Deformable Model Approach Research Articles

Water Cycle Bat Algorithm and Dictionary-Based Deformable Model for Lung Tumor Segmentation.

Among the different types of cancers, lung cancer is one of the widespread diseases which causes the highest number of deaths every year. The early detection of lung cancer is very essential for increasing the survival rate in patients. Although computed tomography (CT) is the preferred choice for lungs imaging, sometimes CT images may produce less tumor visibility regions and unconstructive rates in tumor portions. Hence, the development of an efficient segmentation technique is necessary. In this paper, water cycle bat algorithm- (WCBA-) based deformable model approach is proposed for lung tumor segmentation. In the preprocessing stage, a median filter is used to remove the noise from the input image and to segment the lung lobe regions, and Bayesian fuzzy clustering is applied. In the proposed method, deformable model is modified by the dictionary-based algorithm to segment the lung tumor accurately. In the dictionary-based algorithm, the update equation is modified by the proposed WCBA and is designed by integrating water cycle algorithm (WCA) and bat algorithm (BA).

A Framework for Automated Spine and Vertebrae Interpolation-Based Detection and Model-Based Segmentation.

Automated and semi-automated detection and segmentation of spinal and vertebral structures from computed tomography (CT) images is a challenging task due to a relatively high degree of anatomical complexity, presence of unclear boundaries and articulation of vertebrae with each other, as well as due to insufficient image spatial resolution, partial volume effects, presence of image artifacts, intensity variations and low signal-to-noise ratio. In this paper, we describe a novel framework for automated spine and vertebrae detection and segmentation from 3-D CT images. A novel optimization technique based on interpolation theory is applied to detect the location of the whole spine in the 3-D image and, using the obtained location of the whole spine, to further detect the location of individual vertebrae within the spinal column. The obtained vertebra detection results represent a robust and accurate initialization for the subsequent segmentation of individual vertebrae, which is performed by an improved shape-constrained deformable model approach. The framework was evaluated on two publicly available CT spine image databases of 50 lumbar and 170 thoracolumbar vertebrae. Quantitative comparison against corresponding reference vertebra segmentations yielded an overall mean centroid-to-centroid distance of 1.1 mm and Dice coefficient of 83.6% for vertebra detection, and an overall mean symmetric surface distance of 0.3 mm and Dice coefficient of 94.6% for vertebra segmentation. The results indicate that by applying the proposed automated detection and segmentation framework, vertebrae can be successfully detected and accurately segmented in 3-D from CT spine images.

CeleST: Computer Vision Software for Quantitative Analysis of C. elegans Swim Behavior Reveals Novel Features of Locomotion

In the effort to define genes and specific neuronal circuits that control behavior and plasticity, the capacity for high-precision automated analysis of behavior is essential. We report on comprehensive computer vision software for analysis of swimming locomotion of C. elegans, a simple animal model initially developed to facilitate elaboration of genetic influences on behavior. C. elegans swim test software CeleST tracks swimming of multiple animals, measures 10 novel parameters of swim behavior that can fully report dynamic changes in posture and speed, and generates data in several analysis formats, complete with statistics. Our measures of swim locomotion utilize a deformable model approach and a novel mathematical analysis of curvature maps that enable even irregular patterns and dynamic changes to be scored without need for thresholding or dropping outlier swimmers from study. Operation of CeleST is mostly automated and only requires minimal investigator interventions, such as the selection of videotaped swim trials and choice of data output format. Data can be analyzed from the level of the single animal to populations of thousands. We document how the CeleST program reveals unexpected preferences for specific swim “gaits” in wild-type C. elegans, uncovers previously unknown mutant phenotypes, efficiently tracks changes in aging populations, and distinguishes “graceful” from poor aging. The sensitivity, dynamic range, and comprehensive nature of CeleST measures elevate swim locomotion analysis to a new level of ease, economy, and detail that enables behavioral plasticity resulting from genetic, cellular, or experience manipulation to be analyzed in ways not previously possible.

Automated segmentation and analysis of normal and osteoarthritic knee menisci from magnetic resonance images – data from the Osteoarthritis Initiative

To validate an automatic scheme for the segmentation and quantitative analysis of the medial meniscus (MM) and lateral meniscus (LM) in magnetic resonance (MR) images of the knee. We analysed sagittal water-excited double-echo steady-state MR images of the knee from a subset of the Osteoarthritis Initiative (OAI) cohort. The MM and LM were automatically segmented in the MR images based on a deformable model approach. Quantitative parameters including volume, subluxation and tibial-coverage were automatically calculated for comparison (Wilcoxon tests) between knees with variable radiographic osteoarthritis (rOA), medial and lateral joint space narrowing (mJSN, lJSN) and pain. Automatic segmentations and estimated parameters were evaluated for accuracy using manual delineations of the menisci in 88 pathological knee MR examinations at baseline and 12 months time-points. The median (95% confidence-interval (CI)) Dice similarity index (DSI) (2 ∗|Auto ∩ Manual|/(|Auto|+|Manual|)∗ 100) between manual and automated segmentations for the MM and LM volumes were 78.3% (75.0-78.7), 83.9% (82.1-83.9) at baseline and 75.3% (72.8-76.9), 83.0% (81.6-83.5) at 12 months. Pearson coefficients between automatic and manual segmentation parameters ranged from r = 0.70 to r = 0.92. MM in rOA/mJSN knees had significantly greater subluxation and smaller tibial-coverage than no-rOA/no-mJSN knees. LM in rOA knees had significantly greater volumes and tibial-coverage than no-rOA knees. Our automated method successfully segmented the menisci in normal and osteoarthritic knee MR images and detected meaningful morphological differences with respect to rOA and joint space narrowing (JSN). Our approach will facilitate analyses of the menisci in prospective MR cohorts such as the OAI for investigations into pathophysiological changes occurring in early osteoarthritis (OA) development.

