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1.  Clutter Mitigation in Echocardiography Using Sparse Signal Separation 
In ultrasound imaging, clutter artifacts degrade images and may cause inaccurate diagnosis. In this paper, we apply a method called Morphological Component Analysis (MCA) for sparse signal separation with the objective of reducing such clutter artifacts. The MCA approach assumes that the two signals in the additive mix have each a sparse representation under some dictionary of atoms (a matrix), and separation is achieved by finding these sparse representations. In our work, an adaptive approach is used for learning the dictionary from the echo data. MCA is compared to Singular Value Filtering (SVF), a Principal Component Analysis- (PCA-) based filtering technique, and to a high-pass Finite Impulse Response (FIR) filter. Each filter is applied to a simulated hypoechoic lesion sequence, as well as experimental cardiac ultrasound data. MCA is demonstrated in both cases to outperform the FIR filter and obtain results comparable to the SVF method in terms of contrast-to-noise ratio (CNR). Furthermore, MCA shows a lower impact on tissue sections while removing the clutter artifacts. In experimental heart data, MCA obtains in our experiments clutter mitigation with an average CNR improvement of 1.33 dB.
PMCID: PMC4495184  PMID: 26199622
2.  Automated Feature Extraction in Brain Tumor by Magnetic Resonance Imaging Using Gaussian Mixture Models 
This paper presents a novel method for Glioblastoma (GBM) feature extraction based on Gaussian mixture model (GMM) features using MRI. We addressed the task of the new features to identify GBM using T1 and T2 weighted images (T1-WI, T2-WI) and Fluid-Attenuated Inversion Recovery (FLAIR) MR images. A pathologic area was detected using multithresholding segmentation with morphological operations of MR images. Multiclassifier techniques were considered to evaluate the performance of the feature based scheme in terms of its capability to discriminate GBM and normal tissue. GMM features demonstrated the best performance by the comparative study using principal component analysis (PCA) and wavelet based features. For the T1-WI, the accuracy performance was 97.05% (AUC = 92.73%) with 0.00% missed detection and 2.95% false alarm. In the T2-WI, the same accuracy (97.05%, AUC = 91.70%) value was achieved with 2.95% missed detection and 0.00% false alarm. In FLAIR mode the accuracy decreased to 94.11% (AUC = 95.85%) with 0.00% missed detection and 5.89% false alarm. These experimental results are promising to enhance the characteristics of heterogeneity and hence early treatment of GBM.
PMCID: PMC4469084  PMID: 26136774
4.  Automatic Extraction of Blood Vessels in the Retinal Vascular Tree Using Multiscale Medialness 
We propose an algorithm for vessel extraction in retinal images. The first step consists of applying anisotropic diffusion filtering in the initial vessel network in order to restore disconnected vessel lines and eliminate noisy lines. In the second step, a multiscale line-tracking procedure allows detecting all vessels having similar dimensions at a chosen scale. Computing the individual image maps requires different steps. First, a number of points are preselected using the eigenvalues of the Hessian matrix. These points are expected to be near to a vessel axis. Then, for each preselected point, the response map is computed from gradient information of the image at the current scale. Finally, the multiscale image map is derived after combining the individual image maps at different scales (sizes). Two publicly available datasets have been used to test the performance of the suggested method. The main dataset is the STARE project's dataset and the second one is the DRIVE dataset. The experimental results, applied on the STARE dataset, show a maximum accuracy average of around 94.02%. Also, when performed on the DRIVE database, the maximum accuracy average reaches 91.55%.
PMCID: PMC4421077  PMID: 25977682
5.  Recovering 3D Shape with Absolute Size from Endoscope Images Using RBF Neural Network 
Medical diagnosis judges the status of polyp from the size and the 3D shape of the polyp from its medical endoscope image. However the medical doctor judges the status empirically from the endoscope image and more accurate 3D shape recovery from its 2D image has been demanded to support this judgment. As a method to recover 3D shape with high speed, VBW (Vogel-Breuß-Weickert) model is proposed to recover 3D shape under the condition of point light source illumination and perspective projection. However, VBW model recovers the relative shape but there is a problem that the shape cannot be recovered with the exact size. Here, shape modification is introduced to recover the exact shape with modification from that with VBW model. RBF-NN is introduced for the mapping between input and output. Input is given as the output of gradient parameters of VBW model for the generated sphere. Output is given as the true gradient parameters of true values of the generated sphere. Learning mapping with NN can modify the gradient and the depth can be recovered according to the modified gradient parameters. Performance of the proposed approach is confirmed via computer simulation and real experiment.
