Biomedical subjects

M Unser

Publications and source records attributed to M Unser.

At least 19 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

Design and validation of a tool for neurite tracing and analysis in fluorescence microscopy images.

BACKGROUND: For the investigation of the molecular mechanisms involved in neurite outgrowth and differentiation, accurate and reproducible segmentation and quantification of neuronal processes are a prerequisite. To facilitate this task, we developed a semiautomatic neurite tracing technique. This article describes the design and validation of the technique. METHODS: The technique was compared to fully manual delineation. Four observers repeatedly traced selected neurites in 20 fluorescence microscopy images of cells in culture, using both methods. Accuracy and reproducibility were determined by comparing the tracings to high-resolution reference tracings, using two error measures. Labor intensiveness was measured in numbers of mouse clicks required. The significance of the results was determined by a Student t-test and by analysis of variance. RESULTS: Both methods slightly underestimated the true neurite length, but the differences were not unanimously significant. The average deviation from the true neurite centerline was a factor 2.6 smaller with the developed technique compared to fully manual tracing. Intraobserver variability in the respective measures was reduced by a factor 6.0 and 23.2. Interobserver variability was reduced by a factor 2.4 and 8.8, respectively, and labor intensiveness by a factor 3.3. CONCLUSIONS: Providing similar accuracy in measuring neurite length, significantly improved accuracy in neurite centerline extraction, and significantly improved reproducibility and reduced labor intensiveness, the developed technique may replace fully manual tracing methods.

Animals↗

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↗

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↗

PubMed1998

Unsupervised connectivity-based thresholding segmentation of midsagittal brain MR images.

In this paper, we propose an algorithm for automated segmentation of midsagittal brain MR images. First, we apply thresholding to obtain binary images. From the binary images, we locate some landmarks. Based on the landmarks and anatomical information, we preprocess the binary images, which substantially simplifies the subsequent operations. To separate regions what are incorrectly merged after this initial segmentation, a new connectivity-based threshold algorithm is proposed. Assuming that some prior information about the general shape and location of objects is available, the algorithm finds a boundary between two regions using the path connection algorithm and changing the threshold adaptively. In order to test the robustness of the proposed algorithm we applied the algorithm to 120 midsagittal brain images and obtained satisfactory results.

Algorithms↗

PubMed1998

Statistical analysis of functional MRI data in the wavelet domain.

The use of the wavelet transform is explored for the detection of differences between brain functional magnetic resonance images (fMRI's) acquired under two different experimental conditions. The method benefits from the fact that a smooth and spatially localized signal can be represented by a small set of localized wavelet coefficients, while the power of white noise is uniformly spread throughout the wavelet space. Hence, a statistical procedure is developed that uses the imposed decomposition orthogonality to locate wavelet-space partitions with large signal-to-noise ratio (SNR), and subsequently restricts the testing for significant wavelet coefficients to these partitions. This results in a higher SNR and a smaller number of statistical tests, yielding a lower detection threshold compared to spatial-domain testing and, thus, a higher detection sensitivity without increasing type I errors. The multiresolution approach of the wavelet method is particularly suited to applications where the signal bandwidth and/or the characteristics of an imaging modality cannot be well specified. The proposed method was applied to compare two different fMRI acquisition modalities. Differences of the respective useful signal bandwidths could be clearly demonstrated; the estimated signal, due to the smoothness of the wavelet representation, yielded more compact regions of neuroactivity than standard spatial-domain testing.

Adult↗

PubMed1994

Fast wavelet transformation of EEG.

Wavelet transforms offer certain advantages over Fourier transform techniques for the analysis of EEG. Recent work has demonstrated the applicability of wavelets for both spike and seizure detection, but the computational demands have been excessive. We compare the quality of feature extraction of continuous wavelet transforms using standard numerical techniques, with more rapid algorithms utilizing both polynomial splines and multiresolution frameworks. We further contrast the difference between filtering with and without the use of surrogate data to model background noise, demonstrate the preservation of feature extraction with critical versus redundant sampling, and perform the analyses with wavelets of different shape. Comparison is made with windowed Fourier transforms, similarly filtered, at different data window lengths. We here report a dramatic reduction in computational time required to perform this analysis, without compromising the accuracy of feature extraction. It now appears technically feasible to filter and decompose EEG using wavelet transforms in real time with ordinary microprocessors.

Brain↗

PubMed1993

Minimum views required to characterize cataracts when using the Scheimpflug camera.

We performed Scheimpflug slit lamp photography and computerized image analysis on 20 normal and 25 cataractous lenses using 18 slit images for each lens taken 10 degrees apart. The data gathered from the normals served as the reference to estimate the accuracy of representation of the cataracts by the least number of views (18 and less) using a Fourier interpolative algorithm. Using the error obtained with one view for the normals, our study suggests that the minimum number of views necessary for adequate characterization is two for cortical cataracts, two for nuclear cataracts, and six for posterior subcapsular cataracts. This information will be useful in longitudinal studies of cataracts, since most researchers presently use only one view, which may be adequate for normals but not for cataractous lenses. We found the Fourier interpolative algorithm useful in estimating the minimum views required for the current method of analyzing Scheimpflug images, and it can be easily applied to other similar images.

