Biomedical subjects

S Jonić

Publications and source records attributed to S Jonić.

7 recordsLinked to original sources

PubMed2006

A novel method for improvement of visualization of power spectra for sorting cryo-electron micrographs and their local areas.

In a context of automation of cryo-electron microscopy, we developed a novel method for improving visibility of diffraction rings in the power spectra of cryo-electron micrographs of vitreous ice (without carbon film or high concentration of diffracting material). We used these enhanced spectra to semi-automatically detect and remove micrographs and/or local areas introducing errors in the global 3D map (drifted and charged areas) or those unable to increase global signal-to-noise ratio (non-diffracting areas). Our strategy also allows a detection of micrographs/areas with a strong astigmatism. These images should be removed when using algorithms that do not correct astigmatism. Our sorting method is simple and fast since it uses the normalized cross-correlation between enhanced spectra and their copies rotated by 90 degrees. It owes its success mainly to the novel pre-processing of power spectra. The improved visibility also allows an easier visual check of accuracy of sorting. We show that our algorithm can even improve the visibility of diffraction rings of cryo-electron micrographs of pure water. Moreover, we show that this visibility depends strongly on ice thickness. This algorithm is implemented in the Xmipp (open-source image processing package) and is freely available for implementation in any other software package.

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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.

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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.

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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.

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PubMed1999

Automatic synthesis of synergies for control of reaching--hierarchical clustering.

In this paper we describe a novel method for determining synergies between joint motions in reaching movements by hierarchical clustering. A set of recorded elbow and shoulder trajectories is used in a learning algorithm to determine the relationships between angular velocities at elbow and shoulder joints. The learning algorithm is based on optimal criteria for obtaining the hierarchy of descriptions of movement trajectories. We show that this method finds complex synergism between optimal joint trajectories for a given set of data and angular velocities at the shoulder and elbow joints. Three other machine learning techniques (ML) are used for comparison with our method of hierarchical clustering of trajectories. These MLs are: (1) radial basis functions (RBF), (2) inductive learning (IL), and (3) adaptive-network-based fuzzy inference system (ANFIS). Better error characteristics were obtained using the method of hierarchical clustering in comparison with the other techniques. The advantage of the method of hierarchical clustering with respect to the other MLs is in integrating the spatial and temporal elements of reaching movements. Determination and analysis of spatio-temporal events of movement trajectories is a useful tool in designing control systems for functional electrical stimulation (FES) assisted manipulation.

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PubMed1999

Three machine learning techniques for automatic determination of rules to control locomotion.

Automatic prediction of gait events (e.g., heel contact, flat foot, initiation of the swing, etc.) and corresponding profiles of the activations of muscles is important for real-time control of locomotion. This paper presents three supervised machine learning (ML) techniques for prediction of the activation patterns of muscles and sensory data, based on the history of sensory data, for walking assisted by a functional electrical stimulation (FES). Those ML's are: 1) a multilayer perceptron with Levenberg-Marquardt modification of backpropagation learning algorithm; 2) an adaptive-network-based fuzzy inference system (ANFIS); and 3) a combination of an entropy minimization type of inductive learning (IL) technique and a radial basis function (RBF) type of artificial neural network with orthogonal least squares learning algorithm. Here we show the prediction of the activation of the knee flexor muscles and the knee joint angle for seven consecutive strides based on the history of the knee joint angle and the ground reaction forces. The data used for training and testing of ML's was obtained from a simulation of walking assisted with an FES system [39]. The ability of generating rules for an FES controller was selected as the most important criterion when comparing the ML's. Other criteria such as generalization of results, computational complexity, and learning rate were also considered. The minimal number of rules and the most explicit and comprehensible rules were obtained by ANFIS. The best generalization was obtained by the IL and RBF network.

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PubMed1999

Optimal control of walking with functional electrical stimulation: a computer simulation study.

Bipedal locomotion was simulated to generate a pattern of activating muscles for walking using electrical stimulation in persons with spinal cord injury (SCI) or stroke. The simulation presented in this study starts from a model of the body determined with user-specific parameters, individualized with respect to the lengths, masses, inertia, muscle and joint properties. The trajectory used for simulation was recorded from an able-bodied subject while walking with ankle-foot orthoses. A discrete mathematical model and dynamic programming were used to determine the optimal control. A cost function was selected as the sum of the squares of the tracking errors from the desired trajectories, and the weighted sum of the squares of agonist and antagonist activations of the muscle groups acting around the hip and knee joints. The aim of the simulation was to study plausible trajectories keeping in mind the limitations imposed by the spinal cord injury or stroke (e.g., spasticity, decreased range of movements in some joints, limited strength of paralyzed, externally activated muscles). If the muscles were capable of generating the movements required and the trajectory was achieved, then the simulation provided two kinds of information: 1) timing of the onset and offset of muscle activations with respect to the various gait events and 2) patterns of activation with respect to the maximum activation. These results are important for synthesizing a rule-based controller.

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