http://www.hindawi.comThe latest articles from Hindawi Publishing Corporation&#169; 2010, Hindawi Publishing Corporation. All rights reserved.http://www.hindawi.com/journals/ijbi/2010/308627.htmlViruses are infectious agents that can cause epidemics and pandemics. The understanding of virus formation, evolution, stability, and interaction with host cells is of great importance to the scientific community and public health. Typically, a virus complex in association with its aquatic environment poses a fabulous challenge to theoretical description and prediction. In this work, we propose a differential geometry-based multiscale paradigm to model complex biomolecule systems. In our approach, the differential geometry theory of surfaces and geometric measure theory are employed as a natural means to couple the macroscopic continuum domain of the fluid mechanical description of the aquatic environment from the microscopic discrete domain of the atomistic description of the biomolecule. A multiscale action functional is constructed as a unified framework to derive the governing equations for the dynamics of different scales. We show that the classical Navier-Stokes equation for the fluid dynamics and Newton&#39;s equation for the molecular dynamics can be derived from the least action principle. These equations are coupled through the continuum-discrete interface whose dynamics is governed by potential driven geometric flows.Changjun Chen, Rishu Saxena, and Guo-Wei Wei&#169; 2010, Hindawi Publishing Corporation. All rights reserved.http://www.hindawi.com/journals/ijbi/2010/341242.htmlMyocardial deformation and strain can be investigated using suitably encoded cine MRI that admits disambiguation of material motion. Practical limitations currently restrict the analysis to in-plane motion in cross-sections of the heart (2D + time), but the proposed method readily generalizes to 3D + time. We propose a new, promising methodology, which departs from a multiscale algorithm that exploits local scale selection so as to obtain a robust estimate for the velocity gradient tensor field. Time evolution of the deformation tensor is governed by a first-order ordinary differential equation, which is completely determined by this velocity gradient tensor field. We solve this matrix-ODE analytically and present results obtained from healthy volunteers as well as from patient data. The proposed method requires only off-the-shelf algorithms and is readily applicable to planar or volumetric tagging MRI sampled on arbitrary coordinate grids.Luc Florack and Hans van Assen&#169; 2010, Hindawi Publishing Corporation. All rights reserved.http://www.hindawi.com/journals/ijbi/2009/352954.htmlWe describe a computational framework for the comprehensive assessment of contractile responses of enzymatically dissociated adult cardiac myocytes. The proposed methodology comprises the following stages: digital video recording of the contracting cell, edge preserving total variation-based image smoothing, segmentation of the smoothed images, contour extraction from the segmented images, shape representation by Fourier descriptors, and contractility assessment. The different stages are variants of mathematically sound and computationally robust algorithms very well established in the image processing community. The physiologic application of the methodology is evaluated by assessing overall contraction in enzymatically dissociated adult rat cardiocytes. Our results demonstrate the effectiveness of the proposed approach in characterizing the true, two-dimensional, &#x201C;shortening&#x201D; in the contraction process of adult cardiocytes. We compare the performance of the proposed method to that of a popular edge detection system in the literature. The proposed method not only provides a more comprehensive assessment of the myocyte contraction process but also can potentially eliminate historical concerns and sources of errors caused by myocyte rotation or translation during contraction. Furthermore, the versatility of the image processing techniques makes the method suitable for determining myocyte shortening in cells that usually bend or move during contraction. The proposed method can be utilized to evaluate changes in contractile behavior resulting from drug intervention, disease modeling, transgeneity, or other common applications to mammalian cardiocytes.Carlos Bazan, David Torres Barba, Peter Blomgren, and Paul Paolini&#169; 2010, Hindawi Publishing Corporation. All rights reserved.http://www.hindawi.com/journals/ijbi/2009/847537.htmlAlthough x-ray imaging is widely used in biomedical applications, biological soft tissues have small density changes, leading to low contrast resolution for attenuation-based x-ray imaging. Over the past years, x-ray small-angle scattering was studied as a new contrast mechanism to enhance subtle structural variation within the soft tissue. In this paper, we