Biomedical subjects

D Van Dyck

Publications and source records attributed to D Van Dyck.

At least 19 recordsLinked to original sources

PubMed2006

Electron channelling based crystallography.

Electron channelling occurs when the incident electron beam is parallel to the atom columns of an object, such as a crystal or a particular crystal defect. Then, the electrons are trapped in the electrostatic potential of an atom column in which they scatter dynamically. This picture provides physical insight and explains why a one-to-one correspondence is maintained between the exit wave and the projected structure, even in case of strong dynamical scattering. Moreover, the theory is very useful to invert the dynamical scattering, that is, to derive the projected structure from the exit wave. Finally, it can be used to determine the composition of an atom column with single atom sensitivity or to explain dynamical electron diffraction effects. In this paper, an overview of the channelling theory will be given together with some recent applications.

Journal Article↗

PubMed2006

An efficient way of including thermal diffuse scattering in simulation of scanning transmission electron microscopic images.

We propose an improved image simulation procedure for atomic-resolution annular dark-field scanning transmission electron microscopy (STEM) based on the multislice formulation, which takes thermal diffuse scattering fully into account. The improvement with regard to the classical frozen phonon approach is realized by separating the lattice configuration statistics from the dynamical scattering so as to avoid repetitive calculations. As an example, the influence of phonon scattering on the image contrast is calculated and investigated. STEM image simulation of crystals can be applied with reasonable computing times to problems involving a large number of atoms and thick or large supercells.

Journal Article↗

PubMed2006

High resolution micro-CT scanning as an innovative tool for evaluation of the surgical positioning of cochlear implant electrodes.

X-ray microtomography (micro-CT) is a new technique allowing for visualization of the internal structure of opaque specimens with a quasi-histological quality. Among multiple potential applications, the use of this technique in otology is very promising. Micro-CT appears to be ideally suited for in vitro visualization of the inner ear tissues as well as for evaluation of the electrode damage and/or surgical insertion trauma during implantation of the cochlear implant electrodes. This technique can greatly aid in design and development of new cochlear implant electrodes and is applicable for temporal bone studies. The main advantage of micro-CT is the practically artefact-free preparation of the samples and the possibility of evaluation of the interesting parameters along the whole insertion depth of the electrode. This paper presents the results of the first application of micro-CT for visualization of the inner ear structures in human temporal bones and for evaluation of the surgical positioning of the cochlear implant electrodes relative to the intracochlear soft tissues.

Artifacts↗

PubMed2005

Maximum likelihood estimation of structure parameters from high resolution electron microscopy images. Part I: a theoretical framework.

This paper is the first part of a two-part paper on maximum likelihood (ML) estimation of structure parameters from electron microscopy images. In principle, electron microscopy allows structure determination with a precision that is orders of magnitude better than the resolution of the microscope. This requires, however, a quantitative, model-based method. In our opinion, the ML method is the most appropriate one since it has optimal statistical properties. This paper aims to provide microscopists with the necessary tools to apply this method so as to determine structure parameters as precisely as possible. It reviews the theoretical framework, including model assessment, the derivation of the ML estimator of the parameters, the limits to precision and the construction of confidence regions and intervals for ML parameter estimates. In a companion paper [Van Aert et al., Ultramicroscopy, this issue, 2005], a practical example will be worked out.

Journal Article↗

PubMed2005

Maximum likelihood estimation of structure parameters from high resolution electron microscopy images. Part II: a practical example.

This paper is the second part of a two-part paper on maximum likelihood (ML) estimation of structure parameters from electron microscopy images. In order to show the practical applicability of the theoretical methods described in the first part of this two-part paper, an experimental study of an aluminium crystal is presented. In this study, structure parameters, atom column distances in particular, are estimated from high-resolution transmission electron microscopy (HRTEM) images using the ML method. The necessary steps to be made in the application of this method will be worked out one by one, including model assessment, the computation of the ML parameter estimates, and the construction of confidence intervals for these parameter estimates.

Journal Article↗

PubMed2005

Mathematical framework for simulating diffusion tensor MR neural fiber bundles.

White matter (WM) fiber tractography (i.e., the reconstruction of the 3D architecture of WM fiber pathways) is known to be an important application of diffusion tensor magnetic resonance imaging (DT-MRI). For the quantitative evaluation of several fiber-tracking properties, such as accuracy, noise sensitivity, and robustness, synthetic ground-truth DT-MRI data are required. Moreover, an accurate simulated phantom is also required for optimization of the user-defined tractography parameters, and objective comparisons between fiber-tracking algorithms. Therefore, in this study a mathematical framework for simulating DT-MRI data, based on the physical properties of WM fiber bundles, is presented. We obtained a model of a WM fiber bundle by parameterizing the various features that characterize this bundle. We then evaluated three different synthetic DT-MRI models using experimental data in order to test the proposed methodology, and to determine the optimum model and parameter settings for constructing a realistic simulated DT-MRI phantom. Several examples of how the mathematical framework can be applied to compare fiber-tracking algorithms are presented.

