Enhanced and Flexible Software Tools for X-ray Computed Tomography at the Italian Synchrotron Radiation Facility Elettra

X-ray computed tomography (CT) experiments performed at synchrotron radiation facilities require adequate computing and storage resources due to the large amount of acquired and reconstructed data produced. To satisfy the heterogeneous needs of beamline users, flexible solutions are also required. Moreover, the growing demand of quantitative image analysis impose an easy integration between the CT reconstruction process and the subsequent feature extraction step. This paper presents some of the software solutions adopted by the SYRMEP beamline of the Italian synchrotron radiation facility Elettra. By using the enhanced version of the reconstruction software here presented as well as data reduction and data analysis tools, beamline users can easily implement an integrated and comprehensive approach to the digital image processing and image analysis required by a tomography-oriented scientific workflow

Impact of standardization in tissue processing: the performance of different fixatives

Most tissues in clinical practice are formalin-fixed and paraffin-embedded for histological as well as molecular analyses. The reproducibility and uniformity of molecular analyses is strictly dependent on the quality of the biomolecules, which is highly influenced by pre-analytical processes. In this study, the effect of different fixatives was compared, including formalin, Bouin's solution, RCL2® and TAG-1™ fixatives, by stringent application of ISO standards in mouse liver tissue processing, including formalin-free transport of tissues and tissue grossing in a refrigerated environment. The effect of fixatives was studied in terms of nucleic acid quality at the time of tissue processing and after one year of tissue storage at room temperature in the dark. Furthermore, a microcomputed tomography (CT) scan analysis was applied to investigate the paraffin embedding. The results show that the application of ISO standards in tissue processing allows analysis of 400 bases amplicons from RNA and 1000 bases from DNA, even in extracts from formalin-fixed and paraffin-embedded tissues. However, after one year storage at room temperature in the dark, a degradation of the nucleic acids was observed. Nevertheless, extracts can still be analyzed, but for metachronous tests it is highly recommended to repeat the quantitation of housekeeping genes in order to standardize the extent of nucleic acid degradation

Multiscale X-ray phase-contrast tomography: From breast CT to micro-CT for virtual histology

Phase-contrast imaging techniques address the issue of poor soft-tissue contrast encountered in traditional X-ray imaging. This can be accomplished with the propagation-based phase-contrast technique by employing a coherent photon beam, which is available at synchrotron facilities, as well as long sample-to-detector distances. This study demonstrates the optimization of propagation-based phase-contrast computed tomography (CT) techniques for multiscale X-ray imaging of the breast at the Elettra synchrotron facility (Trieste, Italy). Two whole breast mastectomy samples were acquired with propagation-based breast-CT using a monochromatic synchrotron beam at a pixel size of 60 μm. Paraffin-embedded blocks sampled from the same tissues were scanned with propagation-based micro-CT imaging using a polychromatic synchrotron beam at a pixel size of 4 μm. Images of both methodologies and of the same sample were spatially registered. The resulting images showed the transition from whole breast imaging with propagation-based breast-CT methodology to virtual histology with propagation-based micro-CT imaging of the same sample. Additionally, conventional histological images were matched to virtual histology images. Phase-contrast images offer a high resolution with low noise, which allows for a highly precise match between virtual and conventional histology. Furthermore, those techniques allow a clear discernment of breast structures, lesions, and microcalcifications, being a promising clinically-compatible tool for breast imaging in a multiscale approach, to either assist in the detection of cancer in full volume breast samples or to complement structure identification in paraffin-embedded breast tissue samples

Virtual histological assessment of the prenatal life history and age at death of the Upper Paleolithic fetus from Ostuni (Italy)

The fetal remains from the Ostuni 1 burial (Italy, ca 27 ka) represent a unique opportunity to explore the prenatal biological parameters, and to reconstruct the possible patho-biography, of a fetus (and its mother) in an Upper Paleolithic context. Phase-contrast synchrotron X-ray microtomography imaging of two deciduous tooth crowns and microfocus CT measurements of the right hemimandible of the Ostuni 1b fetus were performed at the SYRMEP beamline and at the TomoLab station of the Elettra - Sincrotrone laboratory (Trieste, Italy) in order to refne age at death and to report the enamel developmental history and dental tissue volumes for this fetal individual. The virtual histology allowed to estimate the age at death of the fetus at 31–33 gestational weeks. Three severe physiological stress episodes were also identifed in the prenatal enamel. These stress episodes occurred during the last two months and half of pregnancy and may relate to the death of both individuals. Compared with modern prenatal standards, Os1b’s skeletal development was advanced. This cautions against the use of modern skeletal and dental references for archaeological fnds and emphasizes the need for more studies on prenatal archaeological skeletal samples

SYRMEP Tomo Project: a graphical user interface for customizing CT reconstruction workflows