present a detection method to extract this type of x-ray scattering data, which are also referred to as dark-field signals. The key idea is to acquire an x-ray projection multiple times with varying collimation before an x-ray detector array. The projection data acquired with a collimator of a sufficiently high collimation aspect ratio contain mainly the primary beam with little scattering, while the data acquired with an appropriately reduced collimation aspect ratio include both the primary beam and small-angle scattering signals. Then, analysis of these corresponding datasets will produce desirable dark-field signals; for example, via digitally subtraction. In the numerical experiments, the feasibility of our dark-field detection technology is demonstrated in Monte Carlo simulation. The results show that the acquired dark field signals can clearly reveal the structural information of tissues in terms of Rayleigh scattering characteristics.Ge Wang, Wenxiang Cong, Haiou Shen, and Yu Zou&#169; 2010, Hindawi Publishing Corporation. All rights reserved.http://www.hindawi.com/journals/ijbi/2010/618747.htmlMagnetization transfer imaging (MT) may have considerable promise for early detection and monitoring of subtle brain changes before they are apparent on conventional magnetic resonance images. At 3 Tesla (T), MT affords higher resolution and increased tissue contrast associated with macromolecules. The reliability and reproducibility of a new high-resolution MT strategy were assessed in brain images acquired from 9 healthy subjects. Repeated measures were taken for 12 brain regions of interest (ROIs): genu, splenium, and the left and right hemispheres of the hippocampus, caudate, putamen, thalamus, and cerebral white matter. Spearman&#39;s correlation coefficient, coefficient of variation, and intraclass correlation coefficient (ICC) were computed. Multivariate mixed-effects regression models were used to fit the mean ROI values and to test the significance of the effects due to region, subject, observer, time, and manual repetition. A sensitivity analysis of various model specifications and the corresponding ICCs was conducted. Our statistical methods may be generalized to many similar evaluative studies of the reliability and reproducibility of various imaging modalities.Kelly H. Zou, Hongyan Du, Shawn Sidharthan, Lisa M. DeTora, Yunmei Chen, <?layout cmd="newline"?>Ann B. Ragin, Robert R. Edelman, and Ying Wu&#169; 2010, Hindawi Publishing Corporation. All rights reserved.http://www.hindawi.com/journals/ijbi/2009/659836.htmlPurpose. To assess the accuracy of high-resolution MR imaging as a means of evaluating mural invasion and lymph node metastasis by colorectal carcinoma in surgical specimens. Materials and Methods. High-resolution T1-weighted and T2-weighted MR images were obtained in 92 surgical specimens containing 96 colorectal carcinomas. Results. T2-weighted MR images clearly depicted the normal colorectal wall as consisting of seven layers. In 90 (94&#37;) of the 96 carcinomas the depth of mural invasion depicted by MR imaging correlated well with the histopathologic stage. Nodal signal intensity on T2-weighted images (93&#37;) and nodal border contour (93&#37;) were more accurate than nodal size (89&#37;) as indicators of lymph node metastasis, and MR imaging provided the highest accuracy (94&#37;&#8211;96&#37;) when they were combined. Conclusion. High-resolution MR imaging is a very accurate method for evaluating both mural invasion and lymph node metastasis by colorectal carcinoma in surgical specimens.Ichiro Yamada, Norio Yoshino, Akemi Tetsumura, Satoshi Okabe, Masayuki Enomoto, Kenichi Sugihara, Jiro Kumagai, and Hitoshi Shibuya&#169; 2010, Hindawi Publishing Corporation. All rights reserved.http://www.hindawi.com/journals/ijbi/2010/195274.htmlA method for three-dimensional (3D) reconstruction of macromolecule assembles, that is, octahedral symmetrical adapted functions (OSAFs) method, was introduced in this paper and a series of formulations for reconstruction by OSAF method were derived. To verify the feasibility and advantages of the method, two octahedral symmetrical macromolecules, that is, heat shock protein Degp24 and the Red-cell L Ferritin, were utilized as examples to implement reconstruction by the OSAF method. The schedule for simulation was designed as follows: 2000 random orientated projections of single particles with predefined Euler angles and centers of origins were generated, then different levels of noises that is signal-to-noise ratio (S/N) =0.1,0.5, and 0.8 were added. The structures reconstructed by the OSAF method were in good agreement with the standard models and the relative errors of the structures reconstructed by the OSAF method to standard structures were very little even for high level noise. The facts mentioned above account for that the OSAF method is feasible and efficient approach to reconstruct structures