Algorithms↗

PubMed1993

Aging studies on normal lens using the Scheimpflug slit-lamp camera.

PURPOSE: To study the changes in density and thickness in normal lenses related to aging, and to study changes in anterior chamber depth related to aging. METHODS: Eighty nine normal volunteers (ages 9-80 yr) were examined and their eyes were photographed to obtain Scheimpflug photographs. The images were digitized and linear densitometry was performed, dividing the lens into five areas: posterior capsular (area 1), posterior cortical (area 2), nuclear (area 3), anterior cortical (area 4), and anterior capsular (area 5). Total lens thickness and anterior chamber depth were similarly measured for 90 normal eyes from the densitometry profiles. These were correlated with age. RESULTS: There was a strong positive correlation between increasing age and the density in all lens areas (area 2: r = 0.805; P < 0.0001; area 3: r = 0.836, P < 0.0001; area 4: r = 0.767, P < 0.0001; and area 5: r = 0.319, P < 0.0023), except the posterior capsular area, where correlation was negative (area 1: r = -0.426; P < 0.0001). In addition, there was a significant correlation between age and overall lens thickness (r = 0.756; P < 0.0001), thickness of nucleus (r = 0.543; P < 0.0001), and cortex (r = 0.632; P < 0.0001), and a negative correlation with anterior chamber depth (r = -0.513, P < 0.0001). CONCLUSION: This report shows human lens changes in density and thickness correlated with aging using Scheimpflug photography and image analysis techniques. The results will aid future development of systems for automated detection, classification, and monitoring of human cataracts, as well as other anterior segment disorders.

Adolescent↗

PubMed1992

Magnification mismatches between micrographs: corrective procedures and implications for structural analysis.

Quantitative structural analysis from electron micrographs of biological macromolecules inevitably requires the synthesis of data from many parts of the same micrograph and, ultimately, from multiple micrographs. Higher resolutions require the inclusion of progressively more data, and for the particles analyzed to be consistent to within ever more stringent limits. Disparities in magnification between micrographs or even within the field of one micrograph, arising from lens hysteresis or distortions, limit the resolution of such analyses. A quantitative assessment of this effect shows that its severity depends on the size of the particle under study: for particles that are 100 nm in diameter, for example, a 2% discrepancy in magnification restricts the resolution to approximately 5 nm. In this study, we derive and describe the properties of a family of algorithms designed for cross-calibrating the magnifications of particles from different micrographs, or from widely differing parts of the same micrograph. This approach is based on the assumption that all of the particles are of identical size: thus, it is applicable primarily to cryo-electron micrographs in which native dimensions are precisely preserved. As applied to icosahedral virus capsids, this procedure is accurate to within 0.1-0.2%, provided that at least five randomly oriented particles are included in the calculation. The algorithm is stable in the presence of noise levels typical of those encountered in practice, and is readily adaptable to non-isometric particles. It may also be used to discriminate subpopulations of subtly different sizes.

Algorithms↗

PubMed1992

Automated detection of the tongue surface in sequences of ultrasound images.

An image processing system has been developed for a Macintosh II personal computer. It is designed to process sequences of sagittal tongue sections that are digitized in real time and stored in standard tagged image file format (TIFF). The successive processing steps are: (a) a low-pass filter for noise reduction, (b) a resampling of the sector of interest in polar coordinates, (c) a matched filter (vertical differentiator) for the enhancement of the tissue/air interface in the surface region of the tongue, and (d) an extraction of border points by searching for an optimal radial path along the angular dimension. This latter task is achieved by dynamic programming, which has the following advantages. First, due to the use of a global criterion to guide the detection, it is very robust. Second, as a result of certain restrictions of the allowable transitions, the extracted contours are smooth. Finally, the method permits the specification of particular predefined contour points. This system was implemented in a program that can handle image sequences in a fully automatic mode. Results obtained using ultrasound data are presented.

Humans↗

PubMed1991

Computerized methods for analyzing two-dimensional agarose gel electropherograms.

Previous methods interpret zonal or polydisperse gel patterns of two-dimensional Serwer-type gels in terms of size and free mobility (surface net charge density). These two parameters have been determined for each component without quantitatively measuring the abundance of the components. The present study advances these previous methods by determining the relative concentration of each component by computer evaluation of densitometrically analyzed gel patterns. Suitable procedures and their underlying algorithms are presented. The mathematical routines are implemented in a user-friendly software package, called GelFit and designed for a Macintosh personal computer. The program input consists of digitized images of gel staining patterns exemplified by those obtained from electrophoresis of native subcellular-sized particles. The data are processed through the following steps: (i) Noise reduction and calibration. (ii) Geometrical transformation of the pattern onto a rectangular size/free mobility coordinate system using rationales of the extended Ogston model. (iii) Analysis of the transformed image to determine density maxima, density profiles along iso-free-mobility or iso-size lines, curve fitting of one-dimensional profiles or two-dimensional surfaces using Gaussian functions and curve stripping of surfaces to determine the possible number of particle populations.

