Classification of Micro Array Protein Crystal Images With Laplacian Pyramidal Filters and Neural Networks

This project is part of the Northeast Structural Genomics Consortium (NESG). The goal of this consortium is to develop efficient and integrated technologies for high-throughput (HTP) protein production and 3D structure determination. This project focuses on the design of an image analysis system to classify protein crystal structures in a production oriented environment. The method presented performs classification of microscopic images as protein precipitates or crystals versus clear solutions. Preliminary experiments are presented, which provided high classification accuracy on large datasets of protein crystallization experiments using expert classification for ground truth

Homogeneity Measures for Multiphase Level Set Segmentation of Brain MRI

This paper presents a new homogeneity measure for variational segmentation with multiple level set functions. We propose to modify the quadratic homogeneity measure to trade off the convexity of the function against a faster rate of convergence. We tested in two series of experiments the performance of this new homogeneity force at converging to appropriate partitioning of brain MRI data sets, over a large range of image spatial resolution and image quality, in terms of tissue homogeneity and contrast

Variational segmentation framework in prolate spheroidal coordinates for 3D real-time echocardiography

This paper presents a new formulation of a deformable model segmentation in prolate spheroidal coordinates for segmentation of 3D cardiac echocardiography data. The prolate spheroidal coordinate system enables a representation of the segmented surface with descriptors specifically adapted to the "ellipsoidal" shape of the ventricle. A simple data energy term, based on gray-level information, guides the segmentation. The segmentation framework provides a very fast and simple algorithm to evolve an initial ellipsoidal object towards the endocardial surface of the myocardium with near real-time deformations. With near real-time performance, additional constraints on landmark points, can be used interactively to prevent leakage of the surface

Assessment of visual quality and spatial accuracy of fast anisotropic diffusion and scan conversion algorithms for real-time three-dimensional spherical ultrasound

Three-dimensional ultrasound machines based on matrix phased-array transducers are gaining predominance for real-time dynamic screening in cardiac and obstetric practice. These transducers array acquire three-dimensional data in spherical coordinates along lines tiled in azimuth and elevation angles at incremental depth. This study aims at evaluating fast filtering and scan conversion algorithms applied in the spherical domain prior to visualization into Cartesian coordinates for visual quality and spatial measurement accuracy. Fast 3d scan conversion algorithms were implemented and with different order interpolation kernels. Downsizing and smoothing of sampling artifacts were integrated in the scan conversion process. In addition, a denoising scheme for spherical coordinate data with 3d anisotropic diffusion was implemented and applied prior to scan conversion to improve image quality. Reconstruction results under different parameter settings, such as different interpolation kernels, scaling factor, smoothing options, and denoising, are reported. Image quality was evaluated on several data sets via visual inspections and measurements of cylinder objects dimensions. Error measurements of the cylinder's radius, reported in this paper, show that the proposed fast scan conversion algorithm can correctly reconstruct three-dimensional ultrasound in Cartesian coordinates under tuned parameter settings. Denoising via three-dimensional anisotropic diffusion was able to greatly improve the quality of resampled data without affecting the accuracy of spatial information after the modification of the introduction of a variable gradient threshold parameter

Tomographic reconstruction with non-linear diagonal estimators

In tomographic reconstruction, the inversion of the Radon transform in the presence of noise is numerically unstable. Reconstruction estimators are studied where the regularization is performed by a thresholding in a wavelet or wavelet packet decomposition. These estimators are efficient and their optimality can be established when the decomposition provides a near-diagonalization of the inverse Radon transform operator and a compact representation of the object to be recovered. Several new estimators are investigated in different decomposition. First numerical results already exhibit a strong metrical and perceptual improvement over current reconstruction methods. These estimators are implemented with fast non-iterative algorithms, and are expected to outperform Filtered Back-Projection and iterative procedures for PET, SPECT and X-ray CT devices

State of the Art of Level Set Methods in Segmentation and Registration of Medical Imaging Modalities

Segmentation of medical images is an important step in various applications such as visualization, quantitative analysis and image-guided surgery. Numerous segmentation methods have been developed in the past two decades for extraction of organ contours on medical images. Low-level segmentation methods, such as pixel-based clustering, region growing, and filter-based edge detection, require additional pre-processing and post-processing as well as considerable amounts of expert intervention or information of the objects of interest. Furthermore the subsequent analysis of segmented objects is hampered by the primitive, pixel or voxel level representations from those region-based segmentation. Deformable models, on the other hand, provide an explicit representation of the boundary and the shape of the object. They combine several desirable features such as inherent connectivity and smoothness, which counteract noise and boundary irregularities, as well as the ability to incorporate knowledge about the object of interest. However, parametric deformable models have two main limitations. First, in situations where the initial model and desired object boundary differ greatly in size and shape, the model must be re-parameterized dynamically to faithfully recover the object boundary. The second limitation is that it has difficulty dealing with topological adaptation such as splitting or merging model parts, a useful property for recovering either multiple objects or objects with unknown topology. This difficulty is caused by the fact that a new parameterization must be constructed whenever topology change occurs, which requires sophisticated schemes. Level set deformable models, also referred to as geometric deformable models, provide an elegant solution to address the primary limitations of parametric deformable models. These methods have drawn a great deal of attention since their introduction in 1988. Advantages of the contour implicit formulation of the deformable model over parametric formulation include: (1) no parameterization of the contour, (2) topological flexibility, (3) good numerical stability, (4) straightforward extension of the 2D formulation to n-D. Recent reviews on the subject include papers from Suri. In this chapter we give a general overview of the level set segmentation methods with emphasize on new frameworks recently introduced in the context of medical imaging problems. We then introduce novel approaches that aim at combining segmentation and registration in a level set formulation. Finally we review a selective set of clinical works with detailed validation of the level set methods for several clinical applications