of macromolecules and have ability to suppress the influence of noise.Songjun Zeng, Hongrong Liu, and Qibin Yang&#169; 2010, Hindawi Publishing Corporation. All rights reserved.http://www.hindawi.com/journals/ijbi/2009/108028.htmlFunctional imaging based on tomographic X-ray imaging relies on the reconstruction of a temporal sequence of images which accurately reproduces the time attenuation curves of the tissue. The main constraints of these techniques are temporal resolution and dose. Using current techniques the data acquisition has to be performed fast so that the dynamic attenuation values can be regarded as static during the scan. Due to the relatively high number of repeated scans the dose per single scan has to be low yielding a poor signal-to-noise ratio (SNR) in the reconstructed images. In a previous publication a temporal interpolation scheme in the projection data space was relaxing the temporal resolution constraint. The aim of this contribution is the improvement of the SNR. A temporal smoothing term is introduced in the temporal interpolation scheme such that only the physiologic relevant bandwidth is considered. A significant increase of the SNR is achieved. The obtained level of noise only depends on the total dose applied and is independent of the number of scans and the SNR of a single reconstructed image. The approach might be the first step towards using slowly rotating CT systems for perfusion imaging like C-arm or small animal CT scanners.Pau Montes and G&#252;nter Lauritsch&#169; 2010, Hindawi Publishing Corporation. All rights reserved.http://www.hindawi.com/journals/ijbi/2009/767805.htmlDetection of clustered microcalcifications (MCs) in mammograms represents a significant step towards successful detection of breast cancer since their existence is one of the early signs of cancer. In this paper, a new framework that integrates Bayesian classifier and a pattern synthesizing scheme for detecting microcalcification clusters is proposed. This proposed work extracts textural, spectral, and statistical features of each input mammogram and generates models of real MCs to be used as training samples through a simplified learning phase of the Bayesian classifier. Followed by an estimation of the classifier&#39;s decision function parameters, a mammogram is segmented into the identified targets (MCs) against background (healthy tissue). The proposed algorithm has been tested using 23 mammograms from the mini-MIAS database. Experimental results achieved MCs detection with average true positive (sensitivity) and false positive (specificity) of 91.3&#37; and 98.6&#37;, respectively. Results also indicate that the modeling of the real MCs plays a significant role in the performance of the classifier and thus should be given further investigation.Imad Zyout, Ikhlas Abdel-Qader, and Christina Jacobs&#169; 2010, Hindawi Publishing Corporation. All rights reserved.http://www.hindawi.com/journals/ijbi/2009/946271.htmlThe purpose of this work is to demonstrate the functionality and performance of a PSF-based geometric distortion correction for high-field functional animal EPI. The EPI method was extended to measure the PSF and a postprocessing chain was implemented in Matlab for offline distortion correction. The correction procedure was applied to phantom and in vivo imaging of mice and rats at 9.4T using different SE-EPI and DWI-EPI protocols. Results show the significant improvement in image quality for single- and multishot EPI. Using a reduced FOV in the PSF encoding direction clearly reduced the acquisition time for PSF data by an acceleration factor of 2 or 4, without affecting the correction quality.Dominik Paul, Maxim Zaitsev, Laura Harsan, Anja Kurutsch, Daniel Nico Splitthoff, Franciszek Hennel, Morwan Choli, and Dominik von Elverfeldt&#169; 2010, Hindawi Publishing Corporation. All rights reserved.http://www.hindawi.com/journals/ijbi/2009/637867.htmlFlat panel detector-based cone beam breast CT (CBBCT) can provide 3D image of the scanned breast with 3D isotropic spatial resolution, overcoming the disadvantage of the structure superimposition associated with X-ray projection mammography. It is very difficult for Mammography to detect a small carcinoma (a few millimeters in size) when the tumor is occult or in dense breast. CBBCT featured with circular scan might be the most desirable mode in breast imaging due to its simple geometrical configuration and potential applications in functional imaging. An inherited large cone angle in CBBCT, however, will yield artifacts in the reconstruction images when only a single circular scan is employed. These artifacts usually manifest themselves as density drop and object geometrical distortion that are more noticeable in the reconstructed image areas that are further away from the circular scanning plane. In order to combat this drawback, a circle plus partial helical scan scheme is proposed. An