PMCID: PMC4408635  PMID: 25949235
6.  Edge Detection in Digital Images Using Dispersive Phase Stretch Transform 
We describe a new computational approach to edge detection and its application to biomedical images. Our digital algorithm transforms the image by emulating the propagation of light through a physical medium with specific warped diffractive property. We show that the output phase of the transform reveals transitions in image intensity and can be used for edge detection.
PMCID: PMC4386678  PMID: 25878656
7.  Classifying Dementia Using Local Binary Patterns from Different Regions in Magnetic Resonance Images 
Dementia is an evolving challenge in society, and no disease-modifying treatment exists. Diagnosis can be demanding and MR imaging may aid as a noninvasive method to increase prediction accuracy. We explored the use of 2D local binary pattern (LBP) extracted from FLAIR and T1 MR images of the brain combined with a Random Forest classifier in an attempt to discern patients with Alzheimer's disease (AD), Lewy body dementia (LBD), and normal controls (NC). Analysis was conducted in areas with white matter lesions (WML) and all of white matter (WM). Results from 10-fold nested cross validation are reported as mean accuracy, precision, and recall with standard deviation in brackets. The best result we achieved was in the two-class problem NC versus AD + LBD with total accuracy of 0.98 (0.04). In the three-class problem AD versus LBD versus NC and the two-class problem AD versus LBD, we achieved 0.87 (0.08) and 0.74 (0.16), respectively. The performance using 3DT1 images was notably better than when using FLAIR images. The results from the WM region gave similar results as in the WML region. Our study demonstrates that LBP texture analysis in brain MR images can be successfully used for computer based dementia diagnosis.
PMCID: PMC4385607  PMID: 25873943
8.  Optic Disc Segmentation by Balloon Snake with Texture from Color Fundus Image 
A well-established method for diagnosis of glaucoma is the examination of the optic nerve head based on fundus image as glaucomatous patients tend to have larger cup-to-disc ratios. The difficulty of optic segmentation is due to the fuzzy boundaries and peripapillary atrophy (PPA). In this paper a novel method for optic nerve head segmentation is proposed. It uses template matching to find the region of interest (ROI). The method of vessel erasing in the ROI is based on PDE inpainting which will make the boundary smoother. A novel optic disc segmentation approach using image texture is explored in this paper. A cluster method based on image texture is employed before the optic disc segmentation step to remove the edge noise such as cup boundary and vessels. We replace image force in the snake with image texture and the initial contour of the balloon snake is inside the optic disc to avoid the PPA. The experimental results show the superior performance of the proposed method when compared to some traditional segmentation approaches. An average segmentation dice coefficient of 94% has been obtained.
PMCID: PMC4378594  PMID: 25861249
9.  High Performance GPU-Based Fourier Volume Rendering 
Fourier volume rendering (FVR) is a significant visualization technique that has been used widely in digital radiography. As a result of its 𝒪(N2log⁡N) time complexity, it provides a faster alternative to spatial domain volume rendering algorithms that are 𝒪(N3) computationally complex. Relying on the Fourier projection-slice theorem, this technique operates on the spectral representation of a 3D volume instead of processing its spatial representation to generate attenuation-only projections that look like X-ray radiographs. Due to the rapid evolution of its underlying architecture, the graphics processing unit (GPU) became an attractive competent platform that can deliver giant computational raw power compared to the central processing unit (CPU) on a per-dollar-basis. The introduction of the compute unified device architecture (CUDA) technology enables embarrassingly-parallel algorithms to run efficiently on CUDA-capable GPU architectures. In this work, a high performance GPU-accelerated implementation of the FVR pipeline on CUDA-enabled GPUs is presented. This proposed implementation can achieve a speed-up of 117x compared to a single-threaded hybrid implementation that uses the CPU and GPU together by taking advantage of executing the rendering pipeline entirely on recent GPU architectures.
