scholarly journals X-ray microtomography–based atlas of mouse cranial development

GigaScience ◽  
2021 ◽  
Vol 10 (3) ◽  
Author(s):  
Jan Matula ◽  
Marketa Tesarova ◽  
Tomas Zikmund ◽  
Marketa Kaucka ◽  
Igor Adameyko ◽  
...  
Keyword(s):  
Mouse Embryo ◽  
Facial Skeleton ◽  
High Quality ◽  
Cranial Development ◽  
X Ray ◽  
Computed Tomography Images ◽  
Complex Process ◽  
Invaluable Tool ◽  
The Face ◽  
3D Scans

Abstract Background X-ray microtomography (μCT) has become an invaluable tool for non-destructive analysis of biological samples in the field of developmental biology. Mouse embryos are a typical model for investigation of human developmental diseases. By obtaining 3D high-resolution scans of the mouse embryo heads, we gain valuable morphological information about the structures prominent in the development of future face, brain, and sensory organs. The development of facial skeleton tracked in these μCT data provides a valuable background for further studies of congenital craniofacial diseases and normal development. Findings In this work, reusable tomographic data from 7 full 3D scans of mouse embryo heads are presented and made publicly available. The ages of these embryos range from E12.5 to E18.5. The samples were stained by phosphotungstic acid prior to scanning, which greatly enhanced the contrast of various tissues in the reconstructed images and enabled precise segmentation. The images were obtained on a laboratory-based μCT system. Furthermore, we provide manually segmented masks of mesenchymal condensations (for E12.5 and E13.5) and cartilage present in the nasal capsule of the scanned embryos. Conclusion We present a comprehensive dataset of X-ray 3D computed tomography images of the developing mouse head with high-quality manual segmentation masks of cartilaginous nasal capsules. The provided μCT images can be used for studying any other major structure within the developing mouse heads. The high quality of the manually segmented models of nasal capsules may be instrumental to understanding the complex process of the development of the face in a mouse model.

An iterative image reconstruction algorithm combined with forward and backward diffusion filtering for in-line X-ray phase-contrast computed tomography

2018 ◽  
Vol 25 (5) ◽  
pp. 1450-1459 ◽  
Author(s):  
Yuqing Zhao ◽  
Mengyu Sun ◽  
Dongjiang Ji ◽  
Changhong Cong ◽  
Wenjuan Lv ◽  
...  
Keyword(s):  
Computed Tomography ◽  
Phase Contrast ◽  
Soft Tissues ◽  
Reconstruction Algorithm ◽  
Projection Data ◽  
Reconstruction Technique ◽  
High Quality ◽  
X Ray ◽  
Diffusion Filtering ◽  
Computed Tomography Images

In-line X-ray phase-contrast computed tomography (IL-PCCT) can reveal fine inner structures for low-Z materials (e.g. biological soft tissues), and shows high potential to become clinically applicable. Typically, IL-PCCT utilizes filtered back-projection (FBP) as the standard reconstruction algorithm. However, the FBP algorithm requires a large amount of projection data, and subsequently a large radiation dose is needed to reconstruct a high-quality image, which hampers its clinical application in IL-PCCT. In this study, an iterative reconstruction algorithm for IL-PCCT was proposed by combining the simultaneous algebraic reconstruction technique (SART) with eight-neighbour forward and backward (FAB8) diffusion filtering, and the reconstruction was performed using the Shepp–Logan phantom simulation and a real synchrotron IL-PCCT experiment. The results showed that the proposed algorithm was able to produce high-quality computed tomography images from few-view projections while improving the convergence rate of the computed tomography reconstruction, indicating that the proposed algorithm is an effective method of dose reduction for IL-PCCT.

Image Quality Analysis of X-ray Grating Interferometer Using Integrating-bucket Method

2020 ◽  
Vol 64 (2) ◽  
pp. 20503-1-20503-5
Author(s):  
Faiz Wali ◽  
Shenghao Wang ◽  
Ji Li ◽  
Jianheng Huang ◽  
Yaohu Lei ◽  
...  
Keyword(s):  
Image Quality ◽  
Phase Contrast ◽  
Quality Analysis ◽  
Phase Contrast Imaging ◽  
Phase Image ◽  
Contrast Imaging ◽  
High Quality ◽  
Image Quality Analysis ◽  
X Ray ◽  
Grating Interferometer