exact circle plus straight line scan scheme is also conducted in computer simulation for the purpose of comparison. Computer simulations using a numerical breast phantom demonstrated the practical feasibility of this new scheme and correction to those artifacts to a certain degree.Dong Yang, Ruola Ning, and Weixing Cai&#169; 2010, Hindawi Publishing Corporation. All rights reserved.http://www.hindawi.com/journals/ijbi/2009/902326.htmlBreast cancer is a serious threat worldwide and is the number two killer of women in the United States. The key to successful management is screening and early detection. What follows is a description of the state of the art in screening and detection for breast cancer as well as a discussion of new and emerging technologies. This paper aims to serve as a starting point for those who are not acquainted with this growing field.Adam B. Nover, Shami Jagtap, Waqas Anjum, Hakki Yegingil, Wan Y. Shih, Wei-Heng Shih, and Ari D. Brooks&#169; 2010, Hindawi Publishing Corporation. All rights reserved.http://www.hindawi.com/journals/ijbi/2009/636240.htmlThis paper describes an algorithm for extracting pulmonary vascular trees (arteries plus veins) from three-dimensional (3D) thoracic computed tomographic (CT) images. The algorithm integrates tube enhancement filter and traversal approaches which are based on eigenvalues and eigenvectors of a Hessian matrix to extract thin peripheral segments as well as thick vessels close to the lung hilum. The resultant algorithm was applied to a simulation data set and 44 scans from 22 human subjects imaged via multidetector-row CT (MDCT) during breath holds at 85&#37; and 20&#37; of their vital capacity. A quantitative validation was performed with more than 1000 manually identified points selected from inside the vessel segments to assess true positives (TPs) and 1000 points randomly placed outside of the vessels to evaluate false positives (FPs) in each case. On average, for both the high and low volume lung images, 99&#37; of the points was properly marked as vessel and 1&#37; of the points were assessed as FPs. Our hybrid segmentation algorithm provides a highly reliable method of segmenting the combined pulmonary venous and arterial trees which in turn will serve as a critical starting point for further quantitative analysis tasks and aid in our overall goal of establishing a normative atlas of the human lung.Hidenori Shikata, Geoffrey McLennan, Eric A. Hoffman, and Milan Sonka&#169; 2010, Hindawi Publishing Corporation. All rights reserved.http://www.hindawi.com/journals/ijbi/2009/313517.htmlThis paper presents a novel method for the generation of myocardial wall surface meshes from segmented 3D MR images, which typically have strongly anisotropic voxels. The method maps a premeshed sphere to the surface of the segmented object. The mapping is defined by the gradient field of the solution of the Laplace equation between the sphere and the surface of the object. The same algorithm is independently used to generate the surface meshes of the epicardium and endocardium of the four cardiac chambers. The generated meshes are smooth despite the strong voxel anisotropy, which is not the case for the marching cubes and related methods. While the proposed method generates more regular mesh triangles than the marching cubes and allows for a complete control of the number of triangles, the generated meshes are still close to the ones obtained by the marching cubes. The method was tested on 3D short-axis cardiac MR images with strongly anisotropic voxels in the long-axis direction. For the five tested subjects, the average in-slice distance between the meshes generated by the proposed method and by the marching cubes was 0.4&#x02009;mm.Oskar &#352;krinjar and Arnaud Bistoquet&#169; 2010, Hindawi Publishing Corporation. All rights reserved.http://www.hindawi.com/journals/ijbi/2009/125871.htmlRecently, in the compressed sensing framework we found that a two-dimensional interior region-of-interest (ROI) can be exactly reconstructed via the total variation minimization if the ROI is piecewise constant (Yu and Wang, 2009). Here we present a general theorem charactering a minimization property for a piecewise constant function defined on a domain in any dimension. Our major mathematical tool to prove this result is functional analysis without involving the Dirac delta function, which was heuristically used by Yu and Wang (2009).Weimin Han, Hengyong Yu, and Ge Wang&#169; 2010, Hindawi Publishing Corporation. All rights reserved.http://www.hindawi.com/journals/ijbi/2009/156234.htmlWe propose and evaluate an automatic segmentation method for extracting striatal brain structures (caudate, putamen, and ventral striatum) from parametric C11-raclopride positron emission tomography (PET) brain images. We focus on the images acquired using a novel brain dedicated high-resolution (HRRT) PET scanner. The segmentation