimator (TLE) module has been coded and implemented for the first time in the open-source Monte Carlo code GATE/Geant4. Results obtained with the module and the procedures used to validate them are presented. A database of energy-absorption coefficients was also generated, which is used by the TLE calculations and is now also included in GATE/Geant4. The validation was carried out by comparing the TLE-simulated doses with experimental data in a synchrotron radiation computed tomography experiment. The TLE technique shows good agreement versus both experimental measurements and the results of a classical Monte Carlo simulation. Compared with the latter, it is possible to reach a pre-defined statistical uncertainty in about two to three orders of magnitude less time for complex geometries without loss of accuracy.

On the possibility of quantitative refractive-index tomography of large biomedical samples with hard X-rays

One of the most promising applications of the X-ray phase-contrast imaging is the three dimensional tomographic reconstruction of the index of refraction. However, results reported so far are limited to relatively small samples. We present here the tomographic reconstruction of the index of refraction distribution of a large biomedical sample (> 10 cm diameter). A quantitative study comparing the absorption and phase contrast (analyzer-based) tomography images shows that the distribution of the index of refraction obtained with the phase contrast method provides a more accurate depiction (3-10 times larger signal to noise ratio values) of the sample internal structure. Thanks to the higher sensitivity of this method, the improved precision was obtained using an incoming photon fluence on the sample several times smaller than in the case of absorption imaging.