Adaptive automated sinogram normalization for ring artifacts suppression in CT.

Ring artifacts pose a major barrier to obtaining precise reconstruction in computed tomography (CT). The presence of ring artifacts complicates the use of automatic means of processing CT reconstruction results, such as segmentation, correction of geometric shapes, alignment of reconstructed volumes. Although there are numerous efficient methods for suppressing ring artifacts, many of them appear to be manual. Along with this, a large proportion of the automatic methods cope unsatisfactorily with the target task while requiring computational capacity. The current work introduces a projection data preprocessing method for suppressing ring artifacts that constitutes a compromise among the outlined aspects - automaticity, high efficiency and computational speed. Derived as the automation of the classical sinogram normalization method, the proposed method specific advantages consist in adaptability in relation to the filtered sinograms and the edge-preservation property proven within the experiments on both synthetic and real CT data. Concerning the challenging open-access data, the method has performed superior quality comparable to that of the advanced methods: it has demonstrated 70.4% ring artifacts suppression percentage (RASP) quality metric. In application to our real laboratory CT data, the proposed method allowed us to gain significant refinement of the reconstruction quality which has not been surpassed by a range of compared manual ring artifacts suppression methods.

Crystal Analyzer Based Multispectral Microtomography Using CCD-Sensor.

To solve the problems of spectral tomography, an X-ray optical scheme was proposed, using a crystal analyzer in Laue geometry between the sample and the detector, which allowed for the selection of predetermined pairs of wavelengths from the incident polychromatic radiation to obtain projection images. On a laboratory X-ray microtomography setup, an experiment was carried out for the first time where a mixture of micro-granules of sodium chloride NaCl, silver behenate AgC22H43O2, and lithium niobate LiNbO3 was used as a test sample to identify their spatial arrangement. The elements were chosen based on the presence of absorption edges in two of the elements in the energy range of the polychromatic spectrum of the probing radiation. The method of projection distortion correction was used to preprocess the obtained projections. To interpret the obtained reconstruction results, the segmentation method based on the analysis of joint histograms was used. This allowed us to identify each of the three substances. To compare the results obtained, additional "reference" tomographic measurements were performed: one in polychromatic and two in monochromatic (MoKα-, MoKß-lines) modes. It took three times less time for the tomographic experiment with the crystal analyzer, while the reconstruction accuracy was comparable to that of the "reference" tomography.

Reducing radiation dose for NN-based COVID-19 detection in helical chest CT using real-time monitored reconstruction.

Computed tomography is a powerful tool for medical examination, which plays a particularly important role in the investigation of acute diseases, such as COVID-19. A growing concern in relation to CT scans is the radiation to which the patients are exposed, and a lot of research is dedicated to methods and approaches to how to reduce the radiation dose in X-ray CT studies. In this paper, we propose a novel scanning protocol based on real-time monitored reconstruction for a helical chest CT using a pre-trained neural network model for COVID-19 detection as an expert. In a simulated study, for the first time, we proposed using per-slice stopping rules based on the COVID-19 detection neural network output to reduce the frequency of projection acquisition for portions of the scanning process. The proposed method allows reducing the total number of X-ray projections necessary for COVID-19 detection, and thus reducing the radiation dose, without a significant decrease in the prediction accuracy. The proposed protocol was evaluated on 163 patients from the COVID-CTset dataset, providing a mean dose reduction of 15.1% while the mean decrease in prediction accuracy amounted to only 1.9% achieving a Pareto improvement over a fixed protocol.

Micromorphology of pineal gland calcification in age-related neurodegenerative diseases.

