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

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

Mathematical Reconstruction of Sample Microstructures Obtained from PIXE Elemental Maps

Abstract not availableJRC.D-Institute for Reference Materials and Measurements (Geel

Polychromatic CT Data Improvement with One-Parameter Power Correction

Standard approaches to tomography reconstruction of the projection data registered with polychromatic emission lead to the appearance of cupping artifacts and irrelevant lines between regions of strong absorption. The main reason for their appearance is the fact that part of the emission with low energy is being absorbed entirely by high absorbing objects. This fact is known as beam hardening (BH). The procedure of processing projection data collected in polychromatic mode is presented; it reduces artifacts relevant to BH and does not require additional calibration experiments. The procedure consists of two steps: the first is to linearize the projection data with one-parameter power correction, and the second is to reconstruct the images from linearized data. Automatic parameter adjustment is the main advantage of the procedure. The optimization problem is formulated. The system flowchart is presented. The reconstruction with different powers of correction is considered to evaluate the quality reconstruction

"Art" in X-ray tomography: Image noise reduction

Reduction of the object dose by reducing X-ray exposure has the inevitable consequence of increasing statistical noise in the projections. A set of projections with a 10% noise, collected during the test experiment at the Institute of Crystallography RAS, were used to reconstruct a water phantom. Two different reconstruction approaches (Algebraic Reconstruction Technique (ART) and Filtered Back Projections (FBP)) were implemented. The reconstructed images also had about 10 % noise in both cases. Median filtering within each ART iterative step and averaging over images, updated and preserved during the final iteration made it possible to lower the image noise to 3%. For ART calculations, the RegART software package developed by the authors was used

X-ray tomography: how to evaluate the reconstruction quality?

Different reconstruction techniques are used to reconstruct the distribution of the physical characteristics, describing a sample under investigation, from a set of tomographic projections. We present a technique for the evaluation of the reconstruction quality. The technique is based on the comparison of two images (phantom and reconstructed image) by means of the correlation coefficient and of the mean square error between them. In parallel, the correlation coefficient and mean square error are calculated for the wavelet transforms of the phantom and reconstructed images. The scales for the wavelet transform are chosen in agreement with the major geometric parameters of the phantom. Then the correlation coefficient of the wavelet transform with the chosen scale yields an evaluation of the quality of the phantom parameters reconstruction. The accuracy of the parameters reconstruction is determined by the mean square error for the selected scale. The phantom used for the analysis is a medium with randomly distributed grains. The distribution is characterized by two parameters: grain size and grain density (average number of grains per unit area). The parameters are used as the scales for the wavelet transform calculation. We make a comparison of the Algebraic Reconstruction Technique (ART) and the Filtered Back Projection Algorithm

FAST X-RAY SUM CALCULATION ALGORITHM FOR COMPUTED TOMOGRAPHY PROBLEM

In iterative methods of computed tomography, each iteration requires to calculate a multitude of sums over values for the current reconstruction approximation. Each summable set is an approximation of a straight line in the three-dimensional space. In a cone-beam tomography, the number of sums to be calculated on each iteration has a cubic dependence on the linear size of the reconstructed image. Direct calculation of these sums requires the number of summations in a quartic dependence on the linear image size, which limits the performance of the iterative methods. The novel algorithm proposed in this paper approximates the three-dimensional straight lines using dyadic patterns, and, using the adjustment of precalculation and inference complexity similar to the adjustment employed in the Method of Four Russians, provides the calculation of these sums with a sub-quartic dependence on the linear size of the reconstructed image

A new nondestructive X-ray method for the determination of the 3D mineralogy at the m scale

The combination of synchrotron-based X-ray absorption and fluorescence computed tomographies (CT) is a new method allowing a noninvasive and nondestructive determination of the three-dimensional (3D) mineralogy with micrometer resolution of sub-millimeter silicate grains, possibly stored in a silica holder. These CT were performed with beams of a few tens of keV from a third-generation synchrotron source on one olivine grain of the NWA817 Martian meteorite presenting a reddish alteration phase. The reconstructed sections show a network of fractures and a few micrometer-thick layers formed on one grain. The 3D facet orientation and the X-ray attenuation coefficient indicate that this grain is an Fo44±9 olivine crystal. The fluorescence section reveals rims enriched in Fe (a major element) or depleted in Ca (a minor element). This CT combination shows that the micrometer-thick layer is preferentially formed on the (010) olivine face and has a lower density (3.5 ± 0.4 g/cm3 ) than the olivine, even though it is enriched in Fe. Its complex nano-petrography and the distributions of nanometer-sized voids and fractures in such a micrometer thick layer, first observed by scanning electron microscopy on focused ion-beam cuts, is not shown by CT. The precision presently achieved, although moderate, is sufficient to obtain a 3D semi-quantitative view of the mineralogy consistent with the one previously established by electron probe microanalyses (Sautter et al. 2002)