Regularization in tomographic reconstruction using thresholding estimators

In tomographic medical devices such as SPECT or PET cameras, image reconstruction is an unstable inverse problem, due to the presence of additive noise. A new family of regularization methods for reconstruction, based on a thresholding procedure in wavelet and wavelet packet decompositions, is studied. This approach is based on the fact that the decompositions provide a near-diagonalization of the inverse Radon transform and of the prior information on medical images. An optimal wavelet packet decomposition is adaptively chosen for the specific image to be restored. Corresponding algorithms have been developed for both 2-D and full 3-D reconstruction. These procedures are fast, non-iterative, flexible, and their performance outperforms Filtered Back-Projection and iterative procedures such as OS-EM

Multi-Phase Three-Dimensional Level Set Segmentation of Brain MRI

Segmentation of cortical structures on clinical brain MRI data is applied for clinical study of depression on elderly subjects. Segmentation of clinical MRI data is more challenging than with simulated data due to intensity overlap among cortical structures and non-homogeneity within each tissue

Segmentation and quantitative evaluation of brain MRI data with a multi-phase three-dimensional implicit deformable model

Segmentation of three-dimensional anatomical brain images into tissue classes has applications in both clinical and research settings. This paper presents the implementation and quantitative evaluation of a four-phase three-dimensional active contour implemented with a level set framework for automated segmentation of brain MRIs. The segmentation algorithm performs an optimal partitioning of three-dimensional data based on homogeneity measures that naturally evolves to the extraction of different tissue types in the brain. Random seed initialization was used to speed up numerical computation and avoid the need for a priori information. This random initialization ensures robustness of the method to variation of user expertise, biased a priori information and errors in input information that could be influenced by variations in image quality. Experimentation on three MRI brain data sets showed that an optimal partitioning successfully labeled regions that accurately identified white matter, gray matter and cerebrospinal fluid in the ventricles. Quantitative evaluation of the segmentation was performed with comparison to manually labeled data and computed false positive and false negative assignments of voxels for the three organs. We report high accuracy for the two comparison cases. These results demonstrate the efficiency and flexibility of this segmentation framework to perform the challenging task of automatically extracting brain tissue volume contours

Tracking motor units longitudinally across experimental sessions with high-density surface electromyography.

KEY POINTS: Classic motor unit (MU) recording and analysis methods do not allow the same MUs to be tracked across different experimental sessions, and therefore, there is limited experimental evidence on the adjustments in MU properties following training or during the progression of neuromuscular disorders. We propose a new processing method to track the same MUs across experimental sessions (separated by weeks) by using high-density surface electromyography. The application of the proposed method in two experiments showed that individual MUs can be identified reliably in measurements separated by weeks and that changes in properties of the tracked MUs across experimental sessions can be identified with high sensitivity. These results indicate that the behaviour and properties of the same MUs can be monitored across multiple testing sessions. The proposed method opens new possibilities in the understanding of adjustments in motor unit properties due to training interventions or the progression of pathologies. ABSTRACT: A new method is proposed for tracking individual motor units (MUs) across multiple experimental sessions on different days. The technique is based on a novel decomposition approach for high-density surface electromyography and was tested with two experimental studies for reliability and sensitivity. Experiment I (reliability): ten participants performed isometric knee extensions at 10, 30, 50 and 70% of their maximum voluntary contraction (MVC) force in three sessions, each separated by 1 week. Experiment II (sensitivity): seven participants performed 2 weeks of endurance training (cycling) and were tested pre-post intervention during isometric knee extensions at 10 and 30% MVC. The reliability (Experiment I) and sensitivity (Experiment II) of the measured MU properties were compared for the MUs tracked across sessions, with respect to all MUs identified in each session. In Experiment I, on average 38.3% and 40.1% of the identified MUs could be tracked across two sessions (1 and 2 weeks apart), for the vastus medialis and vastus lateralis, respectively. Moreover, the properties of the tracked MUs were more reliable across sessions than those of the full set of identified MUs (intra-class correlation coefficients ranged between 0.63-0.99 and 0.39-0.95, respectively). In Experiment II, ∼40% of the MUs could be tracked before and after the training intervention and training-induced changes in MU conduction velocity had an effect size of 2.1 (tracked MUs) and 1.5 (group of all identified motor units). These results show the possibility of monitoring MU properties longitudinally to document the effect of interventions or the progression of neuromuscular disorders