method first extracts the striatum using a deformable surface model and then divides the striatum into its substructures based on a graph partitioning algorithm. The weighted kernel k-means algorithm is used to partition the graph describing the voxel affinities within the striatum into the desired number of clusters. The method was experimentally validated with synthetic and real image data. The experiments showed that our method was able to automatically extract caudate, ventral striatum, and putamen from the images. Moreover, the putamen could be subdivided into anterior and posterior parts. An automatic method for the extraction of striatal structures from high-resolution PET images allows for inexpensive and reproducible extraction of the quantitative information from these images necessary in brain research and drug development.Ricardo J. P. C. Farinha, Ulla Ruotsalainen, Jussi Hirvonen, Lauri Tuominen, Jarmo Hietala, Jos&#233; M. Fonseca, and Jussi Tohka&#169; 2010, Hindawi Publishing Corporation. All rights reserved.http://www.hindawi.com/journals/ijbi/2009/756897.htmlMagnetic Resonance images are normally corrupted by random noise from the measurement process complicating the automatic feature extraction and analysis of clinical data. It is because of this reason that denoising methods have been traditionally applied to improve MR image quality. Many of these methods use the information of a single image without taking into consideration the intrinsic multicomponent nature of MR images. In this paper we propose a new filter to reduce random noise in multicomponent MR images by spatially averaging similar pixels using information from all available image components to perform the denoising process. The proposed algorithm also uses a local Principal Component Analysis decomposition as a postprocessing step to remove more noise by using information not only in the spatial domain but also in the intercomponent domain dealing in a higher noise reduction without significantly affecting the original image resolution. The proposed method has been compared with similar state-of-art methods over synthetic and real clinical multicomponent MR images showing an improved performance in all cases analyzed.Jos&#233; V. Manj&#243;n, Neil A. Thacker, Juan J. Lull, Gracian Garcia-Mart&#237;, Lu&#237;s Mart&#237;-Bonmat&#237;, and Montserrat Robles&#169; 2010, Hindawi Publishing Corporation. All rights reserved.http://www.hindawi.com/journals/ijbi/2009/680508.htmlWe propose a computer aided detection (CAD) system for the detection and classification of suspicious regions in mammographic images. This system combines a dimensionality reduction module (using principal component analysis), a feature extraction module (using independent component analysis), and a feature subset selection module (using rough set model). Rough set model is used to reduce the effect of data inconsistency while a fuzzy classifier is integrated into the system to label subimages into normal or abnormal regions. The experimental results show that this system has an accuracy of 84.03&#37; and a recall percentage of 87.28&#37;.Fadi Abu-Amara and Ikhlas Abdel-Qader&#169; 2010, Hindawi Publishing Corporation. All rights reserved.http://www.hindawi.com/journals/ijbi/2009/968986.htmlThis paper is devoted to the segmentation of cell nuclei from time lapse confocal microscopy images, taken throughout early Zebrafish embryogenesis. The segmentation allows to identify and quantify the number of cells in the animal model. This kind of information is relevant to estimate important biological parameters such as the cell proliferation rate in time and space. Our approach is based on the active contour model without edges. We compare two different formulations of the model equation and evaluate their performances in segmenting nuclei of different shapes and sizes. Qualitative and quantitative comparisons are performed on both synthetic and real data, by means of suitable gold standard. The best approach is then applied on a number of time lapses for the segmentation and counting of cells during the development of a zebrafish embryo between the sphere and the shield stage.Barbara Rizzi and Alessandro Sarti&#169; 2010, Hindawi Publishing Corporation. All rights reserved.http://www.hindawi.com/journals/ijbi/2009/843160.htmlImage restoration is usually viewed as an ill-posed problem in image processing, since there is no unique solution associated with it. The quality of restored image closely depends on the constraints imposed of the characteristics of the solution. In this paper, we propose an original extension of the NAS-RIF restoration technique by using information fusion as prior information with application in SPECT medical imaging. That extension allows the restoration process to be constrained by efficiently incorporating, within the NAS-RIF method, a regularization term which stabilizes the inverse