Biomedical subjects

P Thévenaz

Publications and source records attributed to P Thévenaz.

8 recordsLinked to original sources

PubMed2005

Spline-based image-to-volume registration for three-dimensional electron microscopy.

This paper presents an algorithm based on a continuous framework for a posteriori angular and translational assignment in three-dimensional electron microscopy (3DEM) of single particles. Our algorithm can be used advantageously to refine the assignment of standard quantized-parameter methods by registering the images to a reference 3D particle model. We achieve the registration by employing a gradient-based iterative minimization of a least-squares measure of dissimilarity between an image and a projection of the volume in the Fourier transform (FT) domain. We compute the FT of the projection using the central-slice theorem (CST). To compute the gradient accurately, we take advantage of a cubic B-spline model of the data in the frequency domain. To improve the robustness of the algorithm, we weight the cost function in the FT domain and apply a "mixed" strategy for the assignment based on the minimum value of the cost function at registration for several different initializations. We validate our algorithm in a fully controlled simulation environment. We show that the mixed strategy improves the assignment accuracy; on our data, the quality of the angular and translational assignment was better than 2 voxel (i.e., 6.54 angstroms). We also test the performance of our algorithm on real EM data. We conclude that our algorithm outperforms a standard projection-matching refinement in terms of both consistency of 3D reconstructions and speed.

Algorithms↗

PubMed2005

Spectral signal-to-noise ratio and resolution assessment of 3D reconstructions.

Measuring the quality of three-dimensional (3D) reconstructed biological macromolecules by transmission electron microscopy is still an open problem. In this article, we extend the applicability of the spectral signal-to-noise ratio (SSNR) to the evaluation of 3D volumes reconstructed with any reconstruction algorithm. The basis of the method is to measure the consistency between the data and a corresponding set of reprojections computed for the reconstructed 3D map. The idiosyncrasies of the reconstruction algorithm are taken explicitly into account by performing a noise-only reconstruction. This results in the definition of a 3D SSNR which provides an objective indicator of the quality of the 3D reconstruction. Furthermore, the information to build the SSNR can be used to produce a volumetric SSNR (VSSNR). Our method overcomes the need to divide the data set in two. It also provides a direct measure of the performance of the reconstruction algorithm itself; this latter information is typically not available with the standard resolution methods which are primarily focused on reproducibility alone.

Algorithms↗

PubMed2004

A multiresolution approach to orientation assignment in 3D electron microscopy of single particles.

Three-dimensional (3D) electron microscopy (3DEM) aims at the determination of the spatial distribution of the Coulomb potential of macromolecular complexes. The 3D reconstruction of a macromolecule using single-particle techniques involves thousands of 2D projections. One of the key parameters required to perform such a 3D reconstruction is the orientation of each projection image as well as its in-plane orientation. This information is unknown experimentally and must be determined using image-processing techniques. We propose the use of wavelets to match the experimental projections with those obtained from a reference 3D model. The wavelet decomposition of the projection images provides a framework for a multiscale matching algorithm in which speed and robustness to noise are gained. Furthermore, this multiresolution approach is combined with a novel orientation selection strategy. Results obtained from computer simulations as well as experimental data encourage the use of this approach.

Algorithms↗

PubMed2004

Geometric alignment and chromatic calibration of serial radiographic images.

OBJECTIVE: To develop software for automated registration and intensity calibration of serial dental radiographs for the analysis of longitudinal changes in bone density. METHODS: Serial dental radiographs were acquired using a positioning device designed to minimize projection divergence. Each radiograph included an image of a standardized aluminium wedge. The radiographs were scanned on a flatbed scanner (AGFA Duo Scan) with a spatial resolution of 300 dpi, and pixel intensity coded in 16-bit grey scale. The intensity was calibrated using serial images of selected areas with defined thickness of the aluminium wedge. A robust B-splines multiresolution registration algorithm was implemented to overcome the acquisition misalignment. Radiographs, taken before and after periodontal therapy, were subtracted to assess bone density evolution. RESULTS: The intensity calibration decreased the maximum intensity variations between serial radiographs from 30+/-17% to 1+/-1% (mean+/-standard deviation), and improved the visual comparison between the radiographs. The registration stage allowed correcting the misalignment of the radiographs on the scanner screen and superimposing the radiography contents. The observed residual motion was about 0.02+/-0.01 mm. CONCLUSION: Very user-friendly software was developed. The manipulator needs to scan the radiographs only one time. The software performs all subsequent processing steps.

Absorptiometry, Photon↗

PubMed2001

Chronic inhalation studies of two types of stone wool fibers in rats.