PMCID: PMC4381991  PMID: 25866499
10.  Incidence of Brain Abnormalities Detected on Preoperative Brain MR Imaging and Their Effect on the Outcome of Cochlear Implantation in Children with Sensorineural Hearing Loss 
The incidence of sensorineural hearing loss (SNHL) increased gradually in the past decades. High-resolution computed tomography (HRCT) and magnetic resonance (MR) imaging, as an important part of preimplantation evaluation for children with SNHL, could provide the detailed information about the inner ear, the vestibulocochlear nerve, and the brain, so as to select suitable candidate for cochlear implantation (CI). Brain abnormalities were not rare in the brain MR imaging of SNHL children; however, its influence on the effect of CI has not been clarified. After retrospectively analyzing the CT and MR imaging of 157 children with SNHL that accepted preoperative evaluation from June 2011 to February 2013 in our hospital and following them during a period of 14.09 ± 5.08 months, we found that the white matter change, which might be associated with the history of medical condition, was the most common brain abnormality. Usually CI was still beneficial to the children with brain abnormalities, and the short-term hearing improvement could be achieved. Further study with more patients and longer follow-up time was needed to confirm our results.
PMCID: PMC4320865  PMID: 25685142
11.  Automated Classification of Glandular Tissue by Statistical Proximity Sampling 
Due to the complexity of biological tissue and variations in staining procedures, features that are based on the explicit extraction of properties from subglandular structures in tissue images may have difficulty generalizing well over an unrestricted set of images and staining variations. We circumvent this problem by an implicit representation that is both robust and highly descriptive, especially when combined with a multiple instance learning approach to image classification. The new feature method is able to describe tissue architecture based on glandular structure. It is based on statistically representing the relative distribution of tissue components around lumen regions, while preserving spatial and quantitative information, as a basis for diagnosing and analyzing different areas within an image. We demonstrate the efficacy of the method in extracting discriminative features for obtaining high classification rates for tubular formation in both healthy and cancerous tissue, which is an important component in Gleason and tubule-based Elston grading. The proposed method may be used for glandular classification, also in other tissue types, in addition to general applicability as a region-based feature descriptor in image analysis where the image represents a bag with a certain label (or grade) and the region-based feature vectors represent instances.
PMCID: PMC4312655  PMID: 25685143
12.  Computer-Assisted Segmentation of Videocapsule Images Using Alpha-Divergence-Based Active Contour in the Framework of Intestinal Pathologies Detection 
Visualization of the entire length of the gastrointestinal tract through natural orifices is a challenge for endoscopists. Videoendoscopy is currently the “gold standard” technique for diagnosis of different pathologies of the intestinal tract. Wireless capsule endoscopy (WCE) has been developed in the 1990s as an alternative to videoendoscopy to allow direct examination of the gastrointestinal tract without any need for sedation. Nevertheless, the systematic postexamination by the specialist of the 50,000 (for the small bowel) to 150,000 images (for the colon) of a complete acquisition using WCE remains time-consuming and challenging due to the poor quality of WCE images. In this paper, a semiautomatic segmentation for analysis of WCE images is proposed. Based on active contour segmentation, the proposed method introduces alpha-divergences, a flexible statistical similarity measure that gives a real flexibility to different types of gastrointestinal pathologies. Results of segmentation using the proposed approach are shown on different types of real-case examinations, from (multi)polyp(s) segmentation, to radiation enteritis delineation.
