scholarly journals Noninvasive 3D Structural Analysis of Arthropod by Synchrotron X-Ray Phase Contrast Tomography

2015 ◽  
Vol 2015 ◽  
pp. 1-6 ◽  
Author(s):  
Shengkun Yao ◽  
Yunbing Zong ◽  
Jiadong Fan ◽  
Zhibin Sun ◽  
Huaidong Jiang
Keyword(s):  
Phase Contrast ◽  
Phase Retrieval ◽  
High Efficiency ◽  
Imaging Techniques ◽  
Three Dimensional ◽  
Circulatory System ◽  
Low Contrast ◽  
X Ray ◽  
Potential Applications ◽  
Phase Contrast Tomography

X-ray imaging techniques significantly advanced our understanding of materials and biology, among which phase contrast X-ray microscopy has obvious advantages in imaging biological specimens which have low contrast by conventional absorption contrast microscopy. In this paper, three-dimensional microstructure of arthropod with high contrast has been demonstrated by synchrotron X-ray in-line phase contrast tomography. The external morphology and internal structures of an earthworm were analyzed based upon tomographic reconstructions with and without phase retrieval. We also identified and characterized various fine structural details such as the musculature system, the digestive system, the nervous system, and the circulatory system. This work exhibited the high efficiency, high precision, and wide potential applications of synchrotron X-ray phase contrast tomography in nondestructive investigation of low-density materials and biology.

scholarly journals Three-dimensional virtual histology of human cerebellum by X-ray phase-contrast tomography

2018 ◽  
Vol 115 (27) ◽  
pp. 6940-6945 ◽  
Author(s):  
Mareike Töpperwien ◽  
Franziska van der Meer ◽  
Christine Stadelmann ◽  
Tim Salditt
Keyword(s):  
Phase Contrast ◽  
Spatial Organization ◽  
Granular Layer ◽  
Three Dimensional ◽  
Cell Segmentation ◽  
X Ray ◽  
Human Cerebellum ◽  
Conventional Histology ◽  
3D Information ◽  
Phase Contrast Tomography

To quantitatively evaluate brain tissue and its corresponding function, knowledge of the 3D cellular distribution is essential. The gold standard to obtain this information is histology, a destructive and labor-intensive technique where the specimen is sliced and examined under a light microscope, providing 3D information at nonisotropic resolution. To overcome the limitations of conventional histology, we use phase-contrast X-ray tomography with optimized optics, reconstruction, and image analysis, both at a dedicated synchrotron radiation endstation, which we have equipped with X-ray waveguide optics for coherence and wavefront filtering, and at a compact laboratory source. As a proof-of-concept demonstration we probe the 3D cytoarchitecture in millimeter-sized punches of unstained human cerebellum embedded in paraffin and show that isotropic subcellular resolution can be reached at both setups throughout the specimen. To enable a quantitative analysis of the reconstructed data, we demonstrate automatic cell segmentation and localization of over 1 million neurons within the cerebellar cortex. This allows for the analysis of the spatial organization and correlation of cells in all dimensions by borrowing concepts from condensed-matter physics, indicating a strong short-range order and local clustering of the cells in the granular layer. By quantification of 3D neuronal “packing,” we can hence shed light on how the human cerebellum accommodates 80% of the total neurons in the brain in only 10% of its volume. In addition, we show that the distribution of neighboring neurons in the granular layer is anisotropic with respect to the Purkinje cell dendrites.

High-resolution brain tumor visualization using three-dimensional x-ray phase contrast tomography

2007 ◽  
Vol 52 (23) ◽  
pp. 6923-6930 ◽  
Author(s):  
F Pfeiffer ◽  
O Bunk ◽  
C David ◽  
M Bech ◽  
G Le Duc ◽  
...  
Keyword(s):  
Brain Tumor ◽  
High Resolution ◽  
Phase Contrast ◽  
Three Dimensional ◽  
X Ray ◽  
Tumor Visualization ◽  
Phase Contrast Tomography

Post-reconstruction 3D single-distance phase retrieval for multi-stage phase-contrast tomography with photon-counting detectors

2019 ◽  
Vol 26 (2) ◽  
pp. 510-516 ◽  
Author(s):  
Francesco Brun ◽  
Luca Brombal ◽  
Vittorio Di Trapani ◽  
Pasquale Delogu ◽  
Sandro Donato ◽  
...  
Keyword(s):  
Phase Contrast ◽  
Phase Retrieval ◽  
Photon Counting ◽  
X Ray ◽  
Multi Stage ◽  
Mastectomy Specimen ◽  
X Ray Computed ◽  
Photon Counting Detectors ◽  
3D Volume ◽  
Phase Contrast Tomography