solution. Our restoration method is constrained by anatomical information extracted from a high resolution anatomical procedure such as magnetic resonance imaging (MRI). This structural anatomy-based regularization term uses the result of an unsupervised Markovian segmentation obtained after a preliminary registration step between the MRI and SPECT data volumes from each patient. This method was successfully tested on 30 pairs of brain MRI and SPECT acquisitions from different subjects and on Hoffman and Jaszczak SPECT phantoms. The experiments demonstrated that the method performs better, in terms of signal-to-noise ratio, than a classical supervised restoration approach using a Metz filter.S. Benameur, M. Mignotte, J. Meunier, and J.-P. Soucy&#169; 2010, Hindawi Publishing Corporation. All rights reserved.http://www.hindawi.com/journals/ijbi/2009/960573.htmlA prototype cone-beam micro-CT system for small animal imaging has been developed by our group recently, which consists of a microfocus X-ray source, a three-dimensional programmable stage with object holder, and a flat-panel X-ray detector. It has a large field of view (FOV), which can acquire the whole body imaging of a normal-size mouse in a single scan which usually takes about several minutes or tens of minutes. FDK method is adopted for 3D reconstruction with Graphics Processing Unit (GPU) acceleration. In order to reconstruct images with high spatial resolution and low artifacts, raw data preprocessing and geometry calibration are implemented before reconstruction. A method which utilizes a wire phantom to estimate the residual horizontal offset of the detector is proposed, and 1D point spread function is used to assess the performance of geometric calibration quantitatively. System spatial resolution, image uniformity and noise, and low contrast resolution have been studied. Mouse images with and without contrast agent are illuminated in this paper. Experimental results show that the system is suitable for small animal imaging and is adequate to provide high-resolution anatomic information for bioluminescence tomography to build a dual modality system.Shouping Zhu, Jie Tian, Guorui Yan, Chenghu Qin, and Jinchao Feng&#169; 2010, Hindawi Publishing Corporation. All rights reserved.http://www.hindawi.com/journals/ijbi/2009/715124.htmlThis paper focuses on the detection and segmentation of Multiple Sclerosis (MS) lesions in magnetic resonance (MRI) brain images. To capture the complex tissue spatial layout, a probabilistic model termed Constrained Gaussian Mixture Model (CGMM) is proposed based on a mixture of multiple spatially oriented Gaussians per tissue. The intensity of a tissue is considered a global parameter and is constrained, by a parameter-tying scheme, to be the same value for the entire set of Gaussians that are related to the same tissue. MS lesions are identified as outlier Gaussian components and are grouped to form a new class in addition to the healthy tissue classes. A probability-based curve evolution technique is used to refine the delineation of lesion boundaries. The proposed CGMM-CE algorithm is used to segment 3D MRI brain images with an arbitrary number of channels. The CGMM-CE algorithm is automated and does not require an atlas for initialization or parameter learning. Experimental results on both standard brain MRI simulation data and real data indicate that the proposed method outperforms previously suggested approaches, especially for highly noisy data.Oren Freifeld, Hayit Greenspan, and Jacob Goldberger&#169; 2010, Hindawi Publishing Corporation. All rights reserved.http://www.hindawi.com/journals/ijbi/2009/723912.htmlAs a consequence of misspecification of the hemodynamic response and noise variance models, tests on general linear model coefficients are not valid. Robust estimation of the variance of the general linear model (GLM) coefficients in fMRI time series is therefore essential. In this paper an alternative method to estimate the variance of the GLM coefficients accurately is suggested and compared to other methods. The alternative, referred to as the sandwich, is based primarily on the fact that the time series are obtained from multiple exchangeable stimulus presentations. The analytic results show that the sandwich is unbiased. Using this result, it is possible to obtain an exact statistic which keeps the 5&#37; false positive rate. Extensive Monte Carlo simulations show that the sandwich is robust against misspeci cation of the autocorrelations and of the hemodynamic response model. The sandwich is seen to be in many circumstances robust, computationally efficient, and flexible with respect to correlation structures across the brain. In contrast, the smoothing approach can be robust to a certain extent but only with specific knowledge of the circumstances for the smoothing parameter.Lourens Waldorp&#169; 2010, Hindawi Publishing Corporation. All