Abstract Grating-based x-ray phase-contrast imaging has the potential to enhance image quality and provide inner structure details non-destructively. In this work, using grating-based x-ray phase-contrast imaging system and employing integrating-bucket method, the quantitative expressions of signal-to-noise ratios due to photon statistics and mechanical error are analyzed in detail. Photon statistical noise and mechanical error are the main sources affecting the image noise in x-ray grating interferometry. Integrating-bucket method is a new phase extraction method translated to x-ray grating interferometry; hence, its image quality analysis would be of great importance to get high-quality phase image. The authors’ conclusions provide an alternate method to get high-quality refraction signal using grating interferometer, and hence increases applicability of grating interferometry in preclinical and clinical usage.

Technology of high quality protein crystals’ obtaining aboard the ISS at execution of joint Japanese–Russian experiments

2020 ◽  
pp. 5-25
Author(s):  
Koji INAKA ◽  
Saori ICHIMIZU ◽  
Izumi YOSHIZAKI ◽  
Kiyohito KIHIRA ◽  
Elena G. LAVRENKO ◽  
...  
Keyword(s):  
Drug Design ◽  
International Space Station ◽  
Space Station ◽  
Protein Crystals ◽  
Diffusion Method ◽  
X Ray Diffraction ◽  
High Quality ◽  
International Space ◽  
X Ray ◽  
High Quality Protein

A series of space experiments aboard the International Space Station (ISS) associated with high-quality Protein Crystal Growth (PCG) in microgravity conditions can be considered as a unique and one of the best examples of fruitful collaboration between Japanese and Russian scientists and engineers in space, which includes also other ISS International Partners. X-ray diffraction is still the most powerful tool to determine the protein three dimensional structure necessary for Structure based drug design (SBDD). The major purpose of the experiment is to grow high quality protein crystals in microgravity for X-ray diffraction on Earth. Within one and a half decade, Japan and Russia have established an efficient process over PCG in space to support latest developments over drug design and structural biology. One of the keys for success of the experiment lies in how precisely pre-launch preparations are made. Japanese party provides flight equipment for crystallization and ensures the required environment to support the experiment aboard of the ISS’s Kibo module, and also mainly takes part of the experiment ground support such as protein sample characterization, purification, crystallization screening, and solution optimization for microgravity experiment. Russian party is responsible for integration of the flight items equipped with proteins and precipitants on board Russian transportation space vehicles (Soyuz or Progress), for delivery them at the ISS, transfer to Kibo module, and returning the experiments’ results back on Earth aboard Soyuz manned capsule. Due to close cooperation of the parties and solid organizational structure, samples can be launched at the ISS every half a year if the ground preparation goes smoothly. The samples are crystallized using counter diffusion method at 20 degree C for 1–2.5 months. After samples return, the crystals are carefully taken out from the capillary, and frozen for X-ray diffraction at SPring8 facility in Japan. Extensive support of researchers from both countries is also a part of this process. The paper analyses details of the PCG experiment scheme, unique and reliable technology of its execution, and contains examples of the application. Key words: International Space Station, Protein crystals, Microgravity, International collaboration.

scholarly journals Optimization of X-ray Investigations in Dentistry Using Optical Coherence Tomography

Sensors ◽  
2021 ◽  
Vol 21 (13) ◽  
pp. 4554
Author(s):  
Ralph-Alexandru Erdelyi ◽  
Virgil-Florin Duma ◽  
Cosmin Sinescu ◽  
George Mihai Dobre ◽  
Adrian Bradu ◽  
...  
Keyword(s):  
Optical Coherence Tomography ◽  
Radiation Dose ◽  
Imaging Techniques ◽  
Image Resolution ◽  
Optical Coherence ◽  
X Rays ◽  
High Quality ◽  
X Ray