A summary is given of the pathology results after long-term inhalation in rats of insulation wool representing the new biosoluble types. The pathology results are compared with previously conducted long-term inhalation study with MMVF21 (traditional stone wool). The biosoluble fiber MMVF34/HT (HT) is characterized by a relatively high content of aluminum and a relatively low content of silica compared to the older MMVF21. HT has a high in vitro dissolution rate at pH 4.5, and a relatively low dissolution rate at pH 7.5. Male Fischer 344 rats were exposed at one exposure level of 30 mg/m(3) by nose-only inhalation of a well-characterized fiber test atmosphere. The fibers had been size selected to be largely rat respirable. The negative control group was exposed to filtered air. The exposure duration was 6 h/day, 5 days/wk for 104 wk, with a subsequent nonexposure period lasting until approximately 20% survival in the air control group. Interim sacrifices were performed at wk 13, 26, 52, 78, and 104 to monitor the progression of pulmonary change and fiber numbers. Effectively the main protocol for the previously conducted chronic study with MMVF21 was the same, except that there were three concentration levels (3, 16, and 30 mg/m(3)). In addition to the endpoints measured in the previous study, slides from both studies were evaluated for collagen deposition using a quantitative morphometric method. The results of the comparative study clearly showed a marked difference in the pulmonary pathogenicity of the MMVF21 and HT in terms of their fibrogenic potential. MMVF21 caused pulmonary fibrosis, but the HT fiber did not. The incidence of tumors for both the HT and the MMVF21 fiber was comparable to the control groups.

Adenocarcinoma↗

PubMed2000

Unwarping of unidirectionally distorted EPI images.

Echo-planar imaging (EPI) is a fast nuclear magnetic resonance imaging (MRI) method. Unfortunately, local magnetic field inhomogeneities induced mainly by the subject's presence cause significant geometrical distortion, predominantly along the phase-encoding direction, which must be undone to allow for meaningful further processing. So far, this aspect has been too often neglected. In this paper, we suggest a new approach using an algorithm specifically developed for the automatic registration of distorted EPI images with corresponding anatomically correct MRI images. We model the deformation field with splines, which gives us a great deal of flexibility, while comprising the affine transform as a special case. The registration criterion is least squares. Interestingly, the complexity of its evaluation does not depend on the resolution of the control grid. The spline model gives us good accuracy thanks to its high approximation order. The short support of splines leads to a fast algorithm. A multiresolution approach yields robustness and additional speedup. The algorithm was tested on real as well as synthetic data, and the results were compared with a manual method. A wavelet-based Sobolev-type random deformation generator was developed for testing purposes. A blind test indicates that the proposed automatic method is faster, more reliable, and more precise than the manual one.

Algorithms↗

PubMed2000

Interpolation revisited.

Based on the theory of approximation, this paper presents a unified analysis of interpolation and resampling techniques. An important issue is the choice of adequate basis functions. We show that, contrary to the common belief, those that perform best are not interpolating. By opposition to traditional interpolation, we call their use generalized interpolation; they involve a prefiltering step when correctly applied. We explain why the approximation order inherent in any basis function is important to limit interpolation artifacts. The decomposition theorem states that any basis function endowed with approximation order can be expressed as the convolution of a B-spline of the same order with another function that has none. This motivates the use of splines and spline-based functions as a tunable way to keep artifacts in check without any significant cost penalty. We discuss implementation and performance issues, and we provide experimental evidence to support our claims.

Artifacts↗

PubMed1980

Distribution and attachment of Trypanosoma (Nannomonas) congolense in the proximal part of the proboscis of Glossina morsitans morsitans.

The distribution and attachment of Trypanosoma congolense were investigated in the proximal part of the proboscis of Glossina m. morsitans. In the food canal, epimastigotes and trypomastigotes formed tufts or compact layers. Trypanosomes were attached to the cuticle by their flagella, which formed zonar hemidesmosomes. The flagella were mostly attached parallel to the axis of the labrum and often pointed to its tip. Foot-like processes of the flagella came into contact with adjacent flagella leading to dense grouping of the trypanosomes. Despite narrow contacts between adjacent flagella, no desmosomes were differentiated. The trypanosomes were attached to all parts of the LCI sensilla and might thus impair their function. Uncoated and coated forms were present in the labrum, which indicated that transformation to metacyclic forms is not strictly limited to the hypopharynx. Uncoated forms were often attached to the cuticle of the common salivary duct and hypopharynx by hemidesmosomes. Coated forms could also be attached. Neither compact layers nor tufts of trypanosomes were found. This attachment may partly explain the low number of metacyclics deposited when flies probed on a warm glass slide.

Animals↗