8When considering the acquisition of experimental synchrotron radiation (SR) X-ray CT data, the reconstruction workflow cannot be limited to the essential computational steps of flat fielding and filtered back projection (FBP). More refined image processing is often required, usually to compensate artifacts and enhance the quality of the reconstructed images. In principle, it would be desirable to optimize the reconstruction workflow at the facility during the experiment (beamtime). However, several practical factors affect the image reconstruction part of the experiment and users are likely to conclude the beamtime with sub-optimal reconstructed images. Through an example of application, this article presentsSYRMEP Tomo Project(STP), an open-source software tool conceived to let users design custom CT reconstruction workflows. STP has been designed for post-beamtime (off-line use) and for a new reconstruction of past archived data at user's home institution where simple computing resources are available. Releases of the software can be downloaded at the Elettra Scientific Computing group GitHub repository https://github.com/ElettraSciComp/STP-Gui.openopenBrun, Francesco; Massimi, Lorenzo; Fratini, Michela; Dreossi, Diego; Billé, Fulvio; Accardo, Agostino; Pugliese, Roberto; Cedola, AlessiaBrun, Francesco; Massimi, Lorenzo; Fratini, Michela; Dreossi, Diego; Billé, Fulvio; Accardo, Agostino; Pugliese, Roberto; Cedola, Alessi

Stem photosynthesis contributes to non-structural carbohydrate pool and modulates xylem vulnerability to embolism in Fraxinus ornus L

Stem photosynthesis can significantly contribute to the carbon budget of woody plants, providing an extra carbon gain that might be crucial under drought stress causing leaf photosynthesis impairment and/or a reduced phloem transport.Stems of Fraxinus ornus L. saplings were covered with aluminum foil to test the impact of inhibition of stem photosynthesis on plant vulnerability to drought. Plants were water-stressed to target xylem water potential of-3.5 MPa and were then re-irrigated to field capacity to quantify their recovery capacity. Vulnerability to xylem embolism was assessed in light-exposed and stem-shaded saplings with both the hydraulic method and in vivo with X-ray phase contrast micro-computed tomography. We also measured non-structural carbohydrate (NSC) concentration and osmotic potential in bark and wood, separately.Stem shading increased xylem vulnerability to embolism formation under drought but did not influence the recovery phase. This difference was coupled with modification of the NSC pool and impaired osmoregulation, in particular in the wood of stem-shaded saplings compared to control ones.Our results indicate stem photosynthesis as an important source of local NSCs, directly or indirectly involved in osmoregulation processes, which could be crucial to enhance the hydraulic resistance to embolism formation and to endure drought

Analysis of intracellular magnesium and mineral depositions during osteogenic commitment of 3d cultured saos2 cells

In this study, we explore the behaviour of intracellular magnesium during bone phenotype modulation in a 3D cell model built to mimic osteogenesis. In addition, we measured the amount of magnesium in the mineral depositions generated during osteogenic induction. A two-fold increase of intracellular magnesium content was found, both at three and seven days from the induction of differentiation. By X-ray microscopy, we characterized the morphology and chemical composition of the mineral depositions secreted by 3D cultured differentiated cells finding a marked co-localization of Mg with P at seven days of differentiation. This is the first experimental evidence on the presence of Mg in the mineral depositions generated during biomineralization, suggesting that Mg incorporation occurs during the bone forming process. In conclusion, this study on the one hand attests to an evident involvement of Mg in the process of cell differentiation, and, on the other hand, indicates that its multifaceted role needs further investigation

Synthetic calcium carbonate improves the effectiveness of treatments with nanolime to contrast decay in highly porous limestone

Three synthetized polymorphs of calcium carbonate have been tested in combination with the suspension of nanolime particles as potential consolidating agents for contrasting stone decay and overcome some of the limitations of nanolime agents when applied to substrates with large porosity. The modifications induced in the pore network of the Maastricht limestone were analyzed with microscopy and in a non-invasive fashion with small angle neutron scattering and synchrotron radiation micro-computed tomography. A reduction in porosity and pore accessibility at the micrometric scale was detected with the latter technique, and ascribed to the improved pore-filling capacity of the consolidation agent containing CaCO3 particles. These were found to be effectively bound to the carbonated nanolime, strengthening the pore-matrix microstructure. Penetration depth and positive effect on porosity were found to depend on the particle size and shape. Absence of significant changes in the fractal nature of the pore surface at the nanoscale, was interpreted as indication of the negligible contribution of nanolime-based materials in the consolidation of stones with large porosity. However, the results indicate that in such cases, their effectiveness may be enhanced when used in combination with CaCO3 particles, owing to the synergic effect of chemical/structural compatibility and particle size distribution

Experimental optimization of the energy for breast-CT with synchrotron radiation

Breast Computed Tomography (bCT) is a three-dimensional imaging technique that is raising interest among radiologists as a viable alternative to mammographic planar imaging. In X-rays imaging it would be desirable to maximize the capability of discriminating different tissues, described by the Contrast to Noise Ratio (CNR), while minimizing the dose (i.e. the radiological risk). Both dose and CNR are functions of the X-ray energy. This work aims at experimentally investigating the optimal energy that, at fixed dose, maximizes the CNR between glandular and adipose tissues. Acquisitions of both tissue-equivalent phantoms and actual breast specimens have been performed with the bCT system implemented within the Syrma-3D collaboration at the Syrmep beamline of the Elettra synchrotron (Trieste). The experimental data have been also compared with analytical simulations and the results are in agreement. The CNR is maximized at energies around 26–28 keV. These results are in line with the outcomes of a previously presented simulation study which determined an optimal energy of 28 keV for a large set of breast phantoms with different diameters and glandular fractions. Finally, a study on photon starvation has been carried out to investigate how far the dose can be reduced still having suitable images for diagnostics