The most common imaging technique for dental diagnoses and treatment monitoring is X-ray imaging, which evolved from the first intraoral radiographs to high-quality three-dimensional (3D) Cone Beam Computed Tomography (CBCT). Other imaging techniques have shown potential, such as Optical Coherence Tomography (OCT). We have recently reported on the boundaries of these two types of techniques, regarding. the dental fields where each one is more appropriate or where they should be both used. The aim of the present study is to explore the unique capabilities of the OCT technique to optimize X-ray units imaging (i.e., in terms of image resolution, radiation dose, or contrast). Two types of commercially available and widely used X-ray units are considered. To adjust their parameters, a protocol is developed to employ OCT images of dental conditions that are documented on high (i.e., less than 10 μm) resolution OCT images (both B-scans/cross sections and 3D reconstructions) but are hardly identified on the 200 to 75 μm resolution panoramic or CBCT radiographs. The optimized calibration of the X-ray unit includes choosing appropriate values for the anode voltage and current intensity of the X-ray tube, as well as the patient’s positioning, in order to reach the highest possible X-rays resolution at a radiation dose that is safe for the patient. The optimization protocol is developed in vitro on OCT images of extracted teeth and is further applied in vivo for each type of dental investigation. Optimized radiographic results are compared with un-optimized previously performed radiographs. Also, we show that OCT can permit a rigorous comparison between two (types of) X-ray units. In conclusion, high-quality dental images are possible using low radiation doses if an optimized protocol, developed using OCT, is applied for each type of dental investigation. Also, there are situations when the X-ray technology has drawbacks for dental diagnosis or treatment assessment. In such situations, OCT proves capable to provide qualitative images.

scholarly journals Non-destructive handheld XRF study of archaeological composite silver objects—the case study of the late Roman Seuso Treasure

2021 ◽  
Vol 13 (5) ◽  
Author(s):  
Viktória Mozgai ◽  
Bernadett Bajnóczi ◽  
Zoltán May ◽  
Zsolt Mráv
Keyword(s):  
Fluorescence Analysis ◽  
The Body ◽  
High Quality ◽  
X Ray ◽  
Composite Objects ◽  
Mechanical Attachment ◽  
Non Destructive ◽  
Made In ◽  
Late Roman

AbstractThis study details the non-destructive chemical analysis of composite silver objects (ewers, situlas, amphora and casket) from one of the most significant late Roman finds, the Seuso Treasure. The Seuso Treasure consists of fourteen large silver vessels that were made in the fourth–early fifth centuries AD and used for dining during festive banquets and for washing and beautification. The measurements were systematically performed along a pre-designed grid at several points using handheld X-ray fluorescence analysis. The results demonstrate that all the objects were made from high-quality silver (above 90 wt% Ag), with the exception of the base of the Geometric Ewer B. Copper was added intentionally to improve the mechanical properties of soft silver. The gold and lead content of the objects shows constant values (less than 1 wt% Au and Pb). The chemical composition as well as the Bi/Pb ratio suggests that the parts of the composite objects were manufactured from different silver ingots. The ewers were constructed in two ways: (i) the base and the body were made separately, or (ii) the ewer was raised from a single silver sheet. The composite objects were assembled using three methods: (i) mechanical attachment; (ii) low-temperature, lead-tin soft solders; or (iii) high-temperature, copper-silver hard solders. Additionally, two types of gilding were revealed by the XRF analysis, one with remnants of mercury, i.e. fire-gilding, and another type without remnants of mercury, presumably diffusion bonding.

scholarly journals Visualization Ability of Phase-Contrast Synchrotron-Based X-Ray Imaging Using an X-Ray Interferometer in Soft Tissue Tumors

2021 ◽  
Vol 20 ◽  
pp. 153303382110101
Author(s):  
Thet-Thet Lwin ◽  
Akio Yoneyama ◽  
Hiroko Maruyama ◽  
Tohoru Takeda
Keyword(s):  
Computed Tomography ◽  
Soft Tissue ◽  
Spatial Resolution ◽  
Phase Contrast ◽  
Soft Tissue Tumors ◽  
X Ray ◽  
3 Dimensional ◽  
Computed Tomography Images ◽  
X Ray Imaging ◽  
X Ray Computed

Phase-contrast synchrotron-based X-ray imaging using an X-ray interferometer provides high sensitivity and high spatial resolution, and it has the ability to depict the fine morphological structures of biological soft tissues, including tumors. In this study, we quantitatively compared phase-contrast synchrotron-based X-ray computed tomography images and images of histopathological hematoxylin-eosin-stained sections of spontaneously occurring rat testicular tumors that contained different types of cells. The absolute densities measured on the phase-contrast synchrotron-based X-ray computed tomography images correlated well with the densities of the nuclear chromatin in the histological images, thereby demonstrating the ability of phase-contrast synchrotron-based X-ray imaging using an X-ray interferometer to reliably identify the characteristics of cancer cells within solid soft tissue tumors. In addition, 3-dimensional synchrotron-based phase-contrast X-ray computed tomography enables screening for different structures within tumors, such as solid, cystic, and fibrous tissues, and blood clots, from any direction and with a spatial resolution down to 26 μm. Thus, phase-contrast synchrotron-based X-ray imaging using an X-ray interferometer shows potential for being useful in preclinical cancer research by providing the ability to depict the characteristics of tumor cells and by offering 3-dimensional information capabilities.

