Browse
Submit Data
Databases
API
Help

Dataset Information

22 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Brain Connectivity Exposed by Anisotropic X-ray Dark-field Tomography.

ABSTRACT: To understand the interaction of different parts of the human brain it is essential to know how they are connected. Such connections are predominantly related to the brain's white matter, which forms the neuronal pathways, the axons. These axons, also referred to as nerve fibers, have a size on the micrometer scale and are therefore too small to be imaged by standard X-ray systems. In this paper, we use a grating interferometer and a method based on Anisotropic X-ray Dark-field Tomography (AXDT) with the goal to generate a three-dimensional tomographic reconstruction of these functional structures. A first preclinical survey shows that we successfully reconstruct the orientations of the brain fibers connectivity with our approach.

SUBMITTER: Wieczorek M

PROVIDER: S-EPMC6156569 | biostudies-literature | 2018 Sep

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Publications

Brain Connectivity Exposed by Anisotropic X-ray Dark-field Tomography.

Wieczorek Matthias M Schaff Florian F Jud Christoph C Pfeiffer Daniela D Pfeiffer Franz F Lasser Tobias T

Scientific reports 20180925 1

To understand the interaction of different parts of the human brain it is essential to know how they are connected. Such connections are predominantly related to the brain's white matter, which forms the neuronal pathways, the axons. These axons, also referred to as nerve fibers, have a size on the micrometer scale and are therefore too small to be imaged by standard X-ray systems. In this paper, we use a grating interferometer and a method based on Anisotropic X-ray Dark-field Tomography (AXDT) ...[more]

PMID: 30254282

Similar Datasets

Design of Acquisition Schemes and Setup Geometry for Anisotropic X-ray Dark-Field Tomography (AXDT).

Project description:Anisotropic X-ray Dark-field Tomography (AXDT) is a new imaging technique for reconstructing the three-dimensional scattering profile within a sample using the dark-field signal measured in an X-ray grating interferometry setup. As in any tomographic measurement, the acquisition geometry plays a key role in the accurate reconstruction of the scattering information. More- over, the anisotropic nature of the dark-field signal poses additional challenges for designing the acquisition protocols. In this work, we present an efficient approach to measure scattering orientations spread over the unit sphere and prove its efficacy using the knowledge from conventional tomography. In addition, we conclude (using analytical and experimental results) that placing the gratings such that the grating bars make an angle of 45 degrees with respect to the vertical direction is the optimal setup configuration for AXDT.

| S-EPMC5466688 | biostudies-literature

Grating-based X-ray Dark-field Computed Tomography of Living Mice.

Project description:Changes in x-ray attenuating tissue caused by lung disorders like emphysema or fibrosis are subtle and thus only resolved by high-resolution computed tomography (CT). The structural reorganization, however, is of strong influence for lung function. Dark-field CT (DFCT), based on small-angle scattering of x-rays, reveals such structural changes even at resolutions coarser than the pulmonary network and thus provides access to their anatomical distribution. In this proof-of-concept study we present x-ray in vivo DFCTs of lungs of a healthy, an emphysematous and a fibrotic mouse. The tomographies show excellent depiction of the distribution of structural - and thus indirectly functional - changes in lung parenchyma, on single-modality slices in dark field as well as on multimodal fusion images. Therefore, we anticipate numerous applications of DFCT in diagnostic lung imaging. We introduce a scatter-based Hounsfield Unit (sHU) scale to facilitate comparability of scans. In this newly defined sHU scale, the pathophysiological changes by emphysema and fibrosis cause a shift towards lower numbers, compared to healthy lung tissue.

| S-EPMC4634200 | biostudies-literature

Reconstruction of scalar and vectorial components in X-ray dark-field tomography.

Project description:Grating-based X-ray dark-field imaging is a novel technique for obtaining image contrast for object structures at size scales below setup resolution. Such an approach appears particularly beneficial for medical imaging and nondestructive testing. It has already been shown that the dark-field signal depends on the direction of observation. However, up to now, algorithms for fully recovering the orientation dependence in a tomographic volume are still unexplored. In this publication, we propose a reconstruction method for grating-based X-ray dark-field tomography, which models the orientation-dependent signal as an additional observable from a standard tomographic scan. In detail, we extend the tomographic volume to a tensorial set of voxel data, containing the local orientation and contributions to dark-field scattering. In our experiments, we present the first results of several test specimens exhibiting a heterogeneous composition in microstructure, which demonstrates the diagnostic potential of the method.

| S-EPMC4156746 | biostudies-other

Non-iterative Directional Dark-field Tomography.

Project description:Dark-field imaging is a scattering-based X-ray imaging method that can be performed with laboratory X-ray tubes. The possibility to obtain information about unresolvable structures has already seen a lot of interest for both medical and material science applications. Unlike conventional X-ray attenuation, orientation dependent changes of the dark-field signal can be used to reveal microscopic structural orientation. To date, reconstruction of the three-dimensional dark-field signal requires dedicated, highly complex algorithms and specialized acquisition hardware. This severely hinders the possible application of orientation-dependent dark-field tomography. In this paper, we show that it is possible to perform this kind of dark-field tomography with common Talbot-Lau interferometer setups by reducing the reconstruction to several smaller independent problems. This allows for the reconstruction to be performed with commercially available software and our findings will therefore help pave the way for a straightforward implementation of orientation-dependent dark-field tomography.

| S-EPMC5468257 | biostudies-literature

X-ray absorption, phase and dark-field tomography through a beam tracking approach.