rights reserved.http://www.hindawi.com/journals/ijbi/2009/538389.htmlA conventional 3rd generation Computed Tomography (CT) system with a single circular source trajectory is limited in terms of longitudinal scan coverage since extending the scan coverage beyond 40&#x2009;mm results in significant cone-beam artifacts. A multiaxial CT acquisition is achieved by combining multiple sequential 3rd generation axial scans or by performing a single axial multisource CT scan with multiple longitudinally offset sources. Data from multiple axial scans or multiple sources provide complementary information. For full-scan acquisitions, we present a window-based 3D analytic cone-beam reconstruction algorithm by tessellating data from neighboring axial datasets. We also show that multi-axial CT acquisition can extend the axial scan coverage while minimizing cone-beam artifacts. For half-scan acquisitions, one cannot take advantage of conjugate rays. We propose a cone-angle dependent weighting approach to combine multi-axial half-scan data. We compute the relative contribution from each axial dataset to each voxel based on the X-ray beam collimation, the respective cone-angles, and the spacing between the axial scans. We present numerical experiments to demonstrate that the proposed techniques successfully reduce cone-beam artifacts at very large volumetric coverage.Zhye Yin, Bruno De Man, and Jed Pack&#169; 2010, Hindawi Publishing Corporation. All rights reserved.http://www.hindawi.com/journals/ijbi/2009/149079.htmlCurrently, 3D cone-beam CT image reconstruction speed is still a severe limitation for clinical application. The computational power of modern graphics processing units (GPUs) has been harnessed to provide impressive acceleration of 3D volume image reconstruction. For extra large data volume exceeding the physical graphic memory of GPU, a straightforward compromise is to divide data volume into blocks. Different from the conventional Octree partition method, a new partition scheme is proposed in this paper. This method divides both projection data and reconstructed image volume into subsets according to geometric symmetries in circular cone-beam projection layout, and a fast reconstruction for large data volume can be implemented by packing the subsets of projection data into the RGBA channels of GPU, performing the reconstruction chunk by chunk and combining the individual results in the end. The method is evaluated by reconstructing 3D images from computer-simulation data and real micro-CT data. Our results indicate that the GPU implementation can maintain original precision and speed up the reconstruction process by 110&#x02013;120 times for circular cone-beam scan, as compared to traditional CPU implementation.Xing Zhao, Jing-jing Hu, and Peng Zhang&#169; 2010, Hindawi Publishing Corporation. All rights reserved.http://www.hindawi.com/journals/ijbi/2009/269525.htmlWe propose a constrained version of Mumford and Shah&#39;s (1989) segmentation model with an information-theoretic point of view in order to devise a systematic procedure to segment brain magnetic resonance imaging (MRI) data for parametric T1-Map and T1-weighted images, in both 2-D and 3D settings. Incorporation of a tuning weight in particular adds a probabilistic flavor to our segmentation method, and makes the 3-tissue segmentation possible. Moreover, we proposed a novel method to jointly segment the T1-Map and calibrate RF Inhomogeneity (JSRIC). This method assumes the averageT1 value of white matter is the same across transverse slices in the central brain region, and JSRIC is able to rectify the flip angles to generate calibrated T1-Maps. In order to generate an accurate T1-Map, the determination of optimal flip-angles and the registration of flip-angle images are examined. Our JSRIC method is validated on two human subjects in the 2D T1-Map modality and our segmentation method is validated by two public databases, BrainWeb and IBSR, of T1-weighted modality in the 3D setting.Ping-Feng Chen, R. Grant Steen, Anthony Yezzi, and Hamid Krim&#169; 2010, Hindawi Publishing Corporation. All rights reserved.http://www.hindawi.com/journals/ijbi/2009/231539.htmlCircadian clocks gate cellular proliferation and, thereby, therapeutically target availability within proliferative pathways. This temporal coordination occurs within both cancerous and noncancerous proliferating tissues. The timing within the circadian cycle of the administration of drugs targeting proliferative pathways necessarily impacts the amount of damage done to proliferating tissues and cancers. Concurrently measuring target levels and associated key pathway components in normal and malignant tissues around the circadian clock provides a path toward a fuller understanding of the temporal relationships among the physiologic processes governing the therapeutic index of antiproliferative anticancer therapies. The temporal ordering