BACKGROUND: The formation of concrements in human pineal gland (PG) is a physiological process and, according to many researchers, is associated with the involution of PG structures. The majority of scientific publications concern progressive calcification of PG, leaving out studies on the destruction of already formed calcified concrements. Our study fills the gap in knowledge about calcified zones destruction in PG in normal aging and neuropathological conditions, which has not been addressed until now. PURPOSE: Our objective is to gain insight into human PG tissue impairment in both normal aging and neurodegenerative conditions. X-ray phase-contrast tomography (XPCT) allowed us to study PG tissue degeneration at high spatial resolution and, for the first time, to examine the damaged PG concrements in detail. Our research finding could potentially enhance the understanding of the PG involvement in the process of aging as well as in Alzheimer's disease (AD) and vascular dementia (VD). METHODS: The research was carried out on human PG autopsy material in normal aging, VD, and AD conditions. Laboratory-based micro-computed tomography (micro-CT) was used to collect and evaluate samples of native, uncut, and unstained PG with different degrees of pineal calcification. The detailed high-resolution 3D images of the selected PGs were produced using synchrotron-based XPCT. Histology and immunohistochemistry of soft PG tissue confirmed XPCT results. RESULTS: We performed via micro-CT the evaluation of the morphometric parameters of PG such as total sample volume, calcified concrements volume, and percentage of concrements in the total volume of the sample. XPCT imaging revealed high-resolution details of age-related PG alteration. In particular, we noted signs of moderate degradation of concrements in some PGs from elderly donors. In addition, our analysis revealed noticeable degenerative change in both concrements and soft tissue of PGs with neuropathology. In particular, we observed a hollow core and separated layers as well as deep ragged cracks in PG concrements of AD and VD samples. In parenchyma of some samples, we detected wide pinealocyte-free fluid-filled areas adjacent to the calcified zones. CONCLUSION: The present work provides the basis for future scientific research focused on the dynamic nature of PG calcium deposits and PG soft tissue in normal aging and neurodegenerative diseases.

Deep Learning-Based Segmentation of Post-Mortem Human's Olfactory Bulb Structures in X-ray Phase-Contrast Tomography.

The human olfactory bulb (OB) has a laminar structure. The segregation of cell populations in the OB image poses a significant challenge because of indistinct boundaries of the layers. Standard 3D visualization tools usually have a low resolution and cannot provide the high accuracy required for morphometric analysis. X-ray phase contrast tomography (XPCT) offers sufficient resolution and contrast to identify single cells in large volumes of the brain. The numerous microanatomical structures detectable in XPCT image of the OB, however, greatly complicate the manual delineation of OB neuronal cell layers. To address the challenging problem of fully automated segmentation of XPCT images of human OB morphological layers, we propose a new pipeline for tomographic data processing. Convolutional neural networks (CNN) were used to segment XPCT image of native unstained human OB. Virtual segmentation of the whole OB and an accurate delineation of each layer in a healthy non-demented OB is mandatory as the first step for assessing OB morphological changes in smell impairment research. In this framework, we proposed an effective tool that could help to shed light on OB layer-specific degeneration in patients with olfactory disorder.

Monitored Tomographic Reconstruction-An Advanced Tool to Study the 3D Morphology of Nanomaterials.

Detailed and accurate three-dimensional (3D) information about the morphology of hierarchically structured materials is derived from multi-scale X-ray computed tomography (XCT) and subsequent 3D data reconstruction. High-resolution X-ray microscopy and nano-XCT are suitable techniques to nondestructively study nanomaterials, including porous or skeleton materials. However, laboratory nano-XCT studies are very time-consuming. To reduce the time-to-data by more than an order of magnitude, we propose taking advantage of a monitored tomographic reconstruction. The benefit of this new protocol for 3D imaging is that the data acquisition for each projection is interspersed by image reconstruction. We demonstrate this new approach for nano-XCT data of a novel transition-metal-based materials system: MoNi4 electrocatalysts anchored on MoO2 cuboids aligned on Ni foam (MoNi4/MoO2@Ni). Quantitative data that describe the 3D morphology of this hierarchically structured system with an advanced electrocatalytically active nanomaterial are needed to tailor performance and durability of the electrocatalyst system. We present the framework for monitored tomographic reconstruction, construct three stopping rules for various reconstruction quality metrics and provide their experimental evaluation.

Enhanced Tomographic Sensing Multimodality with a Crystal Analyzer.

This article demonstrates how a combination of well-known tools-a standard 2D detector (CCD (charge-coupled device) camera) and a crystal analyzer-can improve the multimodality of X-ray imaging and tomographic sensing. The use of a crystal analyzer allowed two characteristic lines of the molybdenum anode-Kα and Kß-to be separated from the polychromatic radiation of the conventional X-ray tube. Thus, as a result of one measurement, three radiographic projections (images) were simultaneously recorded. The projection images at different wavelengths were separated in space and registered independently for further processing, which is of interest for the spectral tomography method. A projective transformation to compensate for the geometric distortions that occur during asymmetric diffraction was used. The first experimental results presented here appear promising.

Investigation of the human pineal gland 3D organization by X-ray phase contrast tomography.