PMCID: PMC4281406  PMID: 25587264
13.  Ischemic Stroke Detection System with a Computer-Aided Diagnostic Ability Using an Unsupervised Feature Perception Enhancement Method 
We propose an ischemic stroke detection system with a computer-aided diagnostic ability using a four-step unsupervised feature perception enhancement method. In the first step, known as preprocessing, we use a cubic curve contrast enhancement method to enhance image contrast. In the second step, we use a series of methods to extract the brain tissue image area identified during preprocessing. To detect abnormal regions in the brain images, we propose using an unsupervised region growing algorithm to segment the brain tissue area. The brain is centered on a horizontal line and the white matter of the brain's inner ring is split into eight regions. In the third step, we use a coinciding regional location method to find the hybrid area of locations where a stroke may have occurred in each cerebral hemisphere. Finally, we make corrections and mark the stroke area with red color. In the experiment, we tested the system on 90 computed tomography (CT) images from 26 patients, and, with the assistance of two radiologists, we proved that our proposed system has computer-aided diagnostic capabilities. Our results show an increased stroke diagnosis sensitivity of 83% in comparison to 31% when radiologists use conventional diagnostic images.
PMCID: PMC4276348  PMID: 25610453
14.  Coronary Plaque Boundary Enhancement in IVUS Image by Using a Modified Perona-Malik Diffusion Filter 
We propose a modified Perona-Malik diffusion (PMD) filter to enhance a coronary plaque boundary by considering the conditions peculiar to an intravascular ultrasound (IVUS) image. The IVUS image is commonly used for a diagnosis of acute coronary syndrome (ACS). The IVUS image is however very grainy due to heavy speckle noise. When the normal PMD filter is applied for speckle noise reduction in the IVUS image, the coronary plaque boundary becomes vague. For this problem, we propose a modified PMD filter which is designed in special reference to the coronary plaque boundary detection. It can then not only reduce the speckle noise but also enhance clearly the coronary plaque boundary. After applying the modified PMD filter to the IVUS image, the coronary plaque boundaries are successfully detected further by applying the Takagi-Sugeno fuzzy model. The accuracy of the proposed method has been confirmed numerically by the experiments.
PMCID: PMC4259135  PMID: 25506357
15.  A Comparative Study of Contemporary Color Tongue Image Extraction Methods Based on HSI 
Tongue image with coating is of important clinical diagnostic meaning, but traditional tongue image extraction method is not competent for extraction of tongue image with thick coating. In this paper, a novel method is suggested, which applies multiobjective greedy rules and makes fusion of color and space information in order to extract tongue image accurately. A comparative study of several contemporary tongue image extraction methods is also made from the aspects of accuracy and efficiency. As the experimental results show, geodesic active contour is quite slow and not accurate, the other 3 methods achieve fairly good segmentation results except in the case of the tongue with thick coating, our method achieves ideal segmentation results whatever types of tongue images are, and efficiency of our method is acceptable for the application of quantitative check of tongue image.
PMCID: PMC4258337  PMID: 25505903
16.  Microwave Radar Imaging of Heterogeneous Breast Tissue Integrating A Priori Information 
Conventional radar-based image reconstruction techniques fail when they are applied to heterogeneous breast tissue, since the underlying in-breast relative permittivity is unknown or assumed to be constant. This results in a systematic error during the process of image formation. A recent trend in microwave biomedical imaging is to extract the relative permittivity from the object under test to improve the image reconstruction quality and thereby to enhance the diagnostic assessment. In this paper, we present a novel radar-based methodology for microwave breast cancer detection in heterogeneous breast tissue integrating a 3D map of relative permittivity as a priori information. This leads to a novel image reconstruction formulation where the delay-and-sum focusing takes place in time rather than range domain. Results are shown for a heterogeneous dense (class-4) and a scattered fibroglandular (class-2) numerical breast phantom using Bristol's 31-element array configuration.
PMCID: PMC4243481  PMID: 25435861
17.  Application of Temperature-Dependent Fluorescent Dyes to the Measurement of Millimeter Wave Absorption in Water Applied to Biomedical Experiments 
Temperature sensitivity of the fluorescence intensity of the organic dyes solutions was used for noncontact measurement of the electromagnetic millimeter wave absorption in water. By using two different dyes with opposite temperature effects, local temperature increase in the capillary that is placed inside a rectangular waveguide in which millimeter waves propagate was defined. The application of this noncontact temperature sensing is a simple and novel method to detect temperature change in small biological objects.