Algorithms↗

PubMed2005

In vivo assessment of emphysema in mice by high resolution X-ray microtomography.

High resolution X-ray microtomography (micro-CT) was used for the detection of emphysema in live mice. Emphysema was induced in C57BL/6 J mice by intratracheal instillation of different amounts of porcine pancreatic elastase. This emphysema could be clearly detected by micro-CT seven weeks post-treatment: analysis of the whole data set of virtual cross-sections showed the presence of a dose-dependent level of emphysema.

Animals↗

PubMed2004

How to optimize the experimental design of quantitative atomic resolution TEM experiments?

A quantitative measure is proposed to evaluate and optimize the design of quantitative atomic resolution TEM experiments. It aims at precise measurement of unknown structure parameters. Specifically, the proposed measure quantifies the statistical precision with which positions of atom columns can be estimated. The optimal design is then given by the combination of microscope settings for which this precision is highest. The proposed measure is also used to find out if new instrumental developments improve the precision as compared to existing methods.

Microscopy, Electron↗

PubMed2004

Atomic imaging in aberration-corrected high-resolution transmission electron microscopy.

In recent years, the successful implementation of a spherical-aberration corrector in a Philips CM 200 FEG ST microscope achieved by Haider et al. has attracted a great deal of attention. However, thus far extensive applications of this novel high-resolution transmission electron microscope (HRTEM) to materials research have been hampered by the problems concerning optimum imaging conditions and image interpretation. In this paper, we present our points of view concerning atomic imaging in an aberration-corrected HRTEM. Since atomic resolution images can also be obtained with other techniques such as through-focus exit-wave function reconstruction (TF-EWR), we have to emphasis that the strength of the aberration-corrected HRTEM particularly lies on its ability to resolve the atomic structure in real time. However, for this purpose it is mandatory that the image contrast be related in a one-to-one function with the projected structure of the object. We analyzed the atomic imaging conditions in much detail and we come to the following conclusion: this novel facility is no doubt a powerful and advanced HRTEM instrument in achieving atomic images with its highest resolution (information limit). We furthermore demonstrate that the combination of the new microscope and TF-EWR will yield optimal results.

Journal Article↗

PubMed2004

Physical limits on atomic resolution.

It is shown that the ultimate resolution is not limited by the bandwidth of the microscope but by the bandwidth (i.e., the scattering power) of the object. In the case of a crystal oriented along a zone axis, the scattering is enhanced by the channeling of the electrons. However, if the object is aperiodic along the beam direction, the bandwidth is much more reduced. A particular challenge are the amorphous objects. For amorphous materials, the natural bandwidth is that of the single atom and of the order of 1 angstrom(-1), which can be reached with the present generation of medium voltage microscopes without aberration correctors. A clear distinction is made between resolving a structure and refining, that is, between resolution and precision. In the case of an amorphous structure, the natural bandwidth also puts a limit on the number of atom coordinates that can be refined quantitatively. As a consequence, amorphous structures cannot be determined from one projection, but only by using atomic resolution tomography. Finally a theory of experiment design is presented that can be used to predict the optimal experimental setting or the best instrumental improvement. Using this approach it is suggested that the study of amorphous objects should be done at low accelerating voltage with correction of both spherical and chromatic aberration.

Crystallization↗

PubMed2003

Is atomic resolution transmission electron microscopy able to resolve and refine amorphous structures?

Atomic resolution transmission electron microscopy, even with an aberration free microscope, is only able to resolve and refine amorphous structures at the atomic level for very small foil thicknesses. Then, a precision of the order of 0.01 A is possible, but this may require long recording times, especially for light atoms. For larger thicknesses, amorphous structures can in principle only be resolved and refined using electron tomography.

Journal Article↗

PubMed2003

About forbidden and weak reflections.

Reflections forbidden under the single scattering approximation are not expected to remain extinct for crystal thicknesses for which multiple scattering becomes important, except for reflections of the Gjönnes-Moodie type. However, it has been observed that in many crystals with the incident beam along a zone axis, such as diamond-like crystals along the [110] zone, reflections forbidden under the single scattering approximation remain very weak up to large thicknesses. This is hard to explain in terms of many-beam dynamical scattering in Fourier space. The picture becomes clear if one describes the scattering in real space in terms of the channelling of the electrons along the atom columns parallel to the zone axis. In that case the exit wave of each atom column can be described by the S-state model, which is radially symmetric around the centre of the atom column. As a consequence the exit wave shows the same symmetry as the projected potential, so that the reflections forbidden under the single scattering approximation remain extinct. This condition only breaks down when the crystal thickness becomes so large that the S-state model becomes invalid, which is a function of the distance between neighbouring atom columns and/or the tilt from the exact zone axis. The sensitivity for small tilts is also in agreement with very old observations that have not been explained thus far.