among these relationships, paramount to determining causation, is less well understood using two- or three-dimensional representations. We have created multidimensional multimedia depictions of the temporal unfolding of putatively causative and the resultant therapeutic effects of a drug that specifically targets these ordered processes at specific times of the day. The systems and methods used to create these depictions are provided, as well as three example supplementary movies.Jamil Singletary, Patricia A. Wood, Jovelyn Du-Quiton, Song Wang, Xiaoming Yang, Shobhit Vishnoi, and William J. M. Hrushesky&#169; 2010, Hindawi Publishing Corporation. All rights reserved.http://www.hindawi.com/journals/ijbi/2009/281615.htmlImage registration is a crucial step in many medical image analysis procedures such as image fusion, surgical planning, segmentation and labeling, and shape comparison in population or longitudinal studies. A new approach to volumetric intersubject deformable image registration is presented. The method, called Mjolnir, is an extension of the highly successful method HAMMER. New image features in order to better localize points of correspondence between the two images are introduced as well as a novel approach to generate a dense displacement field based upon the weighted diffusion of automatically derived feature correspondences. An extensive validation of the algorithm was performed on T1-weighted SPGR MR brain images from the NIREP evaluation database. The results were compared with results generated by HAMMER and are shown to yield significant improvements in cortical alignment as well as reduced computation time.Lotta M. Ellingsen and Jerry L. Prince&#169; 2010, Hindawi Publishing Corporation. All rights reserved.http://www.hindawi.com/journals/ijbi/2009/528639.htmlThree-dimensional Oximetric Electron Paramagnetic Resonance Imaging using the Single Point Imaging modality generates unpaired spin density and oxygen images that can readily distinguish between normal and tumor tissues in small animals. It is also possible with fast imaging to track the changes in tissue oxygenation in response to the oxygen content in the breathing air. However, this involves dealing with gigabytes of data for each 3D oximetric imaging experiment involving digital band pass filtering and background noise subtraction, followed by 3D Fourier reconstruction. This process is rather slow in a conventional uniprocessor system. This paper presents a parallelization framework using OpenMP runtime support and parallel MATLAB to execute such computationally intensive programs. The Intel compiler is used to develop a parallel C++ code based on OpenMP. The code is executed on four Dual-Core AMD Opteron shared memory processors, to reduce the computational burden of the filtration task significantly. The results show that the parallel code for filtration has achieved a speed up factor of 46.66 as against the equivalent serial MATLAB code. In addition, a parallel MATLAB code has been developed to perform 3D Fourier reconstruction. Speedup factors of 4.57 and 4.25 have been achieved during the reconstruction process and oximetry computation, for a data set with 23&#x00D7;23&#x00D7;23 gradient steps. The execution time has been computed for both the serial and parallel implementations using different dimensions of the data and presented for comparison. The reported system has been designed to be easily accessible even from low-cost personal computers through local internet (NIHnet). The experimental results demonstrate that the parallel computing provides a source of high computational power to obtain biophysical parameters from 3D EPR oximetric imaging, almost in real-time.Christopher D. Dharmaraj, Kishan Thadikonda, Anthony R. Fletcher, Phuc N. Doan, Nallathamby Devasahayam, Shingo Matsumoto, Calvin A. Johnson, John A. Cook, James B. Mitchell, Sankaran Subramanian, and Murali C. Krishna&#169; 2010, Hindawi Publishing Corporation. All rights reserved.http://www.hindawi.com/journals/ijbi/2009/464235.htmlThermal properties of biological tissues play a critical role in the study of tumor angiogenesis and the design and monitoring of thermal therapies. To map thermal parameters noninvasively, we propose temperature-change-based thermal tomography (TTT) that relies on relative temperature mapping using magnetic resonance imaging (MRI). Our approach is unique in two aspects: (1) the steady-state body temperature in thermal equilibrium is not restricted to be spatially invariant, and (2) absolute temperature mapping is not required. These two features are physiologically realistic and technically convenient. Our numerical simulation indicates that a (9&#x2009;mm)3 tumor inside a breast phantom can be reliably depicted, assuming moderate temperature mapping accuracy of 0.5&#x2218;C.Yong Xu, Xiangyu Wei, and Ge Wang&#169; 2010, Hindawi Publishing Corporation. All rights reserved.