scholarly journals Multi-Cycle-Consistent Adversarial Networks for Edge Denoising of Computed Tomography Images

2021 ◽  
Vol 17 (4) ◽  
pp. 1-16
Author(s):  
Xiaowe Xu ◽  
Jiawei Zhang ◽  
Jinglan Liu ◽  
Yukun Ding ◽  
Tianchen Wang ◽  
...  
Keyword(s):  
Computed Tomography ◽  
Image Denoising ◽  
Ct Images ◽  
High Dose ◽  
Ct Image ◽  
Paired Data ◽  
High Quality ◽  
Computed Tomography Images ◽  
Significant Difference ◽  
Global Cycle

As one of the most commonly ordered imaging tests, the computed tomography (CT) scan comes with inevitable radiation exposure that increases cancer risk to patients. However, CT image quality is directly related to radiation dose, and thus it is desirable to obtain high-quality CT images with as little dose as possible. CT image denoising tries to obtain high-dose-like high-quality CT images (domain Y ) from low dose low-quality CT images (domain X ), which can be treated as an image-to-image translation task where the goal is to learn the transform between a source domain X (noisy images) and a target domain Y (clean images). Recently, the cycle-consistent adversarial denoising network (CCADN) has achieved state-of-the-art results by enforcing cycle-consistent loss without the need of paired training data, since the paired data is hard to collect due to patients’ interests and cardiac motion. However, out of concerns on patients’ privacy and data security, protocols typically require clinics to perform medical image processing tasks including CT image denoising locally (i.e., edge denoising). Therefore, the network models need to achieve high performance under various computation resource constraints including memory and performance. Our detailed analysis of CCADN raises a number of interesting questions that point to potential ways to further improve its performance using the same or even fewer computation resources. For example, if the noise is large leading to a significant difference between domain X and domain Y , can we bridge X and Y with a intermediate domain Z such that both the denoising process between X and Z and that between Z and Y are easier to learn? As such intermediate domains lead to multiple cycles, how do we best enforce cycle- consistency? Driven by these questions, we propose a multi-cycle-consistent adversarial network (MCCAN) that builds intermediate domains and enforces both local and global cycle-consistency for edge denoising of CT images. The global cycle-consistency couples all generators together to model the whole denoising process, whereas the local cycle-consistency imposes effective supervision on the process between adjacent domains. Experiments show that both local and global cycle-consistency are important for the success of MCCAN, which outperforms CCADN in terms of denoising quality with slightly less computation resource consumption.

scholarly journals Crystallographic features of ammonium fluoroelpasolites: dynamic orientational disorder in crystals of (NH4)3HfF7 and (NH4)3Ti(O2)F5

2017 ◽  
Vol 73 (1) ◽  
pp. 1-9 ◽  
Author(s):  
Anatoly A. Udovenko ◽  
Alexander A. Karabtsov ◽  
Natalia M. Laptash
Keyword(s):  
Single Crystal ◽  
Electron Density ◽  
Diffraction Data ◽  
Central Atom ◽  
X Ray Diffraction ◽  
Dynamic Nature ◽  
Orientational Disorder ◽  
High Quality ◽  
Structural Units ◽  
X Ray

A classical elpasolite-type structure is considered with respect to dynamically disordered ammonium fluoro-(oxofluoro-)metallates. Single-crystal X-ray diffraction data from high quality (NH4)3HfF7 and (NH4)3Ti(O2)F5 samples enabled the refinement of the ligand and cationic positions in the cubic Fm \bar 3 m (Z = 4) structure. Electron-density atomic profiles show that the ligand atoms are distributed in a mixed (split) position instead of 24e. One of the ammonium groups is disordered near 8c so that its central atom (N1) forms a tetrahedron with vertexes in 32f. However, a center of another group (N2) remains in the 4b site, whereas its H atoms (H2) occupy the 96k positions instead of 24e and, together with the H3 atom in the 32f position, they form eight spatial orientations of the ammonium group. It is a common feature of all ammonium fluoroelpasolites with orientational disorder of structural units of a dynamic nature.

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