Journal Article↗

PubMed2003

Quantitative analysis of bone mineral content by x-ray microtomography.

A new non-destructive method based on x-ray microtomography (micro-CT) was developed to measure calcium density in bone. X-ray micro-CT was used as a quantitative approach to acquire and reconstruct virtual cross-sections through the sample. Accurate beam-hardening correction was implemented. Grey values in the virtual cross-sections were calibrated as calcium mineral density in bone. From these cross-sections, three-dimensional models were created. Calcium content was calculated directly from images and expressed as percentage per volume and per weight. Calcium mineral density was studied by this method in a unique set of bones isolated from newts (Pleurodeles waltlii Michah) that had travelled into space. A demineralization of 10% was shown as a consequence of sustained micro-gravity.

Animals↗

PubMed2002

An energy-based beam hardening model in tomography.

As a consequence of the polychromatic x-ray source, used in micro-computer tomography (microCT) and in medical CT, the attenuation is no longer a linear function of absorber thickness. If this nonlinear beam hardening effect is not compensated, the reconstructed images will be corrupted by cupping artefacts. In this paper, a bimodal energy model for the detected energy spectrum is presented, which can be used for reduction of artefacts caused by beam hardening in well-specified conditions. Based on the combination of the spectrum of the source and the detector efficiency, the assumption is made that there are two dominant energies which can describe the system. The validity of the proposed model is examined by fitting the model to the experimental datapoints obtained on a microtomograph for different materials and source voltages.

Algorithms↗

PubMed2002

Optimal experimental design of STEM measurement of atom column positions.

A quantitative measure is proposed to evaluate and optimize the design of a high-resolution scanning transmission electron microscopy (STEM) experiment. The proposed measure is related to the measurement of atom column positions. Specifically, it is based on the statistical precision with which the positions of atom columns can be estimated. The optimal design, that is, the combination of tunable microscope parameters for which the precision is highest. is derived for different types of atom columns. The proposed measure is also used to find out if an annular detector is preferable to an axial one and if a C(s)-corrector pays off in quantitative STEM experiments. In addition, the optimal settings of the STEM are compared to the Scherzer conditions for incoherent imaging and their dependence on the type of object is investigated.

Journal Article↗

PubMed2002

The S-state model: a work horse for HRTEM.

The S-state model describes the dynamical scattering of electrons in a specimen foil, consisting of atom columns parallel to the beam direction, such as a crystal or a particular crystal defect. In this model the electrons are considered to be trapped in the electrostatic potential of an atom column, in which it scatters dynamically. This picture allows physical insight, and it explains why a one-to-one correspondence is maintained between the exit wave and the projected structure, even in case of strong dynamical scattering. Furthermore the model can be parameterised in a simple closed analytical form. Apart from the computational advantages, the S-state model proves to be very useful to deduce the projected structure directly from the exit wave, so as to "invert" the dynamical scattering. In this paper the validity of the S-state model, is evaluated in much depth by a proper quantum mechanical treatment. The analytical parameterisation of the 1S eigenfunction and eigenenergy is discussed. It is shown that the method, even in case of small tilts, is valid for most thicknesses, currently used in HRTEM studies. Even for closely spaced atom columns, such as the dumbbells in Si [1 1 0], Sn [1 1 0] and GaN [1 1 0], the positions of the atom columns can be deduced with an accuracy of a few pm.

Journal Article↗

PubMed2002

3D in-vivo X-ray microtomography of living snails.

In this paper we report the first in-vivo scanning of living snails by desktop X-ray microtomograph with a resolution up to 10 m. Consecutive cross-sections were acquired without destroying the specimen. Subsequently, 3D images were reconstructed. The results clearly demonstrate the possibilities of in-vivo scanning. Processes of growth and regeneration of living snails were visualized over a period of time.

Animals↗

PubMed2001

Compositional analysis based on electron holography and a chemically sensitive reflection.

A method for compositional analysis of low-dimensional heterostructures is presented. The suggested procedure is based on electron holography and the exploitation of the chemically sensitive (0 0 2) reflection. We apply an off-axis imaging condition with the (0 0 2) beam strongly excited and centered on the optic axis. The first side band of the hologram is centered using an "empty" reference hologram obtained for a hole of the specimen. From the centered side band we use the phase of the central (0 0 0) and the amplitude of the (0 0 2) reflections to evaluate the local composition and the local specimen thickness in an iterative and self-consistent way. Delocalization effects that lead to a shift of the spatial information of (0 0 0) and (0 0 2) reflections are taken into account. The application of the procedure is demonstrated with an AlAs/GaAs(0 0 1) superlattice with a period of 5 nm. The concentration profiles obtained are discussed in relation to segregation. The measured segregation efficiency is R = 0.51 +/- 0.02.

Journal Article↗