PMCID: PMC4244683  PMID: 25435859
18.  Real-Time Evaluation of Breast Self-Examination Using Computer Vision 
Breast cancer is the most common cancer among women worldwide and breast self-examination (BSE) is considered as the most cost-effective approach for early breast cancer detection. The general objective of this paper is to design and develop a computer vision algorithm to evaluate the BSE performance in real-time. The first stage of the algorithm presents a method for detecting and tracking the nipples in frames while a woman performs BSE; the second stage presents a method for localizing the breast region and blocks of pixels related to palpation of the breast, and the third stage focuses on detecting the palpated blocks in the breast region. The palpated blocks are highlighted at the time of BSE performance. In a correct BSE performance, all blocks must be palpated, checked, and highlighted, respectively. If any abnormality, such as masses, is detected, then this must be reported to a doctor to confirm the presence of this abnormality and proceed to perform other confirmatory tests. The experimental results have shown that the BSE evaluation algorithm presented in this paper provides robust performance.
PMCID: PMC4244695  PMID: 25435860
19.  Robust Initialization of Active Shape Models for Lung Segmentation in CT Scans: A Feature-Based Atlas Approach 
Model-based segmentation methods have the advantage of incorporating a priori shape information into the segmentation process but suffer from the drawback that the model must be initialized sufficiently close to the target. We propose a novel approach for initializing an active shape model (ASM) and apply it to 3D lung segmentation in CT scans. Our method constructs an atlas consisting of a set of representative lung features and an average lung shape. The ASM pose parameters are found by transforming the average lung shape based on an affine transform computed from matching features between the new image and representative lung features. Our evaluation on a diverse set of 190 images showed an average dice coefficient of 0.746 ± 0.068 for initialization and 0.974 ± 0.017 for subsequent segmentation, based on an independent reference standard. The mean absolute surface distance error was 0.948 ± 1.537 mm. The initialization as well as segmentation results showed a statistically significant improvement compared to four other approaches. The proposed initialization method can be generalized to other applications employing ASM-based segmentation.
PMCID: PMC4221988  PMID: 25400660
20.  A Weighted Two-Level Bregman Method with Dictionary Updating for Nonconvex MR Image Reconstruction 
Nonconvex optimization has shown that it needs substantially fewer measurements than l 1 minimization for exact recovery under fixed transform/overcomplete dictionary. In this work, two efficient numerical algorithms which are unified by the method named weighted two-level Bregman method with dictionary updating (WTBMDU) are proposed for solving lp optimization under the dictionary learning model and subjecting the fidelity to the partial measurements. By incorporating the iteratively reweighted norm into the two-level Bregman iteration method with dictionary updating scheme (TBMDU), the modified alternating direction method (ADM) solves the model of pursuing the approximated lp-norm penalty efficiently. Specifically, the algorithms converge after a relatively small number of iterations, under the formulation of iteratively reweighted l 1 and l 2 minimization. Experimental results on MR image simulations and real MR data, under a variety of sampling trajectories and acceleration factors, consistently demonstrate that the proposed method can efficiently reconstruct MR images from highly undersampled k-space data and presents advantages over the current state-of-the-art reconstruction approaches, in terms of higher PSNR and lower HFEN values.
PMCID: PMC4241317  PMID: 25431583
21.  Nonlocal Intracranial Cavity Extraction 
Automatic and accurate methods to estimate normalized regional brain volumes from MRI data are valuable tools which may help to obtain an objective diagnosis and followup of many neurological diseases. To estimate such regional brain volumes, the intracranial cavity volume (ICV) is often used for normalization. However, the high variability of brain shape and size due to normal intersubject variability, normal changes occurring over the lifespan, and abnormal changes due to disease makes the ICV estimation problem challenging. In this paper, we present a new approach to perform ICV extraction based on the use of a library of prelabeled brain images to capture the large variability of brain shapes. To this end, an improved nonlocal label fusion scheme based on BEaST technique is proposed to increase the accuracy of the ICV estimation. The proposed method is compared with recent state-of-the-art methods and the results demonstrate an improved performance both in terms of accuracy and reproducibility while maintaining a reduced computational burden.