Comparative Visualization of Molecular Surfaces Using Deformable Models

AbstractThe comparison of molecular surface attributes is of interest for computer aided drug design and the analysis of biochemical simulations. Due to the non‐rigid nature of molecular surfaces, partial shape matching is feasible for mapping two surfaces onto each other. We present a novel technique to obtain a mapping relation between two surfaces using a deformable model approach. This relation is used for pair‐wise comparison of local surface attributes (e.g. electrostatic potential). We combine the difference value as well as the comparability as derived from the local matching quality in a 3D molecular visualization by mapping them to color. A 2D matrix shows the global dissimilarity in an overview of different data sets in an ensemble. We apply our visualizations to simulation results provided by collaborators from the field of biochemistry to evaluate the effectiveness of our results.

Multiple-object geometric deformable model for segmentation of macular OCT.

Optical coherence tomography (OCT) is the de facto standard imaging modality for ophthalmological assessment of retinal eye disease, and is of increasing importance in the study of neurological disorders. Quantification of the thicknesses of various retinal layers within the macular cube provides unique diagnostic insights for many diseases, but the capability for automatic segmentation and quantification remains quite limited. While manual segmentation has been used for many scientific studies, it is extremely time consuming and is subject to intra- and inter-rater variation. This paper presents a new computational domain, referred to as flat space, and a segmentation method for specific retinal layers in the macular cube using a recently developed deformable model approach for multiple objects. The framework maintains object relationships and topology while preventing overlaps and gaps. The algorithm segments eight retinal layers over the whole macular cube, where each boundary is defined with subvoxel precision. Evaluation of the method on single-eye OCT scans from 37 subjects, each with manual ground truth, shows improvement over a state-of-the-art method.

Correlation Based 3-D Segmentation of the Left Ventricle in Pediatric Echocardiographic Images Using Radio-Frequency Data

Clinical diagnosis of heart disease might be substantially supported by automated segmentation of the endocardial surface in three-dimensional (3-D) echographic images. Because of the poor echogenicity contrast between blood and myocardial tissue in some regions and the inherent speckle noise, automated analysis of these images is challenging. A priori knowledge on the shape of the heart cannot always be relied on, e.g., in children with congenital heart disease, segmentation should be based on the echo features solely. The objective of this study was to investigate the merit of using temporal cross-correlation of radio-frequency (RF) data for automated segmentation of 3-D echocardiographic images. Maximum temporal cross-correlation (MCC) values were determined locally from the RF-data using an iterative 3-D technique. MCC values as well as a combination of MCC values and adaptive filtered, demodulated RF-data were used as an additional, external force in a deformable model approach to segment the endocardial surface and were tested against manually segmented surfaces. Results on 3-D full volume images (Philips, iE33) of 10 healthy children demonstrate that MCC values derived from the RF signal yield a useful parameter to distinguish between blood and myocardium in regions with low echogenicity contrast and incorporation of MCC improves the segmentation results significantly. Further investigation of the MCC over the whole cardiac cycle is required to exploit the full benefit of it for automated segmentation.

Automatic Segmentation of Pelvic Structures From Magnetic Resonance Images for Prostate Cancer Radiotherapy

Target-volume and organ-at-risk delineation is a time-consuming task in radiotherapy planning. The development of automated segmentation tools remains problematic, because of pelvic organ shape variability. We evaluate a three-dimensional (3D), deformable-model approach and a seeded region-growing algorithm for automatic delineation of the prostate and organs-at-risk on magnetic resonance images. Manual and automatic delineation were compared in 24 patients using a sagittal T2-weighted (T2-w) turbo spin echo (TSE) sequence and an axial T1-weighted (T1-w) 3D fast-field echo (FFE) or TSE sequence. For automatic prostate delineation, an organ model-based method was used. Prostates without seminal vesicles were delineated as the clinical target volume (CTV). For automatic bladder and rectum delineation, a seeded region-growing method was used. Manual contouring was considered the reference method. The following parameters were measured: volume ratio (Vr) (automatic/manual), volume overlap (Vo) (ratio of the volume of intersection to the volume of union; optimal value = 1), and correctly delineated volume (Vc) (percent ratio of the volume of intersection to the manually defined volume; optimal value = 100). For the CTV, the Vr, Vo, and Vc were 1.13 (+/-0.1 SD), 0.78 (+/-0.05 SD), and 94.75 (+/-3.3 SD), respectively. For the rectum, the Vr, Vo, and Vc were 0.97 (+/-0.1 SD), 0.78 (+/-0.06 SD), and 86.52 (+/-5 SD), respectively. For the bladder, the Vr, Vo, and Vc were 0.95 (+/-0.03 SD), 0.88 (+/-0.03 SD), and 91.29 (+/-3.1 SD), respectively. Our results show that the organ-model method is robust, and results in reproducible prostate segmentation with minor interactive corrections. For automatic bladder and rectum delineation, magnetic resonance imaging soft-tissue contrast enables the use of region-growing methods.

