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Biomedical subjects

D Van Dyck

Publications and source records attributed to D Van Dyck.

At least 19 recordsLinked to original sources

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↗

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↗

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↗

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↗

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↗

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↗

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↗

Does a monochromator improve the precision in quantitative HRTEM?

This paper addresses the question as to what extent the incorporation of a monochromator in an electron microscope can enhance the performance of high resolution transmission electron microscopy (HRTEM). The monochromator will reduce the chromatic aberration, and hence the information limit, at the expense of beam current, leading to a decrease in signal intensity and a corresponding decrease in signal-to-noise ratio (SNR). Both aspects, information limit and SNR, have been included in a quantitative evaluation based on the statistical precision with which the position of an atom column can be estimated. It is shown that the effect of a monochromator on the attainable precision depends on the microscope and monochromator parameters, as well as on the characteristics of the object.

Journal Article↗

Otolith function after acoustic neuroma surgery.

The response of the vestibular system after acoustic neuroma surgery was investigated in nine patients. The otolith system was studied by means of ocular counterrolling, assessed by video oculography. Horizontal vestibulo-ocular reflex (VOR) function was tested by the sinusoidal harmonic acceleration test using electronystagmography. The results were compared with those obtained from a normal control population. The response to slow rotation tests was symmetric, but the gain was significantly reduced when compared to the normal population. Phase lag was significantly increased. No difference in ocular torsion was observed with lateroflexion of the head to the ipsilateral side in comparison with lateroflexion to the contralateral side. Moreover, the overall ocular counterrolling was well within normal limits. We conclude that the semicircular canal response differs from the otolith response. The component of the torsional VOR mediated by otolith stimulation appears to be more robust than the horizontal VOR mediated mainly by the horizontal semicircular canal system. Ocular counterrolling induced by lateroflexion does not reveal abnormalities in patients with surgically produced unilateral peripheral loss.

Adult↗

Exit wave reconstructions using through focus series of HREM images.

The through focus exit wave reconstruction technique uses a series of high resolution electron microscopy images to reconstruct the complex electron wavefunction at the exit plane of the specimen. The feasibility of the through focus exit wave reconstruction method and its most important limitations are discussed. It is shown that-provided all aberrations of the microscope are well corrected for-a large improvement in the interpretability of the information can be obtained.

Biophysical Phenomena↗

Automatic localization of EEG electrode markers within 3D MR data.

The electrical activity of the brain can be monitored using ElectroEncephaloGraphy (EEG). From the positions of the EEG electrodes, it is possible to localize focal brain activity. Thereby, the accuracy of the localization strongly depends on the accuracy with which the positions of the electrodes can be determined. In this work, we present an automatic, simple, and accurate scheme that detects EEG electrode markers from 3D MR data of the human head.

Electrodes↗

Reduction of ECG and gradient related artifacts in simultaneously recorded human EEG/MRI data.

Nowadays, electroencephalography signals can be acquired from a patient lying in a magnetic resonance imaging system. It is even possible to acquire EEG signals during an MR imaging sequence. However, such EEG signals are severely distorted by artifacts originating from various effects (e.g., MR gradients, ECG). In this paper, a simple method is presented to reduce such artifacts. Thereby, special attention is focused on artifacts related to the patient's electrocardiogram. The method is shown to be effective, adaptive, and automatic.

Artifacts↗

Wavelets as chromatin texture descriptors for the automated identification of neoplastic nuclei.

Chromatin distribution reflects the organization of the DNA of a nucleus and contains important cellular diagnostic and prognostic information. Feulgen staining of breast tissue enables the chromatin distribution of the nucleus to be visualized in the form of texture. Describing texture in an objective and quantitative way by means of a set of texture parameters, combined with the study of the relationship of such parameters to the pathobiological cell properties, is useful both for reduction of the subjectivity inherently coupled to visual observation and for more accurate prognosis or diagnosis. We have presented an automated classification scheme for the diagnosis and grading of invasive breast cancer. The input to this scheme was a digitized microscopical image, from which nuclei were segmented. Chromatin texture was described using a set of textural parameters that include first- and second-order statistics of the image grey levels. The more recently developed wavelet energy parameters were also included in our study. Classification was performed by a Knn-classifier, which is a versatile multivariate statistical classification technique. We investigated the role of the tissue preparation technique and found that parameters derived from cytospins were better texture descriptors than those from sections. A 100% correct classification was achieved in a patient diagnosis experiment and 82% in a nuclear grading experiment.

Breast Neoplasms↗

Adaptive anisotropic noise filtering for magnitude MR data.

Conventional noise filtering schemes applied to magnitude magnetic resonance (MR) images tacitly assume Gauss distributed noise. Magnitude MR data, however, are Rice distributed. Not incorporating this knowledge leads inevitably to biased results, in particular when applying such filters in regions with low signal-to-noise ratio. In this work, we show how the Rice data probability distribution can be incorporated so as to construct a noise filter that is far less biased.

Anisotropy↗

Restoration of MR-induced artifacts in simultaneously recorded MR/EEG data.

During a Magnetic Resonance sequence, simultaneously acquired ElectroEncephaloGraphy (EEG) data are compromised by severe pollution due to artifacts originating from the switching of the magnetic field gradients. In this work, it is shown how these artifacts can be strongly reduced or even removed through application of an adaptive artifact restoration scheme. The method has proved to be fully automatic and to retain high frequency EEG information, which is indispensable for many EEG applications.

Animals↗

A patchy horizontal organization of the somatosensory activation of the rat cerebellum demonstrated by functional MRI.

Blood oxygenation level dependent contrast (BOLD) functional MRI (fMRI) responses, in a 7-T magnet, were observed in the cerebellum of alpha-chloralose anaesthetized rats in response to innocuous electrical stimulation of a forepaw or hindpaw. The responses were imaged in both coronal and sagittal slices which allowed for a clear delineation and localization of the observed activations. We demonstrate the validity of our fMRI protocol by imaging the responses in somatosensory cortex to the same stimuli and by showing reproducibility of the cerebellar responses. Widespread bilateral activations were found with mainly a patchy and mediolateral band organization, more pronounced ipsilaterally. Possible parasagittal bands were observed only in contralateral lobule VI. There was no overlap between the cerebellar activations caused by forepaw and hindpaw stimuli. The overall horizontal organization of these responses was quite remarkable. For both stimulation paradigms most of the activation patches were positioned in either a rostral or caudal broad plane running anteroposteriorly through both anterior and posterior cerebellum. The rostral planes were completely separated, with the forepaw activation closer to the surface, while the caudal plane was common to both stimulation protocols. We relate our findings to the known projection patterns of spinocerebellar and cuneocerebellar mossy fibres, and to human fMRI studies.

Animals↗

Estimation of the noise in magnitude MR images.

Magnitude magnetic resonance data are Rician distributed. In this note a new method is proposed to estimate the image noise variance for this type of data distribution. The method is based on a double image acquisition, thereby exploiting the knowledge of the Rice distribution moments.

Magnetic Resonance Imaging↗

Maximum-likelihood estimation of Rician distribution parameters.

The problem of parameter estimation from Rician distributed data (e.g., magnitude magnetic resonance images) is addressed. The properties of conventional estimation methods are discussed and compared to maximum-likelihood (ML) estimation which is known to yield optimal results asymptotically. In contrast to previously proposed methods, ML estimation is demonstrated to be unbiased for high signal-to-noise ratio (SNR) and to yield physical relevant results for low SNR.

Computer Simulation↗