PMCID: PMC4195262  PMID: 25328511
22.  Transverse Strains in Muscle Fascicles during Voluntary Contraction: A 2D Frequency Decomposition of B-Mode Ultrasound Images 
When skeletal muscle fibres shorten, they must increase in their transverse dimensions in order to maintain a constant volume. In pennate muscle, this transverse expansion results in the fibres rotating to greater pennation angle, with a consequent reduction in their contractile velocity in a process known as gearing. Understanding the nature and extent of this transverse expansion is necessary to understand the mechanisms driving the changes in internal geometry of whole muscles during contraction. Current methodologies allow the fascicle lengths, orientations, and curvatures to be quantified, but not the transverse expansion. The purpose of this study was to develop and validate techniques for quantifying transverse strain in skeletal muscle fascicles during contraction from B-mode ultrasound images. Images were acquired from the medial and lateral gastrocnemii during cyclic contractions, enhanced using multiscale vessel enhancement filtering and the spatial frequencies resolved using 2D discrete Fourier transforms. The frequency information was resolved into the fascicle orientations that were validated against manually digitized values. The transverse fascicle strains were calculated from their wavelengths within the images. These methods showed that the transverse strain increases while the longitudinal fascicle length decreases; however, the extent of these strains was smaller than expected.
PMCID: PMC4195266  PMID: 25328509
23.  Comparison and Supervised Learning of Segmentation Methods Dedicated to Specular Microscope Images of Corneal Endothelium 
The cornea is the front of the eye. Its inner cell layer, called the endothelium, is important because it is closely related to the light transparency of the cornea. An in vivo observation of this layer is performed by using specular microscopy to evaluate the health of the cells: a high spatial density will result in a good transparency. Thus, the main criterion required by ophthalmologists is the cell density of the cornea endothelium, mainly obtained by an image segmentation process. Different methods can perform the image segmentation of these cells, and the three most performing methods are studied here. The question for the ophthalmologists is how to choose the best algorithm and to obtain the best possible results with it. This paper presents a methodology to compare these algorithms together. Moreover, by the way of geometric dissimilarity criteria, the algorithms are tuned up, and the best parameter values are thus proposed to the expert ophthalmologists.
PMCID: PMC4190134  PMID: 25328510
24.  Fiber Visualization with LIC Maps Using Multidirectional Anisotropic Glyph Samples 
Line integral convolution (LIC) is used as a texture-based technique in computer graphics for flow field visualization. In diffusion tensor imaging (DTI), LIC bridges the gap between local approaches, for example directionally encoded fractional anisotropy mapping and techniques analyzing global relationships between brain regions, such as streamline tracking. In this paper an advancement of a previously published multikernel LIC approach for high angular resolution diffusion imaging visualization is proposed: a novel sampling scheme is developed to generate anisotropic glyph samples that can be used as an input pattern to the LIC algorithm. Multicylindrical glyph samples, derived from fiber orientation distribution (FOD) functions, are used, which provide a method for anisotropic packing along integrated fiber lines controlled by a uniform random algorithm. This allows two- and three-dimensional LIC maps to be generated, depicting fiber structures with excellent contrast, even in regions of crossing and branching fibers. Furthermore, a color-coding model for the fused visualization of slices from T1 datasets together with directionally encoded LIC maps is proposed. The methodology is evaluated by a simulation study with a synthetic dataset, representing crossing and bending fibers. In addition, results from in vivo studies with a healthy volunteer and a brain tumor patient are presented to demonstrate the method's practicality.
PMCID: PMC4164306  PMID: 25254038
25.  Choosing the Optimal Spatial Domain Measure of Enhancement for Mammogram Images 
Medical imaging systems often require image enhancement, such as improving the image contrast, to provide medical professionals with the best visual image quality. This helps in anomaly detection and diagnosis. Most enhancement algorithms are iterative processes that require many parameters be selected. Poor or nonoptimal parameter selection can have a negative effect on the enhancement process. In this paper, a quantitative metric for measuring the image quality is used to select the optimal operating parameters for the enhancement algorithms. A variety of measures evaluating the quality of an image enhancement will be presented along with each measure's basis for analysis, namely, on image content and image attributes. We also provide guidelines for systematically choosing the proper measure of image quality for medical images.
PMCID: PMC4142175  PMID: 25177347

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