In the case of single-distance propagation-based phase-contrast X-ray computed tomography with synchrotron radiation, the conventional reconstruction pipeline includes an independent 2D phase retrieval filtering of each acquired projection prior to the actual reconstruction. In order to compensate for the limited height of the X-ray beam or the small sensitive area of most modern X-ray photon-counting detectors, it is quite common to image large objects with a multi-stage approach, i.e. several acquisitions at different vertical positions of the sample. In this context, the conventional reconstruction pipeline may introduce artifacts at the margins of each vertical stage. This article presents a modified computational protocol where a post-reconstruction 3D volume phase retrieval is applied. By comparing the conventional 2D and the proposed 3D reconstructions of a large mastectomy specimen (9 cm in diameter and 3 cm in height), it is here shown that the 3D approach compensates for the multi-stage artifacts, it avoids refined projection stitching, and the image quality in terms of spatial resolution, contrast and contrast-to-noise ratio is preserved.

Three-dimensional morphology of cementite in steel studied by X-ray phase-contrast tomography

2012 ◽  
Vol 67 (3) ◽  
pp. 261-264 ◽  
Author(s):  
Alexander Kostenko ◽  
Hemant Sharma ◽  
E. Gözde Dere ◽  
Andrew King ◽  
Wolfgang Ludwig ◽  
...  
Keyword(s):  
Phase Contrast ◽  
Three Dimensional ◽  
X Ray ◽  
Phase Contrast Tomography

scholarly journals Multiscale three-dimensional imaging of intact human organs down to the cellular scale using hierarchical phase-contrast tomography

2021 ◽  
Author(s):  
C. Walsh ◽  
P. Tafforeau ◽  
Willi L. Wagner ◽  
D. J. Jafree ◽  
A. Bellier ◽  
...  
Keyword(s):  
Phase Contrast ◽  
Soft Tissues ◽  
Structural Information ◽  
Three Dimensional ◽  
High Energy ◽  
X Ray ◽  
Human Organs ◽  
Health And Disease ◽  
Functional Units ◽  
Phase Contrast Tomography

ABSTRACTHuman organs are complex, three-dimensional and multiscale systems. Spatially mapping the human body down through its hierarchy, from entire organs to their individual functional units and specialised cells, is a major obstacle to fully understanding health and disease. To meet this challenge, we developed hierarchical phase-contrast tomography (HiP-CT), an X-ray phase propagation technique utilising the European Synchrotron Radiation Facility’s Extremely Brilliant Source: the world’s first high-energy 4th generation X-ray source. HiP-CT enabled three-dimensional and non-destructive imaging at near-micron resolution in soft tissues at one hundred thousand times the voxel size whilst maintaining the organ’s structure. We applied HiP-CT to image five intact human parenchymal organs: brain, lung, heart, kidney and spleen. These were hierarchically assessed with HiP-CT, providing a structural overview of the whole organ alongside detail of the organ’s individual functional units and cells. The potential applications of HiP-CT were demonstrated through quantification and morphometry of glomeruli in an intact human kidney, and identification of regional changes to the architecture of the air-tissue interface and alveolar morphology in the lung of a deceased COVID-19 patient. Overall, we show that HiP-CT is a powerful tool which can provide a comprehensive picture of structural information for whole intact human organs, encompassing precise details on functional units and their constituent cells to better understand human health and disease.

Hard X-ray phase-contrast tomography of non-homogeneous specimens: grating interferometryversuspropagation-based imaging

2016 ◽  
Vol 23 (5) ◽  
pp. 1202-1209 ◽  
Author(s):  
Maite Ruiz-Yaniz ◽  
Irene Zanette ◽  
Adrian Sarapata ◽  
Lorenz Birnbacher ◽  
Mathias Marschner ◽  
...  
Keyword(s):  
Experimental Data ◽  
Phase Contrast ◽  
Phase Retrieval ◽  
Phase Contrast Imaging ◽  
Contrast Imaging ◽  
Homogeneous Sample ◽  
X Ray ◽  
Practical Applications ◽  
Phase Contrast Tomography ◽  
Complex Valued

X-ray phase-contrast imaging is an effective approach to drastically increase the contrast and sensitivity of microtomographic techniques. Numerous approaches to depict the real part of the complex-valued refractive index of a specimen are nowadays available. A comparative study using experimental data from grating-based interferometry and propagation-based phase contrast combined with single-distance phase retrieval applied to a non-homogeneous sample is presented (acquired at beamline ID19-ESRF). It is shown that grating-based interferometry can handle density gradients in a superior manner. The study underlines the complementarity of the two techniques for practical applications.

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