Three-Dimensional Face Recognition in the Presence of Facial Expressions: An Annotated Deformable Model Approach

In this paper, we present the computational tools and a hardware prototype for 3D face recognition. Full automation is provided through the use of advanced multistage alignment algorithms, resilience to facial expressions by employing a deformable model framework, and invariance to 3D capture devices through suitable preprocessing steps. In addition, scalability in both time and space is achieved by converting 3D facial scans into compact metadata. We present our results on the largest known, and now publicly available, Face Recognition Grand Challenge 3D facial database consisting of several thousand scans. To the best of our knowledge, this is the highest performance reported on the FRGC v2 database for the 3D modality.

Statistical Multi-Object Shape Models

The shape of a population of geometric entities is characterized by both the common geometry of the population and the variability among instances. In the deformable model approach, it is described by a probabilistic model on the deformations that transform a common template into various instances. To capture shape features at various scale levels, we have been developing an object-based multi-scale framework, in which a geometric entity is represented by a series of deformations with different locations and degrees of locality. Each deformation describes a residue from the information provided by previous steps. In this paper, we present how to build statistical shape models of multi-object complexes with such properties based on medial representations and explain how this may lead to more effective shape descriptions as well as more efficient statistical training procedures. We illustrate these ideas with a statistical shape model for a pair of pubic bones and show some preliminary results on using it as a prior in medical image segmentation.

On the digital trail of mobile cells

Cell migration is a field of intense current research, where biologists increasingly rely on methods and expertise from physics and engineering. Signal processing approaches can contribute significantly to this research, most notably to help analyze the exploding quantity of imaging data produced with standard and new microscopy techniques. In this article, we first provide a brief background on the importance of understanding cell movements, then review a selection of current efforts on tracking moving cells, with an emphasis on deformable model approaches (some ideas expressed in this article have been previously discussed. We will point out some of the main difficulties posed by cellular imaging, discuss advantages and limitations of different tracking techniques, and suggest a few directions for future advances

Connectivity-based local adaptive thresholding for carotid artery segmentation using MRA images

The computer algorithms for the delineation of anatomical structures and other regions of interest on the medical imagery are important component in assisting and automating specific radiological tasks. In addition, the segmentation of region is an important first step for variety image related application and visualization tasks. In this paper, we propose a fast and automated connectivity-based local adaptive thresholding (CLAT) algorithm to segment the carotid artery in sequence medical imagery. This algorithm provides the new feature that is the circumscribed quadrangle on the segmented carotid artery for region-of-interest (ROI) determination. By using the preserved connectivity between consecutive slice images, the size of the ROI is adjusted like a moving window according to the segmentation result of previous slice image. The histogram is prepared for each ROI and then smoothed by local averaging for the threshold selection. The threshold value for carotid artery segmentation is locally selected on each slice image and is adaptively determined through the sequence image. In terms of automated features and computing time, this algorithm is more effective than region growing and deformable model approaches. This algorithm is also applicable to segment the cylinder shape structures and tree-like blood vessels such as renal artery and coronary artery in the medical imagery. Experiments have been conducted on synthesized images, phantom and clinical data sets with various Gaussian noise.

An Algorithm For Segmentation Under Interpolation Conditions Using Deformable Models

We present a deformable model technique for geophysical image analysis. Deformable model approaches have been developed extensively in the literature, including prior applications to geophysical or medical image interpretation. In this paper we propose a method to segment a geophysical image under interpolation conditions (well data). The originality of this segmentation method is that it considers the deformable model as a set of articulated curves, which corresponds to the interfaces between different regions. Moreover, the interpolation conditions permit some geometric constraints to be made on the model. The theoretical aspect of the method is given in the case of a three dimensional image. Numerical results are given.

Tomographic reconstruction using 3D deformable models

We address the issue of reconstructing the shape of an object with uniform interior activity from a set of projections. We estimate directly from projection data the position of a triangulated surface describing the boundary of the object while incorporating prior knowledge about the unknown shape. This inverse problem is addressed in a Bayesian framework using the maximum a posteriori (MAP) estimate for the reconstruction. The derivatives needed for the gradient-based optimization of the model parameters are obtained using the adjoint differentiation technique. We present results from a numerical simulation of a dynamic cardiac imaging study. A first-pass exam is simulated with a numerical phantom of the right ventricle using the measured system response of the University of Arizona FASTSPECT imager, which consists of 24 detectors. We demonstrate the usefulness of our approach by reconstructing the shape of the ventricle from 10 000 counts. The comparison with an ML-EM result shows the usefulness of the deformable model approach.