Algorithms↗

PubMed1991

The distribution of particles characterized by size and free mobility within polydisperse populations of protein-polysaccharide conjugates, determined from two-dimensional agarose electropherograms.

New approaches for the characterization of polydisperse particle populations are presented*. The investigated samples contain virus-sized protein-polysaccharide conjugates which had previously been prepared as immunogens against bacterial meningitis (Hib). The analysis is based on two-dimensional agarose electrophoresis (Serwer-type). This method, like the one of O'Farrell, achieves a separation according to size and charge. It relies on a different principle, however, and is applicable to nondenatured particles which are 100 to more than 1000 times larger in mass than regular uncrosslinked proteins. Data from stained gel patterns are evaluated by the computer program ELPHOFIT, which makes it possible to standardize the gel and to construct a nomogram which defines every position on the gel in terms of particle size and free mobility (related to surface net charge density). The output of ELPHOFIT, consisting of nomogram parameters, is transferred to the image processing program GELFIT. This software is used to evaluate the computer images obtained by digitizing the stained gel patterns: (i) The nomogram is electronically superimposed on the computer image. (ii) The gel pattern is transformed from a curvilinear to a rectangular coordinate system of particle size and free mobility. The center of gravity as well as density maxima are given in coordinates of particle size and free mobility. Ranges of grey levels can be accentuated by adding 16 pseudocolors. (iii) Using surface-stripping techniques, GELFIT provides an estimate for the number of major subpopulations within each preparation. (iv) Numerical values for the distribution of particle size and free mobility are determined. Using program IMAGE, the quantitative physical assessment of a given conjugate preparation is presented in the form of a computer-generated three-dimensional plot, the shape of which serves to identify and characterize the preparation visually. The data analysis based on digitized two-dimensional gel patterns is automated to an extent that a technician can perform routine evaluations. It uses the Macintosh II personal computer.

Bacterial Outer Membrane Proteins↗

PubMed1991

Spatial disorders and computational cures.

Image averaging provides a powerful method for enhancing the yield of interpretable information from electron micrographs of biological macromolecules. However, as originally conceived, the full benefit of averaging is achieved only with perfectly ordered two-dimensional crystals. More recent developments, reviewed here, allow one to rectify disordered lattices, straighten randomly bent filaments, and combine multiple images of free-standing particles, thus extending the advantages of image averaging to virtually every class of macromolecular specimen.

Animals↗

PubMed1990

Computerized cataract detection and classification.

156 eyes of patients and normal volunteers were classified at the slit lamp into the following pure groups: normal (n = 50), nuclear (n = 39), cortical (n = 33) and PSC (n = 34). The eyes were photographed with the Topcon SL-45 Scheimpflug camera and the images scanned and processed to obtain one dimensional profiles through a 40 x 440 micron axial window. Of the 156 profiles, 90 were used as reference samples and were processed to obtain average profiles. The remaining 66 "unknown" profiles and each of the reference profiles, were classified into the four groups based on their distance from the average profiles in Euclidean space. The system was found to be very sensitive (98%) in detecting the presence of cataracts and specific (100%) in identifying normal, i.e. cataract negative lenses. In classifying pure cataracts into the various classes 98% of answers were correct.

Adult↗

PubMed1989

Interactions between actin and myosin filaments in skeletal muscle visualized in frozen-hydrated thin sections.

For the purpose of determining net interactions between actin and myosin filaments in muscle cells, perhaps the single most informative view of the myofilament lattice is its averaged axial projection. We have studied frozen-hydrated transverse thin sections with the goal of obtaining axial projections that are not subject to the limitations of conventional thin sectioning (suspect preservation of native structure) or of equatorial x-ray diffraction analysis (lack of experimental phases). In principle, good preservation of native structure may be achieved with fast freezing, followed by low-dose electron imaging of unstained vitrified cryosections. In practice, however, cryosections undergo large-scale distortions, including irreversible compression; furthermore, phase contrast imaging results in a nonlinear relationship between the projected density of the specimen and the optical density of the micrograph. To overcome these limitations, we have devised methods of image restoration and generalized correlation averaging, and applied them to cryosections of rabbit psoas fibers in both the relaxed and rigor states. Thus visualized, myosin filaments appear thicker than actin filaments by a much smaller margin than in conventional thin sections, and particularly so for rigor muscle. This may result from a significant fraction of the myosin S1-cross-bridges averaging out in projection and thus contributing only to the baseline of projected density. Entering rigor incurs a loss of density from an annulus around the myosin filament, with a compensating accumulation of density around the actin filament. This redistribution of mass represents attachment of the fraction of cross-bridges that are visible above background. Myosin filaments in the "nonoverlap" zone appear to broaden on entering rigor, suggesting that on deprivation of ATP, cross-bridges in situ move outwards even without actin in their immediate proximity.

Actins↗