Project description:We present a development of the beam-tracking approach that allows its implementation in computed tomography. One absorbing mask placed before the sample and a high resolution detector are used to track variations in the beam intensity distribution caused by the sample. Absorption, refraction, and dark-field are retrieved through a multi-Gaussian interpolation of the beam. Standard filtered back projection is used to reconstruct three dimensional maps of the real and imaginary part of the refractive index, and of the dark-field signal. While the method is here demonstrated using synchrotron radiation, its low coherence requirements suggest a possible implementation with laboratory sources.

| S-EPMC4635357 | biostudies-other

Time resolved X-ray Dark-Field Tomography Revealing Water Transport in a Fresh Cement Sample.

Project description:Grating-based X-ray dark-field tomography is a promising technique for biomedical and materials research. Even if the resolution of conventional X-ray tomography does not suffice to resolve relevant structures, the dark-field signal provides valuable information about the sub-pixel microstructural properties of the sample. Here, we report on the potential of X-ray dark-field imaging to be used for time-resolved three-dimensional studies. By repeating consecutive tomography scans on a fresh cement sample, we were able to study the hardening dynamics of the cement paste in three dimensions over time. The hardening of the cement was accompanied by a strong decrease in the dark-field signal pointing to microstructural changes within the cement paste. Furthermore our results hint at the transport of water from certain limestone grains, which were embedded in the sample, to the cement paste during the process of hardening. This is indicated by an increasing scattering signal which was observed for two of the six tested limestone grains. Electron microscopy images revealed a distinct porous structure only for those two grains which supports the following interpretation of our results. When the water filled pores of the limestone grains empty during the experiment the scattering signal of the grains increases.

| S-EPMC4928120 | biostudies-other

Dark-field X-ray microscopy for multiscale structural characterization.

Project description:Many physical and mechanical properties of crystalline materials depend strongly on their internal structure, which is typically organized into grains and domains on several length scales. Here we present dark-field X-ray microscopy; a non-destructive microscopy technique for the three-dimensional mapping of orientations and stresses on lengths scales from 100 nm to 1 mm within embedded sampling volumes. The technique, which allows 'zooming' in and out in both direct and angular space, is demonstrated by an annealing study of plastically deformed aluminium. Facilitating the direct study of the interactions between crystalline elements is a key step towards the formulation and validation of multiscale models that account for the entire heterogeneity of a material. Furthermore, dark-field X-ray microscopy is well suited to applied topics, where the structural evolution of internal nanoscale elements (for example, positioned at interfaces) is crucial to the performance and lifetime of macro-scale devices and components thereof.

| S-EPMC4354092 | biostudies-literature

Simultaneous Maximum-Likelihood Reconstruction of Absorption Coefficient, Refractive Index and Dark-Field Scattering Coefficient in X-Ray Talbot-Lau Tomography.

Project description:A maximum-likelihood reconstruction technique for X-ray Talbot-Lau tomography is presented. This technique allows the iterative simultaneous reconstruction of discrete distributions of absorption coefficient, refractive index and a dark-field scattering coefficient. This technique avoids prior phase retrieval in the tomographic projection images and thus in principle allows reconstruction from tomographic data with less than three phase steps per projection. A numerical phantom is defined which is used to evaluate convergence of the technique with regard to photon statistics and with regard to the number of projection angles and phase steps used. It is shown that the use of a random phase sampling pattern allows the reconstruction even for the extreme case of only one single phase step per projection. The technique is successfully applied to measured tomographic data of a mouse. In future, this reconstruction technique might also be used to implement enhanced imaging models for X-ray Talbot-Lau tomography. These enhancements might be suited to correct for example beam hardening and dispersion artifacts and improve overall image quality of X-ray Talbot-Lau tomography.

| S-EPMC5047447 | biostudies-literature

In-vivo dark-field and phase-contrast x-ray imaging.

Project description:Novel radiography approaches based on the wave nature of x-rays when propagating through matter have a great potential for improved future x-ray diagnostics in the clinics. Here, we present a significant milestone in this imaging method: in-vivo multi-contrast x-ray imaging of a mouse using a compact scanner. Of particular interest is the enhanced contrast in regions related to the respiratory system, indicating a possible application in diagnosis of lung diseases (e.g. emphysema).

| S-EPMC3826096 | biostudies-literature

Hard X-ray omnidirectional differential phase and dark-field imaging.

Project description:Ever since the discovery of X-rays, tremendous efforts have been made to develop new imaging techniques for unlocking the hidden secrets of our world and enriching our understanding of it. X-ray differential phase contrast imaging, which measures the gradient of a sample's phase shift, can reveal more detail in a weakly absorbing sample than conventional absorption contrast. However, normally only the gradient's component in two mutually orthogonal directions is measurable. In this article, omnidirectional differential phase images, which record the gradient of phase shifts in all directions of the imaging plane, are efficiently generated by scanning an easily obtainable, randomly structured modulator along a spiral path. The retrieved amplitude and main orientation images for differential phase yield more information than the existing imaging methods. Importantly, the omnidirectional dark-field images can be simultaneously extracted to study strongly ordered scattering structures. The proposed method can open up new possibilities for studying a wide range of complicated samples composed of both heavy, strongly scattering atoms and light, weakly scattering atoms.

| S-EPMC7936267 | biostudies-literature

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data