Pineal gland (PG) is a part of the human brain epithalamus that plays an important role in sleep, circadian rhythm, immunity, and reproduction. The calcium deposits and lesions in PG interfere with normal function of the organ and can be associated with different health disorders including serious neurological diseases. At the moment, the detailed mechanisms of PG calcifications and PG lesions formation as well as their involvement in pathological processes are not fully understood. The deep and comprehensive study of the structure of the uncut human PG with histological details, poses a stiff challenge to most imaging techniques, due to low spatial resolution, low visibility or to exceedingly aggressive sample preparation. Here, we investigate the whole uncut and unstained human post-mortem PGs by X-ray phase contrast tomography (XPCT). XPCT is an advanced 3D imaging technique, that permits to study of both soft and calcified tissue of a sample at different scales: from the whole organ to cell structure. In our research we simultaneously resolved 3D structure of parenchyma, vascular network and calcifications. Moreover, we distinguished structural details of intact and degenerated PG tissue. We discriminated calcifications with different structure, pinealocytes nuclei and the glial cells processes. All results were validated by histology. Our research clear demonstrated that XPCT is a potential tool for the high resolution 3D imaging of PG morphological features. This technique opens a new perspective to investigate PG dysfunction and understand the mechanisms of onset and progression of diseases involving the pineal gland.

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.

Revisiting the Local Structure in Ge-Sb-Te based Chalcogenide Superlattices.

The technological success of phase-change materials in the field of data storage and functional systems stems from their distinctive electronic and structural peculiarities on the nanoscale. Recently, superlattice structures have been demonstrated to dramatically improve the optical and electrical performances of these chalcogenide based phase-change materials. In this perspective, unravelling the atomistic structure that originates the improvements in switching time and switching energy is paramount in order to design nanoscale structures with even enhanced functional properties. This study reveals a high- resolution atomistic insight of the [GeTe/Sb2Te3] interfacial structure by means of Extended X-Ray Absorption Fine Structure spectroscopy and Transmission Electron Microscopy. Based on our results we propose a consistent novel structure for this kind of chalcogenide superlattices.

Monochromatic computed microtomography using laboratory and synchrotron sources and X-ray fluorescence analysis for comprehensive analysis of structural changes in bones.

A combination of X-ray tomography at different wavelengths and X-ray fluorescence analysis was applied in the study of two types of bone tissue changes: prolonged presence in microgravity conditions and age-related bone growth. The proximal tail vertebrae of geckos were selected for investigation because they do not bear the supporting load in locomotion, which allows them to be considered as an independent indicator of gravitational influence. For the vertebrae of geckos no significant differences were revealed in the elemental composition of the flight samples and the synchronous control samples. In addition, the gecko bone tissue samples from the jaw apparatus, spine and shoulder girdle were measured. The dynamics of structural changes in the bone tissue growth was studied using samples of a human fetal hand. The hands of human fetuses of 11-15 weeks were studied. Autonomous zones of calcium accumulation were found not only in individual fingers but in each of the investigated phalanges. The results obtained are discussed.

Computed microtomography and X-ray fluorescence analysis for comprehensive analysis of structural changes in bone.

This paper presents the results of a comprehensive analysis of structural changes in the caudal vertebrae of Turner's thick-toed geckos by computer microtomography and X-ray fluorescence analysis. We present algorithms used for the reconstruction of tomographic images which allow to work with high noise level projections that represent typical conditions dictated by the nature of the samples. Reptiles, due to their ruggedness, small size, belonging to the amniote and a number of other valuable features, are an attractive model object for long-orbital experiments on unmanned spacecraft. Issues of possible changes in their bone tissue under the influence of spaceflight are the subject of discussions between biologists from different laboratories around the world.

Efficient and effective regularised ART for computed tomography.

Algebraic Reconstruction Technique (ART) is a widely employed method in computed tomography since it has certain advantages, such as allowing reconstruction of data with missing projections in some angle ranges, over other techniques such as Filtered Back Projection (FBP). Recently, a regularisation technique for ART, RegART, was introduced which provides greatly reduced noise levels. However, a serious drawback of both ART and RegART is the computational complexity of the methods. In this paper, we present a fast version of RegART, which makes use of nVidia's CUDA technology, and show that this approach performs favourably compared to FBP.

A new FEFF-based wavelet for EXAFS data analysis.

A new mother wavelet function for extended X-ray absorption fine-structure (EXAFS) data analysis has been designed, combining a model EXAFS function derived from the ab initio EXAFS code FEFF8.20 and the complex Morlet wavelet. This new FEFF-Morlet mother wavelet routine allows the generation of wavelets well adapted to specific EXAFS problems. A substantial gain in resolution of the wavelet ridges in k and r space is achieved. The method is applied to a structural problem of Zn-Al double-layer hydroxides, demonstrating unequivocally the homogeneity of the